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ORCIDBMC Bioinformatics, Volume 27
Volume 27, Number 1, December 2026
- Alexandre Chaussard
, Anna Bonnet, Sylvain Le Corff, Harry Sokol:
TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata. 1 - Grigoriy Gogoshin, Andrei S. Rodin:
Correction: Minimum uncertainty as Bayesian network model selection principle. 2 - Jiadong Chu, Yu Wang, Na Sun, Qiang Han, Ziqing Sun, Mengtong Sun, Yuheng Yuan, Qida He, Yueping Shen:
A parametric survival model with bayesian structural equation based on multi-omics integration. 3 - Ramu Gautam, Yang Jiao, Yasong Pang, Mo Weng, Mei Yang:
ProTrack3D: a comprehensive tool for segmentation and tracking of proteins with split and fusion. 4 - Tazin Rahman, Ananth Kalyanaraman:
Density-reducing Jaccard estimators for sketch-based long read applications. 5 - Laura Aviñó-Esteban, Heura Cardona-Blaya, Marco Musy, Antoni Matyjaszkiewicz, James Sharpe, Giovanni Dalmasso:
Limblab: pipeline for 3D analysis and visualisation of limb bud gene expression. 6 - Binbin Wu, William W. Ja:
easyClock: a user-friendly desktop application for circadian rhythm analysis and visualization. 7 - Yaxin Fan, Yichao Mei, Shengbao Bao, Jianyong Wang, Junxiang Gao:
A DSSM network for inferring and prioritizing cell-type-specific regulons using single-cell RNA-seq data. 8 - Chun Hing She, Sophelia Hoi-Shan Chan, Wanling Yang:
SVhet: towards accurate detection of germline heterozygous deletions using short reads. 9 - Martin Engst, Martin Brokes, Tereza Calounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, Ratthachat Chatpatanasiri, Adéla Tajovská, Safa Mert Akmese, Milana Perkovic, Matous Soldát, Josef Sivic, Tomás Pluskal:
MARTS-DB: a database of mechanisms and reactions of terpene synthases. 10 - Amr Mohamed, Kevin H. Lee:
Gradient boosting with knockoff filters: a biostatistical approach to variable selection. 13 - Annekathrin Silvia Nedwed, Arsenij Ustjanzew, Najla Abassi, Leon Dammer, Alicia Schulze, Sara Salome Helbich, Michael Delacher, Konstantin Strauch, Federico Marini:
GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor. 14 - Jacob Pfeil, Liqian Ma, Hin Ching Lo, Tolga Turan, R. Tyler McLaughlin, Xu Shi, Severiano Villarruel, Stephen Wilson, Xi Zhao, Josue Samayoa, Kyle Halliwill:
Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients. 15 - Jack Freeman, Robert J. Millikin, Leo Xu, Ishaan Sharma, Bethany Moore, Cannon Lock, Kevin Shine George, Aviral Bal, Chitrasen Mohanty, Ron M. Stewart:
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation. 16 - Violeta de Anca Prado, Fábio Pértille, Pedro Sá, Marta Gòdia, Joëlle Rüegg, Josep C. Jimenez-Chillaron, Carlos Guerrero-Bosagna:
Benchmarking of methods to analyse data derived from GBS-MeDIP. 17 - Istvan Szepesi-Nagy, Roberta Borosta, Zoltan Szabo, Gabor E. Tusnady, Lorinc S. Pongor, Gergely Rona:
Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments. 18 - Md. Masud Rana, Farjana Tasnim Mukta, Duc Duy Nguyen:
A geometric graph-based deep learning model for drug-target affinity prediction. 19 - Benjamin Lieser, Georgy Belousov, Johannes Söding:
Phylograd: fast column-specific calculation of substitution model gradients. 20 - Szabolcs Makai, Diána Makai, Erika Chonata-Jiménez, Ildikó Karsai, Péter Mikó, Adél Sepsi, András Cseh:
X-cross/over: a web tool for graph-based estimation of meiotic crossover events in plants. 21 - Chiara Schiller, Matthias Lemmer, Sonja Reitter, Janina A. Lehmann, Kai Fenzl, Johanna Schott:
QuAPPro: an R shiny app for quantification and alignment of polysome profiles. 22 - Jiaye Li, Zijian Sun, Shuo Chai, Hangming Li, Yijun Wang, Jingkui Tian:
AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification. 23 - Naafey Aamer, Muhammad Nabeel Asim, Andreas Dengel:
Comic: explainable drug repurposing via contrastive masking for interpretable connections. 24 - Fang Liu, Rui He, Tommy R. Sheeley, David A. Scheiblin, Stephen J. Lockett, Lisa A. Ridnour, David A. Wink, Mark Jensen, Janelle Cortner, George Zaki:
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis. 25 - He Li, Zander Gu, Said el Bouhaddani, Jeanine J. Houwing-Duistermaat:
Statistical modelling of an outcome variable with integrated multi-omics. 26 - Jinxin Li, Xinguo Lu, Zihao Li, Xing Liu, Hongrui Liu, Jingjing Ruan:
MGANSL: multi-network representation generating with generative adversarial network for synthetic lethality prediction. 27 - Lucas F. Jansen Klomp, Xinqi Yan, Rebecca R. Snabel, Gert Jan C. Veenstra, Hil G. E. Meijer, Janine N. Post:
DANSE: a pipeline for dynamic modelling of time-series multi-omics data. 28 - Tristan Cumer, Sotiria Milia, Alexander S. Leonard, Hubert Pausch:
PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers. 29 - Daniel Zyss, Amritansh Sharma, Susana A. Ribeiro, Claire E. Repellin, Oliver Lai, Mary J. C. Ludlam, Thomas Walter, Amin Fehri:
Contrastive learning for cell division detection and tracking in live cell imaging data. 30 - Xiao Han, Xiaochen Cen, Zhijin Li, Xiaobo Zhou, Zhiwei Ji:
DCPR: a deep learning framework for circadian phase reconstruction. 31 - Lei Chen, Jing Yang, Bo Zhou, Yu-Dong Cai:
PLysPTM-HGNN: predicting lysine PTM sites of proteins using hybrid graph neural networks. 32 - Sicheng He, Cheng Chen, Xianrun Pan, Gaogao Xue, Yu Yang, Juan Feng, Hasan Zulfiqar, Yang Zhang, Kejun Deng:
CMsiRNAdb: a database of chemically modified SiRNA silencing efficiency for nucleic acid drug design. 33 - Ponian Li, Guodong Xiao, Haihui Wang, Chunrui Xu, Yusen Zhang:
MODCAN: driver gene identification based on multi-omics features and differential co-association networks for tumor subtypes. 34 - Xiaowen Wang, Yanming Huang, Hongming Zhu, Dongsheng Mao, Xiaoli Zhu, Qin Liu:
Hgtsynergy: a transfer learning method for predicting anticancer synergistic drug combinations based on a drug-drug interaction heterogeneous graph. 35 - Erik D. Huckvale, Hunter N. B. Moseley:
Predicting the pathway involvement of metabolites annotated in the MetaCyc knowledgebase. 36 - David H. Rogers, Cullen Roth, Cameron Tauxe, Jeannie T. Lee, Christina R. Steadman, Karissa Y. Sanbonmatsu, Anna Lappala, Shawn R. Starkenburg:
From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture. 37 - Ivan Ferrari, Mattia Battistella, Francesca Vincenti, Andrea Gobbini, Federico Marini, Samuele Notarbartolo, Jole Costanza, Stefano Biffo, Renata M. Grifantini, Sergio Abrignani, Eugenia Galeota:
CIA: unveiling cellular identities with cluster-independent annotation in single-cell RNA sequencing data for comprehensive cell type characterization and exploration. 38 - Grazia Gargano, Flavia Esposito, Nicoletta Del Buono, Sabino Ciavarella, Maria Carmela Vegliante:
Identification of differentially expressed genes in RNA-seq data via semi-rigid orthogonal sparse KL-NMTF. 39 - Saman Zabihi, Sattar Hashemi, Eghbal Mansoori:
EDEN: multiscale expected density of nucleotide encoding for enhanced DNA sequence classification with hybrid deep learning. 40 - Nabil Rahiman, Michael A. Ochsenkühn, Shady A. Amin, Kristin C. Gunsalus:
MIMI: Molecular Isotope Mass Identifier for stable isotope-labeled Fourier transform ultra-high mass resolution data analysis. 41 - Mehmet Ali Balikci, Cyrille Mesue Njume, Ali Cakmak:
BioMark: biomarker analysis tool. 42 - Gilles Sireta, Gwendal Cueff, Vincent Darbot, Marie Lefebvre, Simon Amiard, Aline V. Probst, Christophe Tatout:
CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool. 43 - Sebastian Raubach, Miriam Schreