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ORCIDBioinformatics, Volume 41
Volume 41, Number 1, 2025
- Daniel Mechtersheimer
, Wenze Ding, Xiangnan Xu, Sanghyun Kim, Carolyn Sue, Yue Cao, Jean Y. H. Yang:
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits. - Danqing Yin, Yue Cao, Junyi Chen, Candice L. Y. Mak, Ken H. O. Yu, Jiaxuan Zhang, Jia Li, Yingxin Lin, Joshua W. K. Ho, Jean Y. H. Yang:
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels. - Fabienne Thelen, Jannis Hochmuth, Sven Griep, Benedikt Schwab, Alexander Goesmann, Frank Förster:
Crypt4GH-JS: securely storing sensitive data online with client-side encryption. - Saul Pierotti, Tomas W. Fitzgerald, Ewan Birney:
FlexLMM: a Nextflow linear mixed model framework for GWAS. - Panagiotis I. Sergouniotis, Adam Diakite, Kumar Gaurav, UK Biobank Eye & Vision Consortium, Ewan Birney, Tomas W. Fitzgerald:
Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers. - Yanfeng Zhou, Liqun Zhong, Zichen Wang, Ge Yang:
A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity. - Zhe Xue, Chenwei Sun, Wenhao Zheng, Jiancheng Lv, Xianggen Liu:
TargetSA: adaptive simulated annealing for target-specific drug design. - Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio:
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning. - Mateo Gray, Luke Trinity, Ulrike Stege, Yann Ponty, Sebastian Will, Hosna Jabbari:
CParty: hierarchically constrained partition function of RNA pseudoknots. - Kevin Volkel, Paul W. Hook, Albert J. Keung, Winston Timp, James M. Tuck:
Nanopore decoding with speed and versatility for data storage. - Nathaniel Smith, Xinyu Yuan, Chesney Melissinos, Gaurav D. Moghe:
FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme-substrate interactions from published manuscripts. - Mark Edward M. Gonzales, Jennifer C. Ureta, Anish Man Singh Shrestha:
PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings. - Timothy Poterba, Christopher Vittal, Daniel King, Daniel Goldstein, Jacqueline I. Goldstein, Patrick Schultz, Konrad J. Karczewski, Cotton Seed, Benjamin M. Neale:
The scalable variant call representation: enabling genetic analysis beyond one million genomes. - Miles D. Woodcock-Girard, Eric C. Bretz, Holly M. Robertson, Karolis Ramanauskas, Jarrad T. Hampton-Marcell, Joseph F. Walker:
Semblans: automated assembly and processing of RNA-seq data. - Duo Xi, Minjianan Zhang, Muheng Shang, Lei Du, Junwei Han:
Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method. - Meng Wang, Wei Fan, Tianrui Wu, Min Li:
TPepRet: a deep learning model for characterizing T-cell receptors-antigen binding patterns. - Darius P. Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri, Victor G. Puelles, Christian F. Krebs, Ulf Panzer, Stefan Bonn:
PCA-based spatial domain identification with state-of-the-art performance. - Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset.
- Wee Loong Chin, Timo Lassmann:
SampleExplorer: using language models to discover relevant transcriptome data. - Iain G. Johnston, Ramon Diaz-Uriarte:
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling. - Lucas R. van Dijk, Abigail L. Manson, Ashlee M. Earl, Kiran V. Garimella, Thomas Abeel:
Fast and exact gap-affine partial order alignment with POASTA. - Yiwei Liu, Hong-Dong Li, Jianxin Wang:
CrossIsoFun: predicting isoform functions using the integration of multi-omics data. - Wannes Mores, Satyajeet S. Bhonsale, Filip Logist, Jan F. M. Van Impe:
Accelerated enumeration of extreme rays through a positive-definite elementarity test. - Jungyong Ji, Sungwon Jung:
PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data. - Jacek Karolczak, Anna Przybylowska, Konrad Szewczyk, Witold Taisner, John M. Heumann, Michael H. B. Stowell, Michal Nowicki, Dariusz Brzezinski:
Ligand identification in CryoEM and X-ray maps using deep learning. - Vít Skrhák, Marián Novotný, Christos P. Feidakis, Radoslav Krivák, David Hoksza:
CryptoBench: cryptic protein-ligand binding sites dataset and benchmark. - Anas Bilal, Fawaz Khaled Alarfaj, Rafaqat Alam Khan, Muhammad Taseer Suleman, Haixia Long:
m5c-iEnsem: 5-methylcytosine sites identification through ensemble models. - Stijn Wittouck, Tom Eilers, Vera van Noort, Sarah Lebeer:
SCARAP: scalable cross-species comparative genomics of prokaryotes. - Tim Cadman, Mariska Slofstra, Marije van der Geest, Demetris Avraam, Tom Bishop, Tommy de Boer, Liesbeth Duijts, Sido Haakma, Eleanor Hyde, Vincent Jaddoe, Tarik Karramass, Fleur D. L. Kelpin, Yannick Marcon, Angela Pinot de Moira, Dick Postma, Clemens Tolboom, Ruben L. Veenstra, Stuart Wheater, Marieke Welten, Rebecca C. Wilson, Erik Zwart, Morris A. Swertz:
MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD. - Manci Li, Damani N. Bryant, Sarah Gresch, Marissa S. Milstein, Peter R. Christenson, Stuart S. Lichtenberg, Peter A. Larsen, Sang-Hyun Oh:
QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data. - Yubo Wang, Haoran Zhu, Yansong Wang, Yuning Yang, Yujian Huang, Jian Zhang, Ka-Chun Wong, Xiangtao Li:
EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events. - Ela Fallik, Nir Friedman:
VarNMF: non-negative probabilistic factorization with source variation. - Yunlu Chen, Feng Ruan, Ji-Ping Wang:
NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data. - Sebastian Vorbrugg, Ilja Bezrukov, Zhigui Bao, Detlef Weigel:
Gretl - variation GRaph Evaluation TooLkit. - Umberto Lupo, Damiano Sgarbossa, Martina Milighetti, Anne-Florence Bitbol:
DiffPaSS - high-performance differentiable pairing of protein sequences using soft scores. - Denis Beslic, Martin Kucklick, Susanne Engelmann, Stephan Fuchs, Bernhard Y. Renard, Nils Körber:
End-to-end simulation of nanopore sequencing signals with feed-forward transformers. - Tam C. Tran, David J. Schlueter, Chenjie Zeng, Huan Mo, Robert J. Carroll, Joshua C. Denny:
PheWAS analysis on large-scale biobank data with PheTK. - Xiaohong Jin, Zimeng Chen, Dan Yu, Qianhui Jiang, Zhuobin Chen, Bin Yan, Jing Qin, Yong Liu, Junwen Wang:
TPepPro: a deep learning model for predicting peptide-protein interactions. - Matei Teleman, Aurélie A. G. Gabriel, Léonard Hérault, David Gfeller:
SuperSpot: coarse graining spatial transcriptomics data into metaspots. - Max Mattessich, Joaquin Reyna, Edel Aron, Ferhat Ay, Misha E. Kilmer, Steven H. Kleinstein, Anna Konstorum:
nipalsMCIA : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares. - Zhaohui Zhan, Lusheng Wang:
Proteoform identification and quantification based on alignment graphs. - Niko Popitsch, Stefan L. Ameres:
Rnalib: a Python library for custom transcriptomics analyses. - Andre C. Faubert, Shang Wang:
Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes. - Jiawei Wu, Jun Wen, Mingyuan Yan, Anqi Dong, Shuai Gao, Ren Wang, Can Chen:
Heterogeneous entity representation for medicinal synergy prediction. - Gang Wen, Limin Li:
MMOSurv: meta-learning for few-shot survival analysis with multi-omics data. - Seonghwan Park, Min Young Kim, Jaewon Jeong, Sohae Yang, Minseok S. Kim, Inkyu Moon:
Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning. - Farid Chaabane, Trestan Pillonel, Claire Bertelli:
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation. - Daniel Zilber, Kyle P. Messier, John House, Fred Parham, Scott S. Auerbach, Matthew W. Wheeler:
Bayesian gene set benchmark dose estimation for "omic" responses. - Clement Bernard, Guillaume Postic, Sahar Ghannay, Fariza Tahi:
RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction. - Jesse Durham, Jing Zhang, Richard D. Schaeffer, Qian Cong:
DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence. - Correction to: Damsel: analysis and visualisation of DamID sequencing in R.
- Chao Gao, Joshua D. Welch:
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks. - Xike Ouyang, Yannuo Feng, Chen Cui, Yunhe Li, Li Zhang, Han Wang:
Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations. - Edo Dotan, Elya Wygoda, Noa Ecker, Michael Alburquerque, Oren Avram, Yonatan Belinkov, Tal Pupko:
BetaAlign: a deep learning approach for multiple sequence alignment. - Yuekai Li, Jiashun Xiao, Jingsi Ming, Yicheng Zeng, Mingxuan Cai:
Funmap: integrating high-dimensional functional annotations to improve fine-mapping. - Davide Buzzao, Lukas Steininger, Dimitri Guala, Erik L. L. Sonnhammer:
The FunCoup Cytoscape App: multi-species network analysis and visualization. - Haozhe Duan, Gavin L. A. Hearne, Robi Polikar, Gail L. Rosen:
The Naïve Bayes classifier++ for metagenomic taxonomic classification - query evaluation. - Jeanine Liebold, Fabian Neuhaus, Janina Geiser, Stefan Kurtz, Jan Baumbach, Khalique Newaz:
Transcription factor prediction using protein 3D secondary structures. - Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J. Treangen:
A near-tight lower bound on the density of forward sampling schemes. - Nicholas E. Newell:
MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins.
