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    Journal: Bioinformatics

    Volume 36, Issue Supplement-2

    0 -- 0Sudhir Kumar 0001, Antonia Chroni, Koichiro Tamura, Maxwell D. Sanderford, Olumide Oladeinde, Vivian Aly, Tracy Vu, Sayaka Miura. PathFinder: Bayesian inference of clone migration histories in cancer
    0 -- 0Jack Lanchantin, Yanjun Qi. Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
    0 -- 0Sarah A. Christensen, Juho Kim, Nicholas Chia, Oluwasanmi Koyejo, Mohammed El-Kebir. Detecting evolutionary patterns of cancers using consensus trees
    0 -- 0Joske Ubels, Tilman Schäfers, Cornelis Punt, Henk-Jan Guchelaar, Jeroen de Ridder. RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials
    0 -- 0Yisu Peng, Shantanu Jain, Yong Fuga Li, Michal Gregus, Alexander R. Ivanov, Olga Vitek, Predrag Radivojac. New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics
    0 -- 0Fuhao Zhang, Wenbo Shi, Jian Zhang, Min Zeng, Min Li 0007, Lukasz A. Kurgan. PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
    0 -- 0Shohag Barman, Yung-Keun Kwon. A neuro-evolution approach to infer a Boolean network from time-series gene expressions
    0 -- 0Emilio Dorigatti, Benjamin Schubert. Joint epitope selection and spacer design for string-of-beads vaccines
    0 -- 0Stefan G. Stark, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Tumor Profiler consortium, Gunnar Rätsch, Kjong-Van Lehmann. SCIM: universal single-cell matching with unpaired feature sets
    0 -- 0Tamim Abdelaal, Paul de Raadt, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Mahfouz. SCHNEL: scalable clustering of high dimensional single-cell data
    0 -- 0Ayse Berceste Dincer, Joseph D. Janizek, Su-In Lee. Adversarial deconfounding autoencoder for learning robust gene expression embeddings
    0 -- 0Milad Mokhtaridoost, Mehmet Gönen. An efficient framework to identify key miRNA-mRNA regulatory modules in cancer
    0 -- 0Gian Marco Messa, Francesco Napolitano, Sarah H. Elsea, Diego di Bernardo, Xin Gao 0001. A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data
    0 -- 0Yahui Long, Min Wu 0008, Yong Liu 0020, Chee-Keong Kwoh 0001, Jiawei Luo 0001, Xiaoli Li 0001. Ensembling graph attention networks for human microbe-drug association prediction
    0 -- 0Wesley Wei Qian, Cassandra Xia, Subhashini Venugopalan, Arunachalam Narayanaswamy, Michelle Dimon, George W. Ashdown, Jake Baum, Jian Peng 0001, D. Michael Ando. Batch equalization with a generative adversarial network
    0 -- 0Sergio Doria-Belenguer, Markus K. Youssef, René Böttcher, Noël Malod-Dognin, Natasa Przulj. Probabilistic graphlets capture biological function in probabilistic molecular networks
    0 -- 0Jason Fan, Xuan Cindy Li, Mark Crovella, Mark D. M. Leiserson. Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information
    0 -- 0Kerem Ayoz, Miray Aysen, Erman Ayday, A. Ercüment Çiçek. The effect of kinship in re-identification attacks against genomic data sharing beacons
    0 -- 0Qiao Liu, Zhiqiang Hu, Rui Jiang 0001, Mu Zhou. DeepCDR: a hybrid graph convolutional network for predicting cancer drug response
    0 -- 0Huy N. Nguyen, Alexey Markin, Iddo Friedberg, Oliver Eulenstein. Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it
    0 -- 0Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D. J. van Dijk. Geometricus represents protein structures as shape-mers derived from moment invariants
    0 -- 0David Merrell, Anthony Gitter. Inferring signaling pathways with probabilistic programming
    0 -- 0Wenjing Xuan, Ning Liu, Neng Huang, Yaohang Li, Jianxin Wang 0001. CLPred: a sequence-based protein crystallization predictor using BLSTM neural network
    0 -- 0Elliot Layne, Erika N. Dort, Richard C. Hamelin, Yue Li, Mathieu Blanchette. Supervised learning on phylogenetically distributed data
    0 -- 0Guillem Ylla, Tianyuan Liu, Ana Conesa. MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants
    0 -- 0Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar 0001. Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
    0 -- 0Salvador Capella-Gutiérrez, Eva Alloza, Edurne Gallastegui, Ioannis Kavakiotis, Jen Harrow, Alberto Langtry, Alfonso Valencia. ECCB2020: the 19th European Conference on Computational Biology
    0 -- 0Dong-Gi Lee, Myungjun Kim, Sang Joon Son, Changhyung Hong, Hyunjung Shin. Dementia key gene identification with multi-layered SNP-gene-disease network
    0 -- 0Charles Abreu Santana, Sabrina de Azevedo Silveira, João P. A. Moraes, Sandro C. Izidoro, Raquel Cardoso de Melo Minardi, António J. M. Ribeiro, Jonathan D. Tyzack, Neera Borkakoti, Janet M. Thornton. GRaSP: a graph-based residue neighborhood strategy to predict binding sites
    0 -- 0Derrick Blakely, Eamon Collins, Ritambhara Singh, Andrew P. Norton, Jack Lanchantin, Yanjun Qi. FastSK: fast sequence analysis with gapped string kernels
    0 -- 0Alina Renz, Lina Widerspick, Andreas Dräger. FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
    0 -- 0Mohammad Lotfollahi, Mohsen Naghipourfar, Fabian J. Theis, F. Alexander Wolf. Conditional out-of-distribution generation for unpaired data using transfer VAE
    0 -- 0Adelme Bazin, Guillaume Gautreau, Claudine Médigue, David Vallenet, Alexandra Calteau. panRGP: a pangenome-based method to predict genomic islands and explore their diversity
    0 -- 0Taiki Fuji, Shiori Nakazawa, Kiyoto Ito. Feasible-metabolic-pathway-exploration technique using chemical latent space
    0 -- 0Salvador Casaní-Galdón, Cécile Pereira, Ana Conesa. Padhoc: a computational pipeline for pathway reconstruction on the fly
    0 -- 0Maor Asif, Yaron Orenstein. DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs
    0 -- 0Marco Varrone, Luca Nanni, Giovanni Ciriello, Stefano Ceri. Exploring chromatin conformation and gene co-expression through graph embedding
    0 -- 0Marleentje Martha Nieboer, Jeroen de Ridder. svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
    0 -- 0Vu Viet Hoang Pham, Lin Liu 0003, Cameron Bracken, Gregory J. Goodall, Jiuyong Li, Thuc Duy Le. DriverGroup: a novel method for identifying driver gene groups
    0 -- 0Christina Huan Shi, Kevin Y. Yip. de novo assembly of 106× human sequence data in 2.7 hours
    0 -- 0Thomas Gumbsch, Christian Bock, Michael Moor, Bastian Rieck, Karsten M. Borgwardt. Enhancing statistical power in temporal biomarker discovery through representative shapelet mining

    Volume 36, Issue Supplement-1

    0 -- 0Erin K. Molloy, Tandy J. Warnow. FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
    0 -- 0Dongjoon Lim, Mathieu Blanchette. EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM
    0 -- 0Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen. The locality dilemma of Sankoff-like RNA alignments
    0 -- 0Gopalakrishnan Venkatesh, Aayush Grover, G. Srinivasaraghavan, Shrisha Rao. MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model
    0 -- 0Chirag Jain, Arang Rhie, Haowen Zhang, Claudia Chu, Brian Walenz, Sergey Koren, Adam M. Phillippy. Weighted minimizer sampling improves long read mapping
    0 -- 0Shaoke Lou, Tianxiao Li, Xiangmeng Kong, Jing Zhang, Jason Liu, Donghoon Lee, Mark Gerstein. TopicNet: a framework for measuring transcriptional regulatory network change
    0 -- 0Amirali Aghazadeh, Orhan Ocal, Kannan Ramchandran. CRISPRL and: Interpretable large-scale inference of DNA repair landscape based on a spectral approach
    0 -- 0Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan. Unsupervised topological alignment for single-cell multi-omics integration
    0 -- 0Zichao Yan, William L. Hamilton, Mathieu Blanchette. Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions
    0 -- 0Torsten Gross, Nils Blüthgen. Identifiability and experimental design in perturbation studies
    0 -- 0Mengshi Zhou, Chunlei Zheng, Rong Xu. Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery
    0 -- 0Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz. Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis
    0 -- 0Xinrui Lyu, Jean Garret, Gunnar Rätsch, Kjong-Van Lehmann. Mutational signature learning with supervised negative binomial non-negative matrix factorization
    0 -- 0Helena Todorov, Robrecht Cannoodt, Wouter Saelens, Yvan Saeys. TinGa: fast and flexible trajectory inference with Growing Neural Gas
    0 -- 0Zichen Wang, Mu Zhou, Corey W. Arnold. Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing
    0 -- 0Sunkyu Kim, Keonwoo Kim, Junseok Choe, Inggeol Lee, Jaewoo Kang. Improved survival analysis by learning shared genomic information from pan-cancer data
    0 -- 0Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi. REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
    0 -- 0Lei Du, Fang Liu, Kefei Liu 0001, Xiaohui Yao, Shannon L. Risacher, Junwei Han, Lei Guo 0002, Andrew J. Saykin, Li Shen 0001. Identifying diagnosis-specific genotype-phenotype associations via joint multitask sparse canonical correlation analysis and classification
    0 -- 0Hirak Sarkar, Avi Srivastava, Héctor Corrada Bravo, Michael I. Love, Rob Patro. Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
    0 -- 0Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac. The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction
    0 -- 0Seung-Hyuk Choi, Eunok Paek. MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search
    0 -- 0Yang Zhang, Yunxuan Xiao, Muyu Yang, Jian Ma 0004. Cancer mutational signatures representation by large-scale context embedding
    0 -- 0Alla Mikheenko, Andrey V. Bzikadze, Alexey A. Gurevich, Karen H. Miga, Pavel A. Pevzner. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
    0 -- 0Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai. Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model
    0 -- 0Caroline Weis, Max Horn, Bastian Rieck, Aline Cuénod, Adrian Egli, Karsten M. Borgwardt. Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra
    0 -- 0Hossein Sharifi Noghabi, Shuman Peng, Olga I. Zolotareva, Colin C. Collins, Martin Ester. AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics
    0 -- 0Berk A. Alpay, Pinar Demetci, Sorin Istrail, Derek Aguiar. Combinatorial and statistical prediction of gene expression from haplotype sequence
    0 -- 0Hongyu Zheng, Carl Kingsford, Guillaume Marçais. Improved design and analysis of practical minimizers
    0 -- 0Nadia El-Mabrouk, Donna K. Slonim. ISMB 2020 proceedings
    0 -- 0Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikic, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, E. Michael Gertz, Chi-Ping Day, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergun, Süleyman Cenk Sahinalp. PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
    0 -- 0JiaQi Wu, Mohammed El-Kebir. ClonArch: visualizing the spatial clonal architecture of tumors
    0 -- 0Spencer Krieger, John D. Kececioglu. Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization
    0 -- 0Anja C. Gumpinger, Kasper Lage, Heiko Horn, Karsten M. Borgwardt. Prediction of cancer driver genes through network-based moment propagation of mutation scores
    0 -- 0Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael. Identifying tumor clones in sparse single-cell mutation data
    0 -- 0He Zhang, Liang Zhang, David H. Mathews, Liang Huang 0001. LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities
    0 -- 0Md Hossain Shuvo, Sutanu Bhattacharya, Debswapna Bhattacharya. QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
    0 -- 0Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten. Distance indexing and seed clustering in sequence graphs
    0 -- 0Yi Liu, Kenneth Barr, John Reinitz. Fully interpretable deep learning model of transcriptional control
    0 -- 0Nour Almadhoun, Erman Ayday, Özgür Ulusoy. Inference attacks against differentially private query results from genomic datasets including dependent tuples
    0 -- 0Alex Warwick Vesztrocy, Christophe Dessimoz. Benchmarking gene ontology function predictions using negative annotations
    0 -- 0Dina Svetlitsky, Tal Dagan, Michal Ziv-Ukelson. Discovery of multi-operon colinear syntenic blocks in microbial genomes
    0 -- 0Mohammad Arifur Rahman, Huzefa Rangwala. IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data
    0 -- 0Kapil Devkota, James M. Murphy, Lenore J. Cowen. GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks
    0 -- 0Mostafa Karimi, Arman Hasanzadeh, Yang Shen. Network-principled deep generative models for designing drug combinations as graph sets
    0 -- 0Vitor Piro, Temesgen Hailemariam Dadi, Enrico Seiler, Knut Reinert, Bernhard Y. Renard. ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
    0 -- 0Noël Malod-Dognin, V. Pancaldi, A. Valencia, Natasa Przulj. Chromatin network markers of leukemia
    0 -- 0Ron Zeira, Benjamin J. Raphael. Copy number evolution with weighted aberrations in cancer
    0 -- 0Avi Srivastava, Laraib Malik, Hirak Sarkar, Rob Patro. A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
    0 -- 0Dan Guo, Melanie Christine Föll, Veronika Volkmann, Kathrin Enderle-Ammour, Peter Bronsert, Oliver Schilling, Olga Vitek. Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations
    0 -- 0Anuradha Wickramarachchi, Vijini Mallawaarachchi, Vaibhav Rajan, Yu Lin. MetaBCC-LR: metagenomics binning by coverage and composition for long reads
    0 -- 0Qiuyu Lian, Hongyi Xin, Jianzhu Ma, Liza Konnikova, Wei Chen, Jin Gu, Kong Chen. Artificial-cell-type aware cell-type classification in CITE-seq
    0 -- 0Yufeng Wu. Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach
    0 -- 0Midori Iida, Michio Iwata, Yoshihiro Yamanishi. Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets
    0 -- 0Zeyang Shen, Marten A. Hoeksema, Zhengyu Ouyang, Christopher Benner, Christopher K. Glass. MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function
    0 -- 0Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp. Identification of conserved evolutionary trajectories in tumors
    0 -- 0Palash Sashittal, Mohammed El-Kebir. Sampling and summarizing transmission trees with multi-strain infections
    0 -- 0Rui Zhu, Chao Jiang, Xiaofeng Wang 0006, Shuang Wang 0002, Hao Zheng, Haixu Tang. Privacy-preserving construction of generalized linear mixed model for biomedical computation
    0 -- 0Metin Balaban, Siavash Mirarab. Phylogenetic double placement of mixed samples
    0 -- 0Yannik Schälte, Jan Hasenauer. Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation
    0 -- 0Kerem Wainer-Katsir, Michal Linial. BIRD: identifying cell doublets via biallelic expression from single cells
    0 -- 0Benjamin Demeo, Bonnie Berger. Hopper: a mathematically optimal algorithm for sketching biological data
    0 -- 0Jeffrey A. Ruffolo, Carlos Guerra, Sai Pooja Mahajan, Jeremias Sulam, Jeffrey J. Gray. Geometric potentials from deep learning improve prediction of CDR H3 loop structures
    0 -- 0Tatiana Dvorkina, Andrey V. Bzikadze, Pavel A. Pevzner. The string decomposition problem and its applications to centromere analysis and assembly
    0 -- 0Marwan Abdellah, Nadir Román Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Benoit Coste, Snigdha Dagar, Jean-Denis Courcol, Henry Markram, Felix Schürmann. Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis
    0 -- 0Assya Trofimov, Joseph Paul Cohen, Yoshua Bengio, Claude Perreault, Sébastien Lemieux. Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition
    0 -- 0Leon Weber, Kirsten Thobe, Oscar Arturo Migueles Lozano, Jana Wolf, Ulf Leser. PEDL: extracting protein-protein associations using deep language models and distant supervision

    Volume 36, Issue 9

    2649 -- 2656Dinh Van Tran, Alessandro Sperduti, Rolf Backofen, Fabrizio Costa. Heterogeneous networks integration for disease-gene prioritization with node kernels
    2657 -- 2664Md Amanullah, Mengqian Yu, Xiwei Sun, Aoran Luo, Qing Zhou, Liyuan Zhou, Ling Hou, Wei Wang, Weiguo Lu, Peng-Yuan Liu, Yan Lu. MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies
    2665 -- 2674Nicola Casiraghi, Francesco Orlando, Yari Ciani, Jenny Xiang, Andrea Sboner, Olivier Elemento, Gerhardt Attard, Himisha Beltran, Francesca Demichelis, Alessandro Romanel. ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA
    2675 -- 2683Evan Gatev, Nicole Gladish, Sara Mostafavi, Michael S. Kobor. CoMeBack: DNA methylation array data analysis for co-methylated regions
    2684 -- 2689Kasidet Hiranniramol, Yuhao Chen, Weijun Liu, Xiaowei Wang. Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency
    2690 -- 2696Jarkko Toivonen, Pratyush K. Das, Jussi Taipale, Esko Ukkonen. MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs
    2697 -- 2704Rui Yin, Emil Luusua, Jan Dabrowski, Yu Zhang 0084, Chee-Keong Kwoh 0001. Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks
    2705 -- 2711Gianvito Urgese, Emanuele Parisi, Orazio M. Scicolone, Santa Di Cataldo, Elisa Ficarra. BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
    2712 -- 2717Ting Yu, Juntao Liu, Xin Gao, Guojun Li. iPAC: a genome-guided assembler of isoforms via phasing and combing paths
    2718 -- 2724Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot, Philippe Ruminy, Hélène Dauchel, Pierre Vera, Fabrice Jardin. UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries
    2725 -- 2730Keisuke Shimmura, Yuki Kato, Yukio Kawahara. Bivartect: accurate and memory-saving breakpoint detection by direct read comparison
    2731 -- 2739Anastasia A. Gulyaeva, Andrey I Sigorskih, Elena S. Ocheredko, Dmitry V. Samborskiy, Alexander E. Gorbalenya. LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins
    2740 -- 2749Henry Xing, Steven W. Kembel, Vladimir Makarenkov. Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks
    2750 -- 2754Sam M. Ireland, Andrew C. R. Martin. atomium - a Python structure parser
    2755 -- 2762Jia-Juan Tu, Le Ou-Yang, Hong Yan 0001, Xiao-fei Zhang, Hong Qin. Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity
    2763 -- 2769Jie-Huei Wang, Yi-Hau Chen. Interaction screening by Kendall's partial correlation for ultrahigh-dimensional data with survival trait
    2770 -- 2777Trang T. Le, Bryan A. Dawkins, Brett A. McKinney. Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding
    2778 -- 2786Shobana V. Stassen, Dickson M. D. Siu, Kelvin C. M. Lee, Joshua W. K. Ho, Hayden K. H. So, Kevin K. Tsia. PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells
    2787 -- 2795Yue Qiu, Tianhuan Lu, Hansaim Lim, Lei Xie. A Bayesian approach to accurate and robust signature detection on LINCS L1000 data
    2796 -- 2804Stephen S. Tran, Qing Zhou, Xinshu Xiao. Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling
    2805 -- 2812Xiangxiang Zeng, Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li, L. Frank Huang, Stephen J. Lewis, Ruth Nussinov, Feixiong Cheng. Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest
    2813 -- 2820N. Suhas Jagannathan, Mario O. Ihsan, Xiao Xuan Kin, Roy E. Welsch, Marie-Véronique Clément, Lisa Tucker-Kellogg. Transcompp: understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions
    2821 -- 2828Omer Basha, Chanan M. Argov, Raviv Artzy, Yazeed Zoabi, Idan Hekselman, Liad Alfandari, Vered Chalifa-Caspi, Esti Yeger Lotem. Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes
    2829 -- 2838So Nakashima, Yuki Sughiyama, Tetsuya J. Kobayashi. Lineage EM algorithm for inferring latent states from cellular lineage trees
    2839 -- 2847Wenjuan Zhang, Hunan Xu, Xiaozhong Li, Qiang Gao, Lin Wang. DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion
    2848 -- 2855Lingwei Xie, Song He, Zhongnan Zhang, Kunhui Lin, Xiaochen Bo, Shu Yang, Boyuan Feng, Kun Wan, Kang Yang, Jie Yang, Yufei Ding. Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds
    2856 -- 2861Gabriel E. Hoffman, Jaroslav Bendl, Kiran Girdhar, Panos Roussos. decorate: differential epigenetic correlation test
    2862 -- 2871Chiung-Ting Wu, Yizhi Wang, Yinxue Wang, Timothy M. D. Ebbels, Ibrahim Karaman, Gonçalo Graça, Rui Pinto, David M. Herrington, Yue Wang, Guoqiang Yu. Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection
    2872 -- 2880Rong Ma, Yi Li, Chenxing Li, Fangping Wan, Hailin Hu, Wei Xu, Jianyang Zeng. Secure multiparty computation for privacy-preserving drug discovery
    2881 -- 2887Joy Roy, Eric Cheung, Junaid Bhatti, Abraar Muneem, Daniel Lobo. Curation and annotation of planarian gene expression patterns with segmented reference morphologies
    2888 -- 2895Zhenyuan Ning, Weihao Pan, Yuting Chen, Qing Xiao, Xinsen Zhang, Jiaxiu Luo, Jian Wang, Yu Zhang. Integrative analysis of cross-modal features for the prognosis prediction of clear cell renal cell carcinoma
    2896 -- 2898Dengfeng Guan, Shane A. McCarthy, Jonathan Wood, Kerstin Howe, Yadong Wang, Richard Durbin. Identifying and removing haplotypic duplication in primary genome assemblies
    2899 -- 2901Quanhu Sheng, Hui Yu, Olufunmilola Oyebamiji, Jiandong Wang, Danqian Chen, Scott Ness, Ying-Yong Zhao, Yan Guo. AnnoGen: annotating genome-wide pragmatic features
    2902 -- 2904Connor A. Horton, Burak Han Alver, Peter J. Park. GiniQC: a measure for quantifying noise in single-cell Hi-C data
    2905 -- 2906Kevin R. Shieh, Christina Kratschmer, Keith E. Maier, John M. Greally, Matthew Levy, Aaron Golden. AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX
    2907 -- 2908Stilianos Louca. Simulating trees with millions of species
    2909 -- 2911Gianluca Tomasello, Ilaria Armenia, Gianluca Molla. The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities
    2912 -- 2914José Luis Velázquez-Libera, Fabio Durán-Verdugo, Alejandro Valdés-Jiménez, Gabriel Núñez-Vivanco, Julio Caballero. LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking
    2915 -- 2916Daniel K. Weber, Songlin Wang, John L. Markley, Gianluigi Veglia, Woonghee Lee. PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins
    2917 -- 2919Christopher W. Wood, Amaurys Ávila Ibarra, Gail J. Bartlett, Andrew J. Wilson, Derek N. Woolfson, Richard B. Sessions. BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan
    2920 -- 2922Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash. incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs
    2923 -- 2925Tomás Tokár, Chiara Pastrello, Igor Jurisica. GSOAP: a tool for visualization of gene set over-representation analysis
    2926 -- 2928Warren D. Anderson, Fabiana M. Duarte, Mete Civelek, Michael J. Guertin. Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R
    2929 -- 2931Hakan Özadam, Michael Geng, Can Cenik. RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution
    2932 -- 2933Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco. BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data
    2934 -- 2935Yi Zheng, Fangqing Zhao. Visualization of circular RNAs and their internal splicing events from transcriptomic data
    2936 -- 2937Gareth Peat, William Jones, Michael Nuhn, José Carlos Marugán, William Newell, Ian Dunham, Daniel R. Zerbino. The open targets post-GWAS analysis pipeline
    2938 -- 2940Olivia Angelin-Bonnet, Patrick J. Biggs, Samantha J. Baldwin, Susan Thomson 0003, Matthieu Vignes. sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R
    2941 -- 2942Stepán Kouril, Julie de Sousa, Jan Václavík, David Friedecký, Tomás Adam. CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data
    2943 -- 2945Francisco Madrid-Gambin, Sergio Oller-Moreno, Luis Fernandez, Simona Bartova, Maria Pilar Giner, Christopher Joyce, Francesco Ferraro, Ivan Montoliu, Sofia Moco, Santiago Marco. AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics
    2946 -- 2947Xingxiang Cheng, Dandan Sun, Dachuan Zhang, Yu Tian, Shaozhen Ding, Pengli Cai, Qian-Nan Hu. RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions
    2948 -- 2949Ervin A. Tasnádi, Timea Toth, Maria Kovacs, Akos Diosdi, Francesco Pampaloni, József Molnár, Filippo Piccinini, Péter Horváth. 3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images
    2950 -- 2951Jacqueline Nowak, Kristin Gennermann, Staffan Persson, Zoran Nikoloski. CytoSeg 2.0: automated extraction of actin filaments
    2952 -- 2954Luciano A. Abriata, Rosalba Lepore, Matteo Dal Peraro. About the need to make computational models of biological macromolecules available and discoverable
    2955 -- 2957Jacopo Di Iorio, Francesca Chiaromonte, Marzia A. Cremona. On the bias of H-scores for comparing biclusters, and how to correct it
    2958 -- 2962Jayvardan S. Naidu, Justin Delano, Scott Mathews, Predrag Radivojac. An examination of citation-based impact of the computational biology conferences
    2963 -- 2965Anastasia Chasapi, Vasilis J. Promponas, Christos A. Ouzounis. The bioinformatics wealth of nations
    2966 -- 2973Gustavo Arango Argoty, G. K. P. Guron, Emily Garner, M. V. Riquelme, Lenwood S. Heath, Amy Pruden, Peter J. Vikesland, Liqing Zhang 0002. ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes
    2974 -- 0Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher. Fast and accurate correction of optical mapping data via spaced seeds

