External Links

    Journal: Bioinformatics

    Volume 39, Issue Supplement-1

    1 -- 2Yann Ponty, Sushmita Roy. ISMB/ECCB 2023 proceedings
    3 -- 4Christiana N. Fogg, Diane E. Kovats, Martin Vingron. 2023 Outstanding Contributions to ISCB Award: Shoba Ranganathan
    5 -- 6Christiana N. Fogg, Diane E. Kovats, Martin Vingron. 2023 ISCB Overton Prize: Jingyi Jessica Li
    7 -- 8Christiana N. Fogg, Diane E. Kovats, Martin Vingron. 2023 ISCB innovator award: Dana Pe'er
    9 -- 10Christiana N. Fogg, Diane E. Kovats, Martin Vingron. 2023 ISCB accomplishments by a senior scientist award: Mark Gerstein
    11 -- 20Thomas Cokelaer, Sarah Cohen Boulakia, Frédéric Lemoine 0002. Reprohackathons: promoting reproducibility in bioinformatics through training
    21 -- 29Shaojun Pan, Xing-Ming Zhao, Luís Pedro Coelho. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
    30 -- 39Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun. PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer
    40 -- 46Mihir Mongia, Romel Baral, Abhinav Adduri, Donghui Yan, Yudong Liu, Yuying Bian, Paul Kim, Bahar Behsaz, Hosein Mohimani. AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes
    47 -- 56Qi Wang 0038, Michael Nute, Todd J. Treangen. Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities
    57 -- 65Wei Wei, Andrew Millward, David Koslicki. L2UniFrac
    66 -- 75Andrew J. Mikalsen, Jaroslaw Zola. Coriolis: enabling metagenomic classification on lightweight mobile devices
    76 -- 85Jonas C. Ditz, Bernhard Reuter, Nico Pfeifer. COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data
    86 -- 93Jonas C. Ditz, Jacqueline Wistuba-Hamprecht, Timo Maier, Rolf Fendel, Nico Pfeifer, Bernhard Reuter. Plasmodium falciparum protein antigen candidate prediction
    94 -- 102Aurélien Beaude, Milad Rafiee Vahid, Franck Augé, Farida Zehraoui, Blaise Hanczar. AttOmics: attention-based architecture for diagnosis and prognosis from omics data
    103 -- 110Alperen Dalkiran, Ahmet Atakan, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Aybar C. Acar, Tunca Dogan, Volkan Atalay. Transfer learning for drug-target interaction prediction
    111 -- 120Alice Lacan, Michèle Sebag, Blaise Hanczar. GAN-based data augmentation for transcriptomics: survey and comparative assessment
    121 -- 130Haoting Zhang, Carl Henrik Ek, Magnus Rattray, Marta Milo. SynBa: improved estimation of drug combination synergies with uncertainty quantification
    131 -- 139Eric Lee, Kevin Chern, Michael Nissen, Xuehai Wang, Chris Huang, Anita K. Gandhi, Alexandre Bouchard-Côté, Andrew P. Weng, Andrew Roth. SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
    140 -- 148Monica T. Dayao, Alexandro Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D'angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar-Joseph. in situ proteomics imaging to enhance cancer survival analysis
    149 -- 157Mohammad Al Olaimat, Jared Martinez, Fahad Saeed, Serdar Bozdag. PPAD: a deep learning architecture to predict progression of Alzheimer's disease
    158 -- 167Ke Zhang, Min Wu 0008, Yong Liu 0020, Yimiao Feng, Jie Zheng 0002. KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality
    168 -- 176Leonard Dervishi, Wenbiao Li, Anisa Halimi, Xiaoqian Jiang, Jaideep Vaidya, Erman Ayday. Privacy preserving identification of population stratification for collaborative genomic research
    177 -- 184Siddhant Grover, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein. Phylogenetic diversity statistics for all clades in a phylogeny
    185 -- 193Yasamin Tabatabaee, Chao Zhang 0055, Tandy J. Warnow, Siavash Mirarab. Phylogenomic branch length estimation using quartets
    194 -- 203Hanqing Zhao, Matthijs Leon Souilljee, Pavlos Pavlidis, Nikolaos Alachiotis 0001. Genome-wide scans for selective sweeps using convolutional neural networks
    204 -- 212Ziyun Guang, Matthew Smith-Erb, Layla Oesper. A weighted distance-based approach for deriving consensus tumor evolutionary trees
    213 -- 221Hartmut Häntze, Paul Horton. Effects of spaced k-mers on alignment-free genotyping
    222 -- 231Alexander J. Petri, Kristoffer Sahlin. isONform: reference-free transcriptome reconstruction from Oxford Nanopore data
    232 -- 241Xiang Li, Qian Shi, Ke Chen, Mingfu Shao. Seeding with minimized subsequence
    242 -- 251Marjan Hosseini, Aaron Palmer, William Manka, Patrick G. S. Grady, Venkata Patchigolla, Jinbo Bi, Rachel J. O'Neill, Zhiyi Chi, Derek Aguiar. Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures
    252 -- 259Camille Marchet, Antoine Limasset. Scalable sequence database search using partitioned aggregated Bloom comb trees
    260 -- 269Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi. k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes
    270 -- 278Sandra Romain, Claire Lemaitre. SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph
    279 -- 287Timofey Prodanov, Vikas Bansal. A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing
    288 -- 296Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve. PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning
    297 -- 307Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh 0002, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu. RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
    308 -- 317Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng. A gated graph transformer for protein complex structure quality assessment and its performance in CASP15
    318 -- 325Frimpong Boadu, Hongyuan Cao, Jianlin Cheng. Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function
    326 -- 336Jia-Ning Li, Guang Yang, Peng-Cheng Zhao, Xue-Xin Wei, Jian-Yu Shi. CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties
    337 -- 346Md. Mahfuzur Rahaman, Nabila Shahnaz Khan, Shaojie Zhang. RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families
    347 -- 356Alexandru Dumitrescu, Emmi Jokinen, Anja Paatero, Juho Kellosalo, Ville O. Paavilainen, Harri Lähdesmäki. TSignal: a transformer model for signal peptide prediction
    357 -- 367Piyumi R. Amarasinghe, Lloyd Allison, Peter J. Stuckey, Maria Garcia de la Banda, Arthur M. Lesk, Arun Siddharth Konagurthu. Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles
    368 -- 376Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang. CellBRF: a feature selection method for single-cell clustering using cell balance and random forest
    377 -- 385Christopher Hill, Sanjarbek Hudaiberdiev, Ivan Ovcharenko. ChromDL: a next-generation regulatory DNA classifier
    386 -- 393Yanlin Zhang, Mathieu Blanchette. Reference panel-guided super-resolution inference of Hi-C data
    394 -- 403Cassandra Burdziak, Chujun Julia Zhao, Doron Haviv, Direna Alonso-Curbelo, Scott W. Lowe, Dana Pe'er. scKINETICS: inference of regulatory velocity with single-cell transcriptomics data
    404 -- 412Kirti Biharie, Lieke Michielsen, Marcel J. T. Reinders, Ahmed Mahfouz. Cell type matching across species using protein embeddings and transfer learning
    413 -- 422Ali Tugrul Balci1, Mark Maher Ebeid, Panayiotis V. Benos, Dennis Kostka, Maria Chikina. An intrinsically interpretable neural network architecture for sequence-to-function learning
    423 -- 430Yueqi Sheng, Boaz Barak, Mor Nitzan. Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates
    431 -- 439Asia Mendelevich, Saumya Gupta, Aleksei Pakharev, Athanasios Teodosiadis, Andrey A. Mironov, Alexander A. Gimelbrant. Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
    440 -- 447Vincent Wagner, Nicole Radde. The impossible challenge of estimating non-existent moments of the Chemical Master Equation
    448 -- 457Mogan Gim, Junseok Choe, Seungheun Baek, Jueon Park, Chaeeun Lee, Minjae Ju, Sumin Lee, Jaewoo Kang. ArkDTA: attention regularization guided by non-covalent interactions for explainable drug-target binding affinity prediction
    458 -- 464Enio Gjerga, Isabel S. Naarmann-de Vries, Christoph Dieterich. Characterizing alternative splicing effects on protein interaction networks with LINDA
    465 -- 474Kerr Ding, Sheng Wang 0012, Yunan Luo. Supervised biological network alignment with graph neural networks
    475 -- 483Zhijian Huang, Pan Zhang, Lei Deng 0002. DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response
    484 -- 493Mihir Bafna, Hechen Li, Xiuwei Zhang. CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics
    494 -- 503Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek. Optimal adjustment sets for causal query estimation in partially observed biomolecular networks
    504 -- 512Addie Woicik, Mingxin Zhang, Hanwen Xu, Sara Mostafavi, Sheng Wang. Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling
    513 -- 522Van-Giang Trinh, Belaid Benhamou, Thomas A. Henzinger, Samuel Pastva. Trap spaces of multi-valued networks: definition, computation, and applications
    523 -- 533Paolo Pellizzoni, Giulia Muzio, Karsten M. Borgwardt. Higher-order genetic interaction discovery with network-based biological priors
    534 -- 543Giulio Ermanno Pibiri, Yoshihiro Shibuya, Antoine Limasset. k-mers
    544 -- 552Yasser Mohseni Behbahani, Elodie Laine, Alessandra Carbone. Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation
    553 -- 562Muyu Yang, Jian Ma 0004. UNADON: transformer-based model to predict genome-wide chromosome spatial position
    563 -- 571Tianshuo Zhou, Ning Dai, Sizhen Li, Max Ward 0001, David H. Mathews, Liang Huang 0001. RNA design via structure-aware multifrontier ensemble optimization

    Volume 39, Issue 9

    0 -- 0Jackson Callaghan, Colleen H. Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Eric Zhou, Rohan Juneja, Yao Yao, Madhumita Narayan, Kristina Hanspers, Ayushi Agrawal, Alexander R. Pico, Chunlei Wu, Andrew I. Su. BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
    0 -- 0Viktoria Schuster, Anders Krogh. The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data
    0 -- 0Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J. O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna. HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
    0 -- 0Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki. RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
    0 -- 0Kyle Smith, Cheng Ye, Yatish Turakhia. Tracking and curating putative SARS-CoV-2 recombinants with RIVET
    0 -- 0Anna Nadtochiy, Peter Luu, Scott E. Fraser, Thai V. Truong. VoDEx: a Python library for time annotation and management of volumetric functional imaging data
    0 -- 0Jonathan Klonowski, Qianqian Liang, Zeynep H. Coban Akdemir, Cecilia Lo, Dennis Kostka. aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants
    0 -- 0. Correction to: Online bias-aware disease module mining with ROBUST-Web
    0 -- 0Saifur R. Khan, Andreea Obersterescu, Erica P. Gunderson, Babak Razani, Michael B. Wheeler, Brian J. Cox. metGWAS 1.0: an R workflow for network-driven over-representation analysis between independent metabolomic and meta-genome-wide association studies
    0 -- 0Ronan M. T. Fleming, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele. Cardinality optimization in constraint-based modelling: application to human metabolism
    0 -- 0Bárbara Zita Peters Couto, Nicholas Robertson, Ellis Patrick, Shila Ghazanfar. MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor
    0 -- 0Yan Zhu, Lingling Zhao, Naifeng Wen, Junjie Wang 0005, Chunyu Wang. DataDTA: a multi-feature and dual-interaction aggregation framework for drug-target binding affinity prediction
    0 -- 0Yan Hu, Vipina Kuttichi Keloth, Kalpana Raja, Yong Chen, Hua Xu. Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach
    0 -- 0David Teschner, David Gomez-Zepeda, Arthur Declercq, Mateusz K. Lacki, Seymen Avci, Konstantin Bob, Ute Distler, Thomas Michna, Lennart Martens, Stefan Tenzer, Andreas Hildebrandt 0001. Ionmob: a Python package for prediction of peptide collisional cross-section values
    0 -- 0Mercedeh Movassagh, Steven J. Schiff, Joseph N. Paulson. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
    0 -- 0Qijie Chen, Haotong Sun, Haoyang Liu, Yinghui Jiang, Ting Ran, Xurui Jin, Xianglu Xiao, Zhimin Lin, Hongming Chen, Zhangming Niu. An extensive benchmark study on biomedical text generation and mining with ChatGPT
    0 -- 0Davide Cozzi, Massimiliano Rossi 0001, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni. μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data
    0 -- 0Steven Grudman, J. Eduardo Fajardo, András Fiser. Optimal selection of suitable templates in protein interface prediction
    0 -- 0Björn Wallner. AFsample: improving multimer prediction with AlphaFold using massive sampling
    0 -- 0Manuel Huth, Jonas Arruda, Roy Gusinow, Lorenzo Contento, Evelina Tacconelli, Jan Hasenauer. Accessibility of covariance information creates vulnerability in Federated Learning frameworks
    0 -- 0Nhan Ly-Trong, Giuseppe M. J. Barca, Bui Quang Minh. AliSim-HPC: parallel sequence simulator for phylogenetics
    0 -- 0Pin Lyu, Yijie Zhai, Taibo Li, Jiang Qian. CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server
    0 -- 0Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt. DrForna: visualization of cotranscriptional folding
    0 -- 0Sarah G. Ayton, Victor Treviño. MuTATE - an R package for comprehensive multi-objective molecular modeling
    0 -- 0. Correction to: Python interfaces for the Smoldyn simulator
    0 -- 0Jeffrey M. Dick, Xun Kang. chem16S: community-level chemical metrics for exploring genomic adaptation to environments
    0 -- 0Wei Qu, Ronghui You, Hiroshi Mamitsuka, Shanfeng Zhu. DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
    0 -- 0Jun-Young Park, Jang Jae Lee, Younghwa Lee, Dongsoo Lee, Jungsoo Gim, Lindsay A. Farrer, Kun Ho Lee, Sungho Won. Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies
    0 -- 0Jace Webster, Hung Mai, Amy Ly, Christopher Maher. INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
    0 -- 0Gherard Batisti Biffignandi, Greta Bellinzona, Greta Petazzoni, Davide Sassera, Gianvincenzo Zuccotti, Claudio Bandi, Fausto Baldanti, Francesco Comandatore, Stefano Gaiarsa. P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics
    0 -- 0Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
    0 -- 0Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song. MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning
    0 -- 0Weiwen Wang, James Barbetti, Thomas Wong, Bryan Thornlow, Russell Corbett-Detig, Yatish Turakhia, Robert Lanfear, Bui Quang Minh. DecentTree: scalable Neighbour-Joining for the genomic era
    0 -- 0Federico Bianca, Emilio Ispano, Ermanno Gazzola, Enrico Lavezzo, Paolo Fontana, Stefano Toppo. FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms
    0 -- 0Matthew D. Smith 0004, Marshall A Case, Emily K. Makowski, Peter M. Tessier. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data
    0 -- 0Lechuan Li, Ruth Dannenfelser, Yu Zhu 0003, Nathaniel Hejduk, Santiago Segarra, Vicky Yao. Joint embedding of biological networks for cross-species functional alignment
    0 -- 0Xinwei He, Kun Qian, Ziqian Wang, Shirou Zeng, Hongwei Li, Wei Vivian Li. scAce: an adaptive embedding and clustering method for single-cell gene expression data
    0 -- 0. Correction to: Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization
    0 -- 0Tudor-Stefan Cotet, Andreas Agrafiotis, Victor Kreiner, Raphael Kuhn, Danielle Shlesinger, Marcos Manero-Carranza, Keywan Khodaverdi, Evgenios Kladis, Aurora Desideri Perea, Dylan Maassen-Veeters, Wiona Glänzer, Solène Massery, Lorenzo Guerci, Kai-Lin Hong, Jiami Han, Kostas Stiklioraitis, Vittoria Martinolli D'arcy, Raphael Dizerens, Samuel Kilchenmann, Lucas Stalder, Leon Nissen, Basil Vogelsanger, Stine Anzböck, Daria Laslo, Sophie Bakker, Melinda Kondorosy, Marco Venerito, Alejandro Sanz García, Isabelle Feller, Annette Oxenius, Sai T. Reddy, Alexander Yermanos. ePlatypus: an ecosystem for computational analysis of immunogenomics data
    0 -- 0Pablo Millan Arias, Kathleen A. Hill, Lila Kari. iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences
    0 -- 0Johannes Smolander, Sini Junttila, Laura L. Elo. Cell-connectivity-guided trajectory inference from single-cell data
    0 -- 0Seong Joon Park, Sunghwan Kim, Jaeho Jeong, Albert No, Jong-Seon No, Hosung Park. Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
    0 -- 0Boris Muzellec, Maria Telenczuk, Vincent Cabeli, Mathieu Andreux. PyDESeq2: a python package for bulk RNA-seq differential expression analysis
    0 -- 0. Correction to: Optimal adjustment sets for causal query estimation in partially observed biomolecular networks
    0 -- 0. Correction to: Clustering spatial transcriptomics data
    0 -- 0Bhanwar Lal Puniya, Andreas Dräger. Advancements in computational modelling of biological systems: seventh annual SysMod meeting
    0 -- 0Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang 0001. MSDRP: a deep learning model based on multisource data for predicting drug response
    0 -- 0Kleanthi Lakiotaki, Zacharias Papadovasilakis, Vincenzo Lagani, Stefanos Fafalios, Paulos Charonyktakis, Michail Tsagris, Ioannis Tsamardinos. Automated machine learning for genome wide association studies
    0 -- 0Chuan-Yuan Wang, Shiyu Xu, Duanchen Sun, Zhi-Ping Liu. ActivePPI: quantifying protein-protein interaction network activity with Markov random fields
    0 -- 0Daoyi Huang, Jianping Jiang, Tingting Zhao, Shengnan Wu, Pin Li, Yongfen Lyu, Jincai Feng, Mingyue Wei, Zhixing Zhu, Jianlei Gu, Yongyong Ren, Guangjun Yu, Hui Lu. diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype
    0 -- 0Lin Wang, Chenhao Sun, Xianyu Xu, Jia Li, Wenjuan Zhang. A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug-side effects
    0 -- 0Megan L. Smith, Matthew W. Hahn. Phylogenetic inference using generative adversarial networks
    0 -- 0Asmita Roy, Jun Chen, Xianyang Zhang. A general framework for powerful confounder adjustment in omics association studies
    0 -- 0En-Yu Lai, Yen-Tsung Huang. Genome-wide multimediator analyses using the generalized Berk-Jones statistics with the composite test
    0 -- 0Anna Paola Muntoni, Andrea Pagnani. DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors
    0 -- 0Wuwei Tan, Yang Shen. Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
    0 -- 0. Correction to: "Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency"
    0 -- 0Brian Johnson, Yubo Shuai, Jason Schweinsberg, Kit Curtius. cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory
    0 -- 0Yuzhong Deng, Jianxiong Tang, Jiyang Zhang, Jianxiao Zou, Que Zhu, Shicai Fan. GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs
    0 -- 0Xin He, Xianhui Huang, Yuexuan Long, Zhenping Liu, Xing Chang, Xianlong Zhang, Maojun Wang. Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms
    0 -- 0Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G. M. Piccirillo, Yan Guo. Somatic mutation effects diffused over microRNA dysregulation
    0 -- 0Yiwei Liu, Changhuo Yang, Hong-Dong Li, Jianxin Wang. IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions
    0 -- 0Adrià Fernández-Torras, Martina Locatelli, Martino Bertoni, Patrick Aloy. BQsupports: systematic assessment of the support and novelty of new biomedical associations

