Journal: Bioinformatics

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