    Volume 36, Issue 8

    2319 -- 2327Jonathan Raad, Georgina Stegmayer, Diego H. Milone. Complexity measures of the mature miRNA for improving pre-miRNAs prediction
    2328 -- 2336Chuanyi Zhang, Idoia Ochoa. VEF: a variant filtering tool based on ensemble methods
    2337 -- 2344Gleb Goussarov, Ilse Cleenwerck, Mohamed Mysara, Natalie Leys, Pieter Monsieurs, Guillaume Tahon, Aurélien Carlier, Peter Vandamme, Rob Van Houdt. PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing
    2345 -- 2351Xinyan Zhang, Nengjun Yi. Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data
    2352 -- 2358Guodong Yang, Aiqun Ma, Zhaohui S. Qin, Li Chen. Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules
    2359 -- 2364Pasi Rastas. Lep-Anchor: automated construction of linkage map anchored haploid genomes
    2365 -- 2374Xiaqiong Wang, Yalu Wen. A U-statistics for integrative analysis of multilayer omics data
    2375 -- 2384Akhilesh Mishra, Sahil Dhanda, Priyanka Siwach, Shruti Aggarwal, B. Jayaram. A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics
    2385 -- 2392Shilpa Garg, John Aach, Heng Li 0002, Isaac Sebenius, Richard Durbin, George M. Church. A haplotype-aware de novo assembly of related individuals using pedigree sequence graph
    2393 -- 2400Haitao Yu, Zhiming Dai. SANPolyA: a deep learning method for identifying Poly(A) signals
    2401 -- 2409Nils Strodthoff, Patrick Wagner, Markus Wenzel 0002, Wojciech Samek. UDSMProt: universal deep sequence models for protein classification
    2410 -- 2416Thomas Bradley, Simon Moxon. FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals
    2417 -- 2428Tobias Brinkjost, Christiane Ehrt, Oliver Koch, Petra Mutzel. SCOT: Rethinking the classification of secondary structure elements
    2429 -- 2437Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function
    2438 -- 2442Yiwei Cao, Sang-Jun Park, Akul Y. Mehta, Richard D. Cummings, Wonpil Im. GlyMDB: Glycan Microarray Database and analysis toolset
    2443 -- 2450Jun Liu, Xiao-gen Zhou, Yang Zhang 0040, Gui-jun Zhang. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm
    2451 -- 2457Louis Becquey, Eric Angel, Fariza Tahi. BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules
    2458 -- 2465Isak Johansson-Åkhe, Claudio Mirabello, Björn Wallner. InterPep2: global peptide-protein docking using interaction surface templates
    2466 -- 2473Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang, Wei Zhang 0076. Platform-integrated mRNA isoform quantification
    2474 -- 2485Zhan-Ying Feng, Xianwen Ren, Yuan Fang, Yining Yin, Chutian Huang, Yimin Zhao, Yong Wang. scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization
    2486 -- 2491Serin Zhang, Jiang Shao, Disa Yu, Xing Qiu, Jinfeng Zhang. MatchMixeR: a cross-platform normalization method for gene expression data integration
    2492 -- 2499Yifan Ji, Chang Yu, Hong Zhang. contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples
    2500 -- 2505Gittu George, Sushrima Gan, Yu Huang, Philip Appleby, A. S. Nar, Radha Venkatesan, Viswanathan Mohan, Colin N. A. Palmer, Alex S. F. Doney. PheGWAS: a new dimension to visualize GWAS across multiple phenotypes
    2506 -- 2514Jingsi Ming, Tao Wang, Can Yang. LPM: a latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations
    2515 -- 2521Kristina Buschur, Maria Chikina, Panayiotis V. Benos. Causal network perturbations for instance-specific analysis of single cell and disease samples
    2522 -- 2529Rasmus Magnusson, Mika Gustafsson. LiPLike: towards gene regulatory network predictions of high certainty
    2530 -- 2537Hui-Zeng Sun, Mi Zhou, Ou Wang, Yanhong Chen, Jian-xin Liu, Le Luo Guan. Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows
    2538 -- 2546Jin Li, Sai Zhang, Tao Liu, Chenxi Ning, Zhuoxuan Zhang, Wei Zhou. Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction
    2547 -- 2553Mayank Baranwal, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, Alfred Hero. A deep learning architecture for metabolic pathway prediction
    2554 -- 2560Xiaohui Yao, Shan Cong, Jingwen Yan, Shannon L. Risacher, Andrew J. Saykin, Jason H. Moore, Li Shen 0001. Regional imaging genetic enrichment analysis
    2561 -- 2568Xia-an Bi, Yingchao Liu, Yiming Xie, Xi Hu, Qinghua Jiang. Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment
    2569 -- 2571Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manu Molina, Toni Gabaldón. HaploTypo: a variant-calling pipeline for phased genomes
    2572 -- 2574Soumitra Pal 0001, Teresa M. Przytycka. Bioinformatics pipeline using JUDI: Just Do It!
    2575 -- 2577Swadha Anand, Bhusan K. Kuntal, Anwesha Mohapatra, Vineet Bhatt, Sharmila S. Mande. FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information
    2578 -- 2580Yu Li 0006, Sheng Wang 0001, Chongwei Bi, Zhaowen Qiu, Mo Li 0005, Xin Gao 0001. DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing
    2581 -- 2583Sophia C. Tintori, Patrick Golden, Bob Goldstein. Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets
    2584 -- 2586Dominika Labudová, Jirí Hon, Matej Lexa. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
    2587 -- 2588Christopher M. Ward, Thu-Hien To, Stephen M. Pederson. ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files
    2589 -- 2591Lorraine A. K. Ayad, Panagiotis Charalampopoulos, Solon P. Pissis. SMART: SuperMaximal approximate repeats tool
    2592 -- 2594Deren A. R. Eaton, Isaac Overcast. ipyrad: Interactive assembly and analysis of RADseq datasets
    2595 -- 2598Bianka Farkas, Georgina Csizmadia, Eszter Katona, Gábor E. Tusnády, Tamás Hegedüs. MemBlob database and server for identifying transmembrane regions using cryo-EM maps
    2599 -- 2601Tomasz Magdziarz, Karolina Mitusinska, Maria Bzówka, Agata Raczynska, Agnieszka Stanczak, Michal Banas, Weronika Bagrowska, Artur Góra. AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective
    2602 -- 2604Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou. ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing
    2605 -- 2607Gui-Yan Xie, Meng Xuan Xia, Ya-Ru Miao, Mei Luo, Qiong Zhang, An-Yuan Guo. FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human
    2608 -- 2610Aritro Nath, Jeremy Chang, R. Stephanie Huang. iMIRAGE: an R package to impute microRNA expression using protein-coding genes
    2611 -- 2613Thang V. Pham, Alex A. Henneman, Connie R. Jimenez. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
    2614 -- 2615Palle Duun Rohde, Izel Fourie Sørensen, Peter Sørensen. qgg: an R package for large-scale quantitative genetic analyses
    2616 -- 2617Andre Schultz, Rehan Akbani. SAMMI: a semi-automated tool for the visualization of metabolic networks
    2618 -- 2619César Parra-Rojas, Esteban A. Hernández-Vargas. PDEparams: parameter fitting toolbox for partial differential equations in python
    2620 -- 2622Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats
    2623 -- 2625Thomas C. Keaty, Paul A. Jensen. Gapsplit: efficient random sampling for non-convex constraint-based models
    2626 -- 2627Corentin Molitor, Matt Brember, Fady R. Mohareb. VarGen: an R package for disease-associated variant discovery and annotation
    2628 -- 2629Steven X. Ge, Dongmin Jung, Runan Yao. ShinyGO: a graphical gene-set enrichment tool for animals and plants
    2630 -- 2631Alexander Keller 0006, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, Markus J. Ankenbrand. BCdatabaser: on-the-fly reference database creation for (meta-)barcoding
    2632 -- 2633Francesco Ceccarelli, Denes Turei, Attila Gabor, Julio Saez-Rodriguez. Bringing data from curated pathway resources to Cytoscape with OmniPath
    2634 -- 2635Sébastien Tosi, Lídia Bardia, Maria Jose Filgueira, Alexandre Calon, Julien Colombelli. LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
    2636 -- 2642Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
    2643 -- 0Nils Koelling, Marie Bernkopf, Eduardo Calpena, Geoffrey J. Maher, Kerry A. Miller, Hannah K. Ralph, Anne Goriely, Andrew O. M. Wilkie. amplimap: a versatile tool to process and analyze targeted NGS data
    2644 -- 0Rui Liu 0009, Pei Chen, Luonan Chen. Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression
    2645 -- 0Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang 0002. SynergyFinder: a web application for analyzing drug combination dose-response matrix data
    2646 -- 0Sergey V. Tarlachkov, Taras V. Shevchuk, Maria del Carmen Montero-Calasanz, Irina P. Starodumova. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments
    2647 -- 0Gabriel Studer, Christine Rempfer, Andrew Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. QMEANDisCo - distance constraints applied on model quality estimation

    Volume 36, Issue 7

    1989 -- 1993Qingsu Cheng, Bahram Parvin. Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure
    1994 -- 2000Kevin R. Amses, William J. Davis, Timothy Y. James. SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes
    2001 -- 2008Samuele Cancellieri, Matthew C. Canver, Nicola Bombieri, Rosalba Giugno, Luca Pinello. CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing
    2009 -- 2016Yi Yang, Xingjie Shi, Yuling Jiao, Jian Huang 0003, Min Chen, Xiang Zhou, Lei Sun, Xinyi Lin, Can Yang, Jin Liu 0011. CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies
    2017 -- 2024Weiwei Zhang, Ziyi Li, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng. Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities
    2025 -- 2032Yuwei Zhang, Tianfei Yi, Huihui Ji, Guofang Zhao, Yang Xi, Changzheng Dong, Lina Zhang, Xiaohong Zhang, Jinshun Zhao, Qi Liao. Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics
    2033 -- 2039Junfeng Liu, Ziyang An, Jianjun Luo, Jing Li, Feifei Li, Zhihua Zhang. Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite
    2040 -- 2046Fabian Klötzl, Bernhard Haubold. Phylonium: fast estimation of evolutionary distances from large samples of similar genomes
    2047 -- 2052Ha-Young Kim, Dongsup Kim. Prediction of mutation effects using a deep temporal convolutional network
    2053 -- 2059Saket Choudhary, Wenzheng Li, Andrew D. Smith. Accurate detection of short and long active ORFs using Ribo-seq data
    2060 -- 2067Sam Friedman, Laura D. Gauthier, Yossi Farjoun, Eric Banks. Lean and deep models for more accurate filtering of SNP and INDEL variant calls
    2068 -- 2075Jing Xu, Han Zhang, Jinfang Zheng, Philippe Dovoedo, Yanbin Yin. eCAMI: simultaneous classification and motif identification for enzyme annotation
    2076 -- 2081Gabriele Orlando, Alexandra Silva 0004, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim F. Vranken. Accurate prediction of protein beta-aggregation with generalized statistical potentials
    2082 -- 2089Tomasz Marek Kowalski, Szymon Grabowski. PgRC: pseudogenome-based read compressor
    2090 -- 2097Zach Dinardo, Kiran Tomlinson, Anna M. Ritz, Layla Oesper. Distance measures for tumor evolutionary trees
    2098 -- 2104Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T. Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie von Dobschütz, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region
    2105 -- 2112Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang 0040. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
    2113 -- 2118Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara. Protein docking model evaluation by 3D deep convolutional neural networks
    2119 -- 2125Zongyang Du, Shuo Pan, Qi Wu, Zhenling Peng, Jianyi Yang. CATHER: a novel threading algorithm with predicted contacts
    2126 -- 2133Ge Liu, Haoyang Zeng, Jonas Mueller, Brandon Carter 0001, Ziheng Wang, Jonas Schilz, Geraldine Horny, Michael E. Birnbaum, Stefan Ewert, David K. Gifford. Antibody complementarity determining region design using high-capacity machine learning
    2134 -- 2141Carlos Martí-Gómez, Enrique Lara Pezzi, Fátima Sánchez-Cabo. dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity
    2142 -- 2149Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra. A framework for exhaustive modelling of genetic interaction patterns using Petri nets
    2150 -- 2156Likun Huang, Weiqi Tang, Suhong Bu, Weiren Wu. BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing
    2157 -- 2164Estelle Geffard, Sophie Limou, Alexandre Walencik, Michelle Daya, Harold Watson, Dara Torgerson, Kathleen C. Barnes, Anne Cesbron Gautier, Pierre-Antoine Gourraud, Nicolas Vince. Easy-HLA: a validated web application suite to reveal the full details of HLA typing
    2165 -- 2172F. Maggioli, Toni Mancini, Enrico Tronci. SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems
    2173 -- 2180Jui Wan Loh, Caitlin Guccione, Frances Di Clemente, Gregory Riedlinger, Shridar Ganesan, Hossein Khiabanian. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data
    2181 -- 2188Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi. Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells
    2189 -- 2194Lars Thielecke, Kerstin Cornils, Ingmar Glauche. genBaRcode: a comprehensive R-package for genetic barcode analysis
    2195 -- 2201Zhe Cui 0001, Jayaram Kancherla, Kyle W. Chang, Niklas Elmqvist, Héctor Corrada Bravo. Proactive visual and statistical analysis of genomic data in Epiviz
    2202 -- 2208Fabio Fabris, Daniel Palmer, Khalid M. Salama, João Pedro de Magalhães, Alex Alves Freitas. Using deep learning to associate human genes with age-related diseases
    2209 -- 2216Herty Liany, Anand Jeyasekharan, Vaibhav Rajan. Predicting synthetic lethal interactions using heterogeneous data sources
    2217 -- 2223Kathryn A. McGurk, Arianna Dagliati, Davide Chiasserini, Dave Lee, Darren Plant, Ivona Baricevic-Jones, Janet Kelsall, Rachael Eineman, Rachel Reed, Bethany Geary, Richard D. Unwin, Anna Nicolaou, Bernard D. Keavney, Anne Barton, Anthony D. Whetton, Nophar Geifman. The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination
    2224 -- 2228Raul Rodriguez-Esteban. Semantic persistence of ambiguous biomedical names in the citation network
    2229 -- 2236Fatima Zohra Smaili, Xin Gao 0001, Robert Hoehndorf. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
    2237 -- 2243Cyril F. Reboul, Simon Kiesewetter, Dominika Elmlund, Hans Elmlund. Point-group symmetry detection in three-dimensional charge density of biomolecules
    2244 -- 2250Wei Long, Yang Yang 0030, Hong-bin Shen. ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images
    2251 -- 2252Takuya Aramaki, Romain Blanc-Mathieu, Hisashi Endo, Koichi Ohkubo, Minoru Kanehisa, Susumu Goto, Hiroyuki Ogata. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
    2253 -- 2255Jiang Hu, Junpeng Fan, Zongyi Sun, Shanlin Liu. NextPolish: a fast and efficient genome polishing tool for long-read assembly
    2256 -- 2257Readman Chiu, Ka Ming Nip, Inanç Birol. Fusion-Bloom: fusion detection in assembled transcriptomes
    2258 -- 2259Gurjit S. Randhawa, Kathleen A. Hill, Lila Kari. MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis
    2260 -- 2261Georgios Fotakis, Dietmar Rieder, Marlene Haider, Zlatko Trajanoski, Francesca Finotello. NeoFuse: predicting fusion neoantigens from RNA sequencing data
    2262 -- 2263Ahmed A. Quadeer, David Morales-Jiménez, Matthew R. McKay. RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins
    2264 -- 2265Mehari B. Zerihun, Fabrizio Pucci, Emanuel K. Peter, Alexander Schug. pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences
    2266 -- 2268Jimmy Caroli, Mattia Forcato, Silvio Bicciato. APTANI2: update of aptamer selection through sequence-structure analysis
    2269 -- 2271Snædís Kristmundsdóttir, Hannes P. Eggertsson, Gudny A. Arnadottir, Bjarni V. Halldórsson. popSTR2 enables clinical and population-scale genotyping of microsatellites
    2272 -- 2274Ammar Tareen, Justin B. Kinney. Logomaker: beautiful sequence logos in Python
    2275 -- 2277Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez. GABAC: an arithmetic coding solution for genomic data
    2278 -- 2279Ahmed A. Quadeer, Matthew R. McKay, John P. Barton, Raymond H. Y. Louie. MPF-BML: a standalone GUI-based package for maximum entropy model inference
    2280 -- 2281Sarah Lutteropp, Alexey M. Kozlov, Alexandros Stamatakis. A fast and memory-efficient implementation of the transfer bootstrap
    2282 -- 2283Jacques Ducasse, Visotheary Ung, Guillaume Lecointre, Aurélien Miralles. LIMES: a tool for comparing species partition
    2284 -- 2285Miguel Romero-Durana, Brian Jiménez-García, Juan Fernández-Recio. pyDockEneRes: per-residue decomposition of protein-protein docking energy
    2286 -- 2287Krisztian Adam, Zoltan Gyorgypal, Zoltan Hegedus. DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments
    2288 -- 2290Shian Su, Luyi Tian, Xueyi Dong, Peter F. Hickey, Saskia Freytag, Matthew E. Ritchie. CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods
    2291 -- 2292Saskia Freytag, Ryan Lister. schex avoids overplotting for large single-cell RNA-sequencing datasets
    2293 -- 2294Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen. SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells
    2295 -- 2297Christina Nieuwoudt, Angela Brooks-Wilson, Jinko Graham. SimRVSequences: an R package to simulate genetic sequence data for pedigrees
    2298 -- 2299Laura M. Zingaretti, Gilles Renand, Diego P. Morgavi, Yuliaxis Ramayo-Caldas. Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities
    2300 -- 2302Maryam Nazarieh, Mohamed Hamed, Christian Spaniol, Thorsten Will, Volkhard Helms. TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks
    2303 -- 2305Junwei Han, Xudong Han, Qingfei Kong, Liang Cheng 0006. psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression
    2306 -- 2307Sergii Domanskyi, Carlo Piermarocchi, George Mias. PyIOmica: longitudinal omics analysis and trend identification
    2308 -- 2310Gongchao Jing, Yufeng Zhang, Ming Yang, Lu Liu, Jian Xu, Xiaoquan Su. Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
    2311 -- 2313Roman Hillje, Pier Giuseppe Pelicci, Lucilla Luzi. Cerebro: interactive visualization of scRNA-seq data
    2314 -- 2315Jacobo de la Cuesta-Zuluaga, Ruth Ley, Nicholas Youngblut. Struo: a pipeline for building custom databases for common metagenome profilers
    2316 -- 2317Bilge Sürün, Charlotta P. I Schärfe, Mathew R. Divine, Julian Heinrich, Nora C. Toussaint, Lukas Zimmermann, Janina Beha, Oliver Kohlbacher. ClinVAP: a reporting strategy from variants to therapeutic options