    Volume 39, Issue 8

    0 -- 0Jennifer Mattock, Marina Martínez-Álvaro, Matthew A Cleveland, Rainer Roehe, Mick Watson. KOunt: a reproducible KEGG orthologue abundance workflow
    0 -- 0Lucas F. Voges, Lukas C. Jarren, Stephan Seifert. Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features
    0 -- 0Göksel Misirli. libSBOLj3: a graph-based library for design and data exchange in synthetic biology
    0 -- 0. Correction to: Joint registration of multiple point clouds for fast particle fusion in localization microscopy
    0 -- 0Jianwen Fang. Predicting thermostability difference between cellular protein orthologs
    0 -- 0Serene W. H. Wong, Chiara Pastrello, Max Kotlyar, Christos Faloutsos, Igor Jurisica. USNAP: fast unique dense region detection and its application to lung cancer
    0 -- 0Guangzhi Xiong, Stefan Bekiranov, Aidong Zhang. ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq
    0 -- 0Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara. Enhancing cryo-EM maps with 3D deep generative networks for assisting protein structure modeling
    0 -- 0Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio. CoCoNat: a novel method based on deep learning for coiled-coil prediction
    0 -- 0Garrett M. Ginell, Aidan J. Flynn, Alex S. Holehouse. SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
    0 -- 0Lena Buck, Tobias Schmidt, Maren Feist, Philipp Schwarzfischer, Dieter Kube, Peter J. Oefner, Helena U. Zacharias, Michael Altenbuchinger, Katja Dettmer, Wolfram Gronwald, Rainer Spang. Anomaly detection in mixed high-dimensional molecular data
    0 -- 0Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne M. Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber. NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
    0 -- 0Elena Krismer, Isabell Bludau, Maximilian T. Strauss, Matthias Mann. AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics
    0 -- 0Kynon J. M. Benjamin, Tarun Katipalli, Apuã C. M. Paquola. dRFEtools: dynamic recursive feature elimination for omics
    0 -- 0Joshua Barnett, Noori Sotudeh, Poorvi Rao, Jonah Silverman, Tamara Jafar, Liya Wang. AtlasXplore: a web platform for visualizing and sharing spatial epigenome data
    0 -- 0Mercè Alemany-Chavarria, Jaime Rodríguez-Guerra, Jean-Didier Maréchal. TALAIA: a 3D visual dictionary for protein structures
    0 -- 0Benjamin Hepp, Florence Lorieux, Augustin Degaugue, Jacques Oberto. VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes
    0 -- 0Yuliang Pan, Yang Wang, Jihong Guan, Shuigeng Zhou. PCGAN: a generative approach for protein complex identification from protein interaction networks
    0 -- 0Hamza Chegraoui, Vincent Guillemot, Amine Rebei, Arnaud Gloaguen, Jacques Grill, Cathy Philippe, Vincent Frouin. Integrating multiomics and prior knowledge: a study of the Graphnet penalty impact
    0 -- 0Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Hang Lou, Hao Ni, Ross D. King. Protein-ligand binding affinity prediction exploiting sequence constituent homology
    0 -- 0Marteinn T. Hardarson, Gunnar Palsson, Bjarni V. Halldórsson. NCOurd: modelling length distributions of NCO events and gene conversion tracts
    0 -- 0Yichen Cheng, Yusen Xia, Xinlei Wang 0001. Bayesian multitask learning for medicine recommendation based on online patient reviews
    0 -- 0Ziqiao Zhang, Ailin Xie, Jihong Guan, Shuigeng Zhou. Molecular property prediction by semantic-invariant contrastive learning
    0 -- 0Minghao Yang, Zhi-an Huang, Wei Zhou, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu. MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations
    0 -- 0Jace Webster, Ha X. Dang, Pradeep S. Chauhan, WenJia Feng, Alex Shiang, Peter K. Harris, Russell K. Pachynski, Aadel A Chaudhuri, Christopher A. Maher. PACT: a pipeline for analysis of circulating tumor DNA
    0 -- 0Eric H. Au, Christiana Fauci, Yanting Luo, Riley J. Mangan, Daniel A Snellings, Chelsea R. Shoben, Seth Weaver, Shae K. Simpson, Craig B. Lowe. Gonomics: uniting high performance and readability for genomics with Go
    0 -- 0Richard Wilton, Alexander S. Szalay. Short-read aligner performance in germline variant identification
    0 -- 0Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad. DeepTraSynergy: drug combinations using multimodal deep learning with transformers
    0 -- 0Bo-Wei Zhao, Xiao-Rui Su, Peng-Wei Hu, Yu-An Huang, Zhu-Hong You, Lun Hu. iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network
    0 -- 0Hans-Ulrich Klein. demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models
    0 -- 0Feifei Wang, Dongzuo Liang, Yang Li, Shuangge Ma. Prior information-assisted integrative analysis of multiple datasets
    0 -- 0Thaidy Moreno, Joaquin Magana, David A. Quigley. AARDVARK: an automated reversion detector for variants affecting resistance kinetics
    0 -- 0Kim Philipp Jablonski, Niko Beerenwinkel. Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression
    0 -- 0Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support
    0 -- 0Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu. Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
    0 -- 0Apurva Kalia, Dilip Krishnan, Soha Hassoun. CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction
    0 -- 0Gabriel Cretin, Charlotte Périn, Nicolas Zimmermann, Tatiana Galochkina, Jean-Christophe Gelly. ICARUS: flexible protein structural alignment based on Protein Units
    0 -- 0Chen Wang, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge. B.subtilis
    0 -- 0Anders Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao. quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics
    0 -- 0Gang Wen, Limin Li. FGCNSurv: dually fused graph convolutional network for multi-omics survival prediction
    0 -- 0Alexander Myronov, Giovanni Mazzocco, Paulina Król, Dariusz Plewczynski. BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
    0 -- 0Philip Hartout, Bojana Pocuca, Celia Méndez-García, Christian Schleberger. Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling
    0 -- 0Bing-Xue Du, Yahui Long, Xiaoli Li, Min Wu, Jian-Yu Shi. CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning
    0 -- 0Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, LiangLiang Zhang. ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
    0 -- 0Tong Xin, Yanan Lv, Haoran Chen, Linlin Li, Lijun Shen, Guangcun Shan, Xi Chen 0031, Hua Han 0001. A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network
    0 -- 0Daniel Liu, Martin Steinegger. Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices
    0 -- 0Anton Zadorozhny, Anton Smirnov, Dmitry Filimonov, Alexey Lagunin. Prediction of pathogenic single amino acid substitutions using molecular fragment descriptors
    0 -- 0Ruohua Shi, Keyan Bi, Kai Du, Lei Ma 0008, Fang Fang, Lingyu Duan, Tingting Jiang 0001, Tie-Jun Huang 0001. PS-Net: human perception-guided segmentation network for EM cell membrane
    0 -- 0Jacob I Marsh, Jakob Petereit, Brady A Johnston, Philipp E. Bayer, Cassandria G. Tay Fernandez, Hawlader A Al-Mamun, Jacqueline Batley, David Edwards. crosshap: R package for local haplotype visualization for trait association analysis
    0 -- 0Md Ashiqur Rahman, Abdullah Aman Tutul, Mahfuza Sharmin, Md. Shamsuzzoha Bayzid. BEENE: deep learning-based nonlinear embedding improves batch effect estimation
    0 -- 0Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova. Sphagnum divinum and proteome-scale annotation
    0 -- 0Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Ivan V. Kulakovskiy. LegNet: a best-in-class deep learning model for short DNA regulatory regions
    0 -- 0Zhenhuan Feng, Peiyang Fang, Hui Zheng, Xiaofei Zhang. DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data
    0 -- 0Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-bin Shen, Dong-jun Yu. MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering
    0 -- 0Longendri Aguilera-Mendoza, Sebastián Ayala-Ruano, Felix Martinez-Rios, Edgar Chávez, César R. García-Jacas, Carlos A. Brizuela, Yovani Marrero-Ponce. StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks
    0 -- 0Amir Feizi, Kamalika Ray. otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
    0 -- 0Xuhua Yan, Ruiqing Zheng, Jinmiao Chen, Min Li. scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization
    0 -- 0Moctard Babatounde Oloulade, Jianliang Gao, Jiamin Chen, Raeed Al-Sabri, Zhenpeng Wu. Cancer drug response prediction with surrogate modeling-based graph neural architecture search
    0 -- 0Yanli Wang, Zhiye Guo, Jianlin Cheng. Single-cell Hi-C data enhancement with deep residual and generative adversarial networks
    0 -- 0Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton. Adjusting for gene-specific covariates to improve RNA-seq analysis
    0 -- 0Eyal Mazuz, Guy Shtar, Nir Kutsky, Lior Rokach, Bracha Shapira. Pretrained transformer models for predicting the withdrawal of drugs from the market
    0 -- 0Emanuel Cunha, Davide Lagoa, José P. Faria, Filipe Liu, Christopher S. Henry, Oscar Días. TranSyT, an innovative framework for identifying transport systems
    0 -- 0Davor Orsolic, Tomislav Smuc. Dynamic applicability domain (dAD): compound-target binding affinity estimates with local conformal prediction
    0 -- 0Andrea Mastropietro, Gianluca De Carlo, Aris Anagnostopoulos. XGDAG: explainable gene-disease associations via graph neural networks
    0 -- 0Chen Li, Xiaoyang Chen, Shengquan Chen, Rui Jiang, Xuegong Zhang. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
    0 -- 0Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota I. Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos. Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
    0 -- 0Peng Chen, Jian Wang, Hongfei Lin, Di Zhao 0003, Zhihao Yang. Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning
    0 -- 0Martin Wegner, Manuel Kaulich. co unting of single and combinatorial CRISPR gRNAs
    0 -- 0Daniel T. Rademaker, Kevin J. van Geemen, Li C. Xue. GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations
    0 -- 0Jack R. Leary, Yi Xu, Ashley B. Morrison, Chong Jin, Emily C. Shen, Peyton C. Kuhlers, Ye Su, Naim U. Rashid, Jen Jen Yeh, Xianlu Laura Peng. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing
    0 -- 0Sehi Park, Mobeen-ur-Rehman, Farman Ullah, Hilal Tayara, Kil To Chong 0001. iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data

    Volume 39, Issue 5

    0 -- 0Ayush Noori, Michelle M. Li, Amelia L. M. Tan, Marinka Zitnik. Metapaths: similarity search in heterogeneous knowledge graphs via meta-paths
    0 -- 0Kyle Ferchen, Nathan Salomonis, H. Leighton Grimes. pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells
    0 -- 0Linda Grob, Anne Bertolini, Matteo Carrara, Ulrike Lischetti, Aizhan Tastanova, Christian Beisel, Mitchell P. Levesque, Daniel J. Stekhoven, Franziska Singer. gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis
    0 -- 0Mengbo Li, Gordon K. Smyth. Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics
    0 -- 0Tanja Holstein, Franziska Kistner, Lennart Martens, Thilo Muth. PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores
    0 -- 0Pierre-Aurélien Gilliot, Thomas E. Gorochowski. Effective design and inference for cell sorting and sequencing based massively parallel reporter assays
    0 -- 0Joung Min Choi, Ming Ji, Layne T. Watson, Liqing Zhang. DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation
    0 -- 0Michal Zurkowski, Maciej Antczak, Marta Szachniuk. High-quality, customizable heuristics for RNA 3D structure alignment
    0 -- 0Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li. AcrNET: predicting anti-CRISPR with deep learning
    0 -- 0Boyan Zhou, Huilin Li. STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
    0 -- 0Jinjuan Wang, Mingya Long, Qizhai Li. A maximum kernel-based association test to detect the pleiotropic genetic effects on multiple phenotypes
    0 -- 0Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List. spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
    0 -- 0Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong 0001, Kwong-Sak Leung, Lixin Cheng. Deciphering associations between gut microbiota and clinical factors using microbial modules
    0 -- 0Sergio Doria-Belenguer, Alexandros Xenos, Gaia Ceddia, Noël Malod-Dognin, Natasa Przulj. A functional analysis of omic network embedding spaces reveals key altered functions in cancer
    0 -- 0Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj. A framework for high-throughput sequence alignment using real processing-in-memory systems
    0 -- 0Artyom A. Egorov, Gemma Catherine Atkinson. uORF4u: a tool for annotation of conserved upstream open reading frames
    0 -- 0. Correction to: Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data
    0 -- 0Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun. HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer
    0 -- 0Kimberly A. Dill-McFarland, Kiana Mitchell, Sashank Batchu, Richard Max Segnitz, Basilin Benson, Tomasz Janczyk, Madison S. Cox, Harriet Mayanja-Kizza, William Henry Boom, Penelope Benchek, Catherine M. Stein, Thomas R. Hawn, Matthew C. Altman. Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data
    0 -- 0Lucas Robidou, Pierre Peterlongo. fimpera: drastic improvement of Approximate Membership Query data-structures with counts
    0 -- 0Ling Luo 0001, Chih-Hsuan Wei, Po-Ting Lai, Robert Leaman, Qingyu Chen 0001, Zhiyong Lu. AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning
    0 -- 0Thomas Büchler, Jannik Olbrich, Enno Ohlebusch. Efficient short read mapping to a pangenome that is represented by a graph of ED strings
    0 -- 0Florin C. Walter, Oliver Stegle, Britta Velten. FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution
    0 -- 0Wouter De Coster, Rosa Rademakers. NanoPack2: population-scale evaluation of long-read sequencing data
    0 -- 0Masaki Tagashira. ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring
    0 -- 0Zixuan Wang, Shuwen Xiong, Yun Yu, Jiliu Zhou, Yongqing Zhang. HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency
    0 -- 0Nicholas A. G. Johnson, Liezel Tamon, Xin Liu, Aleksandr B. Sahakyan. ROptimus: a parallel general-purpose adaptive optimization engine
    0 -- 0Xinran Wang, Zeyun Lu, Arjun Bhattacharya, Bogdan Pasaniuc, Nicholas Mancuso. twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis
    0 -- 0Wancen Mu, Eric S. Davis, Stuart Lee, Mikhail G. Dozmorov, Douglas H. Phanstiel, Michael I. Love. bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing
    0 -- 0Roman Martin, Minh Kien Nguyen, Nick Lowack, Dominik Heider. ODNA: identification of organellar DNA by machine learning
    0 -- 0Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L. Collins, Michael E. Talkowski, Daniel Blankenberg, Rikke S. Møller, Johannes R. Lemke, Michael Nothnagel, Patrick May, Dennis Lal. CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online
    0 -- 0Jinxian Wang, Jihong Guan, Shuigeng Zhou. Molecular property prediction by contrastive learning with attention-guided positive sample selection
    0 -- 0Szymon Grabowski, Wojciech Bieniecki. copMEM2: robust and scalable maximum exact match finding
    0 -- 0Weiyan Zhang, Chuang Chen, Jiacheng Wang, JingPing Liu, Tong Ruan. A co-adaptive duality-aware framework for biomedical relation extraction
    0 -- 0Pietro Hiram Guzzi, Ugo Lomoio, Pierangelo Veltri. GTExVisualizer: a web platform for supporting ageing studies
    0 -- 0Piotr Wlodzimierz, Michael Hong, Ian R. Henderson. TRASH: Tandem Repeat Annotation and Structural Hierarchy
    0 -- 0Camille Juigné, Olivier Dameron, François Moreews, Florence Gondret, Emmanuelle Becker. Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies
    0 -- 0My-Diem Nguyen Pham, Thanh-Nhan Nguyen, Le Son Tran, Que-Tran Bui Nguyen, Thien-Phuc Hoang Nguyen, Thi Mong Quynh Pham, Hoai-Nghia Nguyen, Hoa Giang, Minh-Duy Phan, Vy Nguyen. epiTCR: a highly sensitive predictor for TCR-peptide binding
    0 -- 0. Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks
    0 -- 0Bowen Yang, Minal Khatri, Jinfang Zheng, Jitender S. Deogun, Yanbin Yin. Genome mining for anti-CRISPR operons using machine learning
    0 -- 0Eric S. Davis, Wancen Mu, Stuart Lee, Mikhail G. Dozmorov, Michael I. Love, Douglas H. Phanstiel. matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling
    0 -- 0Robin Paul, Jian Wang, Colleen Reilly, Edgar Sioson, Jaimin Patel, Gavriel Matt, Aleksandar Acic, Xin Zhou. ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping
    0 -- 0Joshua A. M. Kaste, Yair Shachar-Hill. Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
    0 -- 0Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan. RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
    0 -- 0Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A Bradham. ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes
    0 -- 0Tianqi Wu, Zhiye Guo, Jianlin Cheng. Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer
    0 -- 0Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani 0002, Martina Ferri, Francesco Sassi, Luca Alessandrì, Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system
    0 -- 0Lingyu Li, Liangjie Sun, Guangyi Chen, Chi-Wing Wong, Wai-Ki Ching, Zhi-Ping Liu. LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data
    0 -- 0Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu. Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs
    0 -- 0Daniel Krefl, Alessandro Brandulas Cammarata, Sven Bergmann. PascalX: a Python library for GWAS gene and pathway enrichment tests
    0 -- 0Niklas Philipp, Cedric K. Brinkmann, Jens Georg, Daniel Schindler, Bork A Berghoff. DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria
    0 -- 0Ambuj Kumar, Burak T. Kaynak, Karin S. Dorman, Pemra Doruker, Robert L. Jernigan. Predicting allosteric pockets in protein biological assemblages
    0 -- 0Pétur Helgi Einarsson, Páll Melsted. BUSZ: compressed BUS files
    0 -- 0Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang, Changbin Yu. 3D-MSNet: a point cloud-based deep learning model for untargeted feature detection and quantification in profile LC-HRMS data
    0 -- 0Sébastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard I. Kuo, Megan Davey, Alan L. Archibald, Mick Watson. nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
    0 -- 0Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang. DFHiC: a dilated full convolution model to enhance the resolution of Hi-C data
    0 -- 0Xiaobin Zheng, Joseph R. Tran, Yixian Zheng. CscoreTool-M infers 3D sub-compartment probabilities within cell population
    0 -- 0Francesco Monti, David Stewart, Anuradha Surendra, Irina Alecu, Thao Nguyen-Tran, Steffany A. L. Bennett, Miroslava Cuperlovic-Culf. Signed Distance Correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis
    0 -- 0Axel Schmidt, Sebastian Röner, Karola Mai, Hannah Klinkhammer, Martin Kircher, Kerstin U. Ludwig. Predicting the pathogenicity of missense variants using features derived from AlphaFold2
    0 -- 0. Correction to: Integrative analysis of individual-level data and high-dimensional summary statistics
    0 -- 0Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim. VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
    0 -- 0Xueli Zhang, Lingcong Kong, Shunming Liu, Xiayin Zhang, Xianwen Shang, Zhuoting Zhu, Yu Huang, Shuo Ma, Jason Ha, Katerina V. Kiburg, Chunwen Zheng, Yunyan Hu, Cong Li, Guanrong Wu, Yingying Liang, Mengxia He, Yan Wang, Xiaohe Bai, Danli Shi, Wei Wang, Chi Zhang, Ke Zhao, Haining Yuan, Guang Hu, Yijun Hu, Huiying Liang, Honghua Yu, Lei Zhang, Mingguang He. EBD: an eye biomarker database
    0 -- 0Martin Larralde, Georg Zeller. PyHMMER: a Python library binding to HMMER for efficient sequence analysis
    0 -- 0Niema Moshiri. ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
    0 -- 0Yiyan Yang, Xiaofang Jiang. Evolink: a phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multispecies data
    0 -- 0Julian Dosch, Holger Bergmann, Vinh Tran, Ingo Ebersberger. FAS: assessing the similarity between proteins using multi-layered feature architectures
    0 -- 0Rui P. Ribeiro, Alejandro Giorgetti. pyGOMoDo: GPCRs modeling and docking with python
    0 -- 0Anjali Silva, Xiaoke Qin, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi. Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data
    0 -- 0Alfonso De Falco, Christophe M. Olinger, Barbara Klink, Michel Mittelbronn, Daniel Stieber. Digital PCR cluster predictor: a universal R-package and shiny app for the automated analysis of multiplex digital PCR data

