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ORCIDBioinformatics, Volume 42
Volume 42, Number 1, 2026
- Jens Zentgraf
, Johanna Elena Schmitz, Sven Rahmann:
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index. - Yong See Foo, Michael White, Aimee R. Taylor:
Pv3Rs: Plasmodium vivax relapse, recrudescence, and reinfection statistical genetic inference. - Xuan-Tung Trinh, André Abrantes da Costa, David Bouyssié, Adelina Rogowska-Wrzesinska, Veit Schwämmle:
OmicsQ: a user-friendly platform for interactive quantitative omics data analysis. - Aimin Li, Haotian Zhou, Rong Fei, Juntao Zou, Xiguo Yuan, Yajun Liu, Saurav Mallik, Xinhong Hei, Lei Wang:
Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models. - Jun Zhang, Xueer Weng, Tiantian Zhu, Yumeng Liu, Zexuan Zhu:
Molecular-level protein semantic learning via structure-aware coarse-grained language modeling. - Jin Zhang, Yixin Ji, Jinhua Liu, Wenrui Cui, Xiaohui Yao, Hongdong Li, Daoqiang Zhang, Alzheimer's Disease Neuroimaging Initiative:
Mutual learning for joint disease detection and severity prediction reveals multimodal pathogenesis for neurodegenerative disorders. - Chikara Mizukoshi, Yasuhiro Kojima, Shuto Hayashi, Ko Abe, Daisuke Kasugai, Teppei Shimamura:
scSurv: a deep generative model for single-cell survival analysis. - Jennifer T. Fouquier, Maggie Stanislawski, John O'Connor, Ashley Scadden, Catherine A. Lozupone:
EXPLANA: a user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies. - Ruqian Lyu, Annika Vannan, Jonathan A. Kropski, Nicholas E. Banovich, Davis J. McCarthy:
SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset. - Jorge Abreu-Vicente, Hannah Sonntag, Thomas Eidens, Cassie S. Mitchell, Thomas Lemberger:
Integrating curation into scientific publishing to train AI models. - Ira Horecka, Hannes L. Röst:
RISK: a next-generation tool for biological network annotation and visualization. - Yanis Zirem, Léa Ledoux, Isabelle Fournier, Michel Salzet:
Profiler: an open web platform for multi-omics analysis. - Elya Wygoda, Asher Moshe, Nimrod Serok, Edo Dotan, Noa Ecker, Naiel Jabareen, Omer Israeli, Itsik Pe'er, Tal Pupko:
Efficient algorithms for simulating sequences along a phylogenetic tree. - Jan van Eck, Dea Gogishvili, Wilson Silva, Sanne Abeln:
PLM-eXplain: divide and conquer the protein embedding space. - Hu Chen, Ye Qian, Qi Dai, Ying-Feng Zheng, Zhencang Zheng, Zhuoxing Shi:
Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing. - Dongmin Shin, Jeonghwan Henry Kim, Rakbin Sung, Junil Kim, Daewon Lee:
CellCraft: an extensible visual programming application for gene regulatory network inference. - Anna Laddach, Fränze Progatzky, Vassilis Pachnis, Michael Shapiro:
Capturing gene-cell duality in a cat's cradle. - Felix Wiegand, Felix Mölder, Johannes Köster:
Alignoth : portable and interactive visualization of read alignments. - Yong Xie, Jindong Li, Ziyan Zhang, Bin Meng, Shuaijian Dai, Yuchen Zhou, Eamonn Kennedy, Niandong Jiao, Haobin Chen, Zhuxin Dong:
NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores. - Yiran Huang, Xiao Tan, Xiaoyu Li, Feng Xiong, Siu Ming Yiu:
A hybrid unsupervised methodology on artificial intelligence filtering for automatically processing cellular DNA-encoded library (DEL) datasets. - Cameron S. Movassaghi, Amanda Momenzadeh, Jesse G. Meyer:
From articles to code: on-demand generation of core algorithms from scientific publications. - Tim Stohn, Roderick A P. M. van Eijl, Klaas W. Mulder, Lodewyk F. A. Wessels, Evert Bosdriesz:
Reconstructing and comparing signal transduction networks from single-cell protein quantification data. - Nir Nitskansky, Kessem Clein, Barak Raveh:
Building multiscale Markov state models by systematic mapping of temporal communities. - Alemu Takele Assefa, Bie M. P. Verbist, Koen Van den Berge:
Assessing differential cell composition in single-cell studies using voomCLR. - Anna Hadarovich, Maxim Scheremetjew, Hari Raj Singh, HongKee Moon, Lena Hersemann, Ágnes Tóth-Petróczy:
PICNIC web server for predicting proteins involved in biomolecular condensates. - Christine S. Liu, Jerold Chun:
isoSeQL: comparing long-read isoforms across multiple datasets. - Evgeny Tankhilevich, Sergio Martínez Cuesta, Ian P. Barrett, Carolina Berg, Lovisa Holmberg Schiavone, Andrew R. Leach:
RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli. - Sumyyah Toonsi, Paul N. Schofield, Robert Hoehndorf:
Causal knowledge graph analysis identifies adverse drug effects. - Hajime Suzuki, Masahiro Sugawa, Yoshitaka Sakamoto, Yuichi Shiraishi:
mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing. - Lake Noel, Yi-Wen Hsiao, Yimeng He, Andrew Hung, Xiaojiang Cui, Edward Ray, Jason H. Moore, Pei-Chen Peng, Xiuzhen Huang:
Benchmarking large language models for identifying transcription factor regulatory interactions. - Lorenzo Federico Signorini, Martin Kupiec, Roded Sharan:
Signing protein-protein interaction networks. - Huidong Su, Caicai Zhang, Frank Qingyun Wang, Chun Hing She, Xinxin Chen, Xiao Dang, Yao Lei, Ke Ni, Zewei Xiong, Danqing Yin, Xingtian Yang, Hong Feng, Philip H. Li, Wanling Yang:
OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data. - Laurie Prélot, Jiayu Chen, Matthias Hüser, André Kahles, Gunnar Rätsch:
ImmunoPepper: extracting personalized peptides from complex splicing graphs. - Tanya Nandan, Bowen Fan, Samuel Håkansson, Catherine R. Jutzeler, Sarah C. Brüningk:
Joint representation learning for oncology applications. - Genereux Akotenou, Asmaa H. Hassan, Morad M. Mokhtar, Achraf El Allali:
MegaPlantTF: a machine learning framework for comprehensive identification and classification of plant transcription factors. - Darong Li, Lian Shen, Meijia Song, Deyi Li, Juan Liu, Xiangrong Liu:
SurfFold: a unified model for protein inverse folding by integrating surface and structural information. - Nils Peter Petersen, Mia Le, Annick Renevey, Ehizojie Emua, Sarah Ryter, Giuditta Annibaldis, Jacob Camara, Sanaba Boumbaly, Cyril Erameh, Tanja Laske, Jan Baumbach, Philippe Lemey, Stephan Günther, Sophie Duraffour, Liana Eleni Kafetzopoulou:
ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing. - Alan J. S. Beavan, Maria Rosa Domingo-Sananes, James O. McInerney:
PanForest: predicting genes in genomes using random forests. - Fengling Hu, Jiayi Tong, Margaret Gardner, Lifespan Brain Chart Consortium, Andrew A. Chen, Richard A. I. Bethlehem, Jakob Seidlitz, Hongzhe Li, Aaron Alexander-Bloch, Yong Chen, Russell T. Shinohara:
dGAMLSS: an exact, distributed algorithm to fit Generalized Additive Models for Location, Scale, and Shape for privacy-preserving population reference charts. - Sylvère Bastien, Pauline François, Sara Moussadeq, Jérôme Lemoine, Karen Moreau, François Vandenesch:
BPSS: a Nextflow pipeline for Bacterial Peptide Sequence Selection to detect protein diversity. - Rye Howard-Stone, Ion I. Mandoiu:
MHASS: Microbiome HiFi Amplicon Sequencing Simulator. - Yitao Xu, Guanyun Wei, Jingying Zhou, Yuanhua Huang, Weichuan Yu, Zhixiang Lin, Ran Liu, Xiaodan Fan:
RoBep: a region-oriented deep learning model for B-cell epitope prediction. - Zhihua Du, Di Wang, Qiyi Chen, Yuehua Ou, Xinlei Huang, Xiang Zhou, Xubin Zheng:
STAHD: a scalable and accurate method to detect spatial domains in high-resolution spatial transcriptomics data. - Weimin Guo, Yadong Liu, Yadong Wang, Tao Jiang:
cuteSV-OL: a real-time structural variation detection framework for nanopore sequencing devices. - Massimiliano S. Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Tulio de Oliveira, Carla Mavian, Eduan Wilkinson:
CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation. - Jiyuan Yang, Nana Wei, Yang Qu, Congcong Hu, Weiwei Zhang, Lin Liu, Hua-Jun Wu, Xiaoqi Zheng:
Spider: a flexible and unified framework for simulating spatial transcriptomics data. - Andrew Green, Nancy Ontiveros-Palacios, Isaac Jandalala, Simona Panni, Valerie Wood, Giulia Antonazzo, Helen Attrill, Alex Bateman, Blake A. Sweeney:
GOFlowLLM - curating miRNA literature with large language models and flowcharts.
Volume 42, Number 2, 2026
- Alice Cleynen, Agin Ravindran, Nikolay E. Shirokikh:
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data. - Junqi Long, Bo Liu, Jianqiang Li, Shuangtao Zhao:
MCOAN: multimodal contrastive representation learning for cross-omics adaptive disease regulatory network prediction. - Favour James, Dexter Pratt, Christopher Churas, Augustin Luna:
textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape. - Darya Shlyk, Lawrence Hunter:
Improving biomedical entity linking with generative relevance feedback. - David Köhler, Niklas Kleinenkuhnen, Kiarash Rastegar, Till Baar, Chrysa Nikopoulou, Vangelis Kondylis, Vlada Milchevskaya, Matthias Schmid, Peter Tessarz, Achim Tresch:
A spectral dimension reduction technique that improves pattern detection in multivariate spatial data. - Jierui Xu, Elena I. Zavala, Priya Moorjani:
sedimix : a workflow for the analysis of hominin nuclear DNA sequences from sediments. - Hang Wei, Yuran Xie, Wenxiang Zhang, Linyang Li, Shuai Wu, Lin Gao:
Semantic-enhanced heterogeneous graph learning for identifying ncRNAs associated with drug resistance. - Mengni Liu, Lizhen Jiang, Luowanyue Zhang, Tianjian Chen, Xingzhe Wang, Yuan Liang, Xianping Shi, Jian Ren, Yueyuan Zheng:
CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types. - Tohid Ghasemnejad, Yuheng Liang, Khadijeh Jahanian, Milad Eidi, Arash Salmaninejad, Seyedeh Sedigheh Abedini, Fabrizzio Horta, Nigel H. Lovell, Thantrira Porntaveetus, Mark Grosser, Mahmoud Aarabi, Hamid Alinejad-Rokny:
Comprehensive evaluation of ACMG/AMP-based variant classification tools. - Xudong Xiang, Xinxin Mao, Tengfei Luo, Chenbin Liu, Bozhao Li, Pei Yu, Yu Zhang, Dai Wu, Yijing Wang, Qiao Zhou, Yixiao Zhu, Bin Li, Kun Xia, Guihu Zhao, Jinchen Li:
Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker. - Alexandra M. Wong, Cecile P. G. Meier-Scherling, Lorin Crawford:
Characterizing clinical toxicity in cancer combination therapies. - Chenyang Xie, Yingying Song, Song He, Xiaochen Bo, Zhongnan Zhang:
MMPCS: multi-view molecular pretraining based on consistency information and specific information. - Nguyen Khoa Tran, My Ky Huynh, Alexander D. Kotman, Martin Jürgens, Thomas Kurz, Sascha Dietrich, Gunnar W. Klau, Nan Qin:
VUScope: a mathematical model for evaluating image-based drug response measurements and predicting long-term incubation outcomes. - Georgios A. Manios, Sophia Nteli, Panagiota I. Kontou, Pantelis G. Bagos:
PYRAMA: an open-source tool for advanced meta-analysis of genome wide association studies. - Yingtong Liu, Aaron G. Baugh, Evanthia T. Roussos Torres, Adam L. Maclean:
Inference of marker genes of subtle cell state changes via iLR: iterative logistic regression. - Xinyi Tang, Ran Liu:
GAMMA: gap-aware motif mining under incomplete labeling with applications to MHC motifs. - Katalin Ferenc, Lorenzo Martini, Ieva Rauluseviciute, Geir Kjetil Ferkingstad Sandve, Anthony Mathelier:
inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences. - Huda Ahmad, Hannah M. Doherty, Sam T. Benedict, James R. J. Haycocks, Ge Zhou, Patrick J. Moynihan, Danesh Moradigaravand, Manuel Banzhaf:
ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data. - Adrian Weich, Christopher Lischer, Julio Vera:
esloco: simulation-based estimation of local coverage in long-read DNA sequencing. - T. Sophia Luo, Jonathon LeFaive, John Dou, Kelly M. Bakulski, Erin B. Ware, Matthew Zawistowski:
MethylModes: computationally efficient detection of multimodal distributions in DNA methylation data. - Charlotte Collins, Panagiotis Fytas, Ilknur Karadeniz, Huiyuan Zheng, Simon Baker, Ulla Stenius, Anna Korhonen:
BioTriplex : a full-text annotated corpus for fine-tuning language models in gene-disease relation extraction tasks. - Zhao Li, Zaiyi Zheng, Rongbin Li, Wen Chen, Yuntao Yang, Meer A Ali, Jundong Li, W. Jim Zheng:
CeLLTra: aligning cell names with gene expression via a pathway-informed transformer. - Siera Martinez, Tushar Sharma, Luke Johnson, Allen Kim, Vania Ballesteros Prieto, Hovhannes Arestakesyan, Sunisha Harish, Jewel Dias, Joseph Goldfrank, Nathan J. Edwards, Anelia Horvath:
scSNViz: visualization and analysis of cell-specific expressed SNVs. - Daria Smirnova, Anita Ustinova, Viacheslav S. Chukanov, Ekaterina Pchitskaya:
3D dendritic spines shape descriptors for efficient classification and morphology analysis in control and Alzheimer's disease modeling neurons. - Artem Ivanov, Vladimir Popov, Maxim Morozov, Evgenii I Olekhnovich, Vladimir Ulyantsev:
MetaFX: feature extraction from whole-genome metagenomic sequencing data. - Adriana Carolina Gonzalez-Cavazos, Roger Tu, Meghamala Sinha, Andrew I. Su:
A case-based explainable graph neural network framework for mechanistic drug repositioning. - Aidan Tillman, Daniel Ramirez, Mingyang Lu:
sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation. - Christoph Stelz, Lukas Hübner, Alexandros Stamatakis:
Bit-reproducible parallel phylogenetic tree inference. - Daria Meyer, Emanuel Barth, Laura Wiehle, Manja Marz:
diffMONT : predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application. - Isis Narváez-Bandera, Ashley Lui, Yonatan Ayalew Mekonnen, Vanessa Rubio, Augustine Takyi, Noah Sulman, Christopher M. Wilson, Hayley D. Ackerman, Oscar E. Ospina, Guillermo Gonzalez-Calderon, Elsa R. Flores, Qian Li, Ann Chen, Brooke L. Fridley, Paul A. Stewart:
iModMix: integrative module analysis for multi-omics data. - Chaojie Wang, Xin Yu:
STransfer: a transfer learning-enhanced graph convolutional network for clustering spatial transcriptomics data. - Joseph Thorpe, Nina Billows, Gabrielle C. Ngwana-Joseph, Amy Ibrahim, Deborah Nolder, Colin J. Sutherland, Thi Hong Ngoc Nguyen, Thi Huong Binh Nguyen, Quang Thieu Nguyen, Jamille G. Dombrowski, Silvia Maria Di Santi, Claudio R. F. Marinho, Jody Phelan, Tomasz J. Kurowski, Fady R. Mohareb, Susana G. Campino, Taane G. Clark:
Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites. - David Kouril, Trevor Manz, Tereza Clarence, Nils Gehlenborg:
Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks. - Kari Salokas, Salla Keskitalo, Markku Varjosalo:
ProteoGyver: a fast, user-friendly tool for routine QC and analysis of MS-based proteomics data. - Tien-Thanh Bui, Rui Xie, Wei Zhang:
X-intNMF: a cross- and intra-omics regularized NMF framework for multi-omics integration. - Rosan C. M. Kuin, Alexander T. Julian, Jagriti Chander, Sunah Lee, Gerard J. P. van Westen:
PyTEA-O: a Python implementation of Two-Entropies Analysis for protein sequence variation analysis. - Soo Bin Kwon, Jason Ernst:
Learning a pairwise epigenomic and transcription factor binding association score across the human genome. - Matthias Flotho, Philipp Flotho, Andreas Keller:
DicePlot: a package for high-dimensional categorical data visualization. - Kaylee D. Rich, James D. Wasmuth:
mimicDetector: a pipeline for protein motif mimicry detection in host-pathogen interactions. - Stephen Newman, Bruce Budowle, Kristen Mittelman, David Mittelman:
Othram maps: a graph-powered platform for pedigree visualization and forensic intelligence. - Dingyao Zhang, Zhiyuan Chu, Yiran Huo, Yunzhe Jiang, Yuhang Chen, Zhiliang Bai, Rong Fan, Jun Lu, Mark Gerstein:
ASTRO: Automated Spatial-Transcriptome whole RNA Output. - Anja Hess, Dominik Seelow, Helene Kretzmer:
DNAvi: integration, statistics, and visualization of cell-free DNA fragment traces. - Manuel Mangoni, Salvatore Daniele Bianco, Francesco Petrizzelli, Michele Pieroni, Pietro Hiram Guzzi, Viviana Caputo, Tommaso Biagini, Tommaso Mazza:
Unsupervised synchronization of molecular dynamics trajectories via graph embedding and time warping. - Natan Tourne, Gaetan De Waele, Vanessa Vermeirssen, Willem Waegeman:
How negative sampling shapes the performance of transcription factor binding site prediction models. - Massimo Andreatta, Santiago J. Carmona:
UCell and pyUCell: single-cell gene signature scoring for R and Python.
Volume 42, Number 3, 2026
- Grace S. Brown, James Wengler, Aaron Joyce S. Fabelico, Abigail Muir, Anna Tubbs, Amanda Warren, Alexandra N. Millett, Xinrui Xiang Yu, Paul Pavlidis, Sanja Rogic, Stephen R. Piccolo:
Using semantic search to find publicly available gene-expression datasets. - Yojana Gadiya, Javier Millán Acosta, Ammar Ammar, Alejandro Adriaque Lozano, Delano Wetstede, Dominik Martinát, Ana Claudia Sima, Hailiang Mei, Egon L. Willighagen, Tooba Abbassi-Daloii:
pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources. - Joan Segura, Rubén Sánchez García, Sebastian Bittrich, Yana Rose, Stephen K. Burley, Jose M. Duarte:
Multi-scale structural similarity embedding search across entire proteomes. - Lucas Goiriz, Guillermo Rodrigo:
PyEvoMotion: a Python tool for population-based time-course analysis of genome evolution. - Jiaying Hu, Yihang Du, Suyang Hou, Yueyang Ding, Jinyan Li, Hao Wu, Xiaobo Sun:
CEMUSA: a graph-based integrative metric for evaluating clusters in spatial transcriptomics. - Tien-Cuong Bui, Injae Chung, Wonjun Lee, Junsu Ko, Juyong Lee:
IgPose: a generative data-augmented pipeline for robust immunoglobulin-antigen binding prediction. - Husam B. R. Alabed, Dorotea Frongia Mancini, Martina Pergola, Luigina Romani, Sabata Martino, Albert Koulman, Roberto Maria Pellegrino:
Functional lipid analysis via index-based lipidomics profile: a new computational module in LipidOne. - Elnaz Abdollahzadeh, Ali Mortazavi:
Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications. - Ki-Hwa Kim, Avinash Yaganapu, Sai Kosaraju, Aashish Bhatt, Yun Lyna Luo, Sai Phani Parsa, Juyeon Park, Hyun Lee, Jun Hyuck Lee, Tae-Jin Oh, Mingon Kang:
Prediction of bacterial protein-compound interactions with only positive samples. - Haoyu Zhang, Kevin T. Fotso, Marc Subirana-Granés, Milton Pividori:
CCC-GPU: a graphics processing unit (GPU)-accelerated nonlinear correlation coefficient for large-scale transcriptomic analyses. - Ke Xu, Xin Maizie Zhou, Lu Zhang:
stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images. - Serena Rosignoli, Sophie Taraglio, Francesco Di Luzio, Elisa Lustrino, Dario F. Marzella, Arne Elofsson, Massimo Panella, Alessandro Paiardini:
A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins. - Johannes Wirth, Anna Chernysheva, Birthe Lemke, Isabel Giray, Katja Steiger:
InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data. - Qi Zhao, Zhen Zhang, Tingwei Chen, Qian Mao, Haoxuan Shi, Jingjing Chen, Zheng Zhao, Xiaoya Fan:
Mamba6mA: a Mamba-based DNA N6-methyladenine site prediction model. - Grygoriy Zolotarov, Xavier Grau-Bové, Arnau Sebé-Pedrós:
GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis. - Ghanshyam Chandra, Md. Vasimuddin, Sanchit Misra, Chirag Jain:
Accelerating minimap2 for whole-genome alignment. - Olivia Angelin-Bonnet, Lindy Guo, Roy Storey, Susan Thomson:
moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods. - Keyang Yu, Haoquan Zhao, Andrea S. Wilderman, Tierra R. Farris, Jessie E. Arce, David Chen, Andrew R. Jackson, Yiran Guo, Qi Li, Bosko Jevtic, Dubravka Jevtic, Vuk Milinovic, Yuankun Zhu, Jeremy Costanza, Eric Wenger, Christopher Nemarich, Lisa Anderson, Aleksandar Mihajlovic, Kristin Ardlie, Shaine A Morris, Matthew E. Roth, Deanne M. Taylor, Adam C. Resnick, Lilei Zhang, Aleksandar Milosavljevic:
Aggregation of gene regulatory information and knowledge on FAIR principles enables discovery of pathogenic gene regulatory variants. - Wenjing Song, Yesen Sun, Le Ou-Yang:
SeOMLR: one-step multi-view latent representation with self-weighted ensemble learning for multi-omics cancer subtyping. - Leo Carl Foerster, Enrico Frigoli, Xiaoyu Sun, Jooa Hooli, Angela Goncalves, Ana Martin-Villalba:
umite: fast quantification of Smart-seq3 libraries with improved UMI retrieval. - Shangjin Han, Dongsup Kim:
scMix: learning temporal dynamics of gene expression under irregular time intervals. - Kristen Schneider, Simon Walker, Christopher Gignoux, Ryan Layer:
STABIX: summary-statistic-based GWAS indexing and compression. - Alex Rodriguez, Youngdae Kim, Tarak Nath Nandi, Karl Keat, Rachit Kumar, Mitchell Conery, Rohan Bhukar, Molei Liu, John Hessington, Ketan Maheshwari, VA Million Veteran Program, Edmon Begoli, Georgia Tourassi, Pradeep Natarajan, Benjamin F. Voight, John Michael Gaziano, Scott M. Damrauer, Katherine P. Liao, Wei Zhou, Jennifer E. Huffman, Anurag Verma, Ravi K. Madduri:
SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs. - Eli Piliper, Stephanie Goya, Alexander L. Greninger:
RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction. - Remi Trimbour, Julio Saez-Rodriguez, Laura Cantini:
CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data. - Felix Lenner, Anders Jemt, Lucia Peña Pérez, Ramprasad Neethiraj, Peter Pruisscher, Daniel Schmitz, Annick Renevey, Pádraic Corcoran, Daniel Nilsson, Jesper Eisfeldt, Anna Lindstrand, Valtteri Wirta, Adam Ameur, Lars Feuk:
Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis. - Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri-Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, André Kahles, Onur Mutlu:
Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism. - Wen Kong, Lingling Fu, Xingpeng Jiang, Weizhong Zhao:
A dual diffusion model-based representation learning framework for antimicrobial peptides classification. - Sonia García-Ruíz, Hannah Macpherson, Laura Caton, Mina Ryten, Emil K. Gustavsson:
ORFannotate: reproducible coding sequence annotation of transcriptome assemblies. - Pengcheng Li, Kai Zhang, Xiaozhong Liu, Xuhong Zhang:
Knowledge-based citation reasoning for biomedical domain. - Freya E. R. Woods, Emilyanne Leonard, Timothy Ebbels, Jonathan M. Cairns, Rhiannon David:
AutoFlow: an interactive Shiny app for supervised and unsupervised flow cytometry analysis. - Sanjoy Dey, Zhaonan Sun, John Warner, Eileen Koski, Elif Eyigöz, Swati Sathe, Cristina Sampaio, Jianying Hu:
From genes to trajectories: mapping genetic influences on Huntington's disease progression. - Heng Li, Brian Li:
Finding low-complexity DNA sequences with longdust. - Chenglong Sang, Cheng Peng:
BrainConnect: processing brain connectivity and spatial transcriptomics data for integrative analysis. - Gaëlle Letort, Tanya Foley, Ilona Mignerey, Laure Bally-Cuif, Nicolas Dray:
FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues. - Yanan Zhao, TingFang Lee, Boyan Zhou, Chan Wang, Ann Marie Schmidt, Mengling Liu, Huilin Li, Jiyuan Hu:
Joint modeling of longitudinal biomarker and survival outcomes with the presence of competing risk in the nested case-control studies with application to the TEDDY microbiome dataset. - Xiaoqi Tang, Caihua Liu, Chaowang Lan:
scDBic: a novel deep learning-based biclustering algorithm for analyzing scRNA-seq data. - Simon Dellicour, Nuno R. Faria, Rebecca Rose, Philippe Lemey, Oliver G. Pybus:
SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements. - Brydon P. G. Wall, Jonathan D. Ogata, My Nguyen, Amy L. Olex, Konstantinos V. Floros, Anthony C. Faber, Joseph L. McClay, J. Chuck Harrell, Mikhail G. Dozmorov:
Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches. - Emine Beyza Çandir, Halil Ibrahim Kuru, Magnus Rattray, A. Ercüment Çiçek, Öznur Tastan:
One-hot news: drug synergy models shortcut molecular features. - Xu Shi, Yuqi Zhai, Xianshi Yu, Xiaoou Li, Brian L. Hazlehurst, Denis B. Nyongesa, Daniel S. Sapp, Brian D. Williamson, David S. Carrell, Luesa Healy, Kara L. Cushing-Haugen, Jenna Wong, Shirley V. Wang, James S. Floyd, Kathleen Shattuck, Samuel McGown, Sarah Alam, José J. Hernández-Muñoz, Jie Li, Yong Ma, Danijela Stojanovic, Sudha R. Raman, Sharon E. Davis, Tianxi Cai, Jennifer C. Nelson, Patrick J. Heagerty:
Statistical methods to harmonize electronic health record data across healthcare systems: case study and lessons learned. - Chen-Hao Huang, Yen-Jen Oyang, Hsuan-Cheng Huang, Hsueh-Fen Juan:
scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking. - Paul J. Jost, Frank T. Bergmann, Daniel Weindl, Jan Hasenauer:
PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems. - Yiping Zou, Jiaqi Luo, Shuaicheng Li:
CoMBCR: Co-Learning Multi-Modalities of BCRs and gene expressions. - Leonid Chindelevitch, Åsa K. Hedman, Dmitri Bichko, Daniel Ziemek:
ReverseGWAS identifies combined phenotypes associated with a genotype in GWA studies. - Brian Tjaden:
TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria. - Marie Brinkmann, Michael Bonelli, Anela Tosevska:
SummArIzeR: simplifying cross-database enrichment result clustering and annotation via large language models. - Christina Katharina Kuhn, David Schmidt, Michael Rade, Josephine Selke, U. Sandy Tretbar, Maximilian Merz, Jan Grau, Kristin Reiche:
CERTOMICS : trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies. - Xuwen Wang, Zhili Chang, Wansheng Lv, Akhatov Akmal, Xamidov Munis, Xunbiao Liu, Shenjie Wang, Xiaoyan Zhu, Chong Du, Shuqun Zhang, Jiayin Wang:
PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework. - Patrick Barth, Frank Förster, Sebastian Jaenicke, Fabienne Thelen, Oliver Rossbach, Friedemann Weber, Lyudmila Shalamova, Alexander Goesmann:
PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data. - Minindu Weerakoon, Hai Vu, Reza Behboudi, Haynes Heaton:
Souporcell3: robust demultiplexing for high-donor single-cell RNA-seq datasets. - Jacob T. Mitchell, Orian Stapleton, Kavita Krishnan, Sushma Nagaraj, Dmitrijs Lvovs, Christopher Cherry, Amanda Poissonnier, Wesley Horton, Andrew Adey, Varun Rao, Amanda Huff, Jacquelyn W. Zimmerman, Luciane T. Kagohara, Neeha Zaidi, Lisa M. Coussens, Elizabeth M. Jaffee, Jennifer H. Elisseeff, Elana J. Fertig:
Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal. - Jarno N. Alanko, Ilya B. Slizovskiy, Daniel Lokshtanov, Travis Gagie, Noelle R. Noyes, Christina Boucher:
Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes". - Weronika Puchala, Krystyna Grzesiak, Dominik Rafacz, Michal Kistowski, Jochem H. Smit, Julien Marcoux, Michal Dadlez, Michal Burdukiewicz:
HaDeX2: multi-dimensional analysis of hydrogen-deuterium exchange mass spectrometry data. - Robert A. McDonald, Helen M. Byrne, Heather A. Harrington, Thomas Thorne, Bernadette J. Stolz:
Topological model selection: a case-study in tumour-induced angiogenesis. - Benjamin Rombaut, Arne Defauw, Frank Vernaillen, Julien Mortier, Evelien Van Hamme, Sofie Van Gassen, Ruth Seurinck, Yvan Saeys:
Scalable analysis of whole slide spatial proteomics with Harpy. - José-María Castelo, José Ángel Oteo, Gonzalo Oteo-García:
Mixtum: a graphical tool for two-way admixture analysis in population genetics based on f -statistics. - Valentin Schneider-Lunitz, Philip R. Kensche, Landfried Kraatz, Philipp Strubel, Stefan Borufka, Gurudeep Parala, Alexander Kanitz, Roland Eils, Ivo Buchhalter, Sven Twardziok:
Managing workflow executions with WESkit. - Nidia Barco-Armengol, Dèlia Yubero, Clara Xiol, Núria Catasús, Laura Martí-Sánchez, Judith Armstrong, Francesc Palau, Guerau Fernandez:
Identification of autosomal and sex chromosome aneuploidies using next generation sequencing. - Hai Chen, Jingmin Shu, Rekha Mudappathi, Elaine Li, Panwen Wang, Leif Bergsagel, Ping Yang, Zhifu Sun, Logan Zhao, Changxin Shi, Jeffrey P. Townsend, Carlo Maley, Li Liu:
Competing subclones and fitness diversity shape tumor evolution across cancer types. - Lihua Qi, Peng Wang, Hao Liu, Chen Chen, Jin Gu, Cheng Chen:
A hybrid neighborhood enhanced contrastive learning and self-knowledge distillation method for scRNA-seq data clustering analysis. - Marta Sevilla-Porras, Carlos Ruiz-Arenas, Luis A. Pérez-Jurado:
UPDhmm : detecting uniparental disomy from NGS trio data. - Szymon Grabowski, Tomasz Marek Kowalski, Robert Susik:
FFC: a scalable FASTA compressor. - Zhihui Zhu, Huapeng Liu, Xuechen Li, Haojin Zhou, Jiaqi Wang:
Uniform design-embedded predictions of (tetra-)peptide physicochemical properties.
Volume 42, Number 4, 2026
- Yaxiong Ma, Zengfa Dou, Yuhong Zha, Xiaoke Ma:
SA2E: spatial-aware auto-encoder for cell type deconvolution of spatial transcriptomics data. - Susan E. Ott, Giang N. Le, Sayed J. Mohammadi, Jesse Mittertreiner, Erica M. Pasini, Ronald Bontrop, Natasja de Groot, Jesse Bruijnesteijn:
VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions. - Brian B. Merritt, Jeremy Ratcliff, Stanley Ta, Gunars Osis, Matthew R. Mauldin, Peter Thielen:
TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection. - Zhijian Huang, Kai Chen, Xianshu Wang, Junheng Wang, Siyuan Shen, Yuanpeng Zhang, Min Wu, Lei Deng:
DeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA-miRNA interaction prediction. - Stephan Amstler, Lukas Forer, Lara Escherich, Sebastian Schönherr, Stefan Coassin:
Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration. - Yirui Chen, Haotian Zhang, Yu H. Sun, Soumya Negi, Shaolong Cao, Zhengyu Ouyang, Baohong Zhang, Jessica Hurt, Dann Huh:
SpliceHarmonization: an integrated method for identifying RNA splicing events in therapeutics for splicing modulation. - Killian Maudet, Juliette Samaniego, Yoann Pradat, Elsa Bernard:
fRagmentomics : an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation. - Sofia A. Duarte, Rosario Vitale, Sofia Escudero, Emilio Fenoy, Leandro A. Bugnon, Diego H. Milone, Georgina Stegmayer:
ET-Pfam: ensemble transfer learning for protein family prediction. - Rubo Wang, Xingyu Gao, Peilin Zhao:
DrugBLIP: exploring the protein-molecule interaction mechanisms with a multi-task learning graph transformer. - Fangrui Huang, Yitong Wang, Ashok Cutkosky, Janet H. T. Song:
Pretraining improves prediction of genomic datasets across species. - Yiyan Zhou, Jiaheng Hou, Haoling Xie, Nuoshi Lin, Cheng Yang, Hengchuang Yin, Wanqiu Ding, Huaiqiu Zhu:
A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0. - Edward Lukyamuzi, Timothy W. Kimbowa, Alfred Ssekagiri, Ronald Galiwango, Grace Kebirungi, Mugume T. Atwine, Mike Nsubuga, Suresh Maslamoney, Sumir Panji, Nicola J. Mulder, Daudi Jjingo, Jonathan K. Kayondo:
A scalable HPC framework for bioinformatics in resource-limited settings: design principles, implementation, and sustainability from the UVRI experience. - Correction to: Ribotin: automated assembly and phasing of rDNA morphs.
- Wan He, Daniel I. Bolnick, Samuel V. Scarpino, Tina Eliassi-Rad:
Hypergraph representations of single-cell RNA sequencing data for improved cell clustering. - Samuel Fromm, Marko Ludaic, Arne Elofsson:
Evaluating deep learning based structure prediction methods on antibody-antigen complexes. - Casey W. Dunn, Samuel H. Church:
Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR. - Akshata Hegde, Jianlin Cheng:
GRNFormer: accurate gene regulatory network inference using graph transformer. - Ziyang Wang, Yu Zhang, Youli Zhang, Jianwei Huang, Xiaoli Lu, Xiaoping Min, Shengxiang Ge, Jun Zhang, Ningshao Xia:
Predicting antibody-antigen affinity with a dual-level representation model. - Felix Faltings, Hannes Stärk, Tommi S. Jaakkola, Regina Barzilay:
Protein FID: improved evaluation of protein structure generative models. - Kyle C. Weber, Chenlin Lu, Roberto Vera Alvarez, Bruce D. Pascal, Anum Glasgow:
HXMS: a standardized file format for HX-MS data. - Pooria Daneshvar Kakhaki, Neda Ghohabi Esfahani, Stuart Akeson, Miten Jain:
CurrentView: a tool for visualization and comparison of nanopore ionic current signals. - Kunyang Zhang, Thierry D. Marti, Silke I Probst, Serina L. Robinson, Kathrin Fenner:
Enzyme association for environmental biotransformation reactions through contrastive learning of reaction center-specific fingerprints. - Keziah E. Liebenberg, Erin Craig, Robert Tibshirani, Livia S. Eberlin:
Structure-preserving multivariate hypothesis testing for mass spectrometry imaging and single-cell data. - Jiacheng Wang, Yaojia Chen, Quan Zou, Ximei Luo:
AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures. - Shiwei Wu, Nan Xu, Xiaohui Xin, Min Zhang, Haoliang Liu, Hongjia Zhu, Zhenyu Wei, Chengkui Zhao, Lei Yu, Weixing Feng:
Enhancing mutation impact prediction in protein-protein interactions through interpretable graph-based multi-level feature interactions. - Joonhyeok Choi, Sang-yeop Lee, Kyungdoe Han, Marta G. Carneiro, Kyoung-Seok Ryu, Donghan Lee:
ONEST: a web-based platform for the rapid and robust analysis of protein excited states through CEST spectroscopy. - James T. Robinson, Helga Thorvaldsdóttir, Jill P. Mesirov:
igv-reports: embedding interactive genomic visualizations in HTML reports to aid variant review. - Marek Kokot, Amitava Roy, Travis J. Wheeler, Sebastian Deorowicz:
MDCompress: better, faster compression of molecular dynamics simulation trajectories. - Megan Kuo, Kim-Anh Lê Cao, Saritha Kodikara, Jiadong Mao, Kris Sankaran:
phylobar: an R package for multiresolution compositional barplots in omics studies. - Mehmet Efe Akça, Gökçe Uludogan, Arzucan Özgür, Inci M. Baytas:
STAR-GO: improving protein function prediction by learning to hierarchically integrate ontology-informed semantic embeddings. - Fabiana Rodrigues de Góes, Matheus Fujimura Soares, Vitor Gregorio, Bruno Thiago de Lima Nichio, Alisson Gaspar Chiquitto, Flavia Lombardi Lopes, Mark Basham, Douglas Silva Domingues, Alexandre Rossi Paschoal:
mirtronDB 2.0: enhanced database with novel mirtron discoveries. - Akihiro Kitani, Bingyuan Zhang, Koichi Himori, Yusuke Matsui:
GlycanGT: a pretrained graph transformer framework for glycan graph representation and generative learning. - Zhicun Zeng, Yifan Wu, Zhangli Lu, Min Li:
NumMolFormer: an explicit functional group number-guided framework for structure-based drug design. - Carlos J. Rodriguez-Flores, Naroa Barrena, Loïc Paulevé, Francisco J. Planes:
gMISpy: integration of complex regulatory networks and genome scale metabolic models. - Jeffrey Zhong, Alyssa Cantu, Ruth Dannenfelser, Vicky Yao:
Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicing. - Dan Shao, Shengjie Liang, Yucong Xiong, Guangmin Liang:
MAISNet: a multi-species integrated graph neural network for acetylcholinesterase inhibitor screening. - Najla Abassi, Lea Schwarz, Edoardo Filippi, Federico Marini:
DeeDeeExperiment: building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor. - David Wragg, Eunchai Kang, Michael D. Morgan:
Harvesting more reads from single-cell combinatorial barcoding data with scarecrow. - Jure Praznikar:
Fast prediction of protein flexibility. - Chaewon Kim, Sunyong Yoo:
Predicting condition-aware drug-induced transcriptional responses via a latent diffusion model.
Volume 42, Number 5, 2026
- Orsolya Lapohos, Gregory Joseph Fonseca, Amin Emad:
Refining sequence-to-expression modelling with chromatin accessibility. - Peng Wang, Hongyuan Cao, Xiaoquan Wen:
Diagnosing scientific replicability through probabilistic distinguishability. - Susanna Holmström, Antti Häkkinen, Kari Lavikka, Giovanni Marchi, Sampsa Hautaniemi, Alexandra Lahtinen:
FUSE: data-driven functional segmentation of DNA methylation data. - Manjunatha Beduru Krishnamurthy, Pasupula Sridhar Harish, Abhishek Subramanian:
NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks. - Seonggwang Jeon, Jejoong Yoo, Keehyoung Joo, Eunok Paek:
StrucPTM: a database of structurally validated protein modifications and their conformational variation. - Lorién López-Villellas, Cristian Iñiguez, Albert Jiménez-Blanco, Quim Aguado-Puig, Miquel Moretó, Jesús Alastruey-Benedé, Pablo Ibáñez, Santiago Marco-Sola:
Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment. - Guanlan Dong, Nazia Hilal, Shayna Mallett, Bowen Jin, Shulin Mao, Monica Devi Manam, Diane D. Shao, Sangita Choudhury, August Yue Huang, Eunjung Alice Lee:
Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data. - Joon Klaps, Philippe Lemey, Magda Bletsa, Liana Eleni Kafetzopoulou:
nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction. - Fabrícia F. Nascimento, Vinicius B. Franceschi, Erik M. Volz:
treestructure: an R package to detect population structure in phylogenetic trees. - Ahmad Lutfi, Tanja Holstein, Sandro Andreotti, Thilo Muth:
MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing. - Hikaru Nagazumi, Yuki Moriya, Shuichi Kawashima, Toshiaki Katayama, Kana Shimizu:
Accurate SPARQL generation via in-context learning and schema-based query construction. - Krishnendu Sinha:
BABAPPAlign: a multiple sequence alignment engine with a learned residue-level scoring function. - Boyue Cui, Yujuan Li, Shiqu Chen, Jiaming Wei, Xuan Wang, Yadong Wang, Junyi Li:
MZSGO: multimodal zero-shot protein function annotation via evolutionary signals and textual semantics. - John B. Allard, Sudhir Kumar:
Treemble: a graphical tool to generate Newick strings from phylogenetic tree images. - Jakub Adamczyk, Piotr Ludynia, Wojciech Czech:
Molecular fingerprints are strong models for peptide function prediction. - Haeun Moon, Laura Sloofman, Marina Natividad Avila, Lambertus Klei, Bernie Devlin, Joseph D. Buxbaum, Kathryn Roeder:
A framework to infer de novo exonic variants when parental genotypes are missing enhances association studies of autism. - Lukas Buschmann, Sarah Naomi Bolz, Ferras el-Hendi, Negin Malekian, Michael Schroeder:
Much ado about nothing: modeling amino acid replacement with predicted protein structures. - Jingli Zhou, Siyuan Li, Rui Han, Xuan Wang, Yadong Wang, Junyi Li:
GR2ST: spatial transcriptomics prediction based on graph-enhanced multimodal contrastive learning. - Kewei Zhou, Kai Xu, Shaolong Lin, Silong Zhai, Huanxiang Liu, Xiaojun Yao:
Supervised fine-tuning enhances unsupervised learning from 45 million amino acids in TCR and peptide sequences. - Masoud Amiri, Zahra Nasirinia:
HybridMolGen: a unified framework for goal-directed molecular generation via multi-objective reinforcement learning. - Luís L. Marques, Armando J. Pinho, Diogo Pratas:
FALCON2: compression-based metagenomic classification of ancient viruses. - Ugo Lomoio, Pietro Lió, Pietro Hiram Guzzi, Pierangelo Veltri:
Bidirectional Mamba-2 boosts EEG super-resolution via regression and diffusion. - Mateo Gray, Sebastian Will, Hosna Jabbari:
Spark: sparse hierarchical energy minimization for scalable prediction of RNA pseudoknots. - Lukas Burk, John Zobolas, Bernd Bischl, Andreas Bender, Marvin N. Wright, Raphael Sonabend:
A large-scale neutral comparison study of survival models on low-dimensional data. - Yifan Dou, Adam Khadre, Ruben C. Petreaca, Golrokh Mirzaei:
MS-ConTab: multi-scale contrastive learning of mutation signatures for Pan-Cancer representation and stratification. - Basharat Ahmad, Muhammad Hammad Musaddiq, Sebu Aboma Temesgen, Bakanina Kissanga Grace-Mercure, Huma Fida, Hao Lin, Ye-Chen Qi:
HybridGNN: a graph neural network approach for human miRNA-disease association prediction. - Barthélémy Caron, Antonio Rausell:
NCBoost v2: a classifier for non-coding single-nucleotide variants in Mendelian diseases. - Zhenxian Zheng, Minggao He, Xian Yu, Junzhe Li, Lei Chen, Angel On Ki Wong, Jingcheng Zhang, Yekai Zhou, Ruibang Luo:
Accelerated long-read variant calling with Clair3 for whole-genome sequencing. - Leonardo V. Castorina, Christopher W. Wood, Kartic Subr:
From atoms to fragments: a coarse representation for efficient and functional protein design. - Hayden C. Metsky, Katherine J. Siddle, Christian B. Matranga, Pardis C. Sabeti:
Best practices when benchmarking CATCH for the design of genome enrichment probes. - Maryam Astero, Anchen Li, Elena Casiraghi, Juho Rousu:
A cross-attentive multi-task graph learning framework for chemical reaction modeling. - Weizhuang Zhou, Chao Jin, Zexi Yao, Meenatchi Sundaram Muthu Selva Annamalai, Yu En Chan, Sreejith Kumar Ashish Jith, Xiaoxia Deng, Chan Fook Mun, Kok Leong Foong, Rayden Chua Ming Hong, Kok Wai Wong, Roger Foo Sik Yin, Carolyn S. P. Lam, Arthur Mark Richards, Weng Khong Lim, Jonathan Yap, Khung Keong Yeo, Boon Ooi Patrick Tan, Neerja Karnani, Pavitra Krishnaswamy, Sebastian Maurer-Stroh, Khin Mi Mi Aung:
Secure bioinformatics: privacy-preserving federated analytics using homomorphic encryption. - Sinan Ozbay, Aditya Parekh, Rohit Singh:
Local transcriptional covariation produces accurate estimates of cell phenotype. - Criseida G. Zamora-Chimal, Alexander P. S. Darlington:
HySimODE: a hybrid stochastic-deterministic simulation framework for multiscale models of biological systems. - I. A. Dyugay, Aleksandr Poslavsky, Daniil K. Lukyanov, F. M. Polyakov, E. Nikitin, E. Klimuk, A. Dakhnovets, Denis Syrko, Victor V. Kotliar, Dmitry M. Chudakov:
Nested co-expression network analysis identifies compact gene clusters in a black box. - Konstantinos Lazaros, Souzana Logotheti, Christopher Logothetis, Vasiliki Tzelepi, Panagiotis Vlamos, Aristidis G. Vrahatis:
CpGene: a web application for epigenetic signature identification from DNA methylation arrays. - Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin:
Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research. - Yuan Gao, Dongze He, Rob Patro:
QCatch: a framework for quality control assessment and analysis of single-cell sequencing data. - Emmanuel Sapin, Kristen M. Kelly, Matthew C. Keller:
A novel method for across-chromosome phasing without relative data. - Jessica I Murphy, Ryan Barnard, Megan Null, Audrey E. Hendricks:
RAREsim2: flexible simulation of rare variant genetic data using real haplotypes. - Correction to: Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker.
- Shuting Jin, Anqi Huang, Yajie Meng, Zhonghang Zhu, Yinghui Jiang, Junlin Xu, Xiangxiang Zeng:
Learning drug synergy through environment-conditioned feature modulation. - Xu Sun, Xiaoying Liu, Juanjuan Huang, Jiageng Wu, Yuchen Sun, Jiwei Jia:
TSEDTA: a transformer-based neural network with SMILES transformer and ESM2 embeddings for drug-target binding affinity prediction. - Matthijs Brouwer, Jens Bauernfeind, Gouripriya Davuluri, Jorge García Brizuela, Patrick König, Suman Kumar, Matthias Lange, Stephan Weise, Erik Wijnker, Cyril Pommier, Joseph Ruff, Paul J. Kersey:
Integrating plant phenotypic and genotypic data in the AGENT project: a BrAPI service implementation. - Jean-Loup Faulon, Danilo Dursoniah, Paul Ahavi, Antoine Raynal, Enrique Asin-Garcia:
dAMN: a genome-scale neural-mechanistic hybrid model to predict bacterial growth dynamics. - Asmita Roy, Jiuyao Lu, Glen A. Satten, Ni Zhao:
DTH : a nonparametric test for homogeneity of multivariate dispersions. - Wenjian Xu, Yansheng Shen, Xiangfu Liu, Fei Leng, Yang Liu:
AXOLOTL: an accurate method for detecting aberrant gene expression in rare diseases using coexpression constraints. - Nicolas Perrin-Gilbert, Nisma Amjad, Pierre Fumeron, Silvia Tulli, Joshua J. Waterfall:
Yomix: an interactive tool for the exploration of low-dimensional embeddings in omics data. - Markus Lindén, Sebastian I Zúñiga Norman, Tommi Välikangas, Sini Junttila, Tomi Suomi, Kalle T. Rytkönen, Laura L. Elo:
REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research. - Yin Fang, Qiao Jin, Guangzhi Xiong, Bowen Jin, Xianrui Zhong, Siru Ouyang, Yifan Yang, Aidong Zhang, Jiawei Han, Zhiyong Lu:
Cell-o1 : training LLMs to solve single-cell reasoning puzzles with reinforcement learning. - Andrei Preoteasa, Andreas Grigorjew, Alexandru I. Tomescu, Hajk-Georg Drost:
EMERALD-UI: an interactive web application to unveil novel protein biology hidden in the alternative alignment space. - Chenqi Liao, Rui Dou, Danyang Sun, Chengxiu Hu, Hui Hu, Long Cheng, Yuzhong Xu, Xiong Wang:
CancerOmicsStudio (CoS): a web server for integrative and interpretable analysis of multi-omics cancer data. - Kuanghao Wang, Hong Shi:
PyFgsea: a Rust-powered, fgseaMultilevel-aligned GSEA framework with rolling-window enrichment along single-cell trajectories. - Baptiste Hennecart, Eugeni Belda, Raynald de Lahondès, Jean-Daniel Zucker, Edi Prifti:
StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution. - Jin-Xian Hu, Xiaoyong Pan, Ye Yuan, Hong-Bin Shen:
Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder. - Debolina Chatterjee, Justin L. Couetil, Ziyu Liu, Kun Huang, Chao Chen, Jie Zhang, Michael A Kalwat, Travis S. Johnson:
Identification of high-risk cells in single-cell spatially resolved transcriptomics data using Diagnostic Evidence GAuge of Single-cells with spatial smoothing. - Alfred Ferrer Florensa, José Juan Almagro Armenteros, Rolf S. Kaas, Philip Thomas Lanken Conradsen Clausen, Henrik Nielsen, Burkhard Rost, Frank Møller Aarestrup:
Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2. - Heewon Park, Seiya Imoto, Satoru Miyano:
MetaCCI: meta cell-cell interaction inference and its application to CCIs characteristics of MDS. - Nirav N. Shah, Taotao Tan, Jessica Honorato-Mauer, Yi-Sian Lin, Adam X. Maihofer, Clement C. Zai, Elizabeth G. Atkinson, Marcos Santoro, Caroline Nievergelt, Adam Maihofer, Nirav Shah, Clement Zai, M. du Plessis, Jessica Honorato Mauer, Shareefa Dalvie, Estela Bruxel, S. Hemmings, Liriel Almodobar, Caroline M. Nievergelt:
Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies. - Luka Maisuradze, Mark D. Shattuck, Corey S. O'Hern:
SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators. - Rick Beeloo, Ragnar Groot Koerkamp:
Sassy: fuzzy searching DNA sequences using SIMD. - Mickaël Mendez, Yushan Liu, Marc Asenjo Ponce de León, Michael M. Hoffman:
Segzoo: a turnkey system that summarizes genome annotations. - Dan Kalifa, Eric Horvitz, Kira Radinsky:
Learning protein representations with conformational dynamics. - Haimei Wen, Leonidas Bleris, Tian Hong:
EMTscore infers divergent EMT pathways from omics data and enables rapid screening for EMT-associated gene sets. - Hayden Farquhar:
Protein language model embeddings improve HIV drug resistance prediction: a comprehensive benchmark with attention-based interpretability. - Adam B. Rohrlach, Jonathan Tuke, Kay Prüfer, Wolfgang Haak:
ChASM: a statistically rigorous method for the detection of chromosomal aneuploidies in ancient DNA studies. - Andrew Jordan Siciliano, Yifan Bao, Bishal Shrestha, Zheng Wang:
Inferring the qualities of protein-RNA models with graph transformers. - Yebin Ryu, Ha-Eun Jeong, Joon-Yong An:
IDAP: an integrated literature- and knowledge-graph-driven evidence prioritization pipeline for precision oncology. - Huaiwu Zhang, Xinliang Sun, Jianxin Wang, Min Li, Jing Tang:
A causal inference framework for identifying essential genes to enhance drug synergy prediction. - Carolina Lascelles, Morag Raynor, Laura A. Crinnion, Ailsa M. S. Rose, Christine P. Diggle, James A Poulter, Christopher M. Watson, Ian M. Carr:
Utilization of long-read sequencing for the detection of structural rearrangements with AgileStructure. - Haotian Zhuang, Xin Gai, Anru R. Zhang, Wenpin Hou, Zhicheng Ji, Pixu Shi:
Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity. - Jianting Gong, Pengjia Ma, Zilin Ren, Si Li, Zhiguo Fu, Pingping Sun, Ming Ni, Xiaochen Bo:
MuFaDDG: a sequence-based multiscale feature fusion framework for protein stability changes prediction. - Jingqing Hu, Qian Qin, Heng Li, Ying Zhou:
FuFiHLA: a tool for full-field HLA typing from long-read data.
Volume 42, Number 6, 2026
- Zhongyu He, Xiangrong Liu, Yinghui Jiang, Junlin Xu, Yuan Lin, Shuting Jin, Leyi Wei, Youyu Wang:
HKD-CPI: high-order knowledge distillation enhanced inductive compound-protein interaction prediction. - Shiyi Du, Litian Liang, Jiayi Li, Carl Kingsford:
CodonMoE: DNA language models for codon-dependent mRNA prediction. - Bo Wang, Muna Al-Jabri, Udayaraja Gk, Alastair P. Droop, Lucy F. Stead:
ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data. - Bin Yang, Yujie You, Liang Jin, Hongyang Yu, Le Zhang:
CryoPromptSeg: prompt-guided segmentation with integrated denoising for cryo-EM particle picking. - Marta Portasany-Rodríguez, Gonzalo Soria-Alcaide, Elena G. Sánchez, Mariya Ivanova, Ana Gómez, Reyes Giménez, Jaanam Lalchandani, Gonzalo García-Aguilera, Silvia Alemán-Arteaga, Cristina Saiz-Ladera, Manuel Ramirez-Orellana, Jorge Garcia-Martinez:
PULPO: pipeline of understanding large-scale patterns of oncogenomic signatures. - Maryam Haghani, Debswapna Bhattacharya, T. M. Murali:
NEFFy: a versatile tool for computing the number of effective sequences. - Fernando Zhapa-Camacho, Robert Hoehndorf:
INDIGENA: inductive prediction of disease-gene associations using phenotype ontologies. - Abbi Abdel-Rehim, Emma Tate, Larisa N. Soldatova, Ross D. King:
Drug response profile-based machine learning enables strategic cell line and compound selection for drug development. - Sebastian Beier, Anthony M. Bolger, Marie E. Bolger, Rainer Schwacke, Björn Usadel:
Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing. - Wei Zhu, Meredith Yeager, Eric T. Dawson, Komal Jain, Belynda Hicks, Michael Dean, Stephen J. Chanock, Wendy S. W. Wong:
TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent-child trios. - Chenyun Yu, Zihe Xu, Qiong Zeng, Xiaohua Wan, Haythem El-Messiry, Fa Zhang, Renmin Han:
A variational framework with composite sparse regularization for cryo-electron tomography reconstruction. - Chen Peng, Liuyiqi Jiang, Zinuo Huang, Xin Wei, Xiaoping Zhu, Zhen Liu, Qiong Chen, Xiaotao Shen, Peng Gao, Chao Jiang:
MetaNet: a scalable and integrated tool for reproducible omics network analysis. - Quan Zhao, Jiawen Du, Muqing Zhou, Xu-Wen Wang, Quan Sun, Can Chen:
PEARL: integrative multi-omics classification and omics feature discovery via deep graph learning. - Arsham Mikaeili Namini, Ali Saberi, Hamed S. Najafabadi:
Atlas-level single-cell integration and clustering-free differential expression analysis with GEDI 2.0. - Yaowei Jin, Junjie Wang, Yufan Tang, Wenkai Xiang, Duanhua Cao, Dan Teng, Zhehuan Fan, Jiacheng Xiong, Xia Sheng, Chuanlong Zeng, Duo An, Mingyue Zheng, Shuangjia Zheng, Qian Shi:
MolPIF: a parameter interpolation flow model for molecule generation. - Ziqi Zhang, Jongseok Han, Le Song, Xiuwei Zhang:
CeSpGRN: inferring cell-specific gene regulatory networks from single-cell multi-omics and spatial data. - Navya Shukla, Irene Gallego Romero:
Lift&Add - rapid and robust addition of new species to alignments of conserved non-coding sequences. - Nathan Kolbow, Sungsik Kong, Tyler Chafin, Joshua Justison, Cécile Ané, Claudia R. Solís-Lemus:
SNaQ.jl: Improved scalability for level-1 phylogenetic network inference. - Sylvain Mareschal, Valentin Wucher, Sarah Huet, Camille Léonce, Kaddour Chabane, Sandrine Hayette, Pierre-Paul Bringuier, Stéphane Pinson, Marc Barritault, Claire Bardel:
Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline. - Zhenbang Zhang, Jingtong Feng, Hongjia Li, Haythem El-Messiry, Zhiqiang Xu, Renmin Han:
3D registration-guided deformable residual inpainting for ssEM restoration. - Zhilin Huang, Ling Yang, Chujun Qin, Yifei Xing, Hongyang Yu, Xiangxin Zhou, Bing Zheng, Yu Wang, Xin Gao, Wenming Yang:
Disentangled diffusion model for 3D molecular generation with protein-ligand interaction priors. - Hazem Sharaf, Louis-Marie Bobay:
MetaStrainer : accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples. - Sungwoo Goo, Soyoung Lee, Jung-woo Chae, Sangkeun Jung, Hwi-Yeol Yun:
Interpretable deep survival analysis of Alzheimer's disease via metabolic genetic variants. - Tomi Suomi, Jalmari Kettunen, Taneli Pusa, Laura L. Elo:
Clarifying the scope and capabilities of ROTS in differential expression analysis. - Kostiantyn Dreval, Laura K. Hilton, Bruno M. Grande, Giuliano Banco, Krysta M. Coyle, Manuela Cruz, Sierra Gillis, Luke Klossok, Prasath Pararajalingam, Christopher K. Rushton, Haya Shaalan, Nicole Thomas, Helena Winata, Jasper Wong, Jacky Yiu, Christian Steidl, David W. Scott, Ryan D. Morin:
LCR-modules: a collection of workflows for cancer genome analysis. - Marcello Barylli, Joyaditya Saha, Tineke E. Buffart, Jan Koster, Kristiaan J. Lenos, Louis Vermeulen, Roland V. Bumbuc, Vivek M. Sheraton:
Network methods for diagonal integration of unpaired single-cell multiomics data: a review. - Liraz Klausner, Ateret Revital, Todd Lencz, Shai Carmi:
PEStimate : predicting offspring disease risk after polygenic embryo screening. - Md Aynul Islam, M. D. Youshuf Khan Rakib, Zhangjin Huang, Xingfu Wang, Wenjie Du:
HyperSeg-DG: multi-scale hyper feature context for domain-generalized medical image segmentation. - Laura Rumpf, Fatemeh Behjati-Ardakani, Dennis Hecker, Marcel H. Schulz:
Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data. - Jonatan Menger, Sonia Maria Krissmer, Clemens Kreutz, Harald Binder, Maren Hackenberg:
mmContext: an open framework for multimodal contrastive learning of omics and text data. - Anthony Yazdani, Ihor Stepanov, Douglas Teodoro:
GLiNER-BioMed: a suite of efficient models for open biomedical named entity recognition. - Franjo Ivankovic, Dongmei Yu, James Shen, Lingyu Zhan, Maria Niarchou, Ariadne Kaylor, Laura Domènech, Tyne W. Miller-Fleming, Luz M. Porras, Paola Giusti-Rodríguez, Roel A Ophoff, Jeremiah M. Scharf, Carol A Mathews:
MarkerMatch: a proximity-based probe-matching algorithm for joint analysis of copy-number variants from different genotyping arrays. - Hung Pham, Adam P. Lombroso, Esma Cansu Cevik, Hugh S. Taylor, Kieran J. O'Donnell:
slideimp: efficient imputation of DNA methylation data. - Yueshan Huang, Gufeng Yu, Letian Chen, Haoyang Luan, Yang Yang:
EPIC: multi-objective guided diffusion for epitope design in TCR-pMHC complexes. - Ran Song, Yinpu Bai, Xuejun Liu, Hui Liu:
FourierDrug: a domain generalization framework for robust drug response prediction via frequency-space asymmetric attention. - Zhichao Xiao, Haibo Ji, Quan Zou, Yijie Ding, Liang Yu:
Predicting enhancer-promoter interactions using a stacking-based ensemble strategy. - Heming Zhang, Shunning Liang, Tim Xu, Wenyu Li, Di Huang, Yuhan Dong, Guangfu Li, Philip Miller, S. Peter Goedegebuure, Marco Sardiello, Jonathan Cooper, William Buchser, Patricia Dickson, Ryan C. Fields, Carlos Cruchaga, Yixin Chen, Michael A. Province, Philip R. O. Payne, Fuhai Li:
BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation. - Haim Krupkin, Evin M. Padhi, Daniel Nachun, Jessica Kain, Jonathan Z. Long, Stephen B. Montgomery:
Genomics-informed approach identifies which cell types regulate the metabolome. - Yesol Park, Gyujin Son, Taeuk Kim, Mina Rho:
DA-BioNER: data augmentation based on few-shot learning and distant supervision for biomedical named entity recognition. - Chuyao Wang, Tongdong Zhang, Hang Sun, Zhipeng Wu, Shuo Liang, Xueting Wang, Meirong Du, Yanchun Liang, Xin Gao, Qi Tang, Dong Xu, Xiaoyue Feng, An Zeng, Renchu Guan:
A masked generative graph representation learning framework empowering precise spatial domain identification. - Tian Zhang, Zhe Liu, Yiqing Ma, Chenjie Feng, Renmin Han:
Benchmarking deep learning methods for C α atom prediction in cryo-EM density maps. - Takumi Otagaki, Hiroaki Hosokawa, Tsukasa Fukunaga, Junichi Iwakiri, Goro Terai, Kiyoshi Asai:
LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits. - Gregory J. Bedwell, Peter Cherepanov, Alan N. Engelman:
intmap: fast and flexible mapping of mobile DNA integration for basic and translational research. - Laurence H. Pearl, Frances M. G. Pearl:
Using cancer profiles to identify synthetic lethal therapeutic targets and predictive biomarkers in cancer gene dependency data. - Andreas A. Sparre, Ole N. Jensen:
Batch correction for large-scale mass spectrometry imaging experiments. - Stanislav Listopad, Gauri Renjith, Qian Peng:
Evaluation of epistasis detection methods for quantitative phenotypes. - Frimpong Boadu, Yanli Wang, Jianlin Cheng:
A unified multimodal model for generalizable zero-shot and supervised protein function prediction. - Shucheng Si, Xiaoxiao Wang, Siyan Zhan:
Integrated multi-omics strategies for identifying novel therapies in psoriasis. - Darshan Mandge, Anil Tuncel, Aurélien Jaquier, Ilkan Kiliç, Tanguy Damart, Henry Markram, Werner Van Geit, Rajnish Ranjan:
eFEL: electrophysiology feature extraction library. - Adrien Rougny, Marek Ostaszewski, Venkata Sagatopam:
momapy: a Python library to work with molecular maps. - Haixing Piao, Veda Sheersh Boorla, Somtirtha Santra, Costas D. Maranas:
BindPred: a framework for predicting protein-protein binding affinity from language model embeddings. - Anthony Fullam, P. K. Vishnu Prasoodanan, Michael Kuhn, Peer Bork, Thomas S. B. Schmidt:
microntology : a lightweight, data-driven controlled vocabulary to describe earth's microbial habitats.
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