    Volume 36, Issue 6

    1655 -- 1662Nina Baumgarten, Florian Schmidt 0003, Marcel H. Schulz. Improved linking of motifs to their TFs using domain information
    1663 -- 1667Qingsu Cheng, Mina Khoshdeli, Bradley S. Ferguson, Kosar Jabbari, Chongzhi Zang, Bahram Parvin. YY1 is a cis-regulator in the organoid models of high mammographic density
    1668 -- 1672Sergey V. Tarlachkov, Taras V. Shevchuk, Maria del Carmen Montero-Calasanz, Irina P. Starodumova. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments
    1673 -- 1680Judith Bergadà-Pijuan, Carlos Pulido-Quetglas, Adrienne Vancura, Rory Johnson. CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long non-coding RNAs
    1681 -- 1688Joel A. Southgate, Matthew J. Bull, Clare M. Brown, Joanne Watkins, Sally Corden, Benjamin Southgate, Catherine Moore, Thomas R. Connor. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications
    1689 -- 1695Abhay Hukku, Corbin Quick, Francesca Luca, Roger Pique-Regi, Xiaoquan Wen. BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis
    1696 -- 1703Nour Almadhoun, Erman Ayday, Özgür Ulusoy. Differential privacy under dependent tuples - the case of genomic privacy
    1704 -- 1711Artur Jaroszewicz, Jason Ernst. An integrative approach for fine-mapping chromatin interactions
    1712 -- 1717Pramod Chandrashekar, Navid Ahmadinejad, Junwen Wang, Aleksandar Sekulic, Jan B. Egan, Yan W. Asmann, Sudhir Kumar, Carlo Maley, Li Liu. Somatic selection distinguishes oncogenes and tumor suppressor genes
    1718 -- 1724Max E. Schön, Laura Eme, Thijs J. G. Ettema. PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
    1725 -- 1730Sherlyn Jemimah, Masakazu Sekijima, M. Michael Gromiha. ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification
    1731 -- 1739Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan S. Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D'Angelo, Branden Olson, Sai T. Reddy, Victor Greiff, Johannes Trück, Susanna Marquez, William Lees, Enkelejda Miho. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
    1740 -- 1749Raphael Eguchi, Po-Ssu Huang. Multi-scale structural analysis of proteins by deep semantic segmentation
    1750 -- 1756Mark Chonofsky, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane. The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing
    1757 -- 1764Saida S. Mohamed, Gennaro Esposito, Giuseppe Serra 0001, Federico Fogolari. Generalized Born radii computation using linear models and neural networks
    1765 -- 1771Gabriel Studer, Christine Rempfer, Andrew Waterhouse, Rafal Gumienny, Jürgen Haas, Torsten Schwede. QMEANDisCo - distance constraints applied on model quality estimation
    1772 -- 1778Alena Orlenko, Daniel Kofink, Leo-Pekka Lyytikäinen, Kjell Nikus, Pashupati Mishra, Pekka Kuukasjärvi, Pekka J. Karhunen, Mika Kähönen, Jari O. Laurikka, Terho Lehtimäki, Folkert W. Asselbergs, Jason H. Moore. Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning
    1779 -- 1784Chuanqi Wang, Jun Li. SINC: a scale-invariant deep-neural-network classifier for bulk and single-cell RNA-seq data
    1785 -- 1794Jun Li, Qing Lu, Yalu Wen. Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data
    1795 -- 1800David Gerard, Luís Felipe Ventorim Ferrão. Priors for genotyping polyploids
    1801 -- 1806Maureen Kachman, Hani Habra, William Duren, Janis Wigginton, Peter Sajjakulnukit, George Michailidis, Charles F. Burant, Alla Karnovsky. Deep annotation of untargeted LC-MS metabolomics data with Binner
    1807 -- 1813Pau Erola, Johan Björkegren, Tom Michoel. Model-based clustering of multi-tissue gene expression data
    1814 -- 1822Zhibo Wang, Zhezhi He, Milan Shah, Teng Zhang, Deliang Fan, Wei Zhang 0076. Network-based multi-task learning models for biomarker selection and cancer outcome prediction
    1823 -- 1830Wai Kit Ong, Peter E. Midford, Peter D. Karp. Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models
    1831 -- 1839Gal Dinstag, Ron Shamir. PRODIGY: personalized prioritization of driver genes
    1840 -- 1847Kevin McGregor, Aurélie Labbe, Celia M. T. Greenwood. MDiNE: a model to estimate differential co-occurrence networks in microbiome studies
    1848 -- 1854Adrian L. Hauber, Raphael Engesser, Joep Vanlier, Jens Timmer. Estimating chain length for time delays in dynamical systems using profile likelihood
    1855 -- 1863Jianing Xi, Xiguo Yuan, Minghui Wang, Ao Li, Xuelong Li, Qinghua Huang. Inferring subgroup-specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication
    1864 -- 1871Keyao Wang, Jun Wang 0035, Carlotta Domeniconi, Xiangliang Zhang 0001, Guoxian Yu. Differentiating isoform functions with collaborative matrix factorization
    1872 -- 1880Naiara Pérez, Pablo Accuosto, Àlex Bravo, Montse Cuadros, Eva Martínez Garcia, Horacio Saggion, German Rigau. Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English
    1881 -- 1888Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge. Discovery of disease- and drug-specific pathways through community structures of a literature network
    1889 -- 1895Sergio Castillo-Lara, E. Pascual-Carreras, Josep F. Abril. PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources
    1896 -- 1901Anne Morgat, Thierry Lombardot, Elisabeth Coudert, Kristian B. Axelsen, Teresa Batista Neto, Sebastien Gehant, Parit Bansal, Jerven T. Bolleman, Elisabeth Gasteiger, Edouard De Castro, Delphine Baratin, Monica Pozzato, Ioannis Xenarios, Sylvain Poux, Nicole Redaschi, Alan Bridge, The UniProt Consortium. Enzyme annotation in UniProtKB using Rhea
    1902 -- 1907J. Bradley Holmes, Eric Moyer, Lon Phan, Donna R. Maglott, Brandi L. Kattman. SPDI: data model for variants and applications at NCBI
    1908 -- 1914Ying-Ying Xu, Hong-bin Shen, Robert F. Murphy. Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images
    1915 -- 1916Frédéric Escudié, Charles Van Goethem, David Grand, Julie Vendrell, Anna Vigier, Pierre Brousset, Solène M. Evrard, Jérôme Solassol, Janick Selves. MIAmS: microsatellite instability detection on NGS amplicons data
    1917 -- 1919Koustav Pal, Ilario Tagliaferri, Carmen Maria Livi, Francesco Ferrari. HiCBricks: building blocks for efficient handling of large Hi-C datasets
    1920 -- 1922Q. Ferré, G. Charbonnier, N. Sadouni, Frédéric Lopez, Y. Kermezli, Salvatore Spicuglia, Cécile Capponi, Badih Ghattas, Denis Puthier. OLOGRAM: determining significance of total overlap length between genomic regions sets
    1923 -- 1924Yu Jiang, Hongmei Zhang, Shan V. Andrews, Hasan Arshad, Susan Ewart, John W. Holloway, M. Daniele Fallin, Kelly M. Bakulski, Wilfried Karmaus. Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling
    1925 -- 1927Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
    1928 -- 1929Timo Lassmann. Kalign 3: multiple sequence alignment of large datasets
    1930 -- 1932Martijn Cordes, Karin Pike-Overzet, Marja van Eggermond, Sandra Vloemans, Miranda R. Baert, Laura Garcia-Perez, Frank J. T. Staal, Marcel J. T. Reinders, Erik van den Akker. ImSpectR: R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data
    1933 -- 1936Xiangfu Zhong, Albert Pla, Simon Rayner. Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data
    1937 -- 1939Yuhan Fei, Yiyang Mao, Chengji Shen, Rui Wang, Hongsheng Zhang, Ji Huang. WPMIAS: Whole-degradome-based Plant MicroRNA-target Interaction Analysis Server
    1940 -- 1941Nicolaas C. Kist, Robert A. Power, Andrew Skelton, Seth D. Seegobin, Moira Verbelen, Bushan Bonde, Karim Malki. RNASeq_similarity_matrix: visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix
    1942 -- 1943Kai Cheng, Gabrielle Pawlowski, Xinheng Yu, Yusen Zhou, Sriram Neelamegham. DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra
    1944 -- 1945Francesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo. gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles
    1946 -- 1947Debajyoti Sinha, Pradyumn Sinha, Ritwik Saha, Sanghamitra Bandyopadhyay, Debarka Sengupta. Improved dropClust R package with integrative analysis support for scRNA-seq data
    1948 -- 1949James J. Cai. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis
    1950 -- 1951Shijie C. Zheng, Charles E. Breeze, Stephan Beck, Danyue Dong, Tianyu Zhu, Liangxiao Ma, Wei Ye, Guoqing Zhang, Andrew E. Teschendorff. EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI
    1952 -- 1954Matthew Carlucci, Algimantas Krisciunas, Haohan Li, Povilas Gibas, Karolis Koncevicius, Art Petronis, Gabriel Oh. DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity
    1955 -- 1956Carlos Prieto, David Barrios. RaNA-Seq: interactive RNA-Seq analysis from FASTQ files to functional analysis
    1957 -- 1959Alencar Xavier, William M. Muir, Katy Martin Rainey. bWGR: Bayesian whole-genome regression
    1960 -- 1962Laura A. Esteban, Lyubov R. Lonishin, Daniil M. Bobrovskiy, Gregory Leleytner, Natalya S. Bogatyreva, Fyodor A. Kondrashov, Dmitry N. Ivankov. HypercubeME: two hundred million combinatorially complete datasets from a single experiment
    1963 -- 1965Srikanth Ravichandran, András Hartmann, Antonio del Sol. SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies
    1966 -- 1967Stian Holmås, Rafel Riudavets Puig, Marcio Luis Acencio, Vladimir Mironov, Martin Kuiper. The Cytoscape BioGateway App: explorative network building from an RDF store
    1968 -- 1969Maciej Dobrzynski, Marc-Antoine Jacques, Olivier Pertz. Mining single-cell time-series datasets with Time Course Inspector
    1970 -- 1972Deeptanshu Jha, Rahul Singh. SMARTS: the social media-based addiction recovery and intervention targeting server
    1973 -- 1975Jia-Hong Wang, Ling-Feng Zhao, Hua-Feng Wang, Yue-Ting Wen, Kui-Kui Jiang, Xiang-Ming Mao, Zi-Ying Zhou, Kai-Tai Yao, Qing-Shan Geng, Dan Guo, Zhong-Xi Huang. GenCLiP 3: mining human genes' functions and regulatory networks from PubMed based on co-occurrences and natural language processing
    1976 -- 1977Sebastian J. Teran Hidalgo, MengYun Wu, Shuangge Ma. NCutYX: a package for clustering analysis of multilayer omics data
    1978 -- 1980Pieter Moris, Danh Bui-Thi, Kris Laukens, Pieter Meysman. MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks
    1981 -- 1982Radoslav Davidovic, Vladimir Perovic, Branislava Gemovic, Nevena Veljkovic. DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis
    1983 -- 1985Manuel Holtgrewe, Clemens Messerschmidt, Mikko Nieminen, Dieter Beule. DigestiFlow: from BCL to FASTQ with ease
    1986 -- 1988Miguel Ponce de Leon, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes. On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models

    Volume 36, Issue 5

    1317 -- 1325Sandeep Manandhar, Patrick Bouthemy, Erik Welf, Gaudenz Danuser, Philippe Roudot, Charles Kervrann. 3D flow field estimation and assessment for live cell fluorescence microscopy
    1326 -- 1332Victoria A. Sleight, Philipp Antczak, Francesco Falciani, Melody S. Clark. Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways
    1333 -- 1343Renmin Han, Sheng Wang 0001, Xin Gao 0001. Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing
    1344 -- 1350Daiwei Tang, Seyoung Park, Hongyu Zhao. NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution
    1351 -- 1359Liam F. Spurr, Nawaf Alomran, Pavlos Bousounis, Dacian Reece-Stremtan, N. M. Prashant, Hongyu Liu, Piotr Slowinski, Muzi Li, Qianqian Zhang, Justin Sein, Gabriel Asher, Keith A. Crandall, Krasimira Tsaneva-Atanasova, Anelia Horvath. ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data
    1360 -- 1366Bong-Hyun Kim, Kijin Yu, Peter C. W. Lee. Cancer classification of single-cell gene expression data by neural network
    1367 -- 1373Raphaël Mourad. Studying 3D genome evolution using genomic sequence
    1374 -- 1381Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
    1382 -- 1390Kohei Hagiwara, Liang Ding, Michael Edmonson, Stephen V. Rice, Scott Newman, John Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
    1391 -- 1396Jian-Peng Zhou, Lei Chen 0007, Zi-Han Guo. iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs
    1397 -- 1404Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang 0001. Quantifying functional impact of non-coding variants with multi-task Bayesian neural network
    1405 -- 1412Xiao Luo, Xinming Tu, Yang Ding, Ge Gao, Minghua Deng. Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding
    1413 -- 1419Thomas Büchler, Enno Ohlebusch. An improved encoding of genetic variation in a Burrows-Wheeler transform
    1420 -- 1428David Becerra, Alexander Butyaev, Jérôme Waldispühl. Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation
    1429 -- 1438Abdurrahman Elbasir, Raghvendra Mall, Khalid Kunji, Reda Rawi, Zeyaul Islam, Gwo-Yu Chuang, Prasanna R. Kolatkar, Halima Bensmail. BCrystal: an interpretable sequence-based protein crystallization predictor
    1439 -- 1444Puneet Rawat, R. Prabakaran, Sandeep Kumar, M. Michael Gromiha. AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation
    1445 -- 1452Qingzhen Hou, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci. SOLart: a structure-based method to predict protein solubility and aggregation
    1453 -- 1459Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher, Douglas E. V. Pires. mCSM-AB2: guiding rational antibody design using graph-based signatures
    1460 -- 1467Amir Vajdi, Kourosh Zarringhalam, Nurit Haspel. Patch-DCA: improved protein interface prediction by utilizing structural information and clustering DCA scores
    1468 -- 1475Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo. SPARSim single cell: a count data simulator for scRNA-seq data
    1476 -- 1483Runpu Chen, Le Yang, Steve Goodison, Yijun Sun. Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data
    1484 -- 1491Magdalena E. Strauß, Paul D. W. Kirk, John E. Reid, Lorenz Wernisch. GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
    1492 -- 1500Hamed Haselimashhadi, Jeremy C. Mason, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole O. Babalola, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmut Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valérie Gailus-Durner, Tania Sorg, Hiroshi Masuya, Yuichi Obata, Jason D. Heaney, Mary E. Dickinson, Wolfgang Wurst, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Yann Herault, Martin Hrabé de Angelis, Steve D. M. Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen E. Parkinson, Terrence F. Meehan. Soft windowing application to improve analysis of high-throughput phenotyping data
    1501 -- 1508Jia Zhao, Jingsi Ming, Xianghong Hu, Gang Chen, Jin Liu 0011, Can Yang. Bayesian weighted Mendelian randomization for causal inference based on summary statistics
    1509 -- 1516Andrew W. George, Arunas Verbyla, Joshua Bowden. Eagle: multi-locus association mapping on a genome-wide scale made routine
    1517 -- 1521Leilei Cui 0004, Bin Yang, Nikolas Pontikos, Richard Mott, Lusheng Huang. ADDO: a comprehensive toolkit to detect, classify and visualize additive and non-additive quantitative trait loci
    1522 -- 1532Rui Liu 0009, Pei Chen, Luonan Chen. Single-sample landscape entropy reveals the imminent phase transition during disease progression
    1533 -- 1541Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu. FullMeSH: improving large-scale MeSH indexing with full text
    1542 -- 1552Zheng Chen, Meng Pang, Zixin Zhao, Shuainan Li, Rui Miao, Yifan Zhang, Xiaoyue Feng, Xin Feng 0004, Yexian Zhang, Meiyu Duan, Lan Huang, Fengfeng Zhou. Feature selection may improve deep neural networks for the bioinformatics problems
    1553 -- 1561Paolo Mignone, Gianvito Pio, Domenica D'Elia, Michelangelo Ceci. Exploiting transfer learning for the reconstruction of the human gene regulatory network
    1562 -- 1569Antonino Lauria, Salvatore Mannino, Carla Gentile, Giuseppe Mannino, Annamaria Martorana, Daniele Peri. DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets
    1570 -- 1576Nooshin Shomal Zadeh, Sangdi Lin, George C. Runger. Matched Forest: supervised learning for high-dimensional matched case-control studies
    1577 -- 1583Yu Liu, Paul W. Bible, Bin Zou, Qiaoxing Liang, Cong Dong, Xiaofeng Wen, Yan Li, Xiaofei Ge, Xifang Li, Xiuli Deng, Rong Ma, Shixin Guo, Juanran Liang, Tingting Chen, Wenliang Pan, Lixin Liu, Wei Chen, Xueqin Wang, Lai Wei. CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples
    1584 -- 1589Eiru Kim, Dasom Bae, Sunmo Yang, Gunhwan Ko, Sungho Lee, Byungwook Lee, Insuk Lee. BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genome
    1590 -- 1598Daniel Jimenez-Carretero, Mikel Ariz, José Mário T. Morgado, Iván Cortés-Domínguez, Carlos Ortiz-de-Solórzano. NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
    1599 -- 1606Yizhi Wang, Congchao Wang, Petter Ranefall, Gerard Broussard, Yinxue Wang, Guilai Shi, Boyu Lyu, Chiung-Ting Wu, Yue Wang, Lin Tian, Guoqiang Yu. SynQuant: an automatic tool to quantify synapses from microscopy images
    1607 -- 1613Joseph Boyd, Alice Pinheiro, Elaine Del Nery, Fabien Reyal, Thomas Walter 0003. Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen
    1614 -- 1621Jeremy A. Pike, Abdullah O. Khan, Chiara Pallini, Steven G. Thomas, Markus Mund, Jonas Ries, Natalie S. Poulter, Iain B. Styles. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
    1622 -- 1624Andrea Calabria, Stefano Beretta 0001, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini. γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites
    1625 -- 1626Cheng Yee Tang, Rick Twee-Hee Ong. MIRUReader: MIRU-VNTR typing directly from long sequencing reads
    1627 -- 1628Christopher N. Larsen, Guangyu Sun, Xiaomei Li, Sam Zaremba, Hongtao Zhao, Sherry He, Liwei Zhou, Sanjeev Kumar, Vincent Desborough, Edward B. Klem. Mat_peptide: comprehensive annotation of mature peptides from polyproteins in five virus families
    1629 -- 1631Catherine Badel, Violette Da Cunha, Ryan Catchpole, Patrick Forterre, Jacques Oberto. WASPS: web-assisted symbolic plasmid synteny server
    1632 -- 1633Adam T. Lafontaine, Bruce J. Mayer, Kazuya Machida. Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data
    1634 -- 1636Raphaël Leman, Valentin Harter, Alexandre Atkinson, Grégoire Davy, Antoine Rousselin, Etienne Muller, Laurent Castéra, Fréderic Lemoine, Pierre de la Grange, Marine Guillaud-Bataille, Dominique Vaur, Sophie Krieger. SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data
    1637 -- 1639Simon Steffens, Xiuling Fu, Fangfang He, Yuhao Li, Isaac A. Babarinde, Andrew P. Hutchins. DPre: computational identification of differentiation bias and genes underlying cell type conversions
    1640 -- 1641Pencho Yordanov, Jörg Stelling, Irene Otero-Muras. BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks
    1642 -- 1643Yu Tian, Ling Wu, Le Yuan, Shaozhen Ding, Fu Chen, Tong Zhang, Ailin Ren, Dachuan Zhang, Weizhong Tu, Junni Chen, Qian-Nan Hu. BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis
    1644 -- 1646Nikolay Martyushenko, Eivind Almaas. ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models
    1647 -- 1648Bilal Wajid, Hasan Iqbal, Momina Jamil, Hafsa Rafique, Faria Anwar. MetumpX - a metabolomics support package for untargeted mass spectrometry
    1649 -- 1651Moli Huang, Yunpeng Wang, Manqiu Yang, Jun Yan, Henry Yang, Wenzhuo Zhuang, Ying Xu, H. Phillip Koeffler, De-Chen Lin, Xi Chen. dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq
    1652 -- 1653David Sánchez 0001, Sergio Martínez, Josep Domingo-Ferrer, Jordi Soria-Comas, Montserrat Batet. µ-ANT: semantic microaggregation-based anonymization tool