    Volume 39, Issue 4

    0 -- 0Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael I. Love, Mikhail G. Dozmorov. excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
    0 -- 0Massimiliano Volpe, Jyotirmoy Das. methylR: a graphical interface for comprehensive DNA methylation array data analysis
    0 -- 0Natalia V. Loukachevitch, Suresh Manandhar, Elina Baral, Igor Rozhkov, Pavel Braslavski, Vladimir Ivanov 0001, Tatiana Batura, Elena Tutubalina. NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities
    0 -- 0Min Yang, Bo Qiu, Guo-You He, Jian-Yuan Zhou, Hao-Jie Yu, Yu-Ying Zhang, Yan-Shang Li, Tai-Song Li, Jin-Cheng Guo, Xue-Cang Li, Jian-Jun Xie. eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species
    0 -- 0René Staritzbichler, Nikola Ristic, Tülin Stapke, Peter W. Hildebrand. SmoothT - a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling
    0 -- 0Saleh Riahi, Jae-Hyeon Lee, Taylor Sorenson, Shuai Wei, Sven Jager, Reza Olfati-Saber, Yanfeng Zhou, Anna Park, Maria Wendt, Hervé Minoux, Yu Qiu. Surface ID: a geometry-aware system for protein molecular surface comparison
    0 -- 0Xiaoliang Ren, Yanwen Shao, Yiwen Zhang, Ying Ni, Yu Bi, Runsheng Li. Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
    0 -- 0Elisabetta C. Sciacca, Salvatore Alaimo, Gianmarco Silluzio, Alfredo Ferro, Vito Latora, Costantino Pitzalis, Alfredo Pulvirenti, Myles J. Lewis. DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data
    0 -- 0Can (sam) Chen, Jingbo Zhou, Fan Wang, Xue (Steve) Liu, Dejing Dou. Structure-aware protein self-supervised learning
    0 -- 0Ziang Zhang, Lei Sun. The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait
    0 -- 0Hannah M. Doherty, George Kritikos, Marco Galardini, Manuel Banzhaf, Danesh Moradigaravand. ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling
    0 -- 0Benjamin B. Chu, Seyoon Ko, Jin J. Zhou, Aubrey Jensen, Hua Zhou 0001, Janet S. Sinsheimer, Kenneth Lange. Multivariate genome-wide association analysis by iterative hard thresholding
    0 -- 0Can Chen, Scott T. Weiss, Yang-Yu Liu. Graph convolutional network-based feature selection for high-dimensional and low-sample size data
    0 -- 0Bansho Masutani, Riki Kawahara, Shinichi Morishita. Decomposing mosaic tandem repeats accurately from long reads
    0 -- 0Diana F. Sousa, Francisco M. Couto. K-RET: knowledgeable biomedical relation extraction system
    0 -- 0Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals. dipwmsearch: a Python package for searching di-PWM motifs
    0 -- 0Petr Triska, Fabian Amman, Lukas Endler, Andreas Bergthaler. WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) - a web application for visualization of wastewater pathogen sequencing results
    0 -- 0Signe Skog, Lovisa Örkenby, Unn Kugelberg, Anita Öst, Daniel Nätt. Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts
    0 -- 0Tiantian Ye, Yangyang Hu, Sydney Pun, Wenxiu Ma. HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data
    0 -- 0Sheng Fu, Lu Deng, Han Zhang 0003, William Wheeler, Jing Qin, Kai Yu. Integrative analysis of individual-level data and high-dimensional summary statistics
    0 -- 0Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin T. Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson. An expectation-maximization framework for comprehensive prediction of isoform-specific functions
    0 -- 0Steven Shave, John C. Dawson, Abdullah M. Athar, Cuong Q. Nguyen, Richard Kasprowicz, Neil O. Carragher. Phenonaut: multiomics data integration for phenotypic space exploration
    0 -- 0Yi Fang, Xiaoyong Pan, Hong-bin Shen. De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment
    0 -- 0Olivier Mailhot, François Major, Rafael Najmanovich. The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships
    0 -- 0Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek. Boolean network sketches: a unifying framework for logical model inference
    0 -- 0Conrad Leonard. streammd: fast low-memory duplicate marking using a Bloom filter
    0 -- 0. Correction to: Multi-omic integration by machine learning (MIMaL)
    0 -- 0Altay Yuzeir, David Alejandro Bejarano, Stephan Grein, Jan Hasenauer, Andreas Schlitzer, Jiangyan Yu. IntestLine: a shiny-based application to map the rolled intestinal tissue onto a line
    0 -- 0Michael Shaffer, Mikayla A. Borton, Ben Bolduc, José P. Faria, Rory M. Flynn, Parsa Ghadermazi, Janaka N. Edirisinghe, Elisha M. Wood-Charlson, Christopher S. Miller, Siu Hung Joshua Chan, Matthew B. Sullivan, Christopher S. Henry, Kelly C. Wrighton. kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
    0 -- 0Lukas Heumos, Philipp Ehmele, Luis Kuhn Cuellar, Kevin Menden, Edmund Miller, Steffen Lemke 0003, Gisela Gabernet, Sven Nahnsen. mlf-core: a framework for deterministic machine learning
    0 -- 0Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa. Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres
    0 -- 0Yuxin Li, Xuhua Liu, Xueyan Jia, Tao Jiang, Jianghao Wu, Qianlong Zhang, Junhuai Li, Xiangning Li, Anan Li. A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution
    0 -- 0Ke Yan 0003, Yichen Guo, Bin Liu. PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework
    0 -- 0Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data
    0 -- 0Daffodil M. Canson, Aimee L. Davidson, Miguel de la Hoya, Michael T. Parsons, Dylan M. Glubb, Olga Kondrashova, Amanda B. Spurdle. SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
    0 -- 0Yi Liu 0058, Benjamin L. Elsworth, Tom R. Gaunt. Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets
    0 -- 0Chenyang Dong, Siqi Shen, Sündüz Keles. AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver
    0 -- 0Lucas Prates, Renan B. Lemes, Tábita Hünemeier, Florencia G. Leonardi. Population-based change-point detection for the identification of homozygosity islands
    0 -- 0Liangrui Ren, Jun Wang, Zhao Li, Qingzhong Li, Guoxian Yu. scMCs: a framework for single-cell multi-omics data integration and multiple clusterings
    0 -- 0Hanyi Yu, Fusheng Wang 0001, George Teodoro, Fan Chen, Xiaoyuan Guo, John Nickerson, Jun Kong. Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images
    0 -- 0Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li. Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration
    0 -- 0Richard J. Packer, Alex T. Williams, William Hennah, Micaela T. Eisenberg, Nick Shrine, Katherine A Fawcett, Willow Pearson, Anna L. Guyatt, Ahmed Edris, Edward J. Hollox, Mikko Marttila, Balasubramanya S. Rao, John Raymond Bratty, Louise V. Wain, Frank Dudbridge, Martin D. Tobin. DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
    0 -- 0Mohamed Reda El Khili, Safyan Aman Memon, Amin Emad. MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores
    0 -- 0Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu. RNAget: an API to securely retrieve RNA quantifications
    0 -- 0Yuansong Zeng, Zhuoyi Wei, Qianmu Yuan, Sheng Chen, Weijiang Yu, Yutong Lu, Jianzhao Gao, Yuedong Yang. Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
    0 -- 0. Correction to: Continuous chromatin state feature annotation of the human epigenome
    0 -- 0Mingqian Zhang, Wenke Zhang, Yuzhu Chen, Jin Zhao, Shunyao Wu, Xiaoquan Su. Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes
    0 -- 0Shulei Wang. Multiscale adaptive differential abundance analysis in microbial compositional data
    0 -- 0Hyun Jae Cho, Mia Shu, Stefan Bekiranov, Chongzhi Zang, Aidong Zhang. Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment
    0 -- 0Shani Cohen, Eden Maximof, Shay Rokach, Mor Tadeski, Isana Veksler-Lublinsky. Escherichia coli sRNA-mRNA interactions
    0 -- 0Jean-Pierre Borg, Jacques Colinge, Patrice Ravel. Modular response analysis reformulated as a multilinear regression problem
    0 -- 0Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori. Prediction and curation of missing biomedical identifier mappings with Biomappings
    0 -- 0Ruogu Wang, Alex A. Lemus, Colin M. Henneberry, Yiming Ying, Yunlong Feng, Alex M. Valm. Unmixing biological fluorescence image data with sparse and low-rank Poisson regression
    0 -- 0Deliang Bu, Xiao Wang, Qizhai Li. Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants
    0 -- 0Fabio Fassetti, Simona E. Rombo, Cristina Serrao. Discriminative pattern discovery for the characterization of different network populations
    0 -- 0Gözde Yazici, Burcu Kurt Vatandaslar, Ilknur Aydin Canturk, Fatmagul I Aydinli, Ozge Arici Duz, Emre Karakoç, Bilal Ersen Kerman, Can Alkan. Identification of protein-protein interaction bridges for multiple sclerosis
    0 -- 0S. Taylor Head, Elizabeth J. Leslie, David J. Cutler, Michael P. Epstein. POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes
    0 -- 0André L. S. Meirelles, Tahsin M. Kurç, Jun Kong, Renato Ferreira, Joel H. Saltz, George Teodoro. Effective and efficient active learning for deep learning-based tissue image analysis
    0 -- 0Hyunbin Kim, Milot Mirdita, Martin Steinegger. Foldcomp: a library and format for compressing and indexing large protein structure sets
    0 -- 0Heather Marriott, Renata Kabiljo, Ahmad Al Khleifat, Richard J. Dobson, Ammar Al-Chalabi, Alfredo Iacoangeli. DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data
    0 -- 0Edin Salkovic, Mohammad Amin Sadeghi, Abdelkader Baggag, Ahmed Gamal Rashed Salem, Halima Bensmail. OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values