Volume 41, Number 2, 2025
- Guy Durant, Fergus Boyles, Kristian Birchall, Brian D. Marsden, Charlotte M. Deane:
Robustly interrogating machine learning-based scoring functions: what are they learning? - Tatiana A. Gurbich, Martin Beracochea, Nishadi De Silva, Robert D. Finn:
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies. - Nick Laurenz Kaiser, Martin H. Groschup, Balal Sadeghi:
VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing. - Yingfei Wang, Jinsen Li, Tsu-Pei Chiu, Nicolas Gompel, Remo Rohs:
DNAdesign: feature-aware in silico design of synthetic DNA through mutation. - Bernat Bramon Mora, Helen Lindsay, Antonin Thiébaut, Kenneth D. Stuart, Raphael Gottardo:
tagtango: an application to compare single-cell annotations. - Aurélie Mercadié, Éléonore Gravier, Gwendal Josse, Isabelle Fournier, Cécile Viodé, Nathalie Vialaneix, Céline Brouard:
NMFProfiler: a multi-omics integration method for samples stratified in groups. - Yifan Jiang, Disen Liao, Qiyun Zhu, Yang Young Lu:
PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation. - Jinyang Mao, Junlin Xu, Xianfang Tang, Yongjin Liu, Heaven Zhao, Geng Tian, Jialiang Yang:
CAMIL: channel attention-based multiple instance learning for whole slide image classification. - Satoko Namba, Chen Li, Noriko Yuyama Otani, Yoshihiro Yamanishi:
SSL-VQ: vector-quantized variational autoencoders for semi-supervised prediction of therapeutic targets across diverse diseases. - Fabricio Almeida-Silva, Yves Van de Peer:
doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications. - Dmitry Pinchuk, H. M. A. Mohit Chowdhury, Abhishek Pandeya, Oluwatosin Oluwadare:
HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting. - Zhenmiao Zhang, Ishaan Gupta, Pavel A. Pevzner:
GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions. - Javier Delgado, Raul Reche, Damiano Cianferoni, Gabriele Orlando, Rob van der Kant, Frederic Rousseau, Joost Schymkowitz, Luis Serrano:
FoldX force field revisited, an improved version. - Angelos-Michael Papadopoulos, Apostolos Axenopoulos, Anastasia Iatrou, Kostas Stamatopoulos, Federico Alvarez, Petros Daras:
ParaSurf: a surface-based deep learning approach for paratope-antigen interaction prediction. - Yifeng Fu, Hong Qu, Dacheng Qu, Min Zhao:
Trajectory Inference with Cell-Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods. - Francisco J. Pérez-Reche, Nathan J. Cheetham, Ruth C. E. Bowyer, Ellen J. Thompson, Francesca Tettamanzi, Cristina Menni, Claire J. Steves:
ESPClust: unsupervised identification of modifiers for the effect size profile in omics association studies. - Miroslav Kratochvíl, St. Elmo Wilken, Oliver Ebenhöh, Reinhard Schneider, Venkata P. Satagopam:
COBREXA 2: tidy and scalable construction of complex metabolic models. - R. Prabakaran, Yana Bromberg:
Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools. - Thomas-Otavio Peulen, Katherina Hemmen, Annemarie Greife, Benjamin M. Webb, Suren Felekyan, Andrej Sali, Claus A. M. Seidel, Hugo Sanabria, Katrin G. Heinze:
tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. - Seokyoung Hong, Krishna Gopal Chattaraj, Jing Guo, Bernhardt L. Trout, Richard D. Braatz:
Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment. - Ting-Huei Chen, Chia-Jung Lee, Syue-Pu Chen, Shang-Jung Wu, Cathy S. J. Fann:
PNL: a software to build polygenic risk scores using a super learner approach based on PairNet, a Convolutional Neural Network. - Chuanze Kang, Zonghuan Liu, Han Zhang:
A comprehensive graph neural network method for predicting triplet motifs in disease-drug-gene interactions. - Max R. Brown, Pablo Manuel Gonzalez de La Rosa, Mark L. Blaxter:
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. - Dee Velazquez, Jean Fan:
scatterbar: an R package for visualizing proportional data across spatially resolved coordinates. - Victor Paton, Dénes Türei, Olga Ivanova, Sophia Müller-Dott, Pablo Rodríguez-Mier, Veronica Venafra, Livia Perfetto, Martín Garrido-Rodriguez, Julio Saez-Rodriguez:
NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks. - Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal:
ELLIPSIS: robust quantification of splicing in scRNA-seq. - Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru:
SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data. - Miron B. Kursa:
Vistla: identifying influence paths with information theory. - Xiang Tang, Qichang Zhao, Jianxin Wang, Guihua Duan:
MolFCL: predicting molecular properties through chemistry-guided contrastive and prompt learning. - Nicholas Matsumoto, Hyunjun Choi, Jay Moran, Miguel E. Hernandez, Mythreye Venkatesan, Xi Li, Jui-Hsuan Chang, Zhiping Paul Wang, Jason H. Moore:
ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning. - Yujian Lee, Peng Gao, Yongqi Xu, Ziyang Wang, Shuaicheng Li, Jiaxing Chen:
MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network. - Hua Meng, Chuan Qin, Zhiguo Long:
scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss. - Niels Benjamin Paul, Jonas C. Wolber, Malte Lennart Sahrhage, Tim Beißbarth, Martin Haubrock:
Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization. - Weizhong Zhao, Kaijieyi Hou, Yiting Shen, Xiaohua Hu:
A conditional denoising VAE-based framework for antimicrobial peptides generation with preserving desirable properties. - Stephen Salerno, Jiacheng Miao, Awan Afiaz, Kentaro Hoffman, Anna Neufeld, Qiongshi Lu, Tyler H. McCormick, Jeffrey T. Leek:
ipd: an R package for conducting inference on predicted data. - Haoyu Cui, Qinhao Guo, Jun Xu, Xiaohua Wu, Chengfei Cai, Yiping Jiao, Wenlong Ming, Hao Wen, Xiangxue Wang:
Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model. - Tiantian Liu, Xiangnan Xu, Tao Wang, Peirong Xu:
CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data. - Guanhua Chen, Xinyue Wang, Qiang Sun, Zheng-Zheng Tang:
Multidimensional scaling improves distance-based clustering for microbiome data. - Lin Du, Hammad Farooq, Pourya Delafrouz, Jie Liang:
Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.
Volume 41, Number 3, 2025
- Rawan Shraim, Brian Mooney, Karina L. Conkrite, Amber K. Hamilton, Gregg B. Morin, Poul H. Sorensen, John M. Maris, Sharon J. Diskin, Ahmet Sacan:
ImmunoTar - integrative prioritization of cell surface targets for cancer immunotherapy. - Brent S. Pedersen, Aaron R. Quinlan:
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. - Mena Soliman Asaad Kamel, Yiwen Song, Ana Solbas, Sergio Villordo, Amrut Sarangi, Pavel Senin, Sunaal Mathew, Luis Cano Ayestas, Clément Levin, Seqian Wang, Marion Classe, Ziv Bar-Joseph, Albert Pla Planas:
ENACT: End-to-End Analysis of Visium High Definition (HD) Data. - Stephan Michalik, Elke Hammer, Leif Steil, Manuela Gesell Salazar, Christian Hentschker, Kristin Surmann, Larissa M. Busch, Thomas Sura, Uwe Völker:
SpectroPipeR - a streamlining post Spectronaut® DIA-MS data analysis R package. - Yan Yan, Beatriz Jiménez, Michael T. Judge, Toby J. Athersuch, Maria De Iorio, Timothy M. D. Ebbels:
MetAssimulo 2.0: a web app for simulating realistic 1D and 2D metabolomic 1H NMR spectra. - Pavan Holur, Kenneth C. Enevoldsen, Shreyas Rajesh, Lajoyce Mboning, Thalia Georgiou, Louis-S. Bouchard, Matteo Pellegrini, Vwani Roychowdhury:
Embed-Search-Align: DNA sequence alignment using Transformer models. - Jannik Olbrich, Thomas Büchler, Enno Ohlebusch:
Generating multiple alignments on a pangenomic scale. - Wendao Liu, Zhongming Zhao:
Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model. - Jinjin Chen, Ahmed Mohamed, Dharmesh D. Bhuva, Melissa J. Davis, Chin Wee Tan:
mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis. - Jaemin Jeon, Suwan Yu, Sangam Lee, Sang Cheol Kim, Hye-Yeong Jo, Inuk Jung, Kwangsoo Kim:
EpicPred: predicting phenotypes driven by epitope-binding TCRs using attention-based multiple instance learning. - Xindian Wei, Tianyi Chen, Xibiao Wang, Wenjun Shen, Cheng Liu, Si Wu, Hau-San Wong:
COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data. - Antonino Zito, Axel Martinelli, Mauro M. Masiero, Murodzhon Akhmedov, Ivo Kwee:
NPM: latent batch effects correction of omics data by nearest-pair matching. - Anuradha Wickramarachchi, Shakila Tonni, Sonali Majumdar, Sarvnaz Karimi, Sulev Kõks, Brendan Hosking, Jordi Rambla, Natalie A. Twine, Yatish Jain, Denis C. Bauer:
AskBeacon - performing genomic data exchange and analytics with natural language. - Mateusz Staniak, Ting Huang, Amanda M. Figueroa-Navedo, Devon Kohler, Meena Choi, Trent Hinkle, Tracy Kleinheinz, Robert Blake, Christopher M. Rose, Yingrong Xu, Pierre M. Jean Beltran, Liang Xue, Malgorzata Bogdan, Olga Vitek:
Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach. - Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez, Miquel Moretó, Santiago Marco-Sola:
QuickEd: high-performance exact sequence alignment based on bound-and-align. - Ali Hamraoui, Laurent Jourdren, Morgane Thomas-Chollier:
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow. - Vikash Pandey:
MiNEApy: enhancing enrichment network analysis in metabolic networks. - Julia K. Varga, Sergey Ovchinnikov, Ora Schueler-Furman:
actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions. - Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González:
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data. - Sizhe Liu, Yuchen Liu, Haofeng Xu, Jun Xia, Stan Z. Li:
SP-DTI: subpocket-informed transformer for drug-target interaction prediction. - Rui Liu, Zhengwu Zhang, Hyejung Won, J. S. Marron:
Significance in scale space for Hi-C data. - Kari Lavikka, Altti Ilari Maarala, Jaana Oikkonen, Sampsa Hautaniemi:
Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics. - Manuel A. Rivas, Christopher Chang:
Efficient storage and regression computation for population-scale genome sequencing studies. - Weiming Yu, Zerun Lin, Miaofang Lan, Le Ou-Yang:
GCLink: a graph contrastive link prediction framework for gene regulatory network inference. - Jack Kuipers, Mustafa Anil Tuncel, Pedro F. Ferreira, Katharina Jahn, Niko Beerenwinkel:
Single-cell copy number calling and event history reconstruction. - Shunqi Yang, Lingyi Hu, Pengzhou Chen, Xiangxiang Zeng, Shanjun Mao:
AJGM: joint learning of heterogeneous gene networks with adaptive graphical model. - Mina Namazi, Mohammadali Farahpoor, Erman Ayday, Fernando Pérez-González:
Privacy-preserving framework for genomic computations via multi-key homomorphic encryption. - Xirun Wei, Qiao Ning, Kuiyang Che, Zhaowei Liu, Hui Li, Shikai Guo:
Sul-BertGRU: an ensemble deep learning method integrating information entropy-enhanced BERT and directional multi-GRU for S-sulfhydration sites prediction. - Wei Zhang, Tiantian Liu, Han Zhang, Yuanyuan Li:
AcImpute: a constraint-enhancing smooth-based approach for imputing single-cell RNA sequencing data. - Avigail Taylor, Valentine M. Macaulay, Matthieu J. Miossec, Anand K. Maurya, Francesca M. Buffa:
GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation. - Ziqi Kang, Angela Szabo, Teodora Farago, Fernando Perez-Villatoro, Ada Junquera, Saundarya Shah, Inga-Maria Launonen, Ella Anttila, Julia Casado, Kevin Elias, Anni Virtanen, Ulla-Maija Haltia, Anniina Färkkilä:
Tribus: semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic data. - Joel Selvaraj, Liguo Wang, Jianlin Cheng:
CryoTEN: efficiently enhancing cryo-EM density maps using transformers. - Anish K. Simhal, Corey Weistuch, Kevin A. Murgas, Daniel Grange, Jiening Zhu, Jung Hun Oh, Rena Elkin, Joseph O. Deasy:
ORCO: Ollivier-Ricci Curvature-Omics - an unsupervised method for analyzing robustness in biological systems. - Guoyi Zhang, Pekka Ristola, Han Su, Bipin Kumar, Boyu Zhang, Yujin Hu, Michael G. Elliot, Viktor Drobot, Jie Zhu, Jens Staal, Martin Larralde, Shun Wang, Yun Yi, Haoran Yu:
BioArchLinux: community-driven fresh reproducible software repository for life sciences. - Tornike Onoprishvili, Jui-Hung Yuan, Kamen P. Petrov, Vijay Ingalalli, Lila Khederlarian, Niklas Leuchtenmuller, Sona Chandra, Aurelien Duarte, Andreas Bender, Yoann Gloaguen:
SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry. - Jin Sub Lee, Philip M. Kim:
FlowPacker: protein side-chain packing with torsional flow matching. - Tomasz Marek Kowalski, Szymon Grabowski:
PgRC2: engineering the compression of sequencing reads. - Zachary J. Nolen:
PopGLen - a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods. - Ross F. Laidlaw, Emma M. Briggs, Keith R. Matthews, Amir Madany Mamlouk, Richard McCulloch, Thomas D. Otto:
TrAGEDy - trajectory alignment of gene expression dynamics. - Máté Balajti, Rohan Kandhari, Boris Juric, Mihaela Zavolan, Alexander Kanitz:
HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries. - Zeheng Bai, Yao-zhong Zhang, Yuxuan Pang, Seiya Imoto:
PharaCon: a new framework for identifying bacteriophages via conditional representation learning. - Dmitry Molodenskiy, Valentin J. Maurer, Dingquan Yu, Grzegorz Chojnowski, Stefan Bienert, Gerardo Tauriello, Konstantin Gilep, Torsten Schwede, Jan Kosinski:
AlphaPulldown2 - a general pipeline for high-throughput structural modeling. - Xue Zhang, Quan Zou, Mengting Niu, Chunyu Wang:
Predicting circRNA-disease associations with shared units and multi-channel attention mechanisms. - Arthur Cousson, Frédéric Mahé, Ulysse Guyet, Damase Razafimahafaly, Laetitia Bernard:
NanoASV: a snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data analysis. - Constance Creux, Farida Zehraoui, François Radvanyi, Fariza Tahi:
MMnc: multi-modal interpretable representation for non-coding RNA classification and class annotation. - Yanxin Jiao, Hongjia Li, Yang Xue, Guoliang Yang, Lei Qi, Fa Zhang, Dawei Zang, Renmin Han:
TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction. - Wei Zou, Yongxin Ji, Jiaojiao Guan, Yanni Sun:
MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction. - Keisuke Hirota, Felix Salim, Takuji Yamada:
DeepES: deep learning-based enzyme screening to identify orphan enzyme genes. - Riccardo Aucello, Simone Pernice, Dora Tortarolo, Raffaele A. Calogero, Celia Herrera-Rincon, Giulia Ronchi, Stefano Geuna, Francesca Cordero, Pietro Lió, Marco Beccuti:
UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.
Volume 41, Number 4, 2025
- Zhuoyu Wei, Yongqi Shen, Xiang Tang, Jian Wen, Youyi Song, Mingqiang Wei, Jing Cheng, Xiaolei Zhu:
AVPpred-BWR: antiviral peptides prediction via biological words representation. - Hiruna Samarakoon, Yuk Kei Wan, Sri Parameswaran, Jonathan Göke, Hasindu Gamaarachchi, Ira W. Deveson:
Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis. - Pawel Pratyush, Callen Carrier, Suresh Pokharel, Hamid D. Ismail, Meenal Chaudhari, Dukka B. KC:
CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov-Arnold network. - Qiuyan Zhang, Wenjing Xiang, Bo Yang, Hu Yang:
A framework for analyzing EEG data using high-dimensional tests. - Gabriele Leoni, Mauro Petrillo, Victoria Ruiz-Serra, Maddalena Querci, Sandra Coecke, Tobias Wiesenthal:
PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance. - Lucas Chivot, Noé Mathieux, Anna Cosson, Antoine Bridier-Nahmias, Loïc Favennec, Jean-Christophe Gelly, Jérôme Clain, Romain Coppée:
CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure. - Brittany Lasher, David A. Hendrix:
bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity. - Samuel T. N. Aroney, Rhys J. P. Newell, Jakob N. Nissen, Antonio Pedro Camargo, Gene W. Tyson, Ben J. Woodcroft:
CoverM: read alignment statistics for metagenomics. - Wen-Jen Lin, Chia-Hsin Liu, Ming-Siang Huang, Pei-Chun Shen, Hsiu-Cheng Liu, Meng-Hsin Tsai, Yo-Liang Lai, Yu-De Wang, Mien-Chie Hung, Nai-Wen Chang, Wei-Chung Cheng:
LipidFun: a database of lipid functions. - Mete Orhun Minbay, Richard Sun, Vijay Ramachandran, Ahmet Ay, Tamer Kahveci:
OLTA: Optimizing bait seLection for TArgeted sequencing. - Chang-Uk Jeong, Jaesik Kim, Dokyoon Kim, Kyung-Ah Sohn:
GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes. - Na Yeon Kim, Seunggeun Lee:
XPRS: a tool for interpretable and explainable polygenic risk score. - Santosh Tirunagari, Shyamasree Saha, Aravind Venkatesan, Daniel Suveges, Miguel Carmona, Annalisa Buniello, David Ochoa, Johanna R. McEntyre, Ellen M. McDonagh, Melissa Harrison:
Lit-OTAR framework for extracting biological evidences from literature. - Jyoti, Marc-Thorsten Hütt:
Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns. - Yulan B. van Oppen, Andreas Milias-Argeitis:
Gradient matching accelerates mixed-effects inference for biochemical networks. - Tanya Jain, Claire Clelland:
nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data. - Brintha V. P., Manikandan Narayanan:
Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample. - Zheng Deng, Jingli Wu, Xiaorong Chen, Gaoshi Li, Jiafei Liu, Zhipeng Hu, Rongyuan Li, Wansu Deng:
MNMO: discover driver genes from a multi-omics data based-multi-layer network. - Chensheng Zhang, Xintong Shi, Xinyue Yin, Jiayi Sun, Jianhui Zhao, Yi Zhang:
Cleavage-stage embryo segmentation using SAM-based dual branch pipeline: development and evaluation with the CleavageEmbryo dataset. - Chabname Ghassemi Nedjad, Mathieu Bolteau, Lucas Bourneuf, Loïc Paulevé, Clémence Frioux:
Seed2LP: seed inference in metabolic networks for reverse ecology applications. - Nadine Ben Boina, Brigitte Mossé, Anaïs Baudot, Elisabeth Remy:
Refining Boolean models with the partial most permissive scheme. - Xuanwei Chen, Qinghua Ran, Junjie Tang, Zihao Chen, Siyuan Huang, Xingjie Shi, Ruibin Xi:
Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics. - Franziska Kappenberg, Jörg Rahnenführer:
AlertGS: determining alerts for gene sets. - Sachin Mathur, Mathieu Beauvais, Arnau Giribet, Nicolas Aragon Barrero, Chaorui Zhang, Towsif Rahman, Seqian Wang, Jeremy Huang, Nima Nouri, Andre H. Kurlovs, Ziv Bar-Joseph, Peyman Passban:
PyEvoCell: an LLM-augmented single-cell trajectory analysis dashboard. - Xuecong Fu, Zhicheng Luo, Yueqian Deng, William Laframboise, David Bartlett, Russell Schwartz:
Marker selection strategies for circulating tumor DNA guided by phylogenetic inference. - Wenjie Wei, Songtao Gui, Jian Yang, Erik Garrison, Jianbing Yan, Hai-Jun Liu:
wgatools: an ultrafast toolkit for manipulating whole-genome alignments. - Suneth Samarasinghe, Ira W. Deveson, Hasindu Gamaarachchi:
Realfreq: real-time base modification analysis for nanopore sequencing. - Francis Gaudreault, Traian Sulea, Christopher R. Corbeil:
AI-augmented physics-based docking for antibody-antigen complex prediction. - Carlos Cruz-Castillo, Luca Fumis, Chintan Mehta, Ricardo Esteban Martinez Osorio, Juan María Roldán-Romero, Helena Cornu, Prashant Uniyal, Antonio Solano-Román, Miguel Carmona, David Ochoa, Ellen M. McDonagh, Annalisa Buniello:
Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence. - Dennis J. Hazelett:
Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms. - Yuhan Fu, Mengdi Nan, Qing Ren, Xiang Chen, Jie Gao:
A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains. - Alexander Vallmitjana, Belén Torrado, Amanda Durkin, Alexander Dvornikov, Navid Rajil, Suman Ranjit, Mihaela Balu:
GSLab: open-source platform for advanced phasor analysis in fluorescence microscopy. - Keun Hong Son, Je-Yoel Cho:
Gencube: centralized retrieval and integration of multi-omics resources from leading databases. - Bitan Sarkar, Yang Ni:
MR.RGM: an R package for fitting Bayesian multivariate bidirectional Mendelian randomization networks. - Marcelo González, Roberto E. Durán, Michael Seeger, Mauricio Araya, Nicolás A. Jara:
Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters. - Aditya Kashyap, Delip Rao, Mary Regina Boland, Li Shen, Chris Callison-Burch:
Predicting explainable dementia types with LLM-aided feature engineering. - Haiyang Bian, Yinxin Chen, Lei Wei, Xuegong Zhang:
uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization. - Padmapriya Swaminathan, Anu Amallraja, Shivani Kapadia, Casey B. Williams, Tobias Meißner:
CancerTrialMatch: a computational resource for the management of biomarker-based clinical trials at a community cancer center. - Zuqi Li, Sam F. L. Windels, Noël Malod-Dognin, Seth M. Weinberg, Mary L. Marazita, Susan Walsh, Mark D. Shriver, David W. Fardo, Peter Claes, Natasa Przulj, Kristel Van Steen:
Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data. - Jessica Gliozzo, Mauricio Soto Gomez, Arturo Bonometti, Alex Patak, Elena Casiraghi, Giorgio Valentini:
miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources. - Yueying Jing, Dongxue Zhang, Limin Li:
H2GnnDTI: hierarchical heterogeneous graph neural networks for drug-target interaction prediction. - Riki Kawahara, Shinichi Morishita:
Approximating edit distances between complex tandem repeats efficiently. - Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono, Joshua D. Welch:
CytoSimplex: visualizing single-cell fates and transitions on a simplex. - Yiyi Li, Mingzhou Song:
Exact model-free function inference using uniform marginal counts for null population. - Jiwon Yu, Jiwoo Moon, Minseo Kim, Gyeol Han, Insu Jang, Jinyoung Lim, Seungmook Lee, Seok-Hwan Yoon, Woong-Yang Park, Byungwook Lee, Sanghyuk Lee:
HISSTA: a human in situ single-cell transcriptome atlas. - Ghislain Fiévet, Julien Broséus, David Meyre, Sébastien Hergalant:
adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks. - Michail Patsakis, Kimonas Provatas, Fotis A. Baltoumas, Nikol Chantzi, Ioannis Mouratidis, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares:
MAFin: motif detection in multiple alignment files. - Steven Broll, Sumanta Basu, Myung Hee Lee, Martin T. Wells:
PROLONG: penalized regression for outcome guided longitudinal omics analysis with network and group constraints. - Christopher T. Saunders, James M. Holt, Daniel N. Baker, Juniper A Lake, Jonathan R. Belyeu, Zev N. Kronenberg, William J. Rowell, Michael A. Eberle:
Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling. - Min Zeng, Xinyu Zhang, Yiming Li, Chengqian Lu, Rui Yin, Fei Guo, Min Li:
RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model. - Isin Altinkaya, Rasmus Nielsen, Thorfinn Sand Korneliussen:
vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.
Volume 41, Number 5, 2025
- Gabriele Orlando, Rodrigo Gallardo, Alicia Colla, Joost Schymkowitz, Frederic Rousseau:
Charting the structure-sequence landscape of light chain amyloids. - Javed M. Aman, Audrey W. Zhu, Martin Wühr, Stanislav Y. Shvartsman, Mona Singh:
KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics. - Pedro Fontanarrosa, Chania Clare, Alex J. H. Fedorec, Chris P. Barnes:
MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics. - Naama Wagner, Ella Baumer, Iris Lyubman, Yair Shimony, Noam Bracha, Leonor Martins, Neha Potnis, Jeff H. Chang, Doron Teper, Ralf Koebnik, Tal Pupko:
Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors. - Yifan Dai, Di Wu, Ian Carroll, Fei Zou, Baiming Zou:
High-dimensional biomarker identification for interpretable disease prediction via machine learning models. - Svetlana Ugarcina Perovic, Vedanth Ramji, Hui Chong, Yiqian Duan, Finlay Maguire, Luís Pedro Coelho:
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO). - Zhe Liu, Bintao He, Tian Zhang, Chenjie Feng, Fa Zhang, Zhongjun Yang, Renmin Han:
CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features. - Tong Zhang, Zekun Yin, Xiaoming Xu, Lifeng Yan, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu:
RabbitSketch: a high-performance sketching library for genome analysis. - Correction to: Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment.
- Shaun M. Kandathil, Andy M. Lau, Daniel W. A. Buchan, David T. Jones:
Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning. - Ryan K. Krueger, Max Ward:
JAX-RNAfold: scalable differentiable folding. - Van-Giang Trinh, Kyu Hyong Park, Samuel Pastva, Jordan C. Rozum:
Mapping the attractor landscape of Boolean networks with biobalm. - Robyn J. Wright, Morgan G. I. Langille:
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2. - Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin K. Yang, Ava P. Amini:
ProtNote: a multimodal method for protein-function annotation. - Sagara N. S. Gurusinghe, Yibing Wu, William F. DeGrado, Julia M. Shifman:
ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity. - Beibei Wang, Boyue Cui, Shiqu Chen, Xuan Wang, Yadong Wang, Junyi Li:
MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation. - Roger A. R. Moens, Lukasz G. Migas, Jacqueline M. Van Ardenne, Eric P. Skaar, Jeffrey M. Spraggins, Raf Van de Plas:
Preserving full spectrum information in imaging mass spectrometry data reduction. - Omar Melikechi, David B. Dunson, Jeffrey W. Miller:
Nonparametric IPSS: fast, flexible feature selection with false discovery control. - David Gerardus Pieter van IJzendoorn, Magdalena Matusiak, Robert B. West, Matt van de Rijn:
TissueViewer: a web-based multiplexed image viewer. - Chae Eun Lee, Jin Sob Kim, Jinhong Min, Sung Won Han:
SimSon: simple contrastive learning of SMILES for molecular property prediction. - Arash Khoeini, Funda Sar, Yen-Yi Lin, Colin C. Collins, Martin Ester:
scMUSCL: multi-source transfer learning for clustering scRNA-seq data. - Wei Zhang, Ziqi Zhang, Hailong Yang, Te Zhang, Shu Jiang, Ning Qiao, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Shitong Wang:
m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics. - Wenjia Meng, Xueshi Yu, Tingting Zhang, Renmin Han:
A noise-robust classification method for cryo-ET subtomograms with out-of-distribution detection. - James Shiniti Nagai, Tiago Maié, Michael T. Schaub, Ivan G. Costa:
scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis. - Linus Donvil, Joëlle A. J. Housmans, Eveline Peeters, Wim F. Vranken, Gabriele Orlando:
In silico identification of archaeal DNA-binding proteins. - Mayank Mahajan, Martin Hemberg:
Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA. - Ayan Chatterjee, Babak Ravandi, Parham Haddadi, Naomi H. Philip, Mario Abdelmessih, William R. Mowrey, Piero Ricchiuto, Yupu Liang, Wei Ding, Juan Carlos Mobarec, Tina Eliassi-Rad:
Topology-driven negative sampling enhances generalizability in protein-protein interaction prediction. - Joshua Pickard, Ram Prakash, Marc Andrew Choi, Natalie Oliven, Cooper Stansbury, Jillian Cwycyshyn, Nicholas Galioto, Alex A. Gorodetsky, Alvaro Velasquez, Indika Rajapakse:
Automatic biomarker discovery and enrichment with BRAD. - Alexander J. Petri, Kristoffer Sahlin:
De novo clustering of large long-read transcriptome datasets with isONclust3. - James A. McLaughlin, Josh Lagrimas, Haider Iqbal, Helen E. Parkinson, Henriette Harmse:
OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem. - Xiaofei Song, Xiaoqing Yu, Carlos Moran Segura, Hongzhi Xu, Tingyi Li, Joshua T. Davis, Aram Vosoughi, G. Daniel Grass, Roger Li, Xuefeng Wang:
ROICellTrack: a deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues. - Boyu Lyu, Jiangxiong Wang, William Christopher Risher, Guoqiang Yu:
VSOT: volume-surface optimization for accurate ultrastructure analysis of dendritic spines. - Minghui Li, Yao Shi, Shengqing Hu, Shengshan Hu, Peijin Guo, Wei Wan, Leo Yu Zhang, Shirui Pan, Jizhou Li, Lichao Sun, Xiaoli Lan:
MVSF-AB: accurate antibody-antigen binding affinity prediction via multi-view sequence feature learning. - Nils Lundqvist, Mateusz Garbulowski, Thomas Hillerton, Erik L. L. Sonnhammer:
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference. - Gabriel Ruiz-Alías, Sergi Soldevila, Xavier Altafaj, Arnau Cordomí, Mireia Olivella:
Missense variants pathogenicity annotation from homologous proteins. - Lia Obinu, Timothy Booth, Heleen De Weerd, Urmi Trivedi, Andrea Porceddu:
Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly. - Maximillian G. Marin, Natalia Quinones-Olvera, Christoph Wippel, Mahboobeh Behruznia, Brendan M. Jeffrey, Michael Harris, Brendon C. Mann, Alex Rosenthal, Karen R. Jacobson, Robin M. Warren, Heng Li, Conor J. Meehan, Maha R. Farhat:
Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species. - Zhichao Xiao, Yan Li, Yijie Ding, Liang Yu:
EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions. - Mahta Mehdiabadi, Matthias Blum, Giulio Tesei, Sören von Bülow, Kresten Lindorff-Larsen, Silvio C. E. Tosatto, Damiano Piovesan:
MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness. - Misung Yi, Tingting Zhan, Hallgeir Rui, Inna Chervoneva:
Functional protein biomarkers based on distributions of expression levels in single-cell imaging data. - Alison Kyrouz, Lian Liu, Lixin Qin, Brian Tjaden:
Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes. - Sen Yang, Lingli Ju, Peng Cheng, Jianglin Zhou, Yamin Cai, Dawei Feng:
Co-design protein sequence and structure in discrete space via generative flow. - Ruibing Shi, Frank Klawonn, Mark Brönstrup, Raimo Franke:
MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets. - Vincent Mallet, Chiara Rapisarda, Hervé Minoux, Maks Ovsjanikov:
Finding antibodies in cryo-EM maps with CrAI.
Volume 41, Number 6, 2025
- Schuyler D. Smith, Valeria Velásquez-Zapata, Roger P. Wise:
NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein-protein interactions. - Hang Qin, Mateusz Garbulowski, Erik L. L. Sonnhammer, Saikat Chatterjee:
BiGSM: Bayesian inference of gene regulatory network via sparse modelling. - Chiara Cordier, Pascal Jézéquel, Mario Campone, Fabien Panloup, Agnes Basseville:
HABiC: an algorithm based on the exact computation of the Kantorovich-Rubinstein optimizer for binary classification in transcriptomics. - Alp Tartici, Gowri Nayar, Russ B. Altman:
Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations. - Jiyeon Park, Ha Hyeon Jeon, Jeong Wook Lee, Hosung Park:
Sequence analysis and decoding with extra low-quality reads for DNA data storage. - Lujun Zhang, Lu Yang, Yingxue Ren, Shuwen Zhang, Weihua Guan, Jun Chen:
DiSC: a statistical tool for fast differential expression analysis of individual-level single-cell RNA-seq data. - Qianming Xiang, Binbin Lai:
scNucMap: mapping the nucleosome landscapes at single-cell resolution. - Lei Zhang, Yang Wang, Xiao Chen, Jie Hou, Dong Si, Rui Ding, Bo Jiang, Hailey Ledenko, Renzhi Cao:
GOBoost: leveraging long-tail gene ontology terms for accurate protein function prediction. - Kousar Saleem, A. Ercüment Çiçek, Sinem Sav:
Beacon Reconstruction Attack: Reconstruction of genomes in genomic data-sharing beacons using summary statistics. - Kaimiao Hu, Jianguo Wei, Changming Sun, Jie Geng, Leyi Wei, Qi Dai, Ran Su:
Synergizing multimodal data and fingerprint space exploration for mechanism of action prediction. - Sowmya Ramaswamy Krishnan, Arijit Roy, M. Michael Gromiha:
Comment on "Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction" by Sun and Gao. - Siegfried Dubois, Matthias Zytnicki, Claire Lemaitre, Thomas Faraut:
Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. - George Sun, Bryan W. Ting, Fred A. Wright, Yi-Hui Zhou:
HAP-SAMPLE2: data-based resampling for association studies with admixture. - Jiaqi Li, Pengcheng Zhang, Xi Xi, Xiaowo Wang:
esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis. - Mauminah Raina, Hao Cheng, Ricardo Melo Ferreira, Treyden Stansfield, Chandrima Modak, Ying-Hua Cheng, Hari Naga Sai Kiran Suryadevara, Dong Xu, Michael T. Eadon, Qin Ma, Juexin Wang:
Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics. - Xuechen Zhang, Zhuoyang Chen, Junyu Li, Qiong Luo, Longjun Wu, Weichuan Yu:
epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation. - Melania Barile, Shirom Chabra, Tomoya Isobe, Berthold Göttgens:
diffGEK: differential gene expression kinetics. - Xi Zhang, Yining Hu, David Roy Smith, Zhenyu Chen, John M. Archibald:
HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes. - Javier Kipen, Joakim Jaldén:
Brownian motion data augmentation: a method to push neural network performance on nanopore sensors. - Cagri Ozdemir, Yashu Vashishath, Serdar Bozdag, Cagri Ozdemir, Yashu Vashishath, Serdar Bozdag:
IGCN: integrative graph convolution networks for patient level insights and biomarker discovery in multi-omics integration. - Daniel R. Wong, Abby S. Hill, Rob Moccia:
Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations. - Stefano Motta, Lara Callea, Shaziya Ismail Mulla, Hamid Davoudkhani, Laura Bonati, Alessandro Pandini:
SOMMD: an R package for the analysis of molecular dynamics simulations using self-organizing map. - Christoph Waterkamp, Daniel Hoffmann:
BAYAS: simplifying access to Bayesian analysis for biologists. - Rian Pratama, Jason A. Hilton, J. Michael Cherry, Giltae Song:
Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation. - Saul Pierotti, Ian Brettell, Tomas W. Fitzgerald, Cathrin Herder, Narendar Aadepu, Christian Pylatiuk, Joachim Wittbrodt, Ewan Birney, Felix Loosli:
Measurement and classification of bold-shy behaviours in medaka fish. - Daniel S. Hitchcock, Jesse N. Krejci, Chloe E. Sturgeon, Courtney A. Dennis, Sarah T. Jeanfavre, Julian R. Avila-Pacheco, Clary B. Clish:
Eclipse : a Python package for alignment of two or more nontargeted LC-MS metabolomics datasets. - Chowdhury Rafeed Rahman, Zhong Wee Poh, Anders Jacobsen Skanderup, Limsoon Wong:
GCfix: a fast and accurate fragment length-specific method for correcting GC bias in cell-free DNA. - Andrea Raffo, Roberto Rossini, Jonas Paulsen:
StripePy: fast and robust characterization of architectural stripes. - Damiano Sgarbossa, Cyril Malbranke, Anne-Florence Bitbol:
ProtMamba: a homology-aware but alignment-free protein state space model. - Yuqi Hong, Qichang Zhao, Jianxin Wang:
MADSP: predicting anti-cancer drug synergy through multi-source integration and attention-based representation learning. - Md. Hasanul Banna Siam, Md. Akkas Ali, Donald Vardaman, Satwik Acharyya, Mallikarjun Patil, Daniel J. Tyrrell:
CAFE: an integrated web app for high-dimensional analysis and visualization in spectral flow cytometry. - Vanessa E. Kennedy, Ritu Roy, Cheryl A. C. Peretz, Andrew Koh, Elaine Tran, Catherine C. Smith, Adam B. Olshen:
SNACS: a tool for demultiplexing single-cell DNA sequencing data. - Guo-Hua Zeng, Xing-Zheng Zhu, Hong-Rui Yang, Yong-Jia Liang, Yu-Jia Zhai, Ying-Ying Xu:
Knowledge-enhanced protein subcellular localization prediction from 3D fluorescence microscope images. - Joanna Lenkiewicz, Christopher Churas, Mengzhou Hu, Gege Qian, Mayank Jain, Maxwell Adam Levinson, Sadnan Al Manir, Yue Qin, Dylan Fong, Keiichiro Ono, Jing Chen, Chengzhan Gao, Dexter Pratt, Jillian Parker, Timothy W. Clark, Trey Ideker, Leah V. Schaffer:
Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization. - Han Zhou, Kai Cao, Yang Young Lu:
Securing diagonal integration of multimodal single-cell data against ambiguous mapping. - Maxime Maria, Simon Guionnière, Nicolas Dacquay, Cyprien Plateau-Holleville, Valentin Guillaume, Vincent Larroque, Jean Lardé, Yassine Naimi, Jean-Philip Piquemal, Guillaume Levieux, Nathalie Lagarde, Stéphane Mérillou, Matthieu Montès:
VTX: real-time high-performance molecular structure and dynamics visualization software. - Rishika Chowdary, Robert K. Suter, Matthew D'Antuono, Cynthia Gomes, Joshua Stein, Ki-Bum Lee, Jae K. Lee, Nagi G. Ayad:
OrthologAL: a Shiny application for quality-aware humanization of non-human pre-clinical high-dimensional gene expression data. - Alessandro Lisi, Michael C. Campbell:
Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations. - Aurélien Beaude, Franck Augé, Farida Zehraoui, Blaise Hanczar:
CrossAttOmics: multiomics data integration with cross-attention. - Florian Specque, Aurélien Barré, Macha Nikolski, Domitille Chalopin:
SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat. - Haochen Zhao, Dingxi Li, Jian Zhong, Xiao Liang, Guihua Duan, Jianxin Wang:
A deep learning-based method for predicting the frequency classes of drug side effects based on multi-source similarity fusion. - Moaaz Khokhar, Ozlem Keskin, Attila Gürsoy:
DeepAllo: allosteric site prediction using protein language model (pLM) with multitask learning. - Kecheng Wei, Yahang Liu, Chen Huang, Ruilang Lin, Yongfu Yu, Guoyou Qin:
Debiased machine learning for ultra-high dimensional mediation analysis. - Jingxin Yan, Xiaoyu Zhang, Shuying Wang, Jinjuan Wang, Qizhai Li:
The sequence kernel association test for the proportional odds model. - Aaron Chuah, Tim Hewitt, Sidra A. Ali, Maryam May, Tony Xu, Daniel Christiadi, Philip Y.-I Choi, Elizabeth E. Gardiner, T. Daniel Andrews:
EDAmame: interactive exploratory data analyses with explainable models. - Chengfei Cai, Ruidong Chen, Jieyu Chen, Jun Li, Caiyun Lv, Yiping Jiao, Lanqing Wu, Juan Chen, Qi Sun, Qianyun Shi, Jun Xu, Wen Tang, Yao Liu:
Predicting ustekinumab treatment response in Crohn's disease using pre-treatment biopsy images. - Tugçe Oruç, Maria Kadukova, Thomas G. Davies, Marcel L. Verdonk, Carl Poelking:
Mapping the space of protein binding sites with sequence-based protein language models. - Xueying Tian, Yash Patel, Yue Wang:
TRENDY: gene regulatory network inference enhanced by transformer. - Matsvei Tsishyn, Pauline Hermans, Marianne Rooman, Fabrizio Pucci:
Residue conservation and solvent accessibility are (almost) all you need for predicting mutational effects in proteins. - Hester Chapman, Miroslav Kratochvíl, Oliver Ebenhöh, St. Elmo Wilken:
Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models. - Nicolas Maurice, Claire Lemaitre, Riccardo Vicedomini, Clémence Frioux:
Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. - Louis Le Nézet, Jason P. Sinnwell, Anna Letko, Catherine André, Pascale Quignon:
Pedixplorer: a Bioconductor package to streamline pedigree design and visualization. - Correction to: Finding antibodies in cryo-EM maps with CrAI.
- David Porubsky, Xavi Guitart, Dongahn Yoo, Philip C. Dishuck, William T. Harvey, Evan E. Eichler:
SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies. - Debora Monego, Matthias Brosz, Johanna Buck, Vsevolod Viliuga, Paulius Greicius, Jaewoon Jung, Torsten Stuehn, Matthias Schmies, Yuji Sugita, Frauke Gräter:
ColBuilder: flexible structure generation of crosslinked collagen fibrils. - Nikolaos Nakis, Chrysoula Kosma, Anastasia Brativnyk, Michail Chatzianastasis, Iakovos Evdaimon, Michalis Vazirgiannis:
The signed two-space proximity model for learning representations in protein-protein interaction networks. - David Sarrat-González, Xavier Escriba-Montagut, Jared Houghtaling, Juan R. González:
dsOMOP: bridging OMOP CDM and DataSHIELD for secure federated analysis of standardized clinical data. - Thomas Bailly, Eddy Elisée, David Vallenet:
ASMC: investigating the amino acid diversity of enzyme active sites. - Xue Zou, Zachary W. Gomez, Timothy E. Reddy, Andrew S. Allen, William H. Majoros:
Bayesian estimation of allele-specific expression in the presence of phasing uncertainty. - Mei Lang, Thomas Litfin, Ke Chen, Jian Zhan, Yaoqi Zhou:
Benchmarking the methods for predicting base pairs in RNA-RNA interactions. - Correction to: Coding genomes with gapped pattern graph convolutional network.
Volume 41, Number 7, 2025
- Sicen Liu, Shutao Chen, Tao Bai, Bin Liu:
FusionEncoder: identification of intrinsically disordered regions based on multi-feature fusion. - Meiling Liu, Shuangshuang Wang, Zeyu Luo, Guohua Wang, Yuming Zhao:
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction. - Correction to: Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments.
- Omid Arhami, Pejman Rohani:
Topolow: a mapping algorithm for antigenic cross-reactivity and binding affinity assays. - Bing Li, Xin Xiao, Chao Zhang, Ming Xiao, Le Zhang:
DGHNN: a deep graph and hypergraph neural network for pan-cancer related gene prediction. - Amy Glen, Eric W. Deutsch, Stephen A. Ramsey:
PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs. - Zhenru Zhou, Qui T. Phung, Corey E. Bakalarski:
PepMapViz: a versatile toolkit for peptide mapping, visualization, and comparative exploration. - Anchen Li, Elena Casiraghi, Juho Rousu:
CSGL: chemical synthesis graph learning for molecule representation. - Heewon Park, Seiya Imoto, Satory Miyano:
Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity-specific gene networks. - Elysia Saputra, Weiguang Mao, Guillermo Hoffmann Meyer, Nathan Clark, Maria Chikina:
Prediction of local convergent shifts in evolutionary rates with phyloConverge. - Maximilian F. Eggl, Surbhit Wagle, Jean Philip Filling, Thomas E. Chater, Yukiko Goda, Tatjana Tchumatchenko:
SpyDen: simplifying molecular and structural analysis across spines and dendrites. - Ei-Wen Yang, Enrique Velazquez-Villarreal:
AI-HOPE: an AI-driven conversational agent for enhanced clinical and genomic data integration in precision medicine research. - Yang Zhang, Andreas Vitalis:
Nearl: extracting dynamic features from molecular dynamics trajectories for machine learning tasks. - Yunjing Qi, Yulong Kan, Jing Qi, Shuilin Jin:
scGT: integration algorithm for single-cell RNA-seq and ATAC-seq based on graph transformer. - Sepideh Mofidifar, Mojtaba Tefagh:
Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach. - Apurva Kalia, Yan Zhou Chen, Dilip Krishnan, Soha Hassoun:
JESTR: Joint Embedding Space Technique for Ranking candidate molecules for the annotation of untargeted metabolomics data. - Danilo Tomasoni, Luca Marchetti:
CSpace: a concept embedding space for biomedical applications. - Ladislav Hovan, Marieke L. Kuijjer:
SPONGE: simple prior omics network GEnerator. - Yair Pickholz Berliner, Roded Sharan:
PEANUT: Pathway Enrichment Analysis through Network UTilization. - Nicholas Rios, Yuke Shi, Jun Chen, Xiang Zhan, Lingzhou Xue, Qizhai Li:
Composition-on-composition regression analysis for multi-omics integration of metagenomic data. - Jinjiang Liu, Kun Wang, Yawen Yuan, Guangchao Bao, Hang Ci, Mingqin Liu, Yunpan Lyu, Jingxin Tang, Jian Yang, Haoyang Cai:
CCRR: a user-friendly platform for analyzing complex chromosomal rearrangements in tumors. - Jamil Gafur, Olivia W. Lang, William K. M. Lai:
Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture. - Daniele Catanzaro, Henri Dehaybe, Raffaele Pesenti:
New heuristics for phylogeny estimation under the balanced minimum evolution criterion. - Eran Elhaik, Sara Behnamian, Michael Howe, Hongwei Tang, Huihuang Yan, Shulan Tian, Suganti Shivaram, Cinthya Zepeda Mendoza, Kylee Maclachlan, Saad Usmani, Mehdi Pirooznia, Gareth Morgan, Patrick Blaney, Francesco Maura, Linda B. Baughn:
AncestryGeni: a novel genetic ancestry classification pipeline for small and noisy sequence data. - Yingmei Li, Shahid Ullah, Yumei Xian, Yazhou Sun, Zilong Zheng, Xiaoyu Ma, Ming Shi, Changlin Zhang, Tian Li, Leli Zeng, Jie Chen, Yubin Y. B. Deng, Fuxin Wei, Tianshun Gao:
dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data. - Emilia Hurtado, Alexandre Bouchard-Côté, Andrew Roth:
PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing. - Shumin Li, Yiding Wang, Chi-Man Liu, Yuanhua Huang, Tak Wah Lam, Ruibang Luo:
AutoPM3: enhancing variant interpretation via LLM-driven PM3 evidence extraction from scientific literature. - Zarifa Osmanli, Elisa Ferrero, Alexander Miguel Monzon, Silvio C. E. Tosatto, Damiano Piovesan:
GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins. - Reagon Karki, Yojana Gadiya, Andrea Zaliani, Bishab Pokharel, Negin Sadat Babaiha, Marek Ostaszewski, Martin Hofmann-Apitius, Philip Gribbon:
KGG: a fully automated workflow for creating disease-specific knowledge graphs. - Jiaqi Luo, Yiping Zou, Shuai Cheng Li:
AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees. - Axel Alejandro Ramos García, Paulina M. Mejía-Ponce, Nelly Sélem-Mojica, Alejandro Santos-Díaz, Emmanuel Martínez-Ledesma, Cuauhtémoc Licona Cassani:
FuNTB: a functional network clustering tool for the analysis of genome-wide genetic variants in Mycobacterium tuberculosis. - Saisai Sun:
Rebuttal letter of the "comment on "contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction" by Sun and Gao". - Silvia Prieto-Baños, Yannis Nevers, Adrian M. Altenhoff, Alex Warwick Vesztrocy, Christophe Dessimoz, Natasha M. Glover:
Annotation matters: the effect of structural gene annotation on orthology inference. - Alexander Derry, Haim Krupkin, Alp Tartici, Russ B. Altman:
Unsupervised learning reveals landscape of local structural motifs across protein classes. - Yanshuo Chen, Zhengmian Hu, Yihan Wu, Ruibo Chen, Yongrui Jin, Marcus Zhan, Chengjin Xie, Wei Chen, Heng Huang:
Enhancing privacy in biosecurity with watermarked protein design. - Alan Zheng, Ishmeal Lee, Vikram Shivakumar, Omar Y. Ahmed, Ben Langmead:
Fast and flexible minimizer digestion with digest. - Edward S. Ricemeyer, Rachel A. Carroll, Wesley C. Warren:
Agptools: a utility suite for editing genome assemblies. - Amin Nooranikhojasteh, Ghazaleh Tavallaee, Elias Orouji:
Benchmarking peak calling methods for CUT&RUN. - Seung J. Kim, Matthew J. Cecchini, Marco Mura:
shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data. - Qing Wang, Wen-jie Chen, Jing Su, Guangyu Wang, Qianqian Song:
HECLIP: histology-enhanced contrastive learning for imputation of transcriptomics profiles. - Yitong Lin, Jiaying He, Jiahe Chen, Xinnan Zhu, Jianwei Zheng, Tao Bo:
BioGraphFusion: graph knowledge embedding for biological completion and reasoning. - Niloofar Borhani, Iman Izadi, Ali Motahharynia, Mahsa Sheikholeslami, Yousof Gheisari:
DrugTar improves druggability prediction by integrating large language models and gene ontologies. - Zhenglong Cheng, Risheng Lu, Shixiong Zhang:
scMGCL: accurate and efficient integration representation of single-cell multi-omics data. - Kaiyuan Yang, Jiabei Cheng, Shenghao Cao, Xiaoyong Pan, Hongbin Shen, Jin Cheng, Ye Yuan:
Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes. - Junmin Wang:
DOSE-L1000-Viz: an interactive Shiny application for dose-response transcriptomic analysis, target-centric exploration, and signature search. - Kevin C. Lutz, Shengjie Yang, Tejasv Bedi, Michael L. Neugent, Nikita Madhavaram, Bo Yao, Xiaowei Zhan, Nicole J. De Nisco, Qiwei Li:
MiCoDe: a web tool for performing microbiome community detection using a Bayesian weighted stochastic block model. - Zhiqi Xie, Peng Zhang, Zipeng Fan, Qingpeng Zhang, Qianxi Lin:
EM-PLA: environment-aware heterogeneous graph-based multimodal protein-ligand binding affinity prediction. - Lucas De Vrieze, Miguel Biltjes, Sofya Lukashevich, Kodai Tsurumi, Joleen Masschelein:
CAGEcleaner: reducing genomic redundancy in gene cluster mining. - Zhaoyang Li, Yahang Liu, Kecheng Wei, Yongfu Yu, Guoyou Qin, Zhongyi Zhu:
Deconfounded and debiased estimation for high-dimensional linear regression under hidden confounding with application to omics data. - Nicolai Meyerhöfer, Nevan J. Krogan, Benjamin J. Polacco, David B. Blumenthal:
Inference of differential kinase interaction networks with KINference. - Thomas M. O'Connell:
Pathway Volcano: an interactive tool for pathway guided visualization of differential expression data. - Xin Dong, Di Zhao, Jiana Meng, Bocheng Guo, Hongfei Lin:
SyRACT: zero-shot biomedical document-level relation extraction with synergistic RAG and CoT. - Tamsin James, Ben Williamson, Peter Tino, Nicole Wheeler:
Whole-genome phenotype prediction with machine learning: open problems in bacterial genomics. - Xiaoqiang Yan, Shike Du, Quan Zou, Zhen Tian:
Differentiable graph clustering with structural grouping for single-cell RNA-seq data. - Tusharkanti Ghosh, Ryan M. Baxter, Souvik Seal, Victor G. Lui, Pratyaydipta Rudra, Thao Vu, Elena W. Y. Hsieh, Debashis Ghosh:
cytoKernel: robust kernel embeddings for assessing differential expression of single-cell data. - Oluwafemi A. Sarumi, Wilhelm Bertrams, Oliver Schwengers, Jan-Paul Herrmann, Torsten Hain, Laurine Kieper, Markus Petzold, Alexander Goesmann, Bernd Schmeck, Dominik Heider:
LegionProfiler: a computational tool for the identification of virulence factors and classification of Legionella pneumophila serogroup 1 isolates. - Yalin Hou, Yiming Li, Ruiqing Zheng, Fuhao Zhang, Fei Guo, Min Li, Min Zeng:
Leveraging protein language models for cross-variant CRISPR/Cas9 sgRNA activity prediction. - Thomas Jaylet, Florence Jornod, Quentin Capdet, Olivier Armant, Karine Audouze:
AOP-helpFinder 3.0: from text mining to network visualization of key event relationships, and knowledge integration from multiple sources. - David W. Ludwig II, Christopher Guptil, Nicholas R. Alexander, Kateryna Zhalnina, Edi M.-L. Wipf, Albina Khasanova, Nicholas A. Barber, Wesley Swingley, Donald M. Walker, Joshua L. Phillips:
SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing. - Boyan Wang, Yangliao Geng, Xingyi Cheng, Bo Chen, Zhilei Bei, Wei Wang, Jie Tang, Le Song:
ProtGO: universal protein function prediction utilizing multi-modal gene ontology knowledge.