    Volume 36, Issue 4

    985 -- 989Galo A. Goig, Manuela Torres-Puente, Carla Mariner-Llicer, Luis M. Villamayor, Álvaro Chiner-Oms, Ana Gil-Brusola, Rafael Borrás, Iñaki Comas Espadas. Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
    990 -- 993Luis Sánchez-Pulido, Chris P. Ponting. Hexa-Longin domain scaffolds for inter-Rab signalling
    994 -- 999Qian Zhu, Xavier Tekpli, Olga G. Troyanskaya, Vessela N. Kristensen. Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations
    1000 -- 1006Kang Jin Kim, Jaehyun Park, Sang-Chul Park, Sungho Won. Phylogenetic tree-based microbiome association test
    1007 -- 1013Gaia Ceddia, Liuba Nausicaa Martino, Alice C. L. Parodi, Piercesare Secchi, Stefano Campaner, Marco Masseroli. Association rule mining to identify transcription factor interactions in genomic regions
    1014 -- 1021Arif Harmanci, Akdes Serin Harmanci, Jyothishmathi Swaminathan, Vidya Gopalakrishnan. EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements
    1022 -- 1029Deepank R. Korandla, Jacob M. Wozniak, Anaamika Campeau, David J. Gonzalez, Erik S. Wright. AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions
    1030 -- 1036Ziwei Li, Bo He, Weixing Feng. Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases
    1037 -- 1043Zengyan Hong, Xiangxiang Zeng, Leyi Wei, Xiangrong Liu. Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism
    1044 -- 1051Yichao Li, Yating Liu, David Juedes, Frank Drews, Razvan Bunescu, Lonnie R. Welch. Set cover-based methods for motif selection
    1052 -- 1056Xue-qing, Meng Wang, Gerrit Karssen, Patricia Bucki, Wim Bert, Sigal Braun-Miyara. PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes
    1057 -- 1065Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song. DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites
    1066 -- 1073Sen Liu, Yuping Wang, Wuning Tong, Shiwei Wei. A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment
    1074 -- 1081Bin Yu, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma 0003. SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting
    1082 -- 1090Camir Ricketts, Daniel Seidman, Victoria Popic, Fereydoun Hormozdiari, Serafim Batzoglou, Iman Hajirasouliha. Meltos: multi-sample tumor phylogeny reconstruction for structural variants
    1091 -- 1098Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng. Analysis of several key factors influencing deep learning-based inter-residue contact prediction
    1099 -- 1106Amélie Barozet, Kevin Molloy, Marc Vaisset, Thierry Siméon, Juan Cortés. A reinforcement-learning-based approach to enhance exhaustive protein loop sampling
    1107 -- 1113Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou. Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning
    1114 -- 1120Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Yaohang Li, Jianxin Wang, Min Li 0007. Protein-protein interaction site prediction through combining local and global features with deep neural networks
    1121 -- 1128Tanvir Alam, Meshari Alazmi, Rayan Naser, Franceline Huser, Afaque A. Momin, Veronica Astro, SeungBeom Hong, Katarzyna W. Walkiewicz, Christian G. Canlas, Raphaël Huser, Amal J. Ali, Jasmeen Merzaban, Antonio Adamo, Mariusz Jaremko, Lukasz Jaremko, Vladimir B. Bajic, Xin Gao, Stefan T. Arold. Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs
    1129 -- 1134Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk. Topology-based classification of tetrads and quadruplex structures
    1135 -- 1142Xiaoqiang Huang, Robin Pearce, Yang Zhang. EvoEF2: accurate and fast energy function for computational protein design
    1143 -- 1149Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang, Qin Ma 0003. QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data
    1150 -- 1158Abha S. Bais, Dennis Kostka. scds: computational annotation of doublets in single-cell RNA sequencing data
    1159 -- 1166Christopher R. John, David Watson, Michael R. Barnes, Costantino Pitzalis, Myles J. Lewis. Spectrum: fast density-aware spectral clustering for single and multi-omic data
    1167 -- 1173Wilson H. McKerrow, David Fenyö. L1EM: a tool for accurate locus specific LINE-1 RNA quantification
    1174 -- 1181Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei. bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
    1182 -- 1190Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham. Metric learning on expression data for gene function prediction
    1191 -- 1197María Bogaerts-Márquez, Maite G. Barrón, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Raúl Castanera, Josep M. Casacuberta, Josefa González. T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
    1198 -- 1207Mahdi Shafiee Kamalabad, Marco Grzegorczyk. Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters
    1208 -- 1212Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh. CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms
    1213 -- 1218Yuanyue Li, Michael Kuhn 0004, Anne-Claude Gavin, Peer Bork. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features
    1219 -- 1225Saman Salike, Nirav Bhatt. Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach
    1226 -- 1233Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su. Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts
    1234 -- 1240Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang. BioBERT: a pre-trained biomedical language representation model for biomedical text mining
    1241 -- 1251Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy 0001, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun. Graph embedding on biomedical networks: methods, applications and evaluations
    1252 -- 1259Ruijie Yao, Jiaqiang Qian, Qiang Huang. Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules
    1260 -- 1261David Porubsky, Ashley D. Sanders, Aaron Taudt, Maria Colomé-Tatché, Peter M. Lansdorp, Victor Guryev. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
    1262 -- 1264Congting Ye, Qian Zhou, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R. Saban, Qingshun Quinn Li. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data
    1265 -- 1266Marina Marcet-Houben, Toni Gabaldón. EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes
    1267 -- 1269Davide Bolognini, Ashley D. Sanders, Jan O. Korbel, Alberto Magi, Vladimir Benes, Tobias Rausch. VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing
    1270 -- 1272Hongjian Jin, Lawryn H. Kasper, Jon D. Larson, Gang Wu, Suzanne J. Baker, Jinghui Zhang, Yiping Fan. ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in
    1273 -- 1274Ignacio Ferrés, Pablo Fresia, Gregorio Iraola. simurg: simulate bacterial pangenomes in R
    1275 -- 1276Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, Claire Lemaitre. SimkaMin: fast and resource frugal de novo comparative metagenomics
    1277 -- 1278Jun Wang, Pu-Feng Du, Xin-Yu Xue, Guang-Ping Li, Yuan-Ke Zhou, Wei Zhao, Hao Lin, Wei Chen. VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences
    1279 -- 1280Guillermo Serrano, Elizabeth Guruceaga, Victor Segura. DeepMSPeptide: peptide detectability prediction using deep learning
    1281 -- 1282Zhenhua Yu, Fang Du, Xuehong Sun, Ao Li. SCSsim: an integrated tool for simulating single-cell genome sequencing data
    1283 -- 1285Zeynep Baskurt, Scott Mastromatteo, Jiafen Gong, Richard F. Wintle, Stephen W. Scherer, Lisa J. Strug. VikNGS: a C++ variant integration kit for next generation sequencing association analysis
    1286 -- 1288Adrián A. Davín, Théo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szöllosi. Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
    1289 -- 1290Patrick H. Bradley, Katherine S. Pollard. phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
    1291 -- 1292Conrad Stork, Gerd Embruch, Martin Sícho, Christina de Bruyn Kops, Ya Chen, Daniel Svozil, Johannes Kirchmair. NERDD: a web portal providing access to in silico tools for drug discovery
    1293 -- 1295Chao Fang, Zhaoyu Li, Dong Xu 0002, Yi Shang. MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns
    1296 -- 1297Julian Bender, Carla Schmidt. The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
    1298 -- 1299António Cruz, Penousal Machado, Joel P. Arrais. CroP - Coordinated Panel visualization for biological networks analysis
    1300 -- 1302A. Trullo, J. Dufourt, M. Lagha. MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos
    1303 -- 1304Florian P. Breitwieser, Steven L. Salzberg. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
    1305 -- 1306Grégoire Versmée, Laura Versmée, Mikaël Dusenne, Niloofar Jalali, Paul Avillach. dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP)
    1307 -- 1308Anthony Federico, Stefano Monti. hypeR: an R package for geneset enrichment workflows
    1309 -- 1310Kevin McDonnell, Nicholas Waters, Enda Howley, Florence Abram. Chordomics: a visualization tool for linking function to phylogeny in microbiomes
    1311 -- 1313Marcela Aguilera Flores, Iulia M. Lazar. XMAn v2 - a database of Homo sapiens mutated peptides
    1314 -- 1316Pablo Vicente-Munuera, Pedro Gómez-Gálvez, Robert J. Tetley, Cristina Forja, Antonio Tagua, Marta Letrán, Melda Tozluoglu, Yanlan Mao, Luis M. Escudero. EpiGraph: an open-source platform to quantify epithelial organization

    Volume 36, Issue 3

    653 -- 659Ya Wang, Min Qian, Deliang Tang, Julie Herbstman, Frederica Perera, Shuang Wang. A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes
    660 -- 665Ren Hua Chung, Chen-Yu Kang. pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions
    666 -- 675Yaqiang Cao, Zhaoxiong Chen, Xingwei Chen, Daosheng Ai, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, Jing-Dong J. Han. Accurate loop calling for 3D genomic data with cLoops
    676 -- 681Joshua Millstein, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang, Sebastian Stintzing, Volker Heinemann, Heinz-Josef Lenz. Partition: a surjective mapping approach for dimensionality reduction
    682 -- 689Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher. Fast and accurate correction of optical mapping data via spaced seeds
    690 -- 697Tianlei Xu, Peng Jin, Zhaohui S. Qin. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs
    698 -- 703Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API
    704 -- 712Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, ZongYuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song. PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins
    713 -- 720Mary A Wood, Austin Nguyen, Adam J. Struck, Kyle Ellrott, Abhinav Nellore, Reid F. Thompson. neoepiscope improves neoepitope prediction with multivariant phasing
    721 -- 727Robert S. Harris, Paul Medvedev. Improved representation of sequence bloom trees
    728 -- 734Timothy J. Hackmann. Accurate estimation of microbial sequence diversity with Distanced
    735 -- 741M. B. B. Gutierres, C. B. C. Bonorino, M. M. Rigo. ChaperISM: improved chaperone binding prediction using position-independent scoring matrices
    742 -- 750Yufeng Wu. Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach
    751 -- 757Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction
    758 -- 764Fergus Boyles, Charlotte M. Deane, Garrett M. Morris. Learning from the ligand: using ligand-based features to improve binding affinity prediction
    765 -- 772Erney Ramírez-Aportela, Jose Luis Vilas, Alisa Glukhova, Roberto Melero, Pablo Conesa, Marta Martínez, David Maluenda, Javier Mota, Amaya Jiménez, Javier Vargas, Roberto Marabini, Patrick M. Sexton, José María Carazo, Carlos Oscar Sánchez Sorzano. Automatic local resolution-based sharpening of cryo-EM maps
    773 -- 781Hannah De Los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett, Jennifer M. Hurley. ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output
    782 -- 788Jiebiao Wang, Bernie Devlin, Kathryn Roeder. Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression
    789 -- 797Pengchao Ye, Wenbin Ye 0002, Congting Ye, Shuchao Li, Lishan Ye, Guoli Ji, Xiaohui Wu. scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size
    798 -- 804Priyam Das, Christine B. Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani. NExUS: Bayesian simultaneous network estimation across unequal sample sizes
    805 -- 812Wenjiang Deng, Tian Mou, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Trung-Nghia Vu. Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data
    813 -- 818Godwin Woo, Michael Fernandez, Michael Hsing, Nathan A. Lack, Ayse Derya Cavga, Artem Cherkasov. DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules
    819 -- 827Ziyi Chen, Chengyang Ji, Qin Shen, Wei Liu, F. Xiao-Feng Qin, Aiping Wu. Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes
    828 -- 841José Víctor Moreno-Mayar, Thorfinn Sand Korneliussen, Jyoti Dalal, Gabriel Renaud, Anders Albrechtsen, Rasmus Nielsen, Anna-Sapfo Malaspinas. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data
    842 -- 850Cheng Peng, Jun Wang, Isaac Asante, Stan Louie, Ran Jin, Lida Chatzi, Graham Casey, Duncan C. Thomas, David V. Conti. A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits
    851 -- 858Yu-An Huang, Pengwei Hu, Keith C. C. Chan, Zhu-Hong You. Graph convolution for predicting associations between miRNA and drug resistance
    859 -- 864Hongyang Li, Yuanfang Guan. Machine learning empowers phosphoproteome prediction in cancers
    865 -- 871Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca. Gene relevance based on multiple evidences in complex networks
    872 -- 879Rafsan Ahmed, Ilyes Baali, Cesim Erten, Evis Hoxha, Hilal Kazan. MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
    880 -- 889Ashwani Kumar, Ali Hosseinnia, Alla Gagarinova, Sadhna Phanse, Sunyoung Kim, Khaled A Aly, Sandra Zilles, Mohan Babu. A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli
    890 -- 896Xavier Farré, Nino Spataro, Frédéric Haziza, Jordi Rambla, Arcadi Navarro. Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence
    897 -- 903Wei Zhang, Longlong Wang, Ke Liu, Xiaofeng Wei, Kai Yang, Wensi Du, Shiyu Wang, Nannan Guo, Chuanchuan Ma, Lihua Luo, Jinghua Wu, Liya Lin, Fan Yang, Fei Gao, Xie Wang, Tao Li, Ruifang Zhang, Nitin K. Saksena, Huanming Yang, Jian Wang, Lin Fang, Yong Hou, Xun Xu, Xiao Liu. PIRD: Pan Immune Repertoire Database
    904 -- 909Gen Li, Yu Su, Yu-Hang Yan, Jiayi Peng, Qing-Qing Dai, Xiang-Li Ning, Cheng-Long Zhu, Chen Fu, Michael A. McDonough, Christopher J. Schofield, Cheng Huang, Guo-Bo Li. MeLAD: an integrated resource for metalloenzyme-ligand associations
    910 -- 917Blair J. Rossetti, Steven A. Wilbert, Jessica L. Mark Welch, Gary G. Borisy, James G. Nagy. Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs
    918 -- 919Endre Bakken Stovner, Pål Sætrom. PyRanges: efficient comparison of genomic intervals in Python
    920 -- 921Tao Li, Shaokai Wang, Feng Luo, Fang-Xiang Wu, Jianxin Wang. MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries
    922 -- 924Oscar L. Rodriguez, Anna M. Ritz, Andrew J. Sharp, Ali Bashir. MsPAC: a tool for haplotype-phased structural variant detection
    925 -- 927Hrant Hovhannisyan, Ahmed Hafez, Carlos Lloréns, Toni Gabaldón. CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
    928 -- 929Xin Guo, Bo Zhang, Wenqi Zeng, Shuting Zhao, Dongliang Ge. G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram
    930 -- 933Max Lam, Swapnil Awasthi, Hunna J. Watson, Jackie Goldstein, Georgia Panagiotaropoulou, Vassily Trubetskoy, Robert Karlsson, Oleksander Frei, Chun-Chieh Fan, Ward De Witte, Nina R. Mota, Niamh Mullins, Kim Brügger, S. Hong Lee, Naomi R. Wray, Nora Skarabis, Hailiang Huang, Benjamin M. Neale, Mark J. Daly, Manuel Mattheisen, Raymond Walters, Stephan Ripke. RICOPILI: Rapid Imputation for COnsortias PIpeLIne
    934 -- 935Tomasz J. Kurowski, Fady R. Mohareb. Tersect: a set theoretical utility for exploring sequence variant data
    936 -- 937Eric Hugoson, Wai Tin Lam, Lionel Guy. miComplete: weighted quality evaluation of assembled microbial genomes
    938 -- 939Harry J. Whitwell, Peter A. DiMaggio Jr.. HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs
    940 -- 941Riccardo Delli Ponti, Alexandros Armaos, Andrea Vandelli, Gian Gaetano Tartaglia. CROSSalive: a web server for predicting the in vivo structure of RNA molecules
    942 -- 944Tingyang Li, Ashootosh Tripathi, Fengan Yu, David H. Sherman, Arvind Rao. DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases
    945 -- 947Adriano de Bernardi Schneider, Colby T. Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, Daniel Janies. StrainHub: a phylogenetic tool to construct pathogen transmission networks
    948 -- 949Reshmi Ramakrishnan, Bert Houben, Lukasz Kreft, Alexander Botzki, Joost Schymkowitz, Frederic Rousseau. Protein Homeostasis Database: protein quality control in E.coli
    950 -- 952Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jiménez-García. LightDock goes information-driven
    953 -- 955Aleksandra I. Jarmolinska, Anna Gambin, Joanna I. Sulkowska. Knot_pull - python package for biopolymer smoothing and knot detection
    956 -- 958Iñigo Marcos-Alcalde, Eduardo López-Viñas, Paulino Gómez-Puertas. MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces
    959 -- 960Aeri Lee, Dongsup Kim. CRDS: Consensus Reverse Docking System for target fishing
    961 -- 963Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin. pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes
    964 -- 965Krzysztof Polanski, Matthew D. Young, Zhichao Miao, Kerstin B. Meyer, Sarah A. Teichmann, Jong-Eun Park. BBKNN: fast batch alignment of single cell transcriptomes
    966 -- 969A Ozuna, D. Liberto, R. M. Joyce, K. B. Arnvig, Irene Nobeli. baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data
    970 -- 971Mickaël Canouil, Gerard A. Bouland, Amélie Bonnefond, Philippe Froguel, Leen M. 't Hart, Roderick C. Slieker. NACHO: an R package for quality control of NanoString nCounter data
    972 -- 973Vinícius da Silva, Marcel Ramos, Martien Groenen, Richard Crooijmans, Anna Johansson, Luciana C. A. Regitano, Luiz Coutinho, Ralf Zimmer, Levi Waldron, Ludwig Geistlinger. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes
    974 -- 975Zheng Gao, Jonathan Terhorst, Cristopher V. Van Hout, Stilian Stoev. U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies
    976 -- 977Jordi Bartolome, Rui Alves, Francesc Solsona, Ivan Teixido. EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology
    978 -- 979Leonid Stolbov, Dmitry S. Druzhilovskiy, Anastasia V. Rudik, Dmitry Filimonov, Vladimir Poroikov, Marc C. Nicklaus. AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity
    980 -- 981Rafal Cylwa, Kornel Kielczewski, Marta Machnik, Urszula Oleksiewicz, Przemyslaw Biecek. KRAB ZNF explorer - the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas
    982 -- 983Thoba Lose, Peter van Heusden, Alan Christoffels. COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies

    Volume 36, Issue 24

    5567 -- 5570Kyuto Sonehara, Yukinori Okada. Obelisc: an identical-by-descent mapping tool based on SNP streak
    5571 -- 5581Gabriela Alejandra Merino, Jonathan Raad, Leandro A Bugnon, Cristian A. Yones, Laura Kamenetzky, Juan Claus, Federico Ariel, Diego H. Milone, Georgina Stegmayer. Novel SARS-CoV-2 encoded small RNAs in the passage to humans
    5582 -- 5589Taedong Yun, Helen Li, Pi-Chuan Chang, Michael F. Lin, Andrew Carroll, Cory Y. McLean. Accurate, scalable cohort variant calls using DeepVariant and GLnexus
    5590 -- 5599Matteo Chiara, Pietro Mandreoli, Marco Antonio Tangaro, Anna Maria D'Erchia, Sandro Sorrentino, Cinzia Forleo, David Stephen Horner, Federico Zambelli, Graziano Pesole. VINYL: Variant prIoritizatioN bY survivaL analysis
    5600 -- 5609Zhibin Lv, Pingping Wang, Quan Zou 0001, Qinghua Jiang. Identification of sub-Golgi protein localization by use of deep representation learning features
    5610 -- 5617Dipankar Ranjan Baisya, Stefano Lonardi. Prediction of histone post-translational modifications using deep learning
    5618 -- 5622Joana Pereira, Andrei N. Lupas. The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins
    5623 -- 5631Maryam Rabiee, Siavash Mirarab. SODA: multi-locus species delimitation using quartet frequencies
    5632 -- 5639Matthew Kerin, Jonathan Marchini. A non-linear regression method for estimation of gene-environment heritability
    5640 -- 5648Arunabha Majumdar, Kathryn S. Burch, Tanushree Haldar, Sriram Sankararaman, Bogdan Pasaniuc, W. James Gauderman, John S. Witte. A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes
    5649 -- 5655Jingyi Cai, Tianwei Tan, Siu Hung Joshua Chan. Predicting Nash equilibria for microbial metabolic interactions
    5656 -- 5664Chengqian Lu, Min Zeng, Fang-Xiang Wu, Min Li 0007, Jianxin Wang 0001. Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks
    5665 -- 5671Yuanjing Ma, Hongmei Jiang. NinimHMDA: neural integration of neighborhood information on a multiplex heterogeneous network for multiple types of human Microbe-Disease association
    5672 -- 5677Lili Zhao. Deep neural networks for predicting restricted mean survival times
    5678 -- 5685Po-Ting Lai, Zhiyong Lu. BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer
    5686 -- 5694Marne C. Hagemeijer, Annelotte M. Vonk, Nikhil T. Awatade, Iris A. L. Silva, Christian Tischer, Volker Hilsenstein, Jeffrey M. Beekman, Margarida D. Amaral, Hugo M. Botelho. An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay
    5695 -- 5697Taylor Jones, Samuel B. Day, Luke Myers, James E. Crowe Jr., Cinque S. Soto. ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases
    5698 -- 5700Georgios Iakovou, Mousa Alhazzazi, Steven Hayward, Stephen D. Laycock. DockIT: a tool for interactive molecular docking and molecular complex construction
    5701 -- 5702Constantin Ahlmann-Eltze, Wolfgang Huber. glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
    5703 -- 5705Astghik Sargsyan, Alpha Tom Kodamullil, Shounak Baksi, Johannes Darms, Sumit Madan, Stephan Gebel, Oliver Keminer, Geena Mariya Jose, Helena Balabin, Lauren Nicole Delong, Manfred Kohler, Marc Jacobs 0001, Martin Hofmann-Apitius. The COVID-19 Ontology
    5706 -- 5708Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller. cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
    5709 -- 5711Silvia Benevenuta, Emidio Capriotti, Piero Fariselli. Calibrating variant-scoring methods for clinical decision making
    5712 -- 5718Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Saez-Rodriguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper. The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

    Volume 36, Issue 22-23

    5263 -- 5268Jingwen Guo, David Starr, Huazhang Guo. Classification and review of free PCR primer design software
    5269 -- 5274Uriel Singer, Kira Radinsky, Eric Horvitz. On biases of attention in scientific discovery
    5275 -- 5281Bahar Alipanahi, Martin D. Muggli, Musa Jundi, Noelle R. Noyes, Christina Boucher. Metagenome SNP calling via read-colored de Bruijn graphs
    5282 -- 5290Mohammed Alser, Taha Shahroodi, Juan Gómez-Luna, Can Alkan, Onur Mutlu. SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
    5291 -- 5298Felix Stiehler, Marvin Steinborn, Stephan Scholz, Daniela Dey, Andreas P. M. Weber, Alisandra K. Denton. Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
    5299 -- 5303Xiaohua Douglas Zhang, Dandan Wang, Shixue Sun, Heping Zhang. Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies
    5304 -- 5312Roman Feldbauer, Lukas Gosch, Lukas Lüftinger, Patrick Hyden, Arthur Flexer, Thomas Rattei. DeepNOG: fast and accurate protein orthologous group assignment
    5313 -- 5321Shubham Chandak, Kedar Tatwawadi, Srivatsan Sridhar, Tsachy Weissman. Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
    5322 -- 5329Daniel Munro, Mona Singh 0001. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction
    5330 -- 5336Stefan Schulze, Anne Oltmanns, Christian Fufezan, Julia Krägenbring, Michael Mormann, Mechthild Pohlschröder, Michael Hippler. SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
    5337 -- 5343Lennart Langouche, April Joy C. Aralar, Mridu Sinha, Shelley M. Lawrence, Stephanie I Fraley, Todd P. Coleman. Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
    5344 -- 5350Martin C. Frith, Laurent Noé, Gregory Kucherov. Minimally overlapping words for sequence similarity search
    5351 -- 5360Guillaume E. Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi. Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
    5361 -- 5367Xiaoyang Jing, Jinbo Xu. Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
    5368 -- 5376Krzysztof Szczepaniak, Adriana Bukala, Antonio Marinho da Silva Neto, Jan Ludwiczak, Stanislaw Dunin-Horkawicz. A library of coiled-coil domains: from regular bundles to peculiar twists
    5377 -- 5385Tyler Borrman, Brian G. Pierce, Thom Vreven, Brian M. Baker, Zhiping Weng. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides
    5386 -- 5391Benjamin Hsu, Valeriia Sherina, Matthew N. McCall. Autoregressive modeling and diagnostics for qPCR amplification
    5392 -- 5397Markus Ekvall, Michael Höhle, Lukas Käll. Parallelized calculation of permutation tests
    5398 -- 5404Shaked Bergman, Alon Diament, Tamir Tuller. New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region
    5405 -- 5414Wei Wang, Wei Liu. Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction
    5415 -- 5423Yang Hai, Yalu Wen. A Bayesian linear mixed model for prediction of complex traits
    5424 -- 5431Florian Privé, Julyan Arbel, Bjarni J. Vilhjálmsson. LDpred2: better, faster, stronger
    5432 -- 5438Julian Hecker, F. William Townes, Priyadarshini Kachroo, Cecelia A. Laurie, Jessica Lasky-Su, John Ziniti, Michael H. Cho, Scott T. Weiss, Nan M. Laird, Christoph Lange 0003. A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests
    5439 -- 5447Ziqiao Wang, Peng Wei 0005. IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
    5448 -- 5455Da Kuang, Rebecca Truty, Jochen Weile, Britt Johnson, Keith Nykamp, Carlos Araya, Robert L. Nussbaum, Frederick P. Roth. Prioritizing genes for systematic variant effect mapping
    5456 -- 5464Mengyun Yang, Lan Huang, Yunpei Xu, Chengqian Lu, Jianxin Wang 0001. Heterogeneous graph inference with matrix completion for computational drug repositioning
    5465 -- 5472Stefano Sinisi, Vadim Alimguzhin, Toni Mancini, Enrico Tronci, Brigitte Leeners. Complete populations of virtual patients for in silico clinical trials
    5473 -- 5480Rodrigo Santibañez, Daniel Garrido, Alberto J. M. Martin. Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages
    5481 -- 5491Cong Shen, Jiawei Luo, Wenjue Ouyang, Pingjian Ding, Xiangtao Chen. IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors
    5492 -- 5498Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu. FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery
    5499 -- 5506Shuai Wang, Yiqi Jiang, Shuai Cheng Li 0001. PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data
    5507 -- 5513Mateusz Kudla, Kaja Gutowska, Jaroslaw Synak, Mirko Weber, Katrin Sophie Bohnsack, Piotr Lukasiak, Thomas Villmann, Jacek Blazewicz, Marta Szachniuk. Virxicon: a lexicon of viral sequences
    5514 -- 5515Roman Martin, Thomas Hackl, Georges Hattab, Matthias G. Fischer, Dominik Heider. MOSGA: Modular Open-Source Genome Annotator
    5516 -- 5518Fábio K. Mendes, Dan Vanderpool, Ben Fulton, Matthew W. Hahn. CAFE 5 models variation in evolutionary rates among gene families
    5519 -- 5521David Heller, Martin Vingron. SVIM-asm: structural variant detection from haploid and diploid genome assemblies
    5522 -- 5523Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David Stephen Horner, Graziano Pesole. CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
    5524 -- 5525Anand Mayakonda, Maximilian Schönung, Joschka Hey, Rajbir Nath Batra, Clarissa Feuerstein-Akgoz, Kristin Köhler, Daniel B. Lipka, Rocio Sotillo, Christoph Plass, Pavlo Lutsik, Reka Toth. Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data
    5526 -- 5527Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte. RCSB Protein Data Bank 1D tools and services
    5528 -- 5529Arthur Ecoffet, Frédéric Poitevin, Khanh Dao Duc. MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX
    5530 -- 5532Emma H. Gail, Anup D. Shah, Ralf B. Schittenhelm, Chen Davidovich. crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry
    5533 -- 5534Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C. E. Tosatto. MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins
    5535 -- 5536Daniel G. Bunis, Jared Andrews, Gabriela K. Fragiadakis, Trevor D. Burt, Marina Sirota. dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit
    5537 -- 5538Michael F. Lin, Xiaodong Bai, William J. Salerno, Jeffrey G. Reid. Sparse Project VCF: efficient encoding of population genotype matrices
    5539 -- 5541Xiaofan Lu, Jialin Meng, Yujie Zhou, Liyun Jiang, Fangrong Yan. MOVICS: an R package for multi-omics integration and visualization in cancer subtyping
    5542 -- 5544Jeffrey West, Yongqian Ma, Artem Kaznatcheev, Alexander R. A. Anderson. IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations
    5545 -- 5547Kexin Huang, Tianfan Fu, Lucas M. Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun. DeepPurpose: a deep learning library for drug-target interaction prediction
    5548 -- 5550Jan P. Buchmann, Edward C. Holmes. Collecting and managing taxonomic data with NCBI-taxonomist
    5551 -- 5552Gavin Rhys Lloyd, Andris Jankevics, Ralf J. M. Weber. struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
    5553 -- 5555Giuseppe Sgroi, Giulia Russo, Francesco Pappalardo 0001. PETAL: a Python tool for deep analysis of biological pathways
    5556 -- 5557Michael Milton, Natalie Thorne. aCLImatise: automated generation of tool definitions for bioinformatics workflows
    5558 -- 5560Michiel Van Bel, Klaas Vandepoele. Comment on 'Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants': the importance of taking the GO graph structure into account
    5561 -- 0. Corrigendum to: HALPER facilitates the identification of regulatory element orthologs across species
    5562 -- 0Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra Orchard, Andrea H. Auchincloss, Delphine Baratin, Jerven T. Bolleman, Elisabeth Coudert, Edouard De Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia N. Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C. R. Vinayaka, Lai-Su Yeh, Darren A. Natale, Kati Laiho, Maria Jesus Martin, Alexandre Renaux, Klemens Pichler. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
    5563 -- 5564Junlin Xu, Lijun Cai, Bo Liao, Wen Zhu, Jialiang Yang. CMF-Impute: an accurate imputation tool for single cell RNA-seq data
    5565 -- 0Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu. LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations
    5566 -- 0. LFQC: A lossless compression algorithm for FASTQ files

    Volume 36, Issue 21

    5129 -- 5132Diogo Pratas, Jorge Miguel Silva. Persistent minimal sequences of SARS-CoV-2
    5133 -- 5138Shijie Qin, Xinyi Xia, Xuejia Shi, Xinglai Ji, Fei Ma, Liming Chen. Mechanistic insights into SARS-CoV-2 epidemic via revealing the features of SARS-CoV-2 coding proteins and host responses upon its infection
    5139 -- 5144Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos, Glenn Hickey, Vincenza Colonna, Benedict Paten, Erik Garrison. Efficient dynamic variation graphs
    5145 -- 5150Gamze Gürsoy, Charlotte M. Brannon, Fabio C. P. Navarro, Mark Gerstein. FANCY: fast estimation of privacy risk in functional genomics data
    5151 -- 5158Xiyu Peng, Karin S. Dorman. AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data
    5159 -- 5168Xiaoyong Pan, Jasper Zuallaert, Xi Wang, Hong-bin Shen, Elda Posada Campos, Denys O. Marushchak, Wesley De Neve. ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity
    5169 -- 5176Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou. Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network
    5177 -- 5186Yi-Jun Tang, Yihe Pang, Bin Liu. IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning
    5187 -- 5193Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor, Shan He. PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data
    5194 -- 5204Dimitris V. Manatakis, Aaron Vandevender, Elias S. Manolakos. An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures
    5205 -- 5213Mete Akgün, Ali Burak Ünal, Bekir Ergüner, Nico Pfeifer, Oliver Kohlbacher. Identifying disease-causing mutations with privacy protection
    5214 -- 5222Canhong Wen, Hailong Ba, Wenliang Pan, Meiyan Huang. Co-sparse reduced-rank regression for association analysis between imaging phenotypes and genetic variants
    5223 -- 5228Tianzhong Yang, Peng Wei 0005, Wei Pan. Integrative analysis of multi-omics data for discovering low-frequency variants associated with low-density lipoprotein cholesterol levels
    5229 -- 5236Ruey Leng Loo, Queenie Chan, Henrik Antti, Jia V. Li, H. Ashrafian, Paul Elliott, Jeremiah Stamler, Jeremy K. Nicholson, Elaine Holmes, Julien Wist. Strategy for improved characterization of human metabolic phenotypes using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS)
    5237 -- 5246Yasin Ilkagan Tepeli, Ali Burak Ünal, Furkan Mustafa Akdemir, Oznur Tastan. PAMOGK: a pathway graph kernel-based multiomics approach for patient clustering
    5247 -- 5254James H. Joly, William E. Lowry, Nicholas A. Graham. Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets
    5255 -- 5261Keno K. Bressem, Lisa C. Adams, Robert A. Gaudin, Daniel Tröltzsch, Bernd Hamm, Marcus R. Makowski, Chan-Yong Schüle, Janis Lucas Vahldiek, Stefan Markus Niehues. Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports
    5262 -- 5263Legana C. H. W. Fingerhut, David J. Miller, Jan M. Strugnell, Norelle L. Daly, Ira Cooke. ampir: an R package for fast genome-wide prediction of antimicrobial peptides
    5264 -- 5266Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals. PEWO: a collection of workflows to benchmark phylogenetic placement
    5267 -- 5268Jon D. Hill. Gene Teller: an extensible Alexa Skill for gene-relevant databases
    5269 -- 5270Dongliang Liu, Mengying Han, Yu Tian, Linlin Gong, Cancan Jia, Pengli Cai, Weizhong Tu, Junni Chen, Qian-Nan Hu. Cell2Chem: mining explored and unexplored biosynthetic chemical spaces
    5271 -- 5273René L. Warren, Inanç Birol. HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset

    Volume 36, Issue 20

    4977 -- 4983Jing-Bo Zhou, Yao Xiong, Ke An, Zhi-Qiang Ye, Yun-Dong Wu. IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions
    4984 -- 4990Prateek Gupta, Pankaj Singh Dholaniya, Sameera Devulapalli, Nilesh R. Tawari, Yellamaraju Sreelakshmi, Rameshwar Sharma. Reanalysis of genome sequences of tomato accessions and its wild relatives: development of Tomato Genomic Variation (TGV) database integrating SNPs and INDELs polymorphisms
    4991 -- 4999Matej Lexa, Pavel Jedlicka, Ivan Vanat, Michal Cervenanský, Eduard Kejnovský. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
    5000 -- 5006Lucile Broseus, Aubin Thomas, Andrew J. Oldfield, Dany Severac, Emeric Dubois, William Ritchie. TALC: Transcript-level Aware Long-read Correction
    5007 -- 5013Martin R. Smith. Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees
    5014 -- 5020Nina I Ilieva, Nicola Galvanetto, Michele Allegra, Marco Brucale, Alessandro Laio. Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples
    5021 -- 5026Gang Xu, Qinghua Wang, Jianpeng Ma. OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks
    5027 -- 5036Mingzhou Song 0001, Hua Zhong. Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers
    5037 -- 5044Martin E. Guerrero-Gimenez, J. M. Fernandez-Muñoz, B. J. Lang, K. M. Holton, D. R. Ciocca, C. A. Catania, F. C. M. Zoppino. Galgo: a bi-objective evolutionary meta-heuristic identifies robust transcriptomic classifiers associated with patient outcome across multiple cancer types
    5045 -- 5053Moritz Hess, Maren Hackenberg, Harald Binder. Exploring generative deep learning for omics data using log-linear models
    5054 -- 5060Xiangyu Liu, Di Li, Juntao Liu, Zhengchang Su, Guojun Li. RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters
    5061 -- 5067Ali Akbar Jamali, Anthony J. Kusalik, Fang-Xiang Wu. MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization
    5068 -- 5075Yue Wu, Michael T. Judge, Jonathan Arnold, Suchendra M. Bhandarkar, Arthur Edison. RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking
    5076 -- 5085Nikolay Russkikh, Denis V. Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev. Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
    5086 -- 5092Antti Häkkinen, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Luca Pasquini, Mauro Biffoni, Rainer Lehtonen, Sampsa Hautaniemi. qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets
    5093 -- 5103Mark Kittisopikul, Amir Vahabikashi, Takeshi Shimi, Robert D. Goldman, Khuloud Jaqaman. Adaptive multiorientation resolution analysis of complex filamentous network images
    5104 -- 5106Kirill Zinovjev, Marc van der Kamp. Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible
    5107 -- 5108Francesco Ambrosetti, Tobias Hegelund Olsen, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatili, Alexandre M. J. J. Bonvin. proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking
    5109 -- 5111Ren Kong, Guangbo Yang, Rui Xue, Ming Liu, Feng Wang, Jianping Hu, Xiaoqiang Guo, Shan Chang. COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19
    5112 -- 5114Max Hebditch, Jim Warwicker. Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses
    5115 -- 5116August E. Woerner, Jennifer Churchill Cihlar, Utpal Smart, Bruce Budowle. Numt identification and removal with RtN!
    5117 -- 5119Amel Bekkar, Anita Nasrallah, Nicolas Guex, Lluis Fajas, Ioannis Xenarios, Isabel C. Lopez-Mejia. PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling
    5120 -- 5121Arjun Magge, Davy Weissenbacher, Karen O'Connor, Tasnia Tahsin, Graciela Gonzalez-Hernandez, Matthew Scotch. GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography
    5122 -- 5123Christiana N. Fogg, Ron Shamir, Diane E. Kovats. Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient
    5124 -- 5125Christiana N. Fogg, Ron Shamir, Diane E. Kovats. 2019 ISCB Overton Prize: Christophe Dessimoz
    5126 -- 0Christiana N. Fogg, Ron Shamir, Diane E. Kovats. 2019 Outstanding Contributions to ISCB Awarded to Barb Bryant
    5127 -- 5128Christiana N. Fogg, Ron Shamir, Diane E. Kovats. 2019 ISCB Innovator Award Recognizes William Stafford Noble

    Volume 36, Issue 2

    331 -- 338William H. Majoros, Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, Cong Guo, William L. Lowe, Denise M. Scholtens, M. Geoffrey Hayes, Timothy E. Reddy, Andrew S. Allen. Bayesian estimation of genetic regulatory effects in high-throughput reporter assays
    339 -- 346Ran Su, Jiahang Zhang, Xiaofeng Liu 0004, Leyi Wei. Identification of expression signatures for non-small-cell lung carcinoma subtype classification
    347 -- 355Chan Wang, Jiyuan Hu, Martin J. Blaser, Huilin Li. Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data
    356 -- 363Terry Ma, Di Xiao, Xin-xing. MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies
    364 -- 372Sierra S. Nishizaki, Natalie Ng, Shengcheng Dong, Robert S. Porter, Cody Morterud, Colten Williams, Courtney Asman, Jessica A Switzenberg, Alan P. Boyle. Predicting the effects of SNPs on transcription factor binding affinity
    373 -- 379Patrick Sorn, Christoph Holtsträter, Martin Löwer, Ugur Sahin, David Weber. ArtiFuse - computational validation of fusion gene detection tools without relying on simulated reads
    380 -- 387Alfredo Velasco II, Benjamin T. James, Vincent D. Wells, Hani Z. Girgis. Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models
    388 -- 392Cong Pian, Guang-Le Zhang, Fei Li, Xiaodan Fan. MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model
    393 -- 399Michele Berselli, Enrico Lavezzo, Stefano Toppo. QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable
    400 -- 407Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin. Haplotype-aware graph indexes
    408 -- 415Martin C. Frith. How sequence alignment scores correspond to probability models
    416 -- 421Chloé Dimeglio, Stéphanie Raymond, Nicolas Jeanne, Christelle Reynès, Romain Carcenac, Caroline Lefebvre, Michelle Cazabat, Florence Nicot, Pierre Delobel, Jacques Izopet. THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage
    422 -- 429Maxat Kulmanov, Robert Hoehndorf. DeepGOPlus: improved protein function prediction from sequence
    430 -- 436Roberto Del Amparo, Alberto Vicens, Miguel Arenas. The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation
    437 -- 448Di Wang, Ling Geng, Yu-Jun Zhao, Yang Yang 0030, Yan Huang, Yang Zhang, Hong-bin Shen. Artificial intelligence-based multi-objective optimization protocol for protein structure refinement
    449 -- 461Justin Chan, Jinhao Zou, Christopher Llynard Ortiz, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang. DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing
    462 -- 469Gregor Entzian, Martin Raden. pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
    470 -- 477Badri Adhikari. DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout
    478 -- 486Zeyu Wen, Jiahua He, Sheng-You Huang. Topology-independent and global protein structure alignment through an FFT-based algorithm
    487 -- 495Adib Shafi, Tin Nguyen 0001, Azam Peyvandi-Pour, Sorin Draghici. GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis
    496 -- 503Wanwen Zeng, Yong Wang, Rui Jiang 0001. Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
    504 -- 513Christelle Reynès, Guilhem Kister, Marine Rohmer, Tristan Bouschet, Annie Varrault, Emeric Dubois, Stéphanie Rialle, Laurent Journot, Robert Sabatier. ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses
    514 -- 523Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot. MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network
    524 -- 532Zhiguang Huo, Shaowu Tang, Yongseok Park, George C. Tseng. P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications
    533 -- 538Feiyang Ma, Matteo Pellegrini. ACTINN: automated identification of cell types in single cell RNA sequencing
    539 -- 545Li Chen, Feng Wang, Emily C. Bruggeman, Chao Li, Bing Yao. circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
    546 -- 551Kyungsoo Kim, Sunmo Yang, Sang-Jun Ha, Insuk Lee. VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data
    552 -- 557Lerato E. Magosi, Anuj Goel, Jemma C. Hopewell. Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease
    558 -- 567Mikel Hernaez, Charles Blatti, Olivier Gevaert. Comparison of single and module-based methods for modeling gene regulatory networks
    568 -- 577Jiajie Peng, Junya Lu, Donghee Hoh, Ayesha S. Dina, Xuequn Shang, David M. Kramer 0001, Jin Chen. Identifying emerging phenomenon in long temporal phenotyping experiments
    578 -- 585Ning Shi, Zexuan Zhu, Ke Tang, David Parker, Shan He 0001. ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics
    586 -- 593Boseung Choi, Yu-Yu Cheng, Selahattin Cinar, William Ott, Matthew R. Bennett, Kresimir Josic, Jae Kyoung Kim. Bayesian inference of distributed time delay in transcriptional and translational regulation
    594 -- 602Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer, Daniel Weindl. Efficient parameterization of large-scale dynamic models based on relative measurements
    603 -- 610Sameh K. Mohamed, Vít Novácek, Aayah Nounu. Discovering protein drug targets using knowledge graph embeddings
    611 -- 620Peiliang Lou, Antonio Jimeno-Yepes, Zai Zhang, Qinghua Zheng, Xiangrong Zhang, Chen Li 0032. BioNorm: deep learning-based event normalization for the curation of reaction databases
    621 -- 628Siva Rajesh Kasa, Sakyajit Bhattacharya, Vaibhav Rajan. Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping
    629 -- 636Sami Tabib, Denis Larocque. Non-parametric individual treatment effect estimation for survival data with random forests
    637 -- 643Shankai Yan, Ka Chun Wong. Context awareness and embedding for biomedical event extraction
    644 -- 646R. N. Ramirez, K. Bedirian, S. M. Gray, A Diallo. DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data
    647 -- 648Grace Meng, Marva Tariq, Swati Jain, Shereef Elmetwaly, Tamar Schlick. RAG-Web: RNA structure prediction/design using RNA-As-Graphs
    649 -- 650Ramiro Magno, Ana-Teresa Maia. gwasrapidd: an R package to query, download and wrangle GWAS catalog data
    651 -- 0Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

    Volume 36, Issue 19

    4827 -- 4832C. S. Casimiro-Soriguer, M. M. Rigual, A. M. Brokate-Llanos, M. J. Muñoz, A. Garzón, A. J. Pérez-Pulido, J. Jimenez. Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome
    4833 -- 4837Dan Wang, Hui Tang, Jian-feng Liu, Shizhong Xu, Qin Zhang, Chao Ning. Rapid epistatic mixed-model association studies by controlling multiple polygenic effects
    4838 -- 4845Yan Song, Haixu Tang, Haoyu Zhang, Qin Zhang. Overlap detection on long, error-prone sequencing reads via smooth q-gram
    4846 -- 4853Yan Wang, Miguel Correa Marrero, Marnix H. Medema, Aalt D. J. van Dijk. Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines
    4854 -- 4859Nico Borgsmüller, Jose Bonet, Francesco Marass, Abel Gonzalez-Perez, Núria López-Bigas, Niko Beerenwinkel. BnpC: Bayesian non-parametric clustering of single-cell mutation profiles
    4860 -- 4868Kenong Su, Zhijin Wu, Hao Wu 0003. Simulation, power evaluation and sample size recommendation for single-cell RNA-seq
    4869 -- 4875Ruhul Amin, Chowdhury Rafeed Rahman, Sajid Ahmed, Md. Habibur Rahman Sifat, Md Nazmul Khan Liton, Md. Moshiur Rahman, Md Zahid Hossain Khan, Swakkhar Shatabda. iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters
    4876 -- 4884Khalique Newaz, Gabriel Wright, Jacob Piland, Jun Li 0052, Patricia L. Clark, Scott J. Emrich, Tijana Milenkovic. Network analysis of synonymous codon usage
    4885 -- 4893Baoshan Ma, Mingkun Fang, Xiangtian Jiao. Inference of gene regulatory networks based on nonlinear ordinary differential equations
    4894 -- 4901Yi Shi, Zehua Guo, Xianbin Su, Luming Meng, Mingxuan Zhang, Jing Sun, Chao Wu, Minhua Zheng, Xueyin Shang, Xin Zou, Wangqiu Cheng, Yaoliang Yu, Yujia Cai, Chaoyi Zhang, Weidong Cai 0001, Lin-tai Da, Guang He, Zeguang Han. DeepAntigen: a novel method for neoantigen prioritization via 3D genome and deep sparse learning
    4902 -- 4909Peifeng Ruan, Shuang Wang, Hua Liang. mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs
    4910 -- 4917Hai-Long Trieu, Thy Thy Tran, Anh-Khoa Duong Nguyen, Anh Nguyen, Makoto Miwa, Sophia Ananiadou. DeepEventMine: end-to-end neural nested event extraction from biomedical texts
    4918 -- 4927Yahui Long, Min Wu 0008, Chee-Keong Kwoh 0001, Jiawei Luo, Xiaoli Li 0001. Predicting human microbe-drug associations via graph convolutional network with conditional random field
    4928 -- 4934Hongxu Ding, Andrew D. Bailey, Miten Jain, Hugh Olsen, Benedict Paten. Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts
    4935 -- 4941Yao Yao, Ihor Smal, Ilya Grigoriev, Anna Akhmanova, Erik Meijering. Deep-learning method for data association in particle tracking
    4942 -- 4950Canhong Wen, Yuhui Yang, Quan Xiao, Meiyan Huang, Wenliang Pan. Genome-wide association studies of brain imaging data via weighted distance correlation
    4951 -- 4954Lina Yang, Shuang Jiang, Bibo Jiang, Dajiang J. Liu, Xiaowei Zhan. Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset
    4955 -- 4956Lili Dong, Jianan Wang, Guohua Wang. BYASE: a Python library for estimating gene and isoform level allele-specific expression
    4957 -- 4959David B. Blumenthal, Lorenzo Viola, Markus List, Jan Baumbach, Paolo Tieri, Tim Kacprowski. EpiGEN: an epistasis simulation pipeline
    4960 -- 4962Lauren Marazzi, Andrew Gainer-Dewar, Paola Vera-Licona. OCSANA+: optimal control and simulation of signaling networks from network analysis
    4963 -- 4964Mahiar Mahjoub, Daphne Ezer. PAFway: pairwise associations between functional annotations in biological networks and pathways
    4965 -- 4967James Luke Gallant, Tiaan Heunis, Samantha Leigh Sampson, Wilbert Bitter. ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant
    4968 -- 4969Zhicheng Zhang, Xiaokun Liang, Wenjian Qin, Shaode Yu, Yaoqin Xie. matFR: a MATLAB toolbox for feature ranking
    4970 -- 4971Gonzalo Neira, Diego Cortez, Joaquin Jil, David S. Holmes. AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata
    4972 -- 4974Janel L. Davis, Brian Soetikno, Ki-Hee Song, Yang Zhang, Cheng Sun, Hao F. Zhang. RainbowSTORM: an open-source ImageJ plug-in for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction
    4975 -- 0Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

    Volume 36, Issue 18

    4675 -- 4681Yuansheng Liu, Limsoon Wong, Jinyan Li. Allowing mutations in maximal matches boosts genome compression performance
    4682 -- 4690Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Héctor Corrada Bravo. Epiviz File Server: Query, transform and interactively explore data from indexed genomic files
    4691 -- 4698Bikash K. Bhandari, Paul P. Gardner, Chun Shen Lim. Solubility-Weighted Index: fast and accurate prediction of protein solubility
    4699 -- 4705Hamid Bagheri, Andrew J. Severin, Hridesh Rajan. Detecting and correcting misclassified sequences in the large-scale public databases
    4706 -- 4713Connor Morgan-Lang, Ryan McLaughlin, Zachary Armstrong, Grace Zhang, Kevin Chan, Steven J. Hallam. TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
    4714 -- 4720Farzin Sohraby, Mostafa Javaheri Moghadam, Masoud Aliyar, Hassan Aryapour. A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase
    4721 -- 4728Jike Wang, Dongsheng Cao, Cunchen Tang, Xi Chen, Huiyong Sun, Tingjun Hou. Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning
    4729 -- 4738Jian Zhang 0020, Sina Ghadermarzi, Lukasz A. Kurgan. Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins
    4739 -- 4748Jia-Bin Chen, Shan-Shan Dong, Shi Yao, Yuan-Yuan Duan, Wei-Xin Hu, Hao Chen, Nai-Ning Wang, Xiao-Feng Chen, Ruo-Han Hao, Hlaing Nwe Thynn, Ming-Rui Guo, Yu-Jie Zhang, Yu Rong, Yi-Xiao Chen, Fu-Ling Zhou, Yan Guo, Tie-Lin Yang. Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression
    4749 -- 4756Alexey A. Shadrin, Oleksandr Frei, Olav B. Smeland, Francesco Bettella, Kevin S. O'Connell, Osman Gani, Shahram Bahrami, Tea K. E. Uggen, Srdjan Djurovic, Dominic Holland, Ole A. Andreassen, Anders M. Dale. Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR
    4757 -- 4764Liran Juan, Yongtian Wang, Jingyi Jiang, Qi Yang, Guohua Wang, Yadong Wang. Evaluating individual genome similarity with a topic model
    4765 -- 4773Marieke L. Kuijjer, Maud Fagny, Alessandro Marin, John Quackenbush, Kimberly Glass. PUMA: PANDA Using MicroRNA Associations
    4774 -- 4780Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert. Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
    4781 -- 4788Yan Ren, Siva Sivaganesan, Nicholas A. Clark, Lixia Zhang, Jacek Biesiada, Wen Niu, David R. Plas, Mario Medvedovic. Predicting mechanism of action of cellular perturbations with pathway activity signatures
    4789 -- 4796Alessandra Cabassi, Paul D. W. Kirk. Multiple kernel learning for integrative consensus clustering of omic datasets
    4797 -- 4804Shu Yang, Xiaoxi Liu, Raymond T. Ng. ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins
    4805 -- 4809Kieran Walsh, Mircea A. Voineagu, Fatemeh Vafaee, Irina Voineagu. TDAview: an online visualization tool for topological data analysis
    4810 -- 4812Qingxi Meng, Idoia Ochoa, Mikel Hernaez. GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form
    4813 -- 4816Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto. Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens
    4817 -- 4818Gregor Sturm, Tamás Szabo, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data
    4819 -- 4821Anastasiia Kim, James H. Degnan. PRANC: ML species tree estimation from the ranked gene trees under coalescence
    4822 -- 4824Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Céline Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier, David P. Parsons. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
    4825 -- 4826Vo Hong Thanh. RSSALib: a library for stochastic simulation of complex biochemical reactions

    Volume 36, Issue 17

    4535 -- 4543Viivi Halla-aho, Harri Lähdesmäki. LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation
    4544 -- 4550Divya Sharma, Andrew D. Paterson, Wei Xu. TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction
    4551 -- 4559Rongshan Yu, Wenxian Yang. ScaleQC: a scalable lossy to lossless solution for NGS data compression
    4560 -- 4567Mikhail D. Magnitov, Veronika S. Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, Alexander V. Tyakht. Benchmark of software tools for prokaryotic chromosomal interaction domain identification
    4568 -- 4575Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. SVJedi: genotyping structural variations with long reads
    4576 -- 4582Yaobin Ke, Jiahua Rao, Huiying Zhao, Yutong Lu, Nong Xiao, Yuedong Yang. Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting
    4583 -- 4589Safyan Aman Memon, Kinaan Aamir Khan, Hammad Naveed. HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network
    4590 -- 4598Robert Page, Ruriko Yoshida, Leon Zhang. Tropical principal component analysis on the space of phylogenetic trees
    4599 -- 4608Mostofa Rafid Uddin, Sazan Mahbub, Mohammad Saifur Rahman, Md. Shamsuzzoha Bayzid. SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction
    4609 -- 4615Garrett Jenkinson, Yang I Li, Shubham Basu, Margot A. Cousin, Gavin R. Oliver, Eric W. Klee. LeafCutterMD: an algorithm for outlier splicing detection in rare diseases
    4616 -- 4625Theodoulos Rodosthenous, Vahid Shahrezaei, Marina Evangelou. Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study
    4626 -- 4632Yonglin Peng, Meng Yuan, Juncai Xin, Xinhua Liu, Ju Wang 0007. Screening novel drug candidates for Alzheimer's disease by an integrated network and transcriptome analysis
    4633 -- 4642Karim Abbasi, Parvin Razzaghi, Antti Poso, Massoud Amanlou, Jahan B. Ghasemi, Ali Masoudi-Nejad. DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks
    4649 -- 4654Mihai Glont, Chinmay Arankalle, Krishan K. Tiwari, Tung V. N. Nguyen, Henning Hermjakob, Rahuman S. Malik-Sheriff. BioModels Parameters: a treasure trove of parameter values from published systems biology models
    4655 -- 4657Marianne L. Slaten, Yen On Chan, Vivek Shrestha, Alexander E. Lipka, Ruthie Angelovici. HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS
    4658 -- 4659César Piñeiro, José Manuel Abuín, Juan Carlos Pichel. Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies
    4660 -- 4661Milosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco. Molywood: streamlining the design and rendering of molecular movies
    4662 -- 4663Colin Farrell, Sagi Snir, Matteo Pellegrini. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework
    4664 -- 4667Erika Gardini, Federico M. Giorgi, Sergio Decherchi, Andrea Cavalli. Spathial: an R package for the evolutionary analysis of biological data
    4668 -- 4670Tim Scherr, Karolin Streule, Andreas Bartschat, Moritz Böhland, Johannes Stegmaier, Markus Reischl, Véronique Orian-Rousseau, Ralf Mikut. BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images
    4671 -- 4672Alex J. Cornish, Daniel Chubb, Anna Frangou, Phuc H. Hoang, Martin Kaiser, David C. Wedge, Richard S. Houlston. Reference bias in the Illumina Isaac aligner
    4673 -- 0Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing. A Blind and Independent Benchmark Study for Detecting Differentially Methylated Regions in Plants
    4674 -- 0Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay. iBioProVis: interactive visualization and analysis of compound bioactivity space

    Volume 36, Issue 16

    4383 -- 4388Xiaoqiong Wei, Chengxin Zhang, Peter L. Freddolino, Yang Zhang, Zhiyong Lu. Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons
    4389 -- 4398Shouheng Tuo, Haiyan Liu, Hao Chen. Multipopulation harmony search algorithm for the detection of high-order SNP interactions
    4399 -- 4405Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia C. F. Prosperi, Inanc Birol. Portable nanopore analytics: are we there yet?
    4406 -- 4414Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng, Arne Elofsson. TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments
    4415 -- 4422Christopher Heje Grønbech, Maximillian Fornitz Vording, Pascal N. Timshel, Casper Kaae Sønderby, Tune H. Pers, Ole Winther, Bonnie Berger. scVAE: variational auto-encoders for single-cell gene expression data
    4423 -- 4431Wenbo Xu 0003, Yan Tian, Siye Wang, Yupeng Cui, Pier Luigi Martelli. Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing
    4432 -- 4439Yet Nguyen, Dan Nettleton. rmRNAseq: differential expression analysis for repeated-measures RNA-seq data
    4440 -- 4448Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz. Predicting target genes of non-coding regulatory variants with IRT
    4449 -- 4457Florian Privé, Keurcien Luu, Michael G. B. Blum, John J. McGrath, Bjarni J. Vilhjálmsson, Russell Schwartz. Efficient toolkit implementing best practices for principal component analysis of population genetic data
    4458 -- 4465Ruichu Cai, Xuexin Chen, Yuan Fang, Min Wu 0008, Yuexing Hao, Jonathan D. Wren. Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers
    4466 -- 4472Tianyi Zhao, Yang Hu 0008, Jiajie Peng, Liang Cheng 0006, Pier Luigi Martelli. DeepLGP: a novel deep learning method for prioritizing lncRNA target genes
    4473 -- 4482Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu. Automated inference of Boolean models from molecular interaction maps using CaSQ
    4483 -- 4489Zexuan Sun, Shujun Huang, Peiran Jiang, Pingzhao Hu, Zhiyong Lu. DTF: Deep Tensor Factorization for predicting anticancer drug synergy
    4490 -- 4497Siqi Liang, Haiyuan Yu, Jonathan D. Wren. Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach
    4498 -- 4505Sen Li, Qi Yang, Hao Jiang, Jesús A. Cortés-Vecino, Yang Zhang 0057, Alfonso Valencia. Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL)
    4506 -- 4507Guillermo Dufort y Álvarez, Gadiel Seroussi, Pablo Smircich, José Sotelo, Idoia Ochoa, Álvaro Martín, Inanç Birol. ENANO: Encoder for NANOpore FASTQ files
    4508 -- 4509Valentin Zulkower, Susan Rosser, Yann Ponty. DNA Chisel, a versatile sequence optimizer
    4510 -- 4512Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora. SOS: online probability estimation and generation of T-and B-cell receptors
    4513 -- 4515Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty. Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser
    4516 -- 4518Weronika Puchala, Michal Burdukiewicz, Michal Kistowski, Katarzyna A. Dabrowska, Aleksandra E. Badaczewska-Dawid, Dominik Cysewski, Michal Dadlez, Yann Ponty. HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments
    4519 -- 4520Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz. IBDkin: fast estimation of kinship coefficients from identity by descent segments
    4521 -- 4522Ilja M. Nolte, Russell Schwartz. Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics
    4523 -- 4524Enio Gjerga, Panuwat Trairatphisan, Attila Gabor, Hermann Koch, Céline Chevalier, Franceco Ceccarelli, Aurélien Dugourd, Alexander Mitsos, Julio Saez-Rodriguez, Jonathan D. Wren. Converting networks to predictive logic models from perturbation signalling data with CellNOpt
    4525 -- 4526Oriol Canela-Xandri, Samira Anbari, Javier Buceta, Alfonso Valencia. TiFoSi: an efficient tool for mechanobiology simulations of epithelia
    4527 -- 4529Ales Saska, David Tichy, Robert Moore, Achilles Rasquinha, Caner Akdas, Xiaodong Zhao, Renato Fabbri, Ana Jelicic, Gaurav Grover, Himanshu Jotwani, Mohamed Shadab, Resa M. K. Helikar, Tomás Helikar, Jonathan D. Wren. ccNetViz: a WebGL-based JavaScript library for visualization of large networks
    4530 -- 4531Charles E. Vejnar, Antonio J. Giraldez, Pier Luigi Martelli. LabxDB: versatile databases for genomic sequencing and lab management
    4532 -- 4534Joselyn Chávez, Carmina Barberena-Jonas, Jesus E. Sotelo-Fonseca, José Alquicira-Hernández, Heladia Salgado, Leonardo Collado-Torres, Alejandro Reyes. Programmatic access to bacterial regulatory networks with regutools

    Volume 36, Issue 15

    4233 -- 4239Di Ran, Shanshan Zhang, Nicholas Lytal, Lingling An. scDoc: correcting drop-out events in single-cell RNA-seq data
    4240 -- 4247Rohan Shah, Gabriel Keeble-Gagnère, Alex Whan. Accurate calling of homeoallelic genotypes of iSelect markers using inbred structured populations
    4248 -- 4254Nazia Fatima, Luis Rueda. iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps
    4255 -- 4262Si-Yi Chen, Chun-Jie Liu, Qiong Zhang, An-Yuan Guo. An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data
    4263 -- 4268Zijie Shen, Quan Zou 0001. Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites
    4269 -- 4275Haidong Yan, Aureliano Bombarely, Song Li. DeepTE: a computational method for de novo classification of transposons with convolutional neural network
    4276 -- 4282Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song. PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs
    4283 -- 4290Jiajing Xie, Yang Xu, Haifeng Chen, Meirong Chi, Jun He, Meifeng Li, Hui Liu, Jie Xia, Qingzhou Guan, Zheng Guo 0002, Haidan Yan. Identification of population-level differentially expressed genes in one-phenotype data
    4291 -- 4295Philipp Angerer, David S. Fischer, Fabian J. Theis, Antonio Scialdone, Carsten Marr. Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
    4296 -- 4300Maria Solovey, Antonio Scialdone. COMUNET: a tool to explore and visualize intercellular communication
    4301 -- 4308Stephan Seifert, Sven Gundlach, Olaf Junge, Silke Szymczak, Luigi Martelli. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study
    4309 -- 4315Gayathri Sambamoorthy, Karthik Raman 0002. MinReact: a systematic approach for identifying minimal metabolic networks
    4316 -- 4322Yifan Deng, Xinran Xu, Yang Qiu, Jingbo Xia, Wen Zhang, Shichao Liu. A multimodal deep learning framework for predicting drug-drug interaction events
    4323 -- 4330Cong Sun, Zhihao Yang, Leilei Su, Lei Wang, Yin Zhang 0009, Hongfei Lin, Jian Wang. Chemical-protein interaction extraction via Gaussian probability distribution and external biomedical knowledge
    4331 -- 4338Mei Zuo, Yang Zhang. Dataset-aware multi-task learning approaches for biomedical named entity recognition
    4339 -- 4340Xiaoyu Zhang, Irene M. Kaplow, Morgan Wirthlin, Tae-Yoon Park, Andreas R. Pfenning. HALPER facilitates the identification of regulatory element orthologs across species
    4341 -- 4344Christopher J. Neely, Elaina D. Graham, Benjamin J. Tully. MetaSanity: an integrated microbial genome evaluation and annotation pipeline
    4345 -- 4347Loïc Meunier, Pierre Tocquin, Luc Cornet, Damien Sirjacobs, Valérie Leclère, Maude Pupin, Philippe Jacques, Denis Baurain. Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects
    4348 -- 4349Jett Crowdis, Meng Xiao He, Brendan Reardon, Eliezer M. Van Allen. CoMut: visualizing integrated molecular information with comutation plots
    4350 -- 4352Valentin Zulkower, Susan Rosser. DNA Features Viewer: a sequence annotation formatting and plotting library for Python
    4353 -- 4356Pushkala Jayaraman, Timothy Mosbruger, Taishan Hu, Nikolaos G. Tairis, Chao Wu, Peter M. Clark, Monica D'arcy, Deborah Ferriola, Katarzyna Mackiewicz, Xiaowu Gai, Dimitrios Monos, Mahdi Sarmady. AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies
    4357 -- 4359Richard A. Schäfer, Steffen Lott, Jens Georg, Björn A. Grüning, Wolfgang R. Hess, Björn Voß. GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
    4360 -- 4362Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik. Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence
    4363 -- 4365Leslie Solorzano, Gabriele Partel, Carolina Wählby. TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data
    4366 -- 4368Tobias Rohde, Rita Chupalov, Nicholas Shulman, Vagisha Sharma, Josh Eckels, Brian S. Pratt, Michael J. MacCoss, Brendan MacLean. Audit logs to enforce document integrity in Skyline and Panorama
    4369 -- 4371Andrew Whalen, Gregor Gorjanc, John M. Hickey. AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data
    4372 -- 4373James P. Roney, Jeremy Ferlic, Franziska Michor, Thomas O. McDonald. ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes
    4374 -- 4376Ninon Mounier, Zoltán Kutalik. bGWAS: an R package to perform Bayesian genome wide association studies
    4377 -- 4378Giuseppe Agapito, Chiara Pastrello, Pietro Hiram Guzzi, Igor Jurisica, Mario Cannataro. BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways
    4379 -- 4381Florence Jornod, Marylène Rugard, Luc Tamisier, Xavier Coumoul, Helle R. Andersen, Robert Barouki, Karine Audouze. AOP4EUpest: mapping of pesticides in adverse outcome pathways using a text mining tool

    Volume 36, Issue 14

    4103 -- 4105Jiali Yang, Kun Lang, Guang-Le Zhang, Xiaodan Fan, Yuanyuan Chen, Cong Pian. SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species
    4106 -- 4115Yi-Juan Hu, Glen A. Satten. Testing hypotheses about the microbiome using the linear decomposition model (LDM)
    4116 -- 4125Idit Bloch, Dana Sherill-Rofe, Doron Stupp, Irene Unterman, Hodaya Beer, Elad Sharon, Yuval Tabach. Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals
    4126 -- 4129Dmitry Antipov, Mikhail Raiko, Alla Lapidus, Pavel A. Pevzner. Metaviral SPAdes: assembly of viruses from metagenomic data
    4130 -- 4136David J. Burks, Rajeev K. Azad. Higher-order Markov models for metagenomic sequence classification
    4137 -- 4143Hani Jieun Kim, Yingxin Lin, Thomas A. Geddes, Jean Yee Hwa Yang, Pengyi Yang. CiteFuse enables multi-modal analysis of CITE-seq data
    4144 -- 4153Jack LeBien, Gerald McCollam, Joel Atallah. An in silico model of LINE-1-mediated neoplastic evolution
    4154 -- 4162Meiyue Wang, Ruidong Li, Shizhong Xu. Deshrinking ridge regression for genome-wide association studies
    4163 -- 4170Francisco Guil, José F. Hidalgo, José M. García 0001. Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
    4171 -- 4179Caitlin M. A. Simopoulos, Zhibin Ning, Xu Zhang, Leyuan Li, Krystal Walker, Mathieu Lavallée-Adam, Daniel Figeys. pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies
    4180 -- 4188Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu. HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank
    4189 -- 4190Yang Liu, Vinod Kumar Singh, Deyou Zheng. Stereo3D: using stereo images to enrich 3D visualization
    4191 -- 4192Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar. DeepNano-blitz: a fast base caller for MinION nanopore sequencers
    4193 -- 4196Patrick F. McKenzie, Deren A. R. Eaton. ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
    4197 -- 4199Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri. Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
    4200 -- 4202Douglas E. V. Pires, Wandré N. P. Veloso, Yoochan Myung, Carlos H. M. Rodrigues, Michael Silk, Pâmela M. Rezende, Francislon Silva, Joicymara S. Xavier, João P. L. Velloso, Carlos Henrique da Silveira, David B. Ascher. EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening
    4203 -- 4205Eugenia Ulzurrun, Yorley Duarte, Esteban Pérez-Wohlfeil, Fernando D. González Nilo, Oswaldo Trelles. PLIDflow: an open-source workflow for the online analysis of protein-ligand docking using galaxy
    4206 -- 4207Joe G. Greener, Joel Selvaraj, Ben J. Ward. BioStructures.jl: read, write and manipulate macromolecular structures in Julia
    4208 -- 4210Damiano Cianferoni, Leandro G. Radusky, Sarah A. Head, Luis Serrano, Javier Delgado. ProteinFishing: a protein complex generator within the ModelX toolsuite
    4211 -- 4213Xiao Wang, Haidong Yi, Jia Wang, Zhandong Liu, Yanbin Yin, Han Zhang. GDASC: a GPU parallel-based web server for detecting hidden batch factors
    4214 -- 4216Mario Failli, Jussi Paananen, Vittorio Fortino. ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery
    4217 -- 4219Yan Zhang, Yaru Zhang, Jun Hu, Ji Zhang, Fangjie Guo, Meng Zhou, Guijun Zhang, Fulong Yu, Jianzhong Su. scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures
    4220 -- 4221Pieter Verschaffelt, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, Bart Mesuere. Unipept CLI 2.0: adding support for visualizations and functional annotations
    4222 -- 4224Zhong Wang, Nating Wang, Zilu Wang, Libo Jiang, Yaqun Wang, Jiahan Li, Rongling Wu, Janet Kelso. HiGwas: how to compute longitudinal GWAS data in population designs
    4225 -- 4226Ludovic Chaput, Valentin Guillaume, Natesh Singh, Benoit Deprez, Bruno O. Villoutreix. FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases
    4227 -- 4230Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay, Wren Jonathan. iBioProVis: interactive visualization and analysis of compound bioactivity space
    4231 -- 0Kohei Hagiwara, Liang Ding, Michael N. Edmonson, Stephen V. Rice, Scott Newman, John Easton, Juncheng Dai, Soheil Meshinchi, Rhonda E. Ries, Michael Rusch, Jinghui Zhang. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data

    Volume 36, Issue 13

    3951 -- 3958Arnab Kumar Maity, Sang Chan Lee, Bani K. Mallick, Tapasree Roy Sarkar. Bayesian structural equation modeling in multiple omics data with application to circadian genes
    3959 -- 3965Yuanjing Ma, Yuan Luo, Hongmei Jiang. A novel normalization and differential abundance test framework for microbiome data
    3966 -- 3974Ryo Nakabayashi, Shinichi Morishita. HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
    3975 -- 3981Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone. Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A
    3982 -- 3987Yu P. Zhang, Quan Zou 0001. PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning
    3988 -- 3995Pablo A. Goloboff, Martín E. Morales. A phylogenetic C interpreter for TNT
    3996 -- 4003Srivamshi Pittala, Chris Bailey-Kellogg. Learning context-aware structural representations to predict antigen and antibody binding interfaces
    4004 -- 4011Kai Wang, Nan Lyu, Hongjuan Diao, Shujuan Jin, Tao Zeng, Yaoqi Zhou, Ruibo Wu. GM-DockZn: a geometry matching-based docking algorithm for zinc proteins
    4012 -- 4020Alper Sen 0002, Kamyar Kargar, Esma Akgün, Mustafa Ç. Pinar. Codon optimization: a mathematical programing approach
    4021 -- 4029Hyundoo Jeong, Zhandong Liu. PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing
    4030 -- 4037Lifan Liang, Kunju Zhu, Songjian Lu. BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization
    4038 -- 4046Lei Wang, Zhu-Hong You, Yu-An Huang, De-Shuang Huang, Keith C. C. Chan. An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network
    4047 -- 4057Luke A. D. Hutchison, Bonnie Berger, Isaac S. Kohane. Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation
    4058 -- 4064Jie Hu, Huihui Qin, Xiaodan Fan. Can ODE gene regulatory models neglect time lag or measurement scaling?
    4065 -- 4069Abdul Arif Khan, Zakir Khan. COVID-2019-associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak
    4070 -- 4079Evangelos Karatzas, Margarita Zachariou, Marilena M. Bourdakou, George Minadakis, Anastasis Oulas, George Kolios, Alex Delis, George M. Spyrou. PathWalks: identifying pathway communities using a disease-related map of integrated information
    4080 -- 4087Paul D. Tar, Neil A. Thacker, S. Deepaisarn, J. P. B. O'Connor, A. W. McMahon. A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging
    4088 -- 4090Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knights. SHOGUN: a modular, accurate and scalable framework for microbiome quantification
    4091 -- 4092Divon Lan, Raymond Tobler, Yassine Souilmi, Bastien Llamas. genozip: a fast and efficient compression tool for VCF files
    4093 -- 4094Robin Winter, Joren Retel, Frank Noé, Djork-Arné Clevert, Andreas Steffen. grünifai: interactive multiparameter optimization of molecules in a continuous vector space
    4095 -- 4096Matteo Ciciani, Thomas Cantore, Mario Lauria, Janet Kelso. rScudo: an R package for classification of molecular profiles using rank-based signatures
    4097 -- 4098Anna Breit, Simon Ott, Asan Agibetov, Matthias Samwald. OpenBioLink: a benchmarking framework for large-scale biomedical link prediction
    4099 -- 4101Yushu Shi, LiangLiang Zhang, Kim-Anh Do, Christine B. Peterson, Robert R. Jenq. aPCoA: covariate adjusted principal coordinates analysis

    Volume 36, Issue 12

    3625 -- 3631Chenfu Shi, Magnus Rattray, Gisela Orozco. HiChIP-Peaks: a HiChIP peak calling algorithm
    3632 -- 3636Weibo Zheng, Jing Chen, Thomas G. Doak, Weibo Song, Ying Yan. ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data
    3637 -- 3644Mark F. Rogers, Tom R. Gaunt, Colin Campbell. CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome
    3645 -- 3651Lyam Baudry, Gaël A. Millot, Agnes Thierry, Romain Koszul, Vittore F. Scolari. Serpentine: a flexible 2D binning method for differential Hi-C analysis
    3652 -- 3661Iman Deznabi, Busra Arabaci, Mehmet Koyutürk, Oznur Tastan. DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases
    3662 -- 3668Etminan Naznooshsadat, Parvinnia Elham, Sharifi-Zarchi Ali. FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots
    3669 -- 3679Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, Onur Mutlu. Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
    3680 -- 3686Amlan Talukder, Xiaoman Li, Haiyan Hu. Position-wise binding preference is important for miRNA target site prediction
    3687 -- 3692Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert. GenMap: ultra-fast computation of genome mappability
    3693 -- 3702Dandan Zheng, Guansong Pang, Bo Liu, Lihong Chen, Jian Yang 0007. Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors
    3703 -- 3711Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach. CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme
    3712 -- 3718Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead. Vargas: heuristic-free alignment for assessing linear and graph read aligners
    3719 -- 3725Simon Hickinbotham, Sarah Fiddyment, Timothy L. Stinson, Matthew J. Collins. How to get your goat: automated identification of species from MALDI-ToF spectra
    3726 -- 3732Tomer Meirson, David Bomze, Gal Markel, Abraham O. Samson. κ-helix and the helical lock and key model: a pivotal way of looking at polyproline II
    3733 -- 3738Tomer Sidi, Chen Keasar. Redundancy-weighting the PDB for detailed secondary structure prediction using deep-learning models
    3739 -- 3748Abhilesh S. Dhawanjewar, Ankit A. Roy, Mallur S. Madhusudhan. A knowledge-based scoring function to assess quaternary associations of proteins
    3749 -- 3757Wei Zheng, Xiaogen Zhou, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang 0040. FUpred: detecting protein domains through deep-learning-based contact map prediction
    3758 -- 3765Xiaoqiang Huang, Robin Pearce, Yang Zhang 0040. FASPR: an open-source tool for fast and accurate protein side-chain packing
    3766 -- 3772Arezou Rahimi, Mehmet Gönen. A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers
    3773 -- 3780Meenakshi Venkatasubramanian, Kashish Chetal, Daniel J. Schnell, Gowtham Atluri, Nathan Salomonis. Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
    3781 -- 3787Pavel Sulimov, Anastasia Voronkova, Attila Kertész-Farkas. Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics
    3788 -- 3794Wenjian Xu, Xuanshi Liu, Fei Leng, Wei Li. Blood-based multi-tissue gene expression inference with Bayesian ridge regression
    3795 -- 3802Arttu Arjas, Andreas Hauptmann, Mikko J. Sillanpää. Estimation of dynamic SNP-heritability with Bayesian Gaussian process models
    3803 -- 3810Jia Wen, Colby T. Ford, Daniel Janies, Xinghua Shi. A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models
    3811 -- 3817Songshan Yang, Jiawei Wen, Scott T. Eckert, Yaqun Wang, Dajiang J. Liu, Rongling Wu, Runze Li, Xiang Zhan. Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning
    3818 -- 3824Sangseon Lee, Sangsoo Lim, Taeheon Lee, Inyoung Sung, Sun Kim. Cancer subtype classification and modeling by pathway attention and propagation
    3825 -- 3832Wenming Wu, Xiaoke Ma. Joint learning dimension reduction and clustering of single-cell RNA-sequencing data
    3833 -- 3840Ming-Ju Tsai, Jyun-Rong Wang, Shinn-Jang Ho, Li-Sun Shu, Wen-Lin Huang, Shinn-Ying Ho. GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem
    3841 -- 3848Michael Gruenstaeudl. annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA
    3849 -- 3855Jakob Raymaekers, Ruben H. Zamar. Pooled variable scaling for cluster analysis
    3856 -- 3862Di Jin, Peter Szolovits. Advancing PICO element detection in biomedical text via deep neural networks
    3863 -- 3870Mischa Schwendy, Ronald E. Unger, Sapun H. Parekh. EVICAN - a balanced dataset for algorithm development in cell and nucleus segmentation
    3871 -- 3873Xiangyang Li, Fang Chen, Yunpeng Chen. Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
    3874 -- 3876Sergio Arredondo-Alonso, Martin Bootsma, Yaïr Hein, Malbert R. C. Rogers, Jukka Corander, Rob J. L. Willems, Anita C. Schürch. gplas: a comprehensive tool for plasmid analysis using short-read graphs
    3877 -- 3878Mark Grivainis, Zuojian Tang, David Fenyö. TranspoScope: interactive visualization of retrotransposon insertions
    3879 -- 3881Pavel P. Kuksa, Chien-Yueh Lee, Alexandre Amlie-Wolf, Prabhakaran Gangadharan, Elizabeth E. Mlynarski, Yi-Fan Chou, Han-Jen Lin, Heather Issen, Emily Greenfest-Allen, Otto Valladares, Yuk Yee Leung, Li-San Wang. SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
    3882 -- 3884Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Elena N. Ilina, Vadim M. Govorun. Phigaro: high-throughput prophage sequence annotation
    3885 -- 3887Lauren Coombe, Vladimir Nikolic, Justin Chu, Inanç Birol, René L. Warren. ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs
    3888 -- 3889Alexandre Eeckhoutte, Alexandre Houy, Elodie Manié, Manon Reverdy, Ivan Bièche, Elisabetta Marangoni, Oumou Goundiam, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, François-Clément Bidard, Marc-Henri Stern, Tatiana Popova. ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing
    3890 -- 3891Linjie Wu, Han Wang, Yuchao Xia, Ruibin Xi. CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome
    3892 -- 3893Antonio Benítez-Hidalgo, Antonio J. Nebro, José Francisco Aldana Montes. Sequoya: multiobjective multiple sequence alignment in Python
    3894 -- 3896Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré. yacrd and fpa: upstream tools for long-read genome assembly
    3897 -- 3898Mirko Torrisi, Gianluca Pollastri. Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations
    3899 -- 3901Bilal El Houdaigui, Sam Meyer. TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling
    3902 -- 3904Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey. T-Gene: improved target gene prediction
    3905 -- 3906Charlotte A. Darby, Michael J. T. Stubbington, Patrick J. Marks, Álvaro Martínez Barrio, Ian T. Fiddes. scHLAcount: allele-specific HLA expression from single-cell gene expression data
    3907 -- 3909Ruijia Wang, Bin Tian. APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms
    3910 -- 3912Oscar Franzén, Johan L. M. Björkegren. alona: a web server for single-cell RNA-seq analysis
    3913 -- 3915Hemi Luan, Xingen Jiang, Fenfen Ji, Zhangzhang Lan, Zongwei Cai, Wenyong Zhang. CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation
    3916 -- 3917Daniele Mercatelli, Gonzalo Lopez-Garcia, Federico M. Giorgi. corto: a lightweight R package for gene network inference and master regulator analysis
    3918 -- 3919Hendrik A. de Weerd, Tejaswi V. S. Badam, David Martínez-Enguita, Julia Åkesson, Daniel Muthas, Mika Gustafsson, Zelmina Lubovac-Pilav. MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks
    3920 -- 3921Mattia Tomasoni, Sergio Gómez, Jake Crawford, Weijia Zhang, Sarvenaz Choobdar, Daniel Marbach, Sven Bergmann. MONET: a toolbox integrating top-performing methods for network modularization
    3922 -- 3924Brandon Reyes, Irene Otero-Muras, Michael T. Shuen, Alexandre M. Tartakovsky, Vladislav A. Petyuk. CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks
    3925 -- 3926Christian-Alexander Dudek, Carsten Reuse, Regine Fuchs, Janneke Hendriks, Veronique Starck, Karsten Hiller. MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification
    3927 -- 3929Lulu Chen, Chiung-Ting Wu, Niya Wang, David M. Herrington, Robert Clarke, Yue Wang. debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues
    3930 -- 3931Oliver B. Scott, A. W. Edith Chan. ScaffoldGraph: an open-source library for the generation and analysis of molecular scaffold networks and scaffold trees
    3932 -- 3934Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan. EnrichrBot: Twitter bot tracking tweets about human genes
    3935 -- 3937Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar. QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics
    3938 -- 3940Da Kuang, Jochen Weile, Roujia Li, Tom W. Ouellette, Jarry A. Barber, Frederick P. Roth. MaveQuest: a web resource for planning experimental tests of human variant effects
    3941 -- 3943Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla Garcia, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder. GlyGen data model and processing workflow
    3944 -- 3946Shanyu Chen, Xiaoyu He, Ruilin Li, Xiaohong Duan, Beifang Niu. HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures
    3947 -- 3948Jose-Jesus Fernandez, Teobaldo E. Torres, Eva Martin-Solana, Gerardo F. Goya, Maria-Rosario Fernandez-Fernandez. PolishEM: image enhancement in FIB-SEM
    3949 -- 3950Illia Ziamtsov, Saket Navlakha. Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds

    Volume 36, Issue 11

    3295 -- 3298Sen Liu, Qiang Zheng, Zhiying Wang. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus
    3299 -- 3306Ziwei Chen, Fuzhou Gong, Lin Wan, Liang Ma. RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data
    3307 -- 3313Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: refined binning of metagenomic contigs using assembly graphs
    3314 -- 3321Clemens Kreutz, Nilay S. Can, Ralf Schulze Bruening, Rabea Meyberg, Zsuzsanna Mérai, Noé Fernández-Pozo, Stefan A. Rensing. A blind and independent benchmark study for detecting differentially methylated regions in plants
    3322 -- 3326Michael Schwarz, Marius Welzel, Tolganay Kabdullayeva, Anke Becker, Bernd Freisleben, Dominik Heider. MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
    3327 -- 3335Qiang Tang, Juanjuan Kang, Jiaqing Yuan, Hua Tang, Xianhai Li, Hao Lin, Jian Huang 0004, Wei Chen. DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species
    3336 -- 3342Kewei Liu, Wei Chen. iMRM: a platform for simultaneously identifying multiple kinds of RNA modifications
    3343 -- 3349Manaz Kaleel, Yandan Zheng, Jialiang Chen, Xuanming Feng, Jeremy C. Simpson, Gianluca Pollastri, Catherine Mooney. SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks
    3350 -- 3356Md. Mehedi Hasan 0002, Nalini Schaduangrat, Shaherin Basith, Gwang Lee, Watshara Shoombuatong, Balachandran Manavalan. HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation
    3357 -- 3364Tyler Shimko, Polly Fordyce, Yaron Orenstein. DeCoDe: degenerate codon design for complete protein-coding DNA libraries
    3365 -- 3371Yaxin Xue, Anders Lanzén, Inge Jonassen. Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
    3372 -- 3378Alexander Greß, Olga V. Kalinina. SphereCon - a method for precise estimation of residue relative solvent accessible area from limited structural information
    3379 -- 3384Adrien H. Cerdan, Marion Sisquellas, Gilberto Pereira, Diego E. Barreto Gomes, Jean-Pierre Changeux, Marco Cecchini. The Glycine Receptor Allosteric Ligands Library (GRALL)
    3385 -- 3392Zi-Lin Liu, Jing-Hao Hu, Fan Jiang, Yun-Dong Wu. CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning
    3393 -- 3400Vittorio Fortino, Giovanni Scala, Dario Greco. Feature set optimization in biomarker discovery from genome-scale data
    3401 -- 3408Shen Yin, Xinlei Wang, Gaoxiang Jia, Yang Xie. MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples
    3409 -- 3417Lauren Spirko-Burns, Karthik Devarajan. Unified methods for feature selection in large-scale genomic studies with censored survival outcomes
    3418 -- 3421Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter. Interpretable factor models of single-cell RNA-seq via variational autoencoders
    3422 -- 3430Philippe Boileau, Nima S. Hejazi, Sandrine Dudoit. Exploring high-dimensional biological data with sparse contrastive principal component analysis
    3431 -- 3438Ziyi Li, Zhenxing Guo, Ying Cheng, Peng Jin, Hao Wu. Robust partial reference-free cell composition estimation from tissue expression
    3439 -- 3446Daiwei Zhang, Rounak Dey, SeungGeun Lee. Fast and robust ancestry prediction using principal component analysis
    3447 -- 3456Matthew Waas, Shana T. Snarrenberg, Jack Littrell, Rachel A. Jones Lipinski, Polly A. Hansen, John A. Corbett, Rebekah L. Gundry, Janet Kelso. SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates
    3457 -- 3465Renming Liu, Christopher A. Mancuso, Anna Yannakopoulos, Kayla A. Johnson, Arjun Krishnan. Supervised learning is an accurate method for network-based gene classification
    3466 -- 3473Maya Levy, Amit Frishberg, Irit Gat-Viks. Inferring cellular heterogeneity of associations from single cell genomics
    3474 -- 3481Zi-Chao Zhang, Xiao-fei Zhang, Min Wu 0008, Le Ou-Yang, Xing-Ming Zhao, Xiao-Li Li. A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks
    3482 -- 3492Shouyong Jiang, Yong Wang, Marcus Kaiser, Natalio Krasnogor. NIHBA: a network interdiction approach for metabolic engineering design
    3493 -- 3498Yan Ni, Gang Yu, Huan Chen, Yongqiong Deng, Philippa M. Wells, Claire J. Steves, Feng Ju, Junfen Fu. M2IA: a web server for microbiome and metabolome integrative analysis
    3499 -- 3506Leandro A Bugnon, Cristian A. Yones, Jonathan Raad, Matias Gerard, Mariano Rubiolo, Gabriela Alejandra Merino, Milton Pividori, Leandro E. Di Persia, Diego H. Milone, Georgina Stegmayer. DL4papers: a deep learning approach for the automatic interpretation of scientific articles
    3507 -- 3515Yunchuan Kong, Tianwei Yu. forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction
    3516 -- 3521Lixiang Zhang, Lin Lin, Jia Li. CPS analysis: self-contained validation of biomedical data clustering
    3522 -- 3527Emanuele Aliverti, Jeffrey L. Tilson, Dayne L. Filer, Benjamin Babcock, Alejandro Colaneri, Jennifer Ocasio, Timothy R. Gershon, Kirk C. Wilhelmsen, David B. Dunson. Projected t-SNE for batch correction
    3528 -- 3536Bowen Song, Yujiao Tang, Kunqi Chen, Zhen Wei, Rong Rong, Zhiliang Lu, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng. m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human
    3537 -- 3548Nova F. Smedley, Suzie El-Saden, William Hsu. Discovering and interpreting transcriptomic drivers of imaging traits using neural networks
    3549 -- 3551Eddie Ip, Clinton Hadinata, Joshua Wing Kei Ho, Eleni Giannoulatou. dv-trio: a family-based variant calling pipeline using DeepVariant
    3552 -- 3555Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, Tulio de Oliveira. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
    3556 -- 3557M. Anastasiadi, E. Bragin, P. Biojoux, A. Ahamed, J. Burgin, K. de Castro Cogle, S. Llaneza-Lago, R. Muvunyi, M. Scislak, I Aktan, Corentin Molitor, Tomasz J. Kurowski, Fady R. Mohareb. CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances
    3558 -- 3560Emmanuel L. P. Dumont, Benjamin Tycko, Catherine Do. CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation
    3561 -- 3562Kun Sun. Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
    3563 -- 3565Li Chen. powmic: an R package for power assessment in microbiome case-control studies
    3566 -- 3567Sinisa Bidin, Ivan Vujaklija, Tina Paradzik, Ana Bielen, Dusica Vujaklija. Leitmotif: protein motif scanning 2.0
    3568 -- 3569Jian-Peng Zhou, Lei Chen 0007, Tianyun Wang, Min Liu. iATC-FRAKEL: a simple multi-label web server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only
    3570 -- 3572Mindaugas Margelevicius. COMER2: GPU-accelerated sensitive and specific homology searches
    3573 -- 3575Henry Pratt, Zhiping Weng. LogoJS: a Javascript package for creating sequence logos and embedding them in web applications
    3576 -- 3577Marcelo Depólo Polêto, Bruno Iochins Grisci, Márcio Dorn, Hugo Verli. ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories
    3578 -- 3579Michela Quadrini, Luca Tesei, Emanuela Merelli. ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots
    3580 -- 3581Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi, Charlotte M. Deane. TCRBuilder: multi-state T-cell receptor structure prediction
    3582 -- 3584Nathan Lawlor, Eladio J. Márquez, Donghyung Lee, Duygu Ucar. V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data
    3585 -- 3587Lin Wang, Francisca Catalan, Karin Shamardani, Husam Babikir, Aaron Diaz. Ensemble learning for classifying single-cell data and projection across reference atlases
    3588 -- 3589Kaiyi Zhu, Dimitris Anastassiou. 2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions
    3590 -- 3591Simo Kitanovski, Daniel Hoffmann. IgGeneUsage: differential gene usage in immune repertoires
    3592 -- 3593Gaurav Sharma, Carlo Colantuoni, Loyal A. Goff, Elana J. Fertig, Genevieve L. Stein-O'Brien. projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering
    3594 -- 3596Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlovic, Igor Snapkov, Geir Kjetil Sandve, Sai T. Reddy, Victor Greiff. immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
    3597 -- 3599Iurii S. Nagornov, Mamoru Kato. tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes
    3600 -- 3601Tong Zhang, Yu Tian, Le Yuan, Fu Chen, Ailin Ren, Qian-Nan Hu. Bio2Rxn: sequence-based enzymatic reaction predictions by a consensus strategy
    3602 -- 3604Potdar Swapnil, Aleksandr Ianevski, John-Patrick Mpindi, Dmitrii Bychkov, Clément Fiere, Philipp Ianevski, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio, Olli-P. Kallioniemi, Saarela Jani, Päivi Östling. Breeze: an integrated quality control and data analysis application for high-throughput drug screening
    3605 -- 3606Pumin Li, Qi Xu, Xu Hua, Zhongwei Xie, Jie Li, Jin Wang. primirTSS: an R package for identifying cell-specific microRNA transcription start sites
    3607 -- 3609Louis J. Taylor, Arwa Abbas, Frederic D. Bushman. grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories
    3610 -- 3612Qingyang Ding, Siyu Hou, Songpeng Zu, Yonghui Zhang, Shao Li. VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models
    3613 -- 3614Akul Y. Mehta, Richard D. Cummings. GlycoGlyph: a glycan visualizing, drawing and naming application
    3615 -- 3617N. R. Siva Shanmugam, J. Jino Blessy, K. Veluraja, M. Michael Gromiha. ProCaff: protein-carbohydrate complex binding affinity database
    3618 -- 3619Pere Ràfols, Bram Heijs, Esteban del Castillo, Oscar Yanes, Liam A. McDonnell, Jesús Brezmes, Iara Pérez-Taboada, Mario Vallejo, María García-Altares, Xavier Correig. rMSIproc: an R package for mass spectrometry imaging data processing
    3620 -- 3622Alexander Auer, Maximilian T. Strauss, Sebastian Strauss, Ralf Jungmann. nanoTRON: a Picasso module for MLP-based classification of super-resolution data
    3623 -- 0Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge. Discovery of disease- and drug-specific pathways through community structures of a literature network

    Volume 36, Issue 10

    2975 -- 2979Zheng Zhang, Fen Yu, Yuanqiang Zou, Ye Qiu, Aiping Wu, Taijiao Jiang, Yousong Peng. Phage protein receptors have multiple interaction partners and high expressions
    2980 -- 2985Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore. Coolpup.py: versatile pile-up analysis of Hi-C data
    2986 -- 2992Qiang Kang, Jun Meng, Jun Cui, Yushi Luan, Ming Chen. PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction
    2993 -- 3003Pavel Avdeyev, Nikita Alexeev, Yongwu Rong, Max A. Alekseyev. A unified ILP framework for core ancestral genome reconstruction problems
    3004 -- 3010Huang Xu, Xiang Li, Yaning Yang, Yi Li, Jose Pinheiro, Kate Sasser, Hisham Hamadeh, Xu Steven, Min Yuan. High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes
    3011 -- 3017Olga Mineeva, Mateo Rojas-Carulla, Ruth Ley, Bernhard Schölkopf, Nicholas Youngblut. DeepMAsED: evaluating the quality of metagenomic assemblies
    3018 -- 3027Chun-Qiu Xia, Xiaoyong Pan, Hong-bin Shen. Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data
    3028 -- 3034Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng, Quan Zou 0001. StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency
    3035 -- 3042Shiwei Wei, Yuping Wang, Yuanchao Yang, Sen Liu. A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems
    3043 -- 3048Michael A. Peabody, Wing Yin Venus Lau, Gemma Hoad, Baofeng Jia, Finlay Maguire, Kristen L. Gray, Robert G. Beiko, Fiona S. L. Brinkman. PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data
    3049 -- 3055Jae Yong Ryu, Mi-Young Lee, Jeong Hyun Lee, Byung Ho Lee, Kwang-Seok Oh. DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity
    3056 -- 3063Yuan Zhang, Xing Sui, Scott Stagg, Jinfeng Zhang. FTIP: an accurate and efficient method for global protein surface comparison
    3064 -- 3071Rostislav K. Skitchenko, Dmitrii Usoltsev, Mayya Uspenskaya, Andrey V. Kajava, Albert Guskov. Census of halide-binding sites in protein structures
    3072 -- 3076Elena Rivas, Jody Clements, Sean R. Eddy. Estimating the power of sequence covariation for detecting conserved RNA structure
    3077 -- 3083Wentao Shi, Jeffrey Mitchell Lemoine, Abd-El-Monsif A. Shawky, Manali Singha, Limeng Pu, Shuangyan Yang, J. Ramanujam, Michal Brylinski. BionoiNet: ligand-binding site classification with off-the-shelf deep neural network
    3084 -- 3092Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar. Rhapsody: predicting the pathogenicity of human missense variants
    3093 -- 3098Saeid Parvandeh, Hung-Wen Yeh, Martin P. Paulus, Brett A. McKinney. Consensus features nested cross-validation
    3099 -- 3106Burim Ramosaj, Lubna Amro, Markus Pauly. A cautionary tale on using imputation methods for inference in matched-pairs design
    3107 -- 3114Neo Christopher Chung. Statistical significance of cluster membership for unsupervised evaluation of cell identities
    3115 -- 3123Teng Fei, Tianwei Yu. scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment
    3124 -- 3130Wenfei Zhang, Ying Wei, Donghui Zhang, Ethan Y. Xu. ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data
    3131 -- 3138Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan 0001, Xiao-fei Zhang. scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation
    3139 -- 3147Junlin Xu, Lijun Cai, Bo Liao, Wen Zhu, Jialiang Yang. CMF-Impute: an accurate imputation tool for single-cell RNA-seq data
    3148 -- 3155David Bouyssié, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, Magali Rompais, Charlotte Macron, Christine Carapito, Anne Gonzalez de Peredo, Yohann Couté, Véronique Dupierris, Alexandre Burel, Jean-Philippe Menetrey, Andrea Kalaitzakis, Julie Poisat, Aymen Romdhani, Odile Burlet-Schiltz, Sarah Cianférani, Jerome Garin, Christophe Bruley. Proline: an efficient and user-friendly software suite for large-scale proteomics
    3156 -- 3161Chong Chen, Changjing Wu, Linjie Wu, Xiaochen Wang, Minghua Deng, Ruibin Xi. scRMD: imputation for single cell RNA-seq data via robust matrix decomposition
    3162 -- 3168Hong Zhang, Ni Zhao, Devan V. Mehrotra, Judong Shen. Composite Kernel Association Test (CKAT) for SNP-set joint assessment of genotype and genotype-by-treatment interaction in Pharmacogenetics studies
    3169 -- 3176Akio Onogi. Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters
    3177 -- 3184Eshan D. Mitra, William S. Hlavacek. Bayesian inference using qualitative observations of underlying continuous variables
    3185 -- 3191Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens
    3192 -- 3199Stephen Kotiang, Ali Eslami. A probabilistic graphical model for system-wide analysis of gene regulatory networks
    3200 -- 3206Kavishwar B. Wagholikar, Hossein Estiri, Marykate Murphy, Shawn N. Murphy. Polar labeling: silver standard algorithm for training disease classifiers
    3207 -- 3214Rashmie Abeysinghe, Eugene W. Hinderer, Hunter N. B. Moseley, Licong Cui. SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology
    3215 -- 3224Katja Ovchinnikova, Lachlan Stuart, Alexander Rakhlin, Sergey I. Nikolenko, Theodore Alexandrov. ColocML: machine learning quantifies co-localization between mass spectrometry images
    3225 -- 3233Jie Shu, Jingxin Liu, YongMei Zhang, Hao Fu, Mohammad Ilyas, Giuseppe Faraci, Vincenzo Della Mea, Bozhi Liu, Guoping Qiu. Marker controlled superpixel nuclei segmentation and automatic counting on immunohistochemistry staining images
    3234 -- 3235Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. pyBedGraph: a python package for fast operations on 1D genomic signal tracks
    3236 -- 3238Wouter De Coster, Endre Bakken Stovner, Mojca Strazisar. Methplotlib: analysis of modified nucleotides from nanopore sequencing
    3239 -- 3241Zhencheng Fang, Jie Tan, Shufang Wu, Mo Li, Chunhui Wang, Yongchu Liu, Huaiqiu Zhu. PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning
    3242 -- 3243Samuel O'donnell, Gilles Fischer. MUM&Co: accurate detection of all SV types through whole-genome alignment
    3244 -- 3245Lisanna Paladin, Mathieu Schaeffer, Pascale Gaudet, Monique Zahn-Zabal, Pierre-André Michel, Damiano Piovesan, Silvio C. E. Tosatto, Amos Bairoch. The Feature-Viewer: a visualization tool for positional annotations on a sequence
    3246 -- 3247Václav Brázda, Jan Kolomazník, Jean-Louis Mergny, Jiri Stastny. G4Killer web application: a tool to design G-quadruplex mutations
    3248 -- 3250Marta Lovino, Maria Serena Ciaburri, Gianvito Urgese, Santa Di Cataldo, Elisa Ficarra. DEEPrior: a deep learning tool for the prioritization of gene fusions
    3251 -- 3253Congyu Lu, Zena Cai, Yuanqiang Zou, Zheng Zhang, Wenjun Chen, Lizong Deng, Xiangjun Du, Aiping Wu, Lei Yang 0002, Dayan Wang, Yuelong Shu, Taijiao Jiang, Yousong Peng. FluPhenotype - a one-stop platform for early warnings of the influenza A virus
    3254 -- 3256Hang Dai, Yongtao Guan. Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping
    3257 -- 3259Hao-Dong Xu, Ruifeng Hu 0004, Peilin Jia, Zhongming Zhao. 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes
    3260 -- 3262Vladimir Perovic, Jeremy Y. Leclercq, Neven Sumonja, François D. Richard, Nevena Veljkovic, Andrey V. Kajava. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences
    3263 -- 3265Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
    3266 -- 3267Claudio Mirabello, Björn Wallner. InterLig: improved ligand-based virtual screening using topologically independent structural alignments
    3268 -- 3270Matteo P. Ferla, Alistair T. Pagnamenta, David R. Damerell, Jenny C. Taylor, Brian D. Marsden. MichelaNglo: sculpting protein views on web pages without coding
    3271 -- 3272Adrián García-Recio, Gemma Navarro, Rafael Franco, Mireia Olivella, Ramon Guixà-González, Arnau Cordomí. DIMERBOW: exploring possible GPCR dimer interfaces
    3273 -- 3275Elaine Y. Cao, John F. Ouyang, Owen J. L. Rackham. GeneSwitches: ordering gene expression and functional events in single-cell experiments
    3276 -- 3278Alemu Takele Assefa, Jo Vandesompele, Olivier Thas. SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data
    3279 -- 3280Arnaud Becheler, L. Lacey Knowles. Occupancy spectrum distribution: application for coalescence simulation with generic mergers
    3281 -- 3282Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi. GEMtractor: extracting views into genome-scale metabolic models
    3283 -- 3285Jinhwan Kim, Sora Yoon, Dougu Nam. netGO: R-Shiny package for network-integrated pathway enrichment analysis
    3286 -- 3287Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan Kleijn, Michael P. H. Stumpf, Fei He 0002. GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation
    3288 -- 3289Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek. ShinySOM: graphical SOM-based analysis of single-cell cytometry data
    3290 -- 3291Niall Beard, Finn Bacall, Aleksandra Nenadic, Milo Thurston, Carole A. Goble, Susanna-Assunta Sansone, Teresa K. Attwood. TeSS: a platform for discovering life-science training opportunities
    3292 -- 3294Zaki Hasnain, Andrew K. Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S. Bader, Shelly R. Peyton, Andrew J. Ewald, Paul K. Newton. OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics

    Volume 36, Issue 1

    1 -- 9Vahid Jalili, Enis Afgan, James Taylor 0001, Jeremy Goecks. Cloud bursting galaxy: federated identity and access management
    10 -- 16Peng Xu, Timothy Kennell Jr., Min Gao, Human Genome Structural Variation Consortium, Robert P. Kimberly, Zechen Chong. MRLR: unraveling high-resolution meiotic recombination by linked reads
    17 -- 25Adam Kaplan, Eric F. Lock, Mark Fiecas, Alzheimer's Disease Neuroimaging Initiative. Bayesian GWAS with Structured and Non-Local Priors
    26 -- 32Davoud Torkamaneh, Jérôme Laroche, Brian Boyle, François Belzile. DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
    33 -- 40Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan. arcasHLA: high-resolution HLA typing from RNAseq
    41 -- 48Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang. Protein contact prediction using metagenome sequence data and residual neural networks
    49 -- 55Chenwei Lou, Jian Zhao, Ruoyao Shi, Qian Wang, Wenyang Zhou, Yubo Wang, Guoqing Wang, Lan Huang, Xin Feng 0004, Fengfeng Zhou. sefOri: selecting the best-engineered sequence features to predict DNA replication origins
    56 -- 64Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio. DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
    65 -- 72Li Xing, Mary Lesperance, Xuekui Zhang. Simultaneous prediction of multiple outcomes using revised stacking algorithms
    73 -- 80Mohamed Chaabane, Robert M. Williams, Austin T. Stephens, Juw Won Park. circDeep: deep learning approach for circular RNA classification from other long non-coding RNA
    81 -- 89Jakub M. Bartoszewicz, Anja Seidel, Robert Rentzsch, Bernhard Y. Renard. DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks
    90 -- 95Fabian Sievers, Desmond G. Higgins. QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
    96 -- 103Jinfang Zheng, Xu Hong, Juan Xie, Xiaoxue Tong, Shiyong Liu. P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking
    104 -- 111Shuichiro Makigaki, Takashi Ishida. Sequence alignment using machine learning for accurate template-based protein structure prediction
    112 -- 121Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue. iScore: a novel graph kernel-based function for scoring protein-protein docking models
    122 -- 130Jelena Vucinic, David Simoncini, Manon Ruffini, Sophie Barbe, Thomas Schiex. Positive multistate protein design
    131 -- 135Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J. Lanczycki, Renata C. Geer, Thomas Madej, Lon Phan, Minghong Ward, Shennan Lu, Gabriele H. Marchler, Yanli Wang, Stephen H. Bryant, Lewis Y. Geer, Aron Marchler-Bauer. iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures
    136 -- 144Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen, Haiyan Liu. Increasing the efficiency and accuracy of the ABACUS protein sequence design method
    145 -- 153Angela Serra, Serli Önlü, Paola Festa, Vittorio Fortino, Dario Greco. MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling
    154 -- 159Tomer Meirson, David Bomze, Liron Gat Kahlon, Hava Gil-Henn, Abraham O. Samson. A helical lock and key model of polyproline II conformation with SH3
    160 -- 168Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse. Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity
    169 -- 176Yuexu Jiang, Yanchun Liang 0001, Duolin Wang, Dong Xu 0002, Trupti Joshi. A dynamic programing approach to integrate gene expression data and network information for pathway model generation
    177 -- 185John Ferguson, Joseph Chang. An empirical Bayesian ranking method, with applications to high throughput biology
    186 -- 196Erwan Bigan, Satish Sasidharan Nair, François-Xavier Lejeune, Hélissande Fragnaud, Frédéric Parmentier, Lucile Mégret, Marc Verny, Jeff Aaronson, Jim Rosinski, Christian Neri. Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms
    197 -- 204Xin Zhou, Xiaodong Cai. Inference of differential gene regulatory networks based on gene expression and genetic perturbation data
    205 -- 211Elizabeth Guruceaga, Alba Garín-Muga, Victor Segura. MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides
    212 -- 220Jeremy Georges-Filteau, Richard C. Hamelin, Mathieu Blanchette. Mycorrhiza: genotype assignment using phylogenetic networks
    221 -- 231Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu. Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations
    232 -- 240Axel Theorell, Katharina Nöh. Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis
    241 -- 249Rudolf Schill, Stefan Solbrig, Tilo Wettig, Rainer Spang. Modelling cancer progression using Mutual Hazard Networks
    250 -- 256Trang T. Le, Weixuan Fu, Jason H. Moore. Scaling tree-based automated machine learning to biomedical big data with a feature set selector
    257 -- 263Qian Li, Kate Fisher, Wenjun Meng, Bin Fang, Eric A. Welsh, Eric B. Haura, John M. Koomen, Steven A. Eschrich, Brooke L. Fridley, Y. Ann Chen. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis
    264 -- 271Alexander Junge, Lars Juhl Jensen. CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
    272 -- 279Hannah F. Löchel, Dominic Eger, Theodor Sperlea, Dominik Heider. Deep learning on chaos game representation for proteins
    280 -- 286John M. Giorgi, Gary D. Bader. Towards reliable named entity recognition in the biomedical domain
    287 -- 294Arne P. Raulf, Joshua Butke, Claus Küpper, Frederik Großerüschkamp, Klaus Gerwert, Axel Mosig. Deep representation learning for domain adaptable classification of infrared spectral imaging data
    295 -- 302Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser. HUNER: improving biomedical NER with pretraining
    303 -- 310Guoxian Yu, Keyao Wang, Carlotta Domeniconi, Maozu Guo, Jun Wang 0035. Isoform function prediction based on bi-random walks on a heterogeneous network
    311 -- 316Nezar Abdennur, Leonid A. Mirny. Cooler: scalable storage for Hi-C data and other genomically labeled arrays
    317 -- 329Vincent Briane, Myriam Vimond, Cesar Augusto Valades-Cruz, Antoine Salomon, Christian Wunder, Charles Kervrann. A sequential algorithm to detect diffusion switching along intracellular particle trajectories
    330 -- 0Yan Zhao, Xing Chen, Jun Yin. Adaptive boosting-based computational model for predicting potential miRNA-disease associations
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