    Volume 39, Issue 3

    0 -- 0Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman. DeepOM: single-molecule optical genome mapping via deep learning
    0 -- 0Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao 0001, Roger J. Daly, Jiangning Song. Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification
    0 -- 0. Correction to: On the feasibility of deep learning applications using raw mass spectrometry data
    0 -- 0Amy Glen, Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G. Kvarfordt, Ross C. Peene, Shaopeng Liu, Andrew S. Hoffman, Jared C. Roach, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki. ARAX: a graph-based modular reasoning tool for translational biomedicine
    0 -- 0Arya R. Massarat, Michael Lamkin, Ciara Reeve, Amy L. Williams, Matteo D'Antonio, Melissa Gymrek. Haptools: a toolkit for admixture and haplotype analysis
    0 -- 0Ludwig Geistlinger, Roger Vargas, Tyrone Lee, Joshua Pan, Edward L. Huttlin, Robert Gentleman. BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions
    0 -- 0Mohan Rakesh, Hélène Vézina, Catherine Laprise, Ellen E. Freeman, Kelly M. Burkett, Marie-Hélène Roy-Gagnon. GENLIB: new function to simulate haplotype transmission in large complex genealogies
    0 -- 0Iñaki Amatria-Barral, Jorge González-Domínguez, Juan Touriño. PATO: genome-wide prediction of lncRNA-DNA triple helices
    0 -- 0Anupam Gautam, Wenhuan Zeng, Daniel H. Huson. MeganServer: facilitating interactive access to metagenomic data on a server
    0 -- 0Huixi Zou, Tianli Sun, Bangqun Jin, Shengqin Wang. sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome
    0 -- 0. Correction to: SVJedi: genotyping structural variations with long reads
    0 -- 0Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia. PhaGAA: an integrated web server platform for phage genome annotation and analysis
    0 -- 0Gandhar Mahadeshwar, Rafael de Cesaris Araujo Tavares, Han Wan, Zion R. Perry, Anna Marie Pyle. RSCanner: rapid assessment and visualization of RNA structure content
    0 -- 0. M. tuberculosis genome
    0 -- 0Tong Pan, Chen Li 0021, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song. PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships
    0 -- 0Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen 0004, Bin Liu 0014. CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction
    0 -- 0Weiming He, Jian Yang, Yi Jing, Lian Xu, Kang Yu, Xiaodong Fang. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
    0 -- 0Zehao Xiong, Jiawei Luo 0001, Wanwan Shi, Ying Liu, Zhongyuan Xu, Bo Wang. scGCL: an imputation method for scRNA-seq data based on graph contrastive learning
    0 -- 0Xuhua Yan, Ruiqing Zheng, Fang-Xiang Wu, Min Li 0007. CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity
    0 -- 0Andrei Dmitrenko, Michelle Reid, Nicola Zamboni. Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data
    0 -- 0. Correction to: SBbadger: biochemical reaction networks with definable degree distributions
    0 -- 0Tiago Cabral Borelli, Gabriel Santos Arini, Luís G. P. Feitosa, Pieter C. Dorrestein, Norberto Peporine Lopes, Ricardo R. da Silva. Improving annotation propagation on molecular networks through random walks: introducing ChemWalker
    0 -- 0Adrien Rougny, Irina Balaur, Augustin Luna, Alexander Mazein. StonPy: a tool to parse and query collections of SBGN maps in a graph database
    0 -- 0Karel J. van der Weg, Holger Gohlke. TopEnzyme: a framework and database for structural coverage of the functional enzyme space
    0 -- 0. Correction to: Improving annotation propagation on molecular networks through random walks: introducing ChemWalker
    0 -- 0Qizhi Li, Xubin Zheng, Jize Xie, Ran Wang, Mengyao Li, Man Hon Wong 0001, Kwong-Sak Leung, Shuai Li 0010, Qingshan Geng, Lixin Cheng. bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks
    0 -- 0Bin Huang, Tingwen Fan, Kaiyue Wang, Haicang Zhang, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu. Accurate and efficient protein sequence design through learning concise local environment of residues
    0 -- 0Adam Streck, Tom L. Kaufmann, Roland F. Schwarz. SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity
    0 -- 0Zhongshen Li, Junru Jin, Yu Wang, Wentao Long, Yuanhao Ding, Haiyan Hu, Leyi Wei. ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides
    0 -- 0Vladimir Porokhin, Li-Ping Liu 0001, Soha Hassoun. Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products
    0 -- 0Matti Pirinen. linemodels: clustering effects based on linear relationships
    0 -- 0Sebastian Deorowicz, Agnieszka Danek, Heng Li. AGC: compact representation of assembled genomes with fast queries and updates
    0 -- 0Rudolf T. Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M. Gyori, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
    0 -- 0William Haese-Hill, Kathryn Crouch, Thomas D. Otto. peaks2utr: a robust Python tool for the annotation of 3′ UTRs
    0 -- 0João Paulo Pereira Zanetti, Lucas Peres Oliveira, Leonid Chindelevitch, João Meidanis. Generalizations of the genomic rank distance to indels
    0 -- 0Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun. VirBot: an RNA viral contig detector for metagenomic data
    0 -- 0Sanjay K. Srikakulam, Sebastian Keller, Fawaz Dabbaghie, Robert Bals, Olga V. Kalinina. MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants
    0 -- 0Elisabet Munté, Lidia Feliubadaló, Marta Pineda, Eva Tornero, Maribel González, José Marcos Moreno-Cabrera, Carla Roca, Joan Bales Rubio, Laura Arnaldo, Gabriel Capellá, Jose Luis Mosquera, Conxi Lázaro. vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines
    0 -- 0Bianca A. Buchner, Tom J. Clement, Daan H. de Groot, Jürgen Zanghellini. ecmtool: fast and memory-efficient enumeration of elementary conversion modes
    0 -- 0Chirag Jain. Coverage-preserving sparsification of overlap graphs for long-read assembly
    0 -- 0Omid Rohanian, Mohammadmahdi Nouriborji, Samaneh Kouchaki, David A. Clifton. On the effectiveness of compact biomedical transformers
    0 -- 0Jian Cheng, Christian Maltecca, Paul M. Vanraden, Jeffrey R. O'Connell, Li Ma, Jicai Jiang. SLEMM: million-scale genomic predictions with window-based SNP weighting
    0 -- 0Siebren Frölich, Maarten van der Sande, Tilman Schäfers, Simon J. van Heeringen. genomepy: genes and genomes at your fingertips
    0 -- 0Oleksandr Khoroshevskyi, Nathan Leroy, Vincent P. Reuter, Nathan C. Sheffield. GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

    Volume 39, Issue 2

    0 -- 0Rockwell J. Weiner, Chirag M. Lakhani, David A. Knowles, Gamze Gürsoy. LDmat: efficiently queryable compression of linkage disequilibrium matrices
    0 -- 0Dan Guo, Melanie Christine Föll, Kylie A. Bemis, Olga Vitek. A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images
    0 -- 0Dhoha Abid, Michael R. Brent. NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration
    0 -- 0John H. Morris, Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini. The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information
    0 -- 0Lu Chen, Liang Yu, Lin Gao. Potent antibiotic design via guided search from antibacterial activity evaluations
    0 -- 0Julien St-Pierre, Karim Oualkacha, Sahir Rai Bhatnagar. Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data
    0 -- 0Yanlei Kang, Arne Elofsson, Yunliang Jiang, Weihong Huang, Minzhe Yu, Zhong Li. AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network
    0 -- 0Dennis Hecker, Fatemeh Behjati-Ardakani, Alexander Karollus, Julien Gagneur, Marcel H. Schulz. The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
    0 -- 0. CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells
    0 -- 0Seyed Amir Malekpour, Maryam Shahdoust, Rosa Aghdam, Mehdi Sadeghi. wpLogicNet: logic gate and structure inference in gene regulatory networks
    0 -- 0Santiago Marco-Sola, Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó. s) space
    0 -- 0Erwan Moreau. Literature-based discovery: addressing the issue of the subpar evaluation methodology
    0 -- 0Kangwei Wang, ZhengWei Li, Zhu-Hong You, Pengyong Han, Ru Nie. Adversarial dense graph convolutional networks for single-cell classification
    0 -- 0Christopher A. Mancuso, Renming Liu, Arjun Krishnan. PyGenePlexus: a Python package for gene discovery using network-based machine learning
    0 -- 0Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble. MS1Connect: a mass spectrometry run similarity measure
    0 -- 0Xinyi Yu, Jiashun Xiao, Mingxuan Cai, Yuling Jiao, Xiang Wan, Jin Liu 0011, Can Yang 0002. PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations
    0 -- 0Kun Zhu 0023, Hong Su, Zhenling Peng, Jianyi Yang. A unified approach to protein domain parsing with inter-residue distance matrix
    0 -- 0Alexandru Oarga, Bridget Bannerman, Jorge Júlvez. CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities
    0 -- 0Zhongliang Zhou, Wayland Yeung, Nathan Gravel, Mariah Salcedo, Saber Soleymani, Sheng Li 0001, Natarajan Kannan. Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions
    0 -- 0Anton Zhiyanov, Narek Engibaryan, Stepan A. Nersisyan, Maxim U. Shkurnikov, Alexander G. Tonevitsky. Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer
    0 -- 0. Correction to: HOMELETTE: a unified interface to homology modelling software
    0 -- 0Aman Agarwal, Fengdi Zhao, Yuchao Jiang, Li Chen. TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions
    0 -- 0Sehi L'Yi, Mark S. Keller, Ariaki Dandawate, Len Taing, Chen-Hao Chen, Myles Brown, Clifford A. Meyer, Nils Gehlenborg. Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data
    0 -- 0Piotr Klukowski, Roland Riek, Peter Güntert. NMRtist: an online platform for automated biomolecular NMR spectra analysis
    0 -- 0Martin Kern, Sabrina Jaeger-Honz, Falk Schreiber, Björn Sommer 0001. APL@voro - interactive visualization and analysis of cell membrane simulations
    0 -- 0Pooya Borzou, Jafar Ghaisari, Iman Izadi, Yasin Eshraghi, Yousof Gheisari. A novel strategy for dynamic modeling of genome-scale interaction networks
    0 -- 0Weiheng Liao, Xuelian Zhang. Patpat: a public proteomics dataset search framework
    0 -- 0Yunhe Wang 0002, Zhuohan Yu, Shaochuan Li, Chuang Bian, Yanchun Liang, Ka Chun Wong, Xiangtao Li. scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering
    0 -- 0Zhi Jin, Tingfang Wu, Taoning Chen, Deng Pan, Xuejiao Wang, Jingxin Xie, Lijun Quan, Qiang Lyu. CAPLA: improved prediction of protein-ligand binding affinity by a deep learning approach based on a cross-attention mechanism
    0 -- 0Paola Stolfi, Andrea Mastropietro, Giuseppe Pasculli, Paolo Tieri, Davide Vergni. NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification
    0 -- 0Leopold Weidner, Daniel Hemmler, Michael Rychlik, Philippe Schmitt-Kopplin. DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry
    0 -- 0Martin C. Frith, Jim Shaw, John L. Spouge. How to optimally sample a sequence for rapid analysis
    0 -- 0Xiang Cheng, Md Amanullah, Weigang Liu, Yi Liu, Xiaoqing Pan, Honghe Zhang, Haiming Xu, Peng-Yuan Liu, Yan Lu. WMDS.net: a network control framework for identifying key players in transcriptome programs
    0 -- 0Limin Li, Yameng Zhao, Huiran Li, Shuqin Zhang. BLTSA: pseudotime prediction for single cells by branched local tangent space alignment
    0 -- 0Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant S. Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min. Binding peptide generation for MHC Class I proteins with deep reinforcement learning
    0 -- 0Yang Hua, Xiaoning Song, Zhen-Hua Feng, Xiaojun Wu 0001. MFR-DTA: a multi-functional and robust model for predicting drug-target binding affinity and region
    0 -- 0Dylan Feldner-Busztin, Panos Firbas Nisantzis, Shelley Jane Edmunds, Gergely Boza, Fernando Racimo, Shyam Gopalakrishnan, Morten Tønsberg Limborg, Leo Lahti, Gonzalo G. de Polavieja. Dealing with dimensionality: the application of machine learning to multi-omics data
    0 -- 0Daniel Chang, Vinod K. Gupta, Benjamin Hur, Kevin Cunningham, Jaeyun Sung. GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
    0 -- 0Samuel Neuenschwander, Diana I Cruz Dávalos, Lucas Anchieri, Bárbara Sousa da Mota, Davide Bozzi, Simone Rubinacci, Olivier Delaneau, Simon Rasmussen, Anna-Sapfo Malaspinas. Mapache: a flexible pipeline to map ancient DNA
    0 -- 0Weijie Zhang, Yichu Shan, Lili Zhao, Zhen Liang, Chao Liu, Lihua Zhang, Yukui Zhang. ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry
    0 -- 0Abhijit Mondal, Luiz Thibério Rangel, Jack G. Payette, Gregory Fournier, Mukul S. Bansal. DaTeR: error-correcting phylogenetic chronograms using relative time constraints
    0 -- 0Jun Wen, Xiang Zhang, Everett Neil Rush, Vidul Ayakulangara Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J. Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P. Liao, Marinka Zitnik, Tianxi Cai. Multimodal representation learning for predicting molecule-disease relations
    0 -- 0Yan Zhu, Yuhuan Zhou, Yang Liu, Xuan Wang, Junyi Li. SLGNN: synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network
    0 -- 0Xabier Rey-Barreiro, Alejandro F. Villaverde. Benchmarking tools for a priori identifiability analysis
    0 -- 0Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad. GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations

    Volume 39, Issue 12

    0 -- 0Harshavardhan Khare, Nathaly Dongo Mendoza, Chiara Zurzolo. CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images
    0 -- 0Eszter Csibra, Guy-Bart Stan. Parsley: a web app for parsing data from plate readers
    0 -- 0Omar G. Younis, Matteo Turchetta, Daniel Ariza Suarez, Steven Yates, Bruno Studer, Ioannis N. Athanasiadis, Andreas Krause, Joachim M. Buhmann, Luca Corinzia. ChromaX: a fast and scalable breeding program simulator
    0 -- 0Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals. k-mers
    0 -- 0Cuifang Xu, Jiating Huang, Yongqiang Gao, Weixing Zhao, Yiqi Shen, Feihong Luo, Gang Yu, Feng Zhu, Yan Ni. OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases
    0 -- 0. Correction to: GIL: a python package for designing custom indexing primers
    0 -- 0William DeGroat, Dinesh Mendhe, Atharva Bhusari, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed 0001. IntelliGenes: a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles
    0 -- 0Zi Hao Liu, João M. C. Teixeira, Oufan Zhang, Thomas E. Tsangaris, Jie Li, Claudiu C. Gradinaru, Teresa Head-Gordon, Julie D. Forman-Kay. Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments
    0 -- 0Weihua Zheng, Wenwen Min, Shunfang Wang. TsImpute: an accurate two-step imputation method for single-cell RNA-seq data
    0 -- 0Herve Emissah, Bengt Ljungquist, Giorgio A. Ascoli. Bibliometric analysis of neuroscience publications quantifies the impact of data sharing
    0 -- 0Armin Rauschenberger, Zied Landoulsi, Mark A. van de Wiel, Enrico Glaab. Penalized regression with multiple sources of prior effects
    0 -- 0Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro. VSCode-Antimony: a source editor for building, analyzing, and translating antimony models
    0 -- 0Mikolaj Spytek, Mateusz Krzyzinski, Sophie Hanna Langbein, Hubert Baniecki, Marvin N. Wright, Przemyslaw Biecek. survex: an R package for explaining machine learning survival models
    0 -- 0Yang Li, Zihou Guo, Xin Gao, Guohua Wang. MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning
    0 -- 0Yitian Fang, Yi Jiang, Leyi Wei, Qin Ma, Zhixiang Ren, Qianmu Yuan, Dong-Qing Wei. DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model
    0 -- 0Hikmet Emre Kaya, Kevin J. Naidoo. CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform
    0 -- 0Rui Ren, Kuangnan Fang, Qingzhao Zhang, Shuangge Ma. FunctanSNP: an R package for functional analysis of dense SNP data (with interactions)
    0 -- 0Min Zeng, Yifan Wu, Yiming Li, Rui Yin, Chengqian Lu, Junwen Duan, Min Li 0007. LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism
    0 -- 0Bede Constantinides, Martin Hunt, Derrick W. Crook. Hostile: accurate decontamination of microbial host sequences
    0 -- 0Yu Huo, Hongpei Li, Xiao Wang, Xiaochen Du, Peter S. Swain. Nunchaku: optimally partitioning data into piece-wise contiguous segments
    0 -- 0Wunna Kyaw, Ryan C. Chai, Weng Hua Khoo, Leonard D. Goldstein, Peter I Croucher, John M. Murray, Tri Giang Phan. ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate
    0 -- 0Anisha Haldar, Vishal H. Oza, Nathaniel S. Devoss, Amanda D. Clark, Brittany N. Lasseigne. CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis
    0 -- 0Brendan S. McConnell, Matthew W. Parker. Protein intrinsically disordered regions have a non-random, modular architecture
    0 -- 0Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S. M. Ashiqul Islam, Ian Vermes, Stephen Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah J. Moody, Sergey Senkin, Paul Brennan, Michael R. Stratton, Ludmil B. Alexandrov. Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
    0 -- 0Herui Liao, Jiayu Shang, Yanni Sun. GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data
    0 -- 0Ze-Gang Wei, Peng-Yu Bu, Xiao-dan Zhang, Fei Liu, Yu Qian, Fang-Xiang Wu. invMap: a sensitive mapping tool for long noisy reads with inversion structural variants
    0 -- 0Hongjing Xie, Xuewei Cao, Shuanglin Zhang, Qiuying Sha. Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies using multi-layer network
    0 -- 0Jacob Morrison, Wanding Zhou, Benjamin K. Johnson, Hui Shen. Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing
    0 -- 0Gianluca Vozza, Emanuele Bonetti, Giulia Tini, Valentina Favalli, Gianmaria Frige, Gabriele Bucci, Simona De Summa, Mario Zanfardino, Francesco Zapelloni, Luca Mazzarella. Benchmarking and improving the performance of variant-calling pipelines with RecallME
    0 -- 0Mingzhi Yuan, Ao Shen, Kexue Fu, Jiaming Guan, Yingfan Ma, Qin Qiao, Manning Wang. ProteinMAE: masked autoencoder for protein surface self-supervised learning
    0 -- 0Duy T. Pham, Kenneth E. Westerman, Cong Pan, Ling Chen, Shylaja Srinivasan, Elvira Isganaitis, Mary Ellen Vajravelu, Fida Bacha, Steve Chernausek, Rose Gubitosi-Klug, Jasmin Divers, Catherine Pihoker, Santica M. Marcovina, Alisa K. Manning, Han Chen. Re-analysis and meta-analysis of summary statistics from gene-environment interaction studies
    0 -- 0Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar S. Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar. PDBImages: a command-line tool for automated macromolecular structure visualization
    0 -- 0Md. Abdullah-Al-Kamran Khan, Jian Wu, Yuhan Sun, Alexander D. Barrow, Anthony T. Papenfuss, Stefano Mangiola. cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling
    0 -- 0Kazim Kivanç Eren, Esra Çinar, Hamza Umut Karakurt, Arzucan Özgür. Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics
    0 -- 0Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Diego Armando Esquivel-Hernandez, Yoscelina Estrella Martinez Lopez, Daniel Neri-Rosario, Jean Paul Sánchez-Castañeda, David Giron-Villalobos, Osbaldo Resendis-Antonio. mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data
    0 -- 0Jae-Won Lee, Jong-Hyun Won, Seonggwang Jeon, Yujin Choo, Yubin Yeon, Jin-Seon Oh, Minsoo Kim, Seonhwa Kim, InSuk Joung, Cheongjae Jang, Sung-Jong Lee, Tae-Hyun Kim, Kyong Hwan Jin, Giltae Song, Eun-Sol Kim, Jejoong Yoo, Eunok Paek, Yung-Kyun Noh, Keehyoung Joo. DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
    0 -- 0. Correction to: PEMT: a patent enrichment tool for drug discovery
    0 -- 0Jian Liu, Fubin Ma, Yongdi Zhu, Naiqian Zhang, Lingming Kong, Jia Mi, Haiyan Cong, Rui Gao, Mingyi Wang, Yusen Zhang. MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules
    0 -- 0Daniel Stribling, Lauren A. Gay, Rolf Renne. Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods
    0 -- 0. Correction to: DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
    0 -- 0Nima Nouri, Andre H. Kurlovs, Giorgio Gaglia, Emanuele de Rinaldis, Virginia Savova. Scaling up single-cell RNA-seq data analysis with CellBridge workflow
    0 -- 0Bassel Ghaddar, Subhajyoti De. Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census
    0 -- 0Susan L. Hoops, Dan Knights. LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients
    0 -- 0Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo 0001, Zhiyong Lu, Peter N. Robinson. Term-BLAST-like alignment tool for concept recognition in noisy clinical texts
    0 -- 0Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu. COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods
    0 -- 0. Correction to: NeoFox: annotating neoantigen candidates with neoantigen features
    0 -- 0Kyriakos Soulios, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, Jana Schor. deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks
    0 -- 0Emil Hägglund, Siv G. E. Andersson, Lionel Guy. TADA: taxonomy-aware dataset aggregator
    0 -- 0Giovanni Visonà, Diane Duroux, Lucas Miranda, Emese Sükei, Yiran Li, Karsten M. Borgwardt, Carlos G. Oliver. Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information
    0 -- 0Nolan H. Hamilton, Terrence S. Furey. ROCCO: a robust method for detection of open chromatin via convex optimization
    0 -- 0. Correction to: Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads
    0 -- 0Kaspar Märtens, Michele Bortolomeazzi, Lucia Montorsi, Jo Spencer, Francesca D. Ciccarelli, Christopher Yau. Rarity: discovering rare cell populations from single-cell imaging data
    0 -- 0. Correction to: Prediction of gene co-expression from chromatin contacts with graph attention network
    0 -- 0Jaskaran Singh, Yingzhou Edward Pan, Shunmoogum A Patten. NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish
    0 -- 0Quim Aguado-Puig, Max Doblas, Christos Matzoros, Antonio Espinosa, Juan Carlos Moure, Santiago Marco-Sola, Miquel Moretó. WFA-GPU: gap-affine pairwise read-alignment using GPUs
    0 -- 0Jose Espejo Valle-Inclán, Isidro Cortés-Ciriano. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
    0 -- 0Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-jun Yu. Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues
    0 -- 0Dani Korpela, Emmi Jokinen, Alexandru Dumitrescu, Jani Huuhtanen, Satu Mustjoki, Harri Lähdesmäki. EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings
    0 -- 0. Correction to: KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality

    Volume 39, Issue 11

    0 -- 0Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß, Nils Bundgaard, Frederik Graw, Lutz Brusch, Jan Hasenauer. FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes
    0 -- 0Trisevgeni Rapakoulia, Sara Lopez Ruiz De Vargas, Persia Akbari Omgba, Verena Laupert, Igor Ulitsky, Martin Vingron. CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction
    0 -- 0Peihong Hu, Qi Ye, Weiyan Zhang, JingPing Liu, Tong Ruan. Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure
    0 -- 0Hyukpyo Hong, Mark Jayson Cortez, Yu-Yu Cheng, Hang Joon Kim, Boseung Choi, Kresimir Josic, Jae Kyoung Kim. Inferring delays in partially observed gene regulation processes
    0 -- 0Xuehua Bi, Weiyang Liang, Qichang Zhao, Jianxin Wang. SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data
    0 -- 0Yannik Schälte, Fabian Fröhlich, Paul J. Jost, Jakob Vanhoefer, Dilan Pathirana, Paul Stapor, Polina A. Lakrisenko, Dantong Wang, Elba Raimúndez-Álvarez, Simon Merkt, Leonard Schmiester, Philipp Städter, Stephan Grein, Erika Dudkin, Domagoj Doresic, Daniel Weindl, Jan Hasenauer. pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
    0 -- 0Qian Wang, Zhiqiang Wei, Xiaotong Hu, Zhuoya Wang, Yujie Dong, Hao Liu. Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design
    0 -- 0Dmitry Konanov, Vladislav V. Babenko, Aleksandra M. Belova, Arina G. Madan, Daria I Boldyreva, Oksana E. Glushenko, Ivan Butenko, Dmitry E. Fedorov, Alexander I Manolov, Danil V. Krivonos, Vassili N. Lazarev, Vadim M. Govorun, Elena N. Ilina. Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads
    0 -- 0. Correction to: HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition
    0 -- 0Leon Weber, Fabio Barth, Leonie Lorenz, Fabian Konrath, Kirsten Huska, Jana Wolf, Ulf Leser. PEDL+: protein-centered relation extraction from PubMed at your fingertip
    0 -- 0Xiaoqing Ru, Quan Zou 0001, Chen Lin. Optimization of drug-target affinity prediction methods through feature processing schemes
    0 -- 0Divya Sharma, Wei Xu. ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction
    0 -- 0Pingping Sun, Shijie Fan, Shaochuan Li, Yingwei Zhao, Chang Lu, Ka Chun Wong, Xiangtao Li. Automated exploitation of deep learning for cancer patient stratification across multiple types
    0 -- 0Michail Chatzianastasis, Michalis Vazirgiannis, Zijun Zhang. Explainable Multilayer Graph Neural Network for cancer gene prediction
    0 -- 0Jun Wu, Jian Ouyang, Haipeng Qing, Jiajia Zhou, Ruth Roberts, Rania Siam, Lan Wang, Weida Tong, Zhichao Liu, Tieliu Shi. PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model
    0 -- 0Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung. hipFG: high-throughput harmonization and integration pipeline for functional genomics data
    0 -- 0Javier D. Gomez, Martha L. Wall, Mohsin Rahim, Shrikaar Kambhampati, Bradley S. Evans, Doug K. Allen, Maciek R. Antoniewicz, Jamey D. Young. Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID)
    0 -- 0Yuliia Varenyk, Thomas Spicher, Ivo L. Hofacker, Ronny Lorenz. Modified RNAs and predictions with the ViennaRNA Package
    0 -- 0. Correction to: CITEdb: a manually curated database of cell-cell interactions in human
    0 -- 0Elena S. Dimitrova, Adam C. Knapp, Brandilyn Stigler, Michael Eugene Stillman. Cyclone: open-source package for simulation and analysis of finite dynamical systems
    0 -- 0Abdul Rehman Khan, Marcel J. T. Reinders, Indu Khatri. Determining epitope specificity of T-cell receptors with transformers
    0 -- 0Dat Thanh Nguyen. An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells

    Volume 39, Issue 10

    0 -- 0Peishun Jiao, Beibei Wang, Xuan Wang, Bo Liu, Yadong Wang, Junyi Li. Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information
    0 -- 0Mario Fruzangohar, Paula Moolhuijzen, Nicolette Bakaj, Julian Taylor. CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes
    0 -- 0Cheng Zhong, Tian Tian, Zhi Wei 0001. Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics
    0 -- 0Fernando H. C. Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu. A safety framework for flow decomposition problems via integer linear programming
    0 -- 0Serena Rosignoli, Luisa Di Paola, Alessandro Paiardini. PyPCN: protein contact networks in PyMOL
    0 -- 0Wenyi Yang, Pingping Wang, Meng Luo 0001, Yideng Cai, Chang Xu, Guangfu Xue, Xiyun Jin, Rui Cheng 0003, Jinhao Que, Fenglan Pang, Yuexin Yang, Huan Nie, Qinghua Jiang, Zhigang Liu, Zhaochun Xu. DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data
    0 -- 0Mohammad Nuwaisir Rahman, Abdullah Al Noman, Abir Mohammad Turza, Mohammed Abid Abrar, Md. Abul Hassan Samee, M. Saifur Rahman. ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data
    0 -- 0Junmin Wang, Steven Novick. DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes
    0 -- 0Luca R. Genz, Thomas Mulvaney, Sanjana Nair, Maya Topf. PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX
    0 -- 0Qiao Jin 0001, Won Kim 0003, Qingyu Chen 0001, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu. MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval
    0 -- 0Ping Han Hsieh, Camila Miranda Lopes-Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data
    0 -- 0Kamil Kaminski, Jan Ludwiczak, Kamil Pawlicki, Vikram Alva, Stanislaw Dunin-Horkawicz. pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models
    0 -- 0Grant Greenberg, Aditya Narayan Ravi, Ilan Shomorony. LexicHash: sequence similarity estimation via lexicographic comparison of hashes
    0 -- 0Ugo Bastolla, David Abia, Oscar Piette. PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score
    0 -- 0Gun Kaynar, Doruk Cakmakci, Caroline Bund, Julien Todeschi, Izzie-Jacques Namer, A. Ercüment Çiçek. PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas
    0 -- 0Luiz Felipe Piochi, António J. Preto, Irina S. Moreira. DELFOS - drug efficacy leveraging forked and specialized networks - benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity
    0 -- 0Zeeshan Abbas, Mobeen-ur-Rehman, Hilal Tayara, Kil To Chong 0001. ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion
    0 -- 0Maria Theiss, Jean-Karim Hériché, Craig Russell, David Helekal, Alisdair Soppitt, Jonas Ries, Jan Ellenberg, Alvis Brazma, Virginie Uhlmann. Simulating structurally variable nuclear pore complexes for microscopy
    0 -- 0Jianting Gong, Lili Jiang, Yongbing Chen, Yixiang Zhang, Xue Li, Zhiqiang Ma, Zhiguo Fu, Fei He, Pingping Sun, Zilin Ren, Mingyao Tian. THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model
    0 -- 0Yuhang Liu, Hao Yuan, Qiang Zhang, Zixuan Wang, Shuwen Xiong, Naifeng Wen, Yongqing Zhang. Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding
    0 -- 0Ali Osman Berk Sapci, Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Tastan, Sündüz Keles. MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing
    0 -- 0Huiling Liu, Wenxiu Ma. scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data
    0 -- 0Patrick Gohl, Jaume Bonet, Oriol Fornes, Joan Planas-Iglesias, Narcis Fernandez-Fuentes, Baldo Oliva. SBILib: a handle for protein modeling and engineering
    0 -- 0Dhaivat Joshi, Suhas N. Diggavi, Mark J. P. Chaisson, Sreeram Kannan. HQAlign: aligning nanopore reads for SV detection using current-level modeling
    0 -- 0Yi-Juan Hu, Glen A. Satten. Compositional analysis of microbiome data using the linear decomposition model (LDM)
    0 -- 0Richard A Schäfer, Qingxiang Guo, Rendong Yang. ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations
    0 -- 0Yujie Guo, Xiaowen Feng, Heng Li. Evaluation of haplotype-aware long-read error correction with hifieval
    0 -- 0Natália Teruel, Vinicius Magalhães Borges, Rafael Najmanovich. Surfaces: a software to quantify and visualize interactions within and between proteins and ligands
    0 -- 0Rachel Colquhoun, Ben Jackson, Áine Niamh O'toole, Andrew Rambaut. SCORPIO: a utility for defining and classifying mutation constellations of virus genomes
    0 -- 0Richard A. Schäfer, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß. RNA interaction format: a general data format for RNA interactions
    0 -- 0Cyprien Plateau-Holleville, Simon Guionnière, Benjamin Boyer, Brian Jiménez-García, Guillaume Levieux, Stéphane Mérillou, Maxime Maria, Matthieu Montès. UDock2: interactive real-time multi-body protein-protein docking software
    0 -- 0Kevin Volkel, Kevin N. Lin, Paul W. Hook, Winston Timp, Albert J. Keung, James M. Tuck. FrameD: framework for DNA-based data storage design, verification, and validation
    0 -- 0Anowarul Kabir, Manish Bhattarai, Kim Ø. Rasmussen, Amarda Shehu, Anny Usheva, Alan R. Bishop, Boian S. Alexandrov. Examining DNA breathing with pyDNA-EPBD
    0 -- 0Noriaki Sato, Miho Uematsu, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto. ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics
    0 -- 0Roberto Malinverni, David Corujo, Bernat Gel, Marcus Buschbeck. regioneReloaded: evaluating the association of multiple genomic region sets
    0 -- 0Kwan-Ling Wu, Melisa A. Martinez-Paniagua, Kate Reichel, Prashant Menon, Shravani Deo, Badrinath Roysam, Navin Varadarajan. Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks
    0 -- 0Hyunjun Choi, Jay Moran, Nicholas Matsumoto, Miguel E. Hernandez, Jason H. Moore. Aliro: an automated machine learning tool leveraging large language models
    0 -- 0Andrea Gasparin, Federico Julian Camerota Verdù, Daniele Catanzaro, Lorenzo Castelli. An evolution strategy approach for the balanced minimum evolution problem
    0 -- 0Vijini Mallawaarachchi, Michael J. Roach 0001, Przemyslaw Decewicz, Bhavya Nalagampalli Papudeshi, Sarah K. Giles, Susanna R. Grigson, George Bouras, Ryan D. Hesse, Laura K. Inglis, Abbey L. K. Hutton, Elizabeth A. Dinsdale, Robert A. Edwards. Phables: from fragmented assemblies to high-quality bacteriophage genomes
    0 -- 0Jared G. Galloway, Kevin Sung, Samuel S. Minot, Meghan E. Garrett, Caitlin I Stoddard, Alexandra C. Willcox, Zak A. Yaffe, Ryan Yucha, Julie Overbaugh, Frederick A. Matsen. phippery: a software suite for PhIP-Seq data analysis
    0 -- 0Xiaoming Xu, Zekun Yin, Lifeng Yan, Huiguang Yi, Hua Wang, Bertil Schmidt, Weiguo Liu. RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
    0 -- 0Felix Teufel, Jan C. Refsgaard, Christian T. Madsen, Carsten Stahlhut, Mads Grønborg, Ole Winther, Dennis Madsen. DeepPeptide predicts cleaved peptides in proteins using conditional random fields
    0 -- 0Thomas Naake, Johannes Rainer, Wolfgang Huber. MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data
    0 -- 0Ryo Yamamoto, Zhiheng Liu, Mudra Choudhury, Xinshu Xiao. in silico identification of dsRNA regions using long-read RNA-seq data
    0 -- 0Huaying Fang. gmcoda: Graphical model for multiple compositional vectors in microbiome studies
    0 -- 0KyungPyo Ham, Lee Sael. Evidential meta-model for molecular property prediction
    0 -- 0Haifan Gong, Yumeng Zhang, Chenhe Dong, Yue Wang, Guanqi Chen, Bilin Liang, Haofeng Li, Lanxuan Liu, Jie Xu, Guanbin Li. Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction
    0 -- 0Yiming Wu, Bing Qian, Anqi Wang, Heng Dong, Enqiang Zhu, Baoshan Ma. iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion
    0 -- 0Zerong Feng, Jiejie Feng, Baoyi Zhang, Yuhan Fei, Hongsheng Zhang, Ji Huang. PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences
    0 -- 0Chih-Hsuan Wei, Ling Luo 0001, Rezarta Islamaj, Po-Ting Lai, Zhiyong Lu. GNorm2: an improved gene name recognition and normalization system
    0 -- 0Shihu Jiao, Xiucai Ye, Chunyan Ao, Tetsuya Sakurai, Quan Zou 0001, Lei Xu. Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
    0 -- 0. Correction to: Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
    0 -- 0Chen Li, Ting-Fung Chan, Can Yang, Zhixiang Lin. stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics
    0 -- 0Carlos Sequeiros, Manuel Pájaro, Carlos Vázquez 0002, Julio R. Banga, Irene Otero-Muras. IDESS: a toolbox for identification and automated design of stochastic gene circuits
    0 -- 0. Correction to: BIODICA: a computational environment for Independent Component Analysis of omics data
    0 -- 0Yevgeni Nogin, Daniella Bar-Lev, Dganit Hanania, Tahir Detinis Zur, Yuval Ebenstein, Eitan Yaakobi, Nir Weinberger, Yoav Shechtman. Design of optimal labeling patterns for optical genome mapping via information theory
    0 -- 0Michal Wlasnowolski, Pawel Z. Grabowski, Damian Roszczyk, Krzysztof Kaczmarski, Dariusz Plewczynski. cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling
    0 -- 0Neng Huang, Heng Li. compleasm: a faster and more accurate reimplementation of BUSCO
    0 -- 0Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan. BondGraphs.jl: composable energy-based modelling in systems biology
    0 -- 0Jun Liu, Dong Liu, Gui-jun Zhang. DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes
    0 -- 0Edgar E. Robles, Ye Jin, Padhraic Smyth, Richard H. Scheuermann, Jack D. Bui, Huan-You Wang, Jean Oak, Yu Qian. A cell-level discriminative neural network model for diagnosis of blood cancers
    0 -- 0Luis Francisco Hernández Sánchez, Bram Burger, Rodrigo Alexander Castro Campos, Stefan Johansson, Pål R. Njølstad, Harald Barsnes, Marc Vaudel. Extending protein interaction networks using proteoforms and small molecules
    0 -- 0Yanglan Gan, Xingyu Huang, Wenjing Guo, Cairong Yan, Guobing Zou. Predicting synergistic anticancer drug combination based on low-rank global attention mechanism and bilinear predictor
    0 -- 0Axel von Kamp, Steffen Klamt. Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
    0 -- 0Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro. An automated model annotation system (AMAS) for SBML models
    0 -- 0Xinyue Wang, Leonard Dervishi, Wen-tao Li, Erman Ayday, Xiaoqian Jiang, Jaideep Vaidya. Privacy-preserving federated genome-wide association studies via dynamic sampling
    0 -- 0Romain Derelle, John Lees, Jody Phelan, Ajit Lalvani, Nimalan Arinaminpathy, Leonid Chindelevitch. Mycobacterium tuberculosis complex lineage typing
    0 -- 0Dmitriy Umerenkov, Fedor Nikolaev, Tatiana I Shashkova, Pavel V. Strashnov, Maria Sindeeva, Andrey Shevtsov, Nikita V. Ivanisenko, Olga L. Kardymon. PROSTATA: a framework for protein stability assessment using transformers
    0 -- 0Samuel Sledzieski, Kapil Devkota, Rohit Singh 0001, Lenore Cowen, Bonnie Berger. TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions
    0 -- 0Aakriti Jain, Neelja Singhal, Manish Kumar 0005. AFRbase: a database of protein mutations responsible for antifungal resistance
    0 -- 0Shabnam Sahay, Shishir Adhikari, Sahand Hormoz, Shaon Chakrabarti. An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
    0 -- 0Nicolas Buton, François Coste, Yann Le Cunff. Predicting enzymatic function of protein sequences with attention
    0 -- 0Bastian Pfeifer, Hryhorii Chereda, Roman Martin, Anna Saranti, Sandra Clemens, Anne-Christin Hauschild, Tim Beißbarth, Andreas Holzinger, Dominik Heider. Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification
    0 -- 0Ruoyu Tang, Xinyu He, Ruiqi Wang. Constructing maps between distinct cell fates and parametric conditions by systematic perturbations
    0 -- 0Olli Sarala, Tanja Pyhäjärvi, Mikko J. Sillanpää. BELMM: Bayesian model selection and random walk smoothing in time-series clustering
    0 -- 0Vincenzo Laveglia, Milana Bazayeva, Claudia Andreini, Antonio Rosato. Hunting down zinc(II)-binding sites in proteins with distance matrices
    0 -- 0Anthony J. Aylward, Semar Petrus, Allen Mamerto, Nolan T. Hartwick, Todd P. Michael. k-mer-based and reference-free pangenome analysis
    0 -- 0Yao-zhong Zhang, Zeheng Bai, Seiya Imoto. Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings
    0 -- 0Megan M. Shuey, William W. Stead, Ida Aka, April L. Barnado, Lisa Bastarache, Elly Brokamp, Meredith Campbell, Robert J. Carroll, Jeffrey A. Goldstein, Adam Lewis, Beth A. Malow, Jonathan D. Mosley, Travis Osterman, Dolly A Padovani-Claudio, Andrea Ramirez, Dan M. Roden, Bryce A Schuler, Edward Siew, Jennifer Sucre, Isaac Thomsen, Rory J. Tinker, Sara Van Driest, Colin Walsh, Jeremy L. Warner, Quinn Stanton Wells, Lee E. Wheless. Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics
    0 -- 0Mhaned Oubounyt, Lorenz Adlung, Fabio Patroni, Nina Kerstin Wenke, Andreas Maier, Michael Hartung, Jan Baumbach, Maria L. Elkjaer. Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet
    0 -- 0Dong Pei, Rachel Griffard, Nanda Kumar Yellapu, Emily Nissen, Devin C. Koestler. optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis
    0 -- 0Ieva Kerseviciute, Juozas Gordevicius. aPEAR: an R package for autonomous visualization of pathway enrichment networks
    0 -- 0Michele Fontanesi, Alessio Micheli, Paolo Milazzo, Marco Podda. Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs
    0 -- 0Xinmeng Liao, Mehmet Ozcan, Mengnan Shi, Woonghee Kim, Han Jin, Xiangyu Li, Hasan Turkez, Adnane Achour, Mathias Uhlén, Adil Mardinoglu, Cheng Zhang 0002. Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy
    0 -- 0Dabin Jeong, Bonil Koo, Minsik Oh, Tae-Bum Kim, Sun Kim. GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype
    0 -- 0Xiao Wang, Wei-Cheng Gu, Jie Li, Bin-Guang Ma. EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient
    0 -- 0Samuele Garda, Leon Weber-Genzel, Robert Martin, Ulf Leser. BELB: a biomedical entity linking benchmark
    0 -- 0Bilal Shaker, Jingyu Lee, Yunhyeok Lee, Myeong-Sang Yu, Hyang-Mi Lee, Eunee Lee, Hoon-Chul Kang, Kwang-Seok Oh, Hyung Wook Kim, Dokyun Na. A machine learning-based quantitative model (LogBB_Pred) to predict the blood-brain barrier permeability (logBB value) of drug compounds
    0 -- 0Thomas Weber, Marco Raffaele Cosenza, Jan Korbel. MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq
    0 -- 0Yang Hai, Jixiang Ma, Kaixin Yang, Yalu Wen. Bayesian linear mixed model with multiple random effects for prediction analysis on high-dimensional multi-omics data
    0 -- 0Palle Duun Rohde, Izel Fourie Sørensen, Peter Sørensen. Expanded utility of the R package, qgg, with applications within genomic medicine
    0 -- 0Luca Del Core, Danilo Pellin, Ernst C. Wit, Marco Grzegorczyk. Scalable inference of cell differentiation networks in gene therapy clonal tracking studies of haematopoiesis
    0 -- 0Xu Han, Wanli Wang, Li-Hua Ma, Ismael Ai-Ramahi, Juan Botas, Kevin Mackenzie, Genevera I. Allen, Damian W. Young, Zhandong Liu, Mirjana Maletic-Savatic. SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra
    0 -- 0Barbara Bodinier, Dragana Vuckovic, Sabrina Rodrigues, Sarah Filippi, Julien Chiquet, Marc Chadeau-Hyam. Automated calibration of consensus weighted distance-based clustering approaches using sharp
    0 -- 0Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun. EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction
    0 -- 0Fabio Barteri, Alejandro Valenzuela, Xavier Farré, David de Juan, Gerard Muntané, Borja Esteve-Altava, Arcadi Navarro. CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
    0 -- 0Marco Teixeira, Stephanie Pillay, Aysun Urhan, Thomas Abeel. SHIP: identifying antimicrobial resistance gene transfer between plasmids
    0 -- 0Ludvig Larsson, Lovisa Franzén, Patrik L. Ståhl, Joakim Lundeberg. Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization
    0 -- 0Kristian K. Ullrich, Nikoleta E. Glytnasi. oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data
    0 -- 0Dongze He, Rob Patro. simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry
    0 -- 0Zahed Khatooni, Navid Teymourian, Heather L. Wilson. Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development

    Volume 39, Issue 1

    0 -- 0Antonios Klonizakis, Christoforos Nikolaou, Thomas Graf. SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data
    0 -- 0. Expression of Concern: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking
    0 -- 0Xavier Didelot, David Helekal, Michelle Kendall, Paolo Ribeca. Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease
    0 -- 0Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam. Insights from incorporating quantum computing into drug design workflows
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