Volume 41, Number 8, 2025
- Louis Paré, Philippe Bordron, Laurent David, Maxime Mahé, Audrey Bihouée, Damien Eveillard:
HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures. - Chen Liu, Mingchen Li, Yang Tan, Wenrui Gou, Guisheng Fan, Bingxin Zhou:
Sequence-only prediction of binding affinity changes: a robust and interpretable model for antibody engineering. - Haowen Zhou, Pratibha Panwar, Boyi Guo, Caleb Hallinan, Shila Ghazanfar, Stephanie C. Hicks:
Spatial mutual nearest neighbors for spatial transcriptomics data. - Goro Terai, Kiyoshi Asai:
Deep generative model of RNAs based on variational autoencoder with context-free grammar. - Louis Kraft, Thorfinn Sand Korneliussen, Peter Wad Sackett, Gabriel Renaud:
AdDeam : a fast and scalable tool for estimating and clustering reference-level damage profiles. - Zongli Xu, Alison A. Motsinger-Reif, Liang Niu:
Efficient gene set analysis for DNA methylation addressing probe dependency and bias. - Georgi I. Nikov, Daniella Pretorius, James W. Murray:
SOLeNNoID: a deep learning pipeline for solenoid residue detection in protein structures. - Zheng Chen, Peng Ni, Jianxin Wang:
Identifying DNA methylation types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network. - Weihua Zheng, Wenwen Min, Shunfang Wang:
IGCLAPS: an interpretable graph contrastive learning method with adaptive positive sampling for scRNA-seq data analysis. - Mengyu Li, Bencong Zhu, Cheng Meng, Xiaodan Fan:
Double optimal transport for differential gene regulatory network inference with unpaired samples. - Xiang Li, Ke Chen, Mingfu Shao:
Efficient seeding for error-prone sequences with SubseqHash2. - Sourish S. Iyengar, Alex R. Qin, Nicholas Robertson, Andrew N. Harman, Ellis Patrick:
SpatioMark: quantifying the impact of spatial proximity on cell phenotype. - Candace Guzman-Cole, Andrew D. Huang:
nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets. - Roman Stratiichuk, Mykola Melnychenko, Ihor Koleiev, Taras Voitsitskyi, Vladyslav Husak, Nazar Shevchuk, Zakhar Ostrovsky, Volodymyr G. Bdzhola, Semen O. Yesylevskyy, Serhii Starosyla, Alan Nafiiev:
Leveraging large language models for literature-driven prioritization of protein binding pockets. - Kerim Heber, Shuchang Tian, Daniela Betancurt-Anzola, Heejung Koo, Jordan E. Bisanz:
StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities. - François Lamoline, Isabel Haasler, Johan Karlsson, Jorge Gonçalves, Atte Aalto:
Dynamic gene regulatory network inference from single-cell data using optimal transport. - Pierre-Yves Libouban, Camille Parisel, Maxime Song, Samia Aci-Sèche, José Carlos Gómez-Tamayo, Gary Tresadern, Pascal Bonnet:
Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction. - Yixiao Zhai, Pinglu Zhang, Quan Zou, Ximei Luo:
ReAlign-P: a vertical iterative realignment method for protein multiple sequence alignment. - Qianpei Liu, Min Zeng, Yiming Li, Chengqian Lu, Shichao Kan, Fei Guo, Min Li:
2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model. - Zhicong Wang, Zicheng Ma, Ziqiang Cao, Changlong Zhou, Jun Zhang, Yi Qin Gao:
Prot2Chat: protein large language model with early fusion of text, sequence, and structure. - Craig Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Jason R. Swedlow, Alvis Brazma, Matthew Hartley, Virginie Uhlmann:
bia-binder: a web-native cloud compute service for the bioimage analysis community. - Vijayaraj Nagarajan, Guangpu Shi, Samyuktha Arunkumar, Chunhong Liu, Jaanam Gopalakrishnan, Pulak R. Nath, Junseok Jang, Rachel R. Caspi:
SCassist: an AI based workflow assistant for single-cell analysis. - Dan Kalifa, Kira Radinsky, Eric Horvitz:
Beyond the leaderboard: leveraging predictive modeling for protein-ligand insights and discovery. - Qinze Yu, Chang Zhou, Jiyue Jiang, Xiangyu Shi, Yu Li:
GS-DTI: a graph-structure-aware framework leveraging large language models for drug-target interaction prediction. - Jonathan Feldman, Jeffrey Skolnick:
AF3Complex yields improved structural predictions of protein complexes. - Elizabeth Wynn, Kara J. Mould, Brian Vestal, Camille M. Moore:
Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim. - Yifan Dou, Golrokh Mirzaei:
MO-GCAN: multi-omics integration based on graph convolutional and attention networks. - Andrea Pozzi:
Pedigree Painter (pepa): a tool for the visualization of genetic inheritance in chromosomal context. - Jordy Bollon, Michael R. Shortreed, Erin Jeffery, Ben T. Jordan, Rachel Miller, Andrea Cavalli, Lloyd M. Smith, Colin N. Dewey, Gloria M. Sheynkman, Simone Tiberi:
IsoBayes: a Bayesian approach for single-isoform proteomics inference. - Sandra Castillo, Osmo Henri Samuli Ollila:
ActSeek: fast and accurate search algorithm of active sites in alphafold database. - Yuhong Zha, Shaoqing Feng, Peng Gao, Quan Zou, Xiaoke Ma:
Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model. - William Knottenbelt, William McGough, Rebecca Wray, Woody Zhidong Zhang, Jiashuai Liu, Inês Prata Machado, Zeyu Gao, Mireia Crispin-Ortuzar:
CoxKAN: Kolmogorov-Arnold networks for interpretable, high-performance survival analysis. - Tianjiao Zhang, Zhongqian Zhao, Hongfei Zhang, Zhenao Wu, Fang Wang, Guohua Wang:
Multi-omics single-cell data alignment and integration with enhanced contrastive learning and differential attention mechanism. - Hamza Gamouh, Marián Novotný, David Hoksza:
Hybrid protein-ligand binding residue prediction with protein language models: does the structure matter? - Giulio Formenti, Bonhwang Koo, Marco Sollitto, Jennifer Balacco, Nadolina Brajuka, Richard Burhans, Erick Duarte, Alice Giani, Kirsty McCaffrey, Jack A. Medico, Eugene W. Myers, Patrik Smeds, Anton Nekrutenko, Erich D. Jarvis:
Evaluation of sequencing reads at scale using rdeval. - Tomás Racek, Dusan Vel'ký, Gabriela Buceková, Ondrej Schindler, Ivana Hutarová Vareková, Anna Spacková, Václav Bazgier, Karel Berka, Radka Svobodová Vareková:
MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update). - Marek Justyna, Craig L. Zirbel, Maciej Antczak, Marta Szachniuk:
Graph neural network and diffusion model for modeling RNA interatomic interactions. - Shanming Chen, Fan Nie, Jianxin Wang:
NanoFilter: enhancing phasing performance by utilizing highly consistent INDELs and SNVs in nanopore sequencing. - Yan Zhong, Yuntong Hou, Yongjian Yang, Xinyue Zheng, James J. Cai:
scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation. - Jingmao Li, Yaqing Xu, Shuangge Ma, Kuangnan Fang:
GE-IA-NAM: gene-environment interaction analysis via imaging-assisted neural additive model. - Dewei Hu, Damian Szklarczyk, Christian von Mering, Lars Juhl Jensen:
SPACE: STRING proteins as complementary embeddings. - Shumin Yang, Yuhan Su, Yuchen Lin, Qin Lin, Zhong Chen:
PF-AGCN: an adaptive graph convolutional network for protein-protein interaction-based function prediction. - Yang An, Valter Bergant, Samuele Firmani, Corinna Grünke, Batiste Bonnal, Alexander Henrici, Andreas Pichlmair, Benjamin Schubert, Annalisa Marsico:
TransFactor - prediction of pro-viral SARS-CoV-2 host factors using a protein language model. - LeAnn M. Lindsey, Nicole L. Pershing, Anisa Habib, Keith Dufault-Thompson, W. Zac Stephens, Anne J. Blaschke, Xiaofang Jiang, Hari Sundar:
The impact of tokenizer selection in genomic language models. - Ibrahim Alsaggaf, Daniel W. A. Buchan, Cen Wan:
Less is more: improving cell-type identification with augmentation-free single-cell RNA-Seq contrastive learning. - Guannan Yang, Ellen Menkhorst, Evdokia Dimitriadis, Kim-Anh Lê Cao:
PLSKO: a robust knockoff generator to control false discovery rate in omics variable selection. - Pierre Millard, Loïc Le Grégam, Svetlana Dubiley, Valeria Gabrielli, Thomas Gosselin-Monplaisir, Guy Lippens, Cyril Charlier:
MultiNMRFit: a software to fit 1D and pseudo-2D NMR spectra. - Olivier Dennler, Elisa Chenel, François Coste, Samuel Blanquart, Catherine Belleannée, Nathalie Théret:
FUSE-PhyloTree: linking functions and sequence conservation modules of a protein family through phylogenomic analysis. - Qingsong Zhang, Fei Liu, Xin Lai:
HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes. - Herson H. M. Soares, João P. R. Romanelli, Patrick J. Fleming, Carlos Henrique da Silveira:
FIBOS: R and python packages for analyzing protein packing and structure. - Maharshi Chakraborty, Laura Morgan, Quin Scacheri, Alexandra D'yan, Hyunmin Kim, Yaw Asante, Diana Chin, Olivia Corradin, Peter C. Scacheri, Richard C. Sallari, Berkley E. Gryder:
AQuA Tools: clear and reliable BEDPE operations for 3D genomics. - Zahra Nozari, Paul Hüttl, Jakob Simeth, Marian Schön, James A. Hutchinson, Rainer Spang:
Harp: data harmonization for computational tissue deconvolution across diverse transcriptomics platforms. - Homa Mohammadi Peyhani, Edith Lee, Richard Bonneau, Vladimir Gligorijevic, Jae Hyeon Lee:
deepNGS navigator: exploring antibody NGS datasets using deep contrastive learning. - Lilu Guo, Zongtao He, Hongwei Huo:
Panaln: indexing pangenome for read alignment. - Woo Dae Jang, Changdai Gu, Yumi Noh, Kwang-Seok Oh, Jae Yong Ryu:
ChemBounce: a computational framework for scaffold hopping in drug discovery. - Zirui Wang, Ke Xu, Yang Liu, Yu Xu, Lu Zhang:
Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon. - Bencong Zhu, Alberto Cassese, Marina Vannucci, Michele Guindani, Qiwei Li:
BISON: bi-clustering of spatial omics data with feature selection. - Correction to: OLTA: Optimizing bait seLection for TArgeted sequencing.
- Samuel Olowofila, Oluwatosin Oluwadare:
DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data. - Yang Li, Chang Liu, Xin Gao, Guohua Wang:
MolPrompt: improving multi-modal molecular pre-training with knowledge prompts. - Leonie J. Lorenz, Antoine Andréoletti, Tung V. N. Nguyen, Henning Hermjakob, Richard G. FitzJohn, Rahuman S. Malik-Sheriff, John A. Lees:
SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences. - Rosan C. M. Kuin, Meindert H. Lamers, Gerard J. P. van Westen:
PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries. - Andres Aldana, Michael Sebek, Gordana Ispirova, Rodrigo Dorantes Gilardi, Joseph Loscalzo, Albert-László Barabási, Giulia Menichetti:
NetMedPy: a Python package for large-scale network medicine screening. - Camille Aucouturier, Nicolas Goardon, Laurent Castéra, Alexandre Atkinson, Thibaut Lavolé, Angélina Legros, Agathe Ricou, Flavie Boulouard, Sophie Krieger, Raphaël Leman:
Decipher RNA isoform combinations from minigene splicing assays and massive parallel sequencing with MAGIC. - Jixin Deng, Jingxiao Zhang, Song Tian, John Dicarlo, Hong Xu, Samuel J. Rulli, Jonathan M. Shaffer, Vikas Gupta, Töresin Karakoyun:
UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification. - Jeffrey J. Czajka, Joonhoon Kim, Yinjie J. Tang, Kyle R. Pomraning, Aindrila Mukhopadhyay, Héctor García Martín:
FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets. - Gianna Serafina Monti, Meritxell Pujolassos, Malu Calle Rosingana, Peter Filzmoser:
Robust multivariate regression controlling false discoveries for microbiome data. - Sophie-Marie Wind, Thea Reinkens, Yvonne Lisa Behrens, Sarah Sandmann:
scafari: exploring scDNA-seq data. - Austyn Trull, Elizabeth A. Worthey, Lara Ianov:
scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing. - Grzegorz Chojnowski:
gapTrick - structural characterization of protein-protein interactions using AlphaFold. - Saisai Sun, Jianyi Yang, Lin Gao, Pengyong Li, Yumeng Liu:
RNA language model and graph attention network for RNA and small molecule binding sites prediction. - Mallek Mziou-Sallami, Pierrick Roger, Arnaud Gloaguen, Claire Dandine-Roulland, Thierry Jiogho Ngaho, Solène Brohard, Kévin Muret, Florian Sandron, Eric Bonnet, Jean-Francois Deleuze, Edith Le Floch, Vincent Meyer:
GNNenrich: a novel method for pathway enrichment analysis based on graph neural network. - Ferdoos Hossein Nezhad, Namir Oues, Massimiliano Meli, Alessandro Pandini:
MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles. - Junchao Wang, Ling Sun, Nana Wei, Yisheng Huang, Naiqian Zhang:
A semi-supervised Bayesian approach for marker gene trajectory inference from single-cell RNA-seq data. - Meiling Liu, Shujuan Su, Guohua Wang, Shan Huang:
KGCLMDA: a computational model for predicting latent associations of microbial drugs using knowledge graphs and contrastive learning. - Guy Baele, Luiz Max Carvalho, Marius Brusselmans, Gytis Dudas, Xiang Ji, John T. McCrone, Philippe Lemey, Marc A. Suchard, Andrew Rambaut:
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X. - Tomasz Chady, Zuzanna Karolina Filutowska:
Parsing GTF and FASTA files using the eccLib Library. - Ruite Xiang, Christian Domínguez-Dalmases, Albert Cañellas-Solé, Victor Guallar:
aMLProt: an automated machine learning library for protein applications. - Kylee Degatano, Aseel Awdeh, Robert Sidney Cox III, Wes Dingman, George Grant, Farzaneh Khajouei, Elizabeth Kiernan, Kishori M. Konwar, Kaylee L. Mathews, Kevin Palis, Nikelle Petrillo, Geraldine Van der Auwera, Chengchen (Rex) Wang, Jessica Way:
Warp analysis research pipelines: cloud-optimized workflows for biological data processing and reproducible analysis. - Adrian Chan, Isabel S. Naarmann-de Vries, Christoph Dieterich:
Ψ-co-mAFiA: concurrent detection of pseudouridine and m6A in single RNA molecules. - Peng Liu, David Page, Paul Ahlquist, Irene M. Ong, Anthony Gitter:
MPAC: a computational framework for inferring pathway activities from multi-omic data. - Mihaly Badonyi, Joseph A. Marsh:
acmgscaler : an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework. - Guido Barzaghi, Arnaud R. Krebs, Judith B. Zaugg:
FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data. - Arangasamy Yazhini, Johannes Söding:
Enhancing genome recovery across metagenomic samples using MAGmax.
Volume 41, Number 9, 2025
- Asato Yoshinaga, Osamu Maruyama:
CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning. - Tianci Wang, Xin Lai, Shenjie Wang, Yuqian Liu, Xiaoyan Zhu, Jiayin Wang:
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples. - Tong Wang, Zhi-Ping Liu:
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection. - Helena García-Cebollada, Alfonso López, Vladimir Espinosa Angarica, Juan José Galano-Frutos, Javier Sancho:
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins. - Carl M. Kobel, Velma T. E. Aho, Ove Øyås, Niels Nørskov-Lauritsen, Ben J. Woodcroft, Phillip B. Pope:
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. - Shuang Wang, Tianle Ma, Kaiyu Dong, Peifu Han, Xue Li, Junteng Ma, Mao Li, Tao Song:
MVSO-PPIS: a structured objective learning model for protein-protein interaction sites prediction via multi-view graph information integration. - Joseph L. Hellerstein, Lucian P. Smith, Lillian T. Tatka, Steven S. Andrews, Michael A Kochen, Herbert M. Sauro:
Discovering subnetworks in SBML models. - Ryan R. Wick, Benjamin P. Howden, Timothy P. Stinear:
Autocycler: long-read consensus assembly for bacterial genomes. - Johannes Hingerl, Alexander Karollus, Julien Gagneur:
Flashzoi: an enhanced Borzoi for accelerated genomic analysis. - Ke Yan, Shutao Chen, Bin Liu, Hao Wu:
Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework. - Xiang Liu, Yi-Han Tang, James Blachly, Stephen Edge, Yasminka A Jakubek, Martin McCarter, Abdul Rafeh Naqash, Kenneth G. Nepple, Afaf Osman, Matthew J. Reilley, Gregory Riedlinger, Bodour Salhia, Bryan P. Schneider, Craig Shriver, Michelle L. Churchman, Robert J. Rounbehler, Jamie K. Teer, Nancy Gillis, Mingxiang Teng:
qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics. - Sebastian Persson, Fabian Fröhlich, Stephan Grein, Torkel Loman, Damiano Ognissanti, Viktor Hasselgren, Jan Hasenauer, Marija Cvijovic:
PEtab.jl: advancing the efficiency and utility of dynamic modelling. - Seokjun On, Yujin Jeong, Eun-Sol Kim:
Structure-guided sequence representation learning for generalizable protein function prediction.
Volume 41, Number 10, 2025
- Armin Rauschenberger, Petr V. Nazarov, Enrico Glaab:
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation. - Marcos Lopez-De-Castro, Alberto García-Galindo, José González-Gomariz, Rubén Armañanzas:
Conformal inference for reliable single cell RNA-seq annotation. - Daniel Kim, Carissa Chen, Lijia Yu, Jean Yee Hwa Yang, Pengyi Yang:
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data. - Wouter Duverger, Georg Ramer, Nikolaos N. Louros, Joost Schymkowitz, Frederic Rousseau:
AXZ viewer: a web application to visualize unprocessed AFM-IR data. - L. Moritz Blumer, Jeffrey M. Good, Richard Durbin:
WinPCA: a package for windowed principal component analysis. - Chunfeng He, Yue Xu, Yuan Zhou, Jiayao Fan, Chunxiao Cheng, Ran Meng, Lang Wu, Ruiyuan Pan, Ravi V. Shah, Eric R. Gamazon, Dan Zhou:
Integrating population-level and cell-based signatures for drug repositioning. - Qicheng Zhao, Anji Deng, Qihuang Zhang:
DiSTect: a Bayesian model for disease-associated gene discovery and prediction in spatial transcriptomics. - Cem Ata Baykara, Ali Burak Ünal, Nico Pfeifer, Mete Akgün:
Privacy-preserving federated unsupervised domain adaptation with application to age prediction from DNA methylation data. - Austin M. Marcus, Jordan C. Rozum, Herbert Sizek, Luis M. Rocha:
CANA v1.0.0: efficient quantification of canalization in automata networks. - Shengli Zhang, Jingyi Ren, Yunyun Liang:
An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection. - Hongxin Xiang, Mingquan Liu, Linlin Hou, Shuting Jin, Jianmin Wang, Jun Xia, Wenjie Du, Sisi Yuan, Xiangzheng Fu, Xinyu Yang, Li Zeng, Lei Xu:
An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training. - Xinyu Zhou, Yi Yan, Kevin Hu, Haixu Tang, Yijie Wang, Lu Wang, Chi Zhang, Sha Cao:
Predicting the trend of SARS-CoV-2 mutation frequencies using historical data. - Elias Dohmen, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger, Anna Grandchamp:
DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation. - Güliz Akkaya, Nesli Erdogmus, Mete Akgün:
PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption. - Hung-Ching Chang, Yusi Fang, Michael T. Gorczyca, Kayhan Batmanghelich, George C. Tseng:
High-dimensional causal mediation analysis by partial sum statistic and sample splitting strategy in imaging genetics application. - Hukam C. Rawal, Qi Chen, Tong Zhou:
FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. - Trevor Schneggenburger, Jaroslaw Zola:
SKiM: accurately classifying metagenomic ONT reads in limited memory. - Daniel E. Schäffer, Samuel Sledzieski, Lenore Cowen, Bonnie Berger:
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT. - Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T. Reddy, Alexander Yermanos:
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests. - Cecilia B. Rodriguez, Ronaldo Romario Tunque Cahui, Nicolás Demitroff, Layla Hirsh, Damien P. Devos, Graciela Boccaccio, Gustavo D. Parisi:
BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins. - Evan Komp, Kristoffer E. Johansson, Nicholas Paul Gauthier, Japheth E. Gado, Kresten Lindorff-Larsen, Gregg T. Beckham:
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE. - Dickson Aruhomukama:
Balancing complexity and clarity - towards clinician-ready antibiotic resistance prediction models. - Jiaqing Xie, Yuqiang Li, Tianfan Fu:
DeepProtein: deep learning library and benchmark for protein sequence learning. - Yue Luo, Lei Deng:
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction. - Suleiman Aminu, Abdulaziz Ascandari, Rachid Benhida, Rachid Daoud:
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk. - Donn Liew, Akesha Dinuli Dharmatilleke, Edwin See, Ee Hou Yong:
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration. - Rok Kogoj, Mauro Petrillo, Samo Zakotnik, Alen Suljic, Misa Korva, Gabriele Leoni:
Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows. - Md Masud Rana, Md. Nurul Haque Mollah, Mohammed H. Albujja, Sibte Syed Hadi, Fan Liu:
ToxAssay: a hierarchical model-driven tool for advanced toxicogenomics biomarker discovery. - Michael L. Sierk, Daniel Danis, Sujay Patil, Nobal Kishor, Rajdeep Mondal, Abhishek Jha, Qingrong Chen, Chunhua Yan, Monica C. Munoz-Torres, Daoud M. Meerzaman, Peter N. Robinson, Justin T. Reese:
Oncopacket: integration of cancer research data using GA4GH phenopackets. - Alexandre Boulay, Emma Cremelie, Clovis Galiez, Yves Briers, Elsa Rousseau, Roberto Vázquez Fernández:
SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains. - Sunjae Lee, Jaebeom Kim, Milot Mirdita, Cameron L. M. Gilchrist, Martin Steinegger:
Easy and interactive taxonomic profiling with Metabuli App. - Melis Gencel, David Gagné-Leroux, Adrian W. R. Serohijos:
Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series. - Wenzhe Xu, Xiaorong Liu, Jie Wang, Fan Zhang, Dongfeng Hu, Liansong Zong:
UAMRL: multi-granularity uncertainty-aware multimodal representation learning for drug-target affinity prediction. - Nigreisy Montalvo, Francisco Requena, Emidio Capriotti, Antonio Rausell:
Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings. - Yurou Wang, Zhixiang Lin, Tao Wang:
InterVelo: a mutually enhancing model for estimating pseudotime and RNA velocity in multi-omic single-cell data. - Xiaoyi Liu, Na Zhang, Chenglong Kang, Chengwei Ai, Hongpeng Yang, Jijun Tang, Fei Guo:
HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning. - Thomas Minotto, Antoine Claessens, Thomas D. Otto:
Exploring homology detection via k-means clustering of proteins embedded with a large language model. - Saba Zerefa, Jesse Cool, Pramesh Singh, Samantha Petti:
An interpretable alphabet for local protein structure search based on amino acid neighborhoods. - Bokeum Cho, Seunggeun Lee:
PTL-PRS: an R package for transfer learning of polygenic risk scores with pseudovalidation. - Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T. Eadon, Qin Ma, Juexin Wang, Dong Xu:
scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. - Alberto Cattaneo, Stephen Bonner, Thomas Martynec, Edward R. Morrissey, Carlo Luschi, Ian P. Barrett, Daniel Justus:
The role of graph topology in the performance of biomedical Knowledge Graph Completion models. - Nele P. Quast, Charlotte M. Deane, Matthew I. J. Raybould:
STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation. - Mariia Pospelova, Yana Safonova:
PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences. - Zirui Chen, Jiao Hua, Lu Ba, Tianyun He, Boran Yang, Jing Qi, Shuilin Jin:
reDA: differential abundance testing on scATAC-seq data using random walk with restart. - Omri Peleg, Maya Raytan, Elhanan Borenstein:
KADAIF: an anomaly detection method for complex microbiome data. - Pavel P. Kuksa, Matei Ionita, Luke Carter, Jeffrey Cifello, Prabhakaran Gangadharan, Kaylyn Clark, Otto Valladares, Yuk Yee Leung, Li-San Wang:
BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets. - Huiying Jiang, Wenlan Chen, Fei Guo, Cheng Liang:
Cancer survival prediction based on soft-label guided contrastive learning and global feature fusion. - Taushif Khan, Mohammed Toufiq, Marina Yurieva, Nitaya Indrawattana, Akanitt Jittmittraphap, Nathamon Kosoltanapiwat, Pornpan Pumirat, Passanesh Sukphopetch, Muthita Vanaporn, Karolina Palucka, Basirudeen Syed Ahamed Kabeer, Darawan Rinchai, Damien Chaussabel:
Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation. - Shawn T. O'Neil, Brian M. Schilder, Kevin Schaper, Corey Cox, Daniel R. Korn, Sarah Gehrke, Christopher J. Mungall, Melissa A. Haendel:
monarchr: an R package for querying biomedical knowledge graphs.
Volume 41, Number 11, 2025
- Leo Hermet, Leo Laoubi, Martial Scavino, Anne-Claire Doffin, Alexia Gazeu, Justine Berthet, Berenice Pillat, Stephanie Tissot, Sylvie Rusakiewicz, Marie-Cécile Michallet, Nathalie Bendriss-Vermare, Jenny Valladeau-Guilemond, Jean Hausser, Christophe Caux, Margaux Hubert:
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment. - Tiberiu Totu, Rafael Riudavets Puig, Lukas Jonathan Häuser, Mattia Tomasoni, Hella Anna Bolck, Marija Buljan:
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline. - Amir Hassan Shariatmadari, Alireza Jafari, Sikun Guo, Sneha Srinivasan, Nathan C. Sheffield, Aidong Zhang, Kishlay Jha:
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation. - Yu Xu, Chonghao Wang, Ke Xu, Yi Ding, Aiping Lyu, Lu Zhang:
TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction. - Oscar Rojas Labra, Carla M. Martinez-Garcia, Nelly Beatriz Santoyo-Rivera, Daniel Montiel-Garcia, Vijay S. Reddy:
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs. - Enzo Battistella, Nick Jiang, Chris Rohlicek, Ilya Shlyakhter, Victoria Popic:
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement. - Stefaan Verwimp, Rob Lavigne, Cédric Lood, Vera van Noort:
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures. - Yanli Wang, Frimpong Boadu, Jianlin Cheng:
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs. - Ryuichiro Nakato, Luis Augusto Eijy Nagai:
ShortCake: an integrated platform for efficient and reproducible single-cell analysis. - William Gilpin:
The cell as a token: high-dimensional geometry in language models and cell embeddings. - Melissa Van Norden, William Mangione, Zackary Falls, Ram Samudrala:
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. - Charles Tapley Hoyt, Klas Karis, Benjamin M. Gyori:
Assembly and reasoning over semantic mappings at scale for biomedical data integration. - Kangsheng Qi, Can Cenik:
Topological and functional characterization of human translation efficiency covariation network. - Feng Chen, Chunhe Li:
Reconstructing gene network structure and dynamics from single cell data. - Florestan De Moor, Olivier Boulle, Dominique Lavenier:
De-Bruijn graph partitioning for scalable and accurate DNA storage processing. - Philip Hartout, Dexiong Chen, Paolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt:
Endowing protein language models with structural knowledge. - Yangyang Chen, Zixu Wang, Pengyong Li, Li Zeng, Xiangxiang Zeng, Lei Xu:
ZeroGEN: leveraging language models for zero-shot ligand design from protein sequences. - Andrew J. Bass, David J. Cutler, Michael P. Epstein:
A powerful framework for differential co-expression analysis of general risk factors. - Jan Pielesiak, Maciej Antczak, Marta Szachniuk, Tomasz Zok:
RNAtive to recognize native-like structure in a set of RNA 3D models. - Mark Chernyshev, Aron Stålmarck, Martin Corcoran, Gunilla B. Karlsson Hedestam, Ben Murrell:
Detection of PCR chimeras in adaptive immune receptor repertoire sequences. - Ana Laura Chenoweth Galaz, Nadia Tahiri:
aPhyloGeo: a Python application for correlating genetic and climatic conditions. - Yicong Mao, Zhiwen Jiang, Tianying Wang, Yijuan Hu, Xiang Zhan:
TCVS: tree-guided compositional variable selection analysis of microbiome data. - Yinan Zheng, Feng Gao, Lifang Hou:
PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework. - Minsoo Kim, Hanjin Bae, Gyeongpil Jo, Kunwoo Kim, Sung Jong Lee, Jejoong Yoo, Keehyoung Joo:
DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models. - Michael B. Hall, Chenxi Zhou, Lachlan J. M. Coin:
Genome size estimation from long read overlaps. - Jacqueline M. Boccacino, Martin Del Castillo Velasco-Herrera, Mathew A Beale, Jamie Billington, Ian Vermes, Sofia Obolenski, Kim Wong, Laura Torrens, Sarah J. Moody, Sandra Perdomo, Saamin Cheema, Bailey Francis, Victoria Offord, Adam P. Butler, David J. Adams:
SPARKI: a tool for the statistical analysis of pathogen identification results. - Giorgia Migliaccio, Lena Möbus, Giusy del Giudice, Jack Morikka, Antonio Federico, Angela Serra, Dario Greco:
OpTiles: an R package for adaptive tiling and methylation variability profiling. - Liyuan Shu, Deyu Zhuang, Jiao Tang, Junyong Zhao, Wei Shao, Xiaoyu Guan, Daoqiang Zhang:
DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing. - Zhenqian Shen, Mingyang Zhou, Yongqi Zhang, Quanming Yao:
Benchmarking drug-drug interaction prediction methods: a perspective of distribution changes. - Junhao Gu, Nandor Laszik, Christopher E. Miles, Jun Allard, Timothy L. Downing, Elizabeth L. Read:
Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data. - Kevin Dradjat, Massinissa Hamidi, Pierre Bartet, Blaise Hanczar:
Self-supervised representation learning on gene expression data. - Junyi Song, Shadi Zabad, Archer Yang, Simon Gravel, Yue Li:
Sparse polygenic risk score inference with the spike-and-slab LASSO. - Jacob Schreiber:
Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring. - Daniel R. Bergman, Jeanette A. I. Johnson, Marwa Naji, Max Booth, Heber L. Rocha, Atul Deshpande, Dimitrios N. Sidiropoulos, Tamara Lopez-Vidal, Randy W. Heiland, Luciane T. Kagohara, Robert A. Anders, Lei Zheng, Elizabeth M. Jaffee, Genevieve L. Stein-O'Brien, Paul Macklin, Elana J. Fertig:
BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells. - Tuomas Borman, Artur Sannikov, Robert D. Finn, Morten Tønsberg Limborg, Alexander B. Rogers, Varsha Kale, Kati Hanhineva, Leo Lahti:
HoloFoodR: a statistical programming framework for holo-omics data integration workflows. - Correction to: Learning meaningful representation of single-neuron morphology via large-scale pre-training.
- Xiyuan Mei, Hanbo Liu, Yuheng Zhu, Enshuang Zhao, Longyi Li, Hao Zhang:
TVAE-RNA: ensemble-based RNA secondary structure prediction via transformer variational autoencoders. - Javier De La Fuente, Diego Londoño-Correa, Elliot M. Tucker-Drob:
Distinguishing specific from broad genetic associations between external correlates and common factors. - Yutong Zhou, Shuyang Hou, Xinhao Miao, Guangxin Zhang, Zining Li, Di Zhang, Yongjie Lin, Yihan Lin:
Decoding cell fate: integrated experimental and computational analysis at the single-cell level. - Kosuke Hamazaki, Hiroyoshi Iwata, Koji Tsuda:
DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies. - Sajjad Ghaffarinasab, Hugo Dourado:
GBA Solver: a user-friendly web server for growth balance analysis. - Emine Ayse Sunar, Zeynep Isik, Mert Pekey, Ramazan Gökberk Cinbis, Öznur Tastan:
DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models. - Jeff Gauthier, Irena Kukavica-Ibrulj, Roger C. Levesque:
PDP-Miner: an AI/ML tool to detect prophage tail proteins with depolymerase domains across thousands of bacterial genomes. - Qingxiang Guo, Yangyang Li, Ting-You Wang, Abhirami Ramakrishnan, Rendong Yang:
OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. - Yuheng Lai, Dongyuan Song, Lucy Xia, Jingyi Jessica Li:
PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime. - Zhengfa Xue, Jingyu Zeng, Xuwen Wang, Jiajing Yuan, Tianci Wang, Xin Lai, Lin Wang, Yu Wang, Huanhuan Zhu, Xin Jin, Jiayin Wang:
ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing. - Marek S. Wiewiórka, Pavel Khamutou, Marek Zbysinski, Tomasz Gambin:
polars-bio - fast, scalable, and out-of-core operations on large genomic interval datasets. - Abiodun S. Oyedele, Allison S. Walker:
Benchmarking methods for measuring biosynthetic gene cluster similarity and determination of gene cluster families. - Mark A. Burgess, Brendan Hosking, Roc Reguant, Anubhav Kaphle, Mitchell J. O'Brien, Letitia M. F. Sng, Yatish Jain, Denis C. Bauer:
Privacy-hardened and hallucination-resistant synthetic data generation with logic-solvers. - Xiaowen Sun, Jiahao Li, Guiying Yan, Renmin Han:
ADMGCN: graph convolutional network for Alzheimer's disease diagnosis with a meta-learning paradigm. - Samson Weiner, Mukul S. Bansal:
SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection. - Timothy D. J. Kirkwood, Jack A. Connolly, Ee Lui Ang, Huimin Zhao, Eriko Takano, Rainer Breitling:
Synteny plot quality control with SyntenyQC. - Joonas Kartau, Matti Pirinen:
FINEMAP-miss: fine-mapping genome-wide association studies with missing genotype information. - Alexander L. R. Lubbock, Lauren E.-A. Eyssen, Kelly Parker, Mark Basham, Laura Shemilt, Raymond J. Owens:
AntigenApp: a laboratory data management system for nanobody generation and sequence analysis. - Mehrdad Zandigohar, Jalees Rehman, Yang Dai:
scRegulate: single-cell regulatory-embedded variational inference of transcription factor activity from gene expression.
Volume 41, Number 12, 2025
- Jingong Huang, Rui Ma, Michael Strobel, Yangyang Hu, Tiantian Ye, Tao Jiang, Wenxiu Ma:
SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing. - Rakbin Sung, Seongmi Woo, Dongmin Shin, Junil Kim, Daewon Lee:
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors. - Ali Mostafa Anwar, Akewak Jeba, Leo Lahti, Eleanor Coffey:
LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis. - Jin Young Lee, Jeremiah Holt, Xiaobei Zhao, Katherine A Hoadley, D. Neil Hayes, Hyo Young Choi:
ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution. - Hongyao Li, Yunrui Liu, Pengcheng Zeng:
Guided co-clustering transfer across unpaired and paired single-cell multi-omics data. - Bhupesh Dewangan, Debjyoti Ray, Yijie Ren, Shraddha Srivastava, Lei Jiang, Muneendra Ojha, Dong Xu, Gyan Srivastava:
Target and biomarker exploration portal for drug discovery. - Vijay Subramanian, Rajeswari Appadurai, Harikrishnan Venkatesh, Ashok Sekhar, Anand Srivastava:
Morpheus: a fragment-based algorithm to predict fold-switching behaviour in proteins across proteomes. - Noah A. Wahl, Georgios Koutsovoulos, Ben Bettisworth, Alexandros Stamatakis:
raxtax : a k -mer-based non-Bayesian taxonomic classifier. - Mohit Chawla, Utkarsh Kalra, Andrea Petta, Suraj Sharma, Abdul Rajjak Shaikh, Luigi Cavallo, Romina Oliva:
COCOMAPS 2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes. - Antonino Zito, Xavier Escriba-Montagut, Gabriela Scorici, Axel Martinelli, Murodzhon Akhmedov, Ivo Kwee:
PLAID: ultrafast single-sample gene set enrichment scoring. - Zilong Li, Frederik Filip Stæger, Robert W. Davies, Ida Moltke, Anders Albrechtsen:
SVUPP: Pre-phasing long reads improves structural variant genotyping. - Anton Stratmann, Martin Beyß, Johann F. Jadebeck, Wolfgang Wiechert, Katharina Nöh:
13CFLUX - third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis. - Tessa R. Macnish, Hawlader A. Al-Mamun, Thomas Bergmann, Mitchell S. Bestry, Jacob I Marsh, David Edwards:
HaploVar: an R package for defining local haplotype variants for trait association and trait prediction analyses. - Alexandra M. Kasianova, Anna V. Klepikova, Oleg A Gusev, Guzel R. Gazizova, Maria D. Logacheva, Aleksey A. Penin:
Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads. - Tianci Wang, Guanyu Qiao, Guohua Wang, Yang Li:
PLiSAGE: enhancing protein-ligand interaction prediction with multimodal surface and geometry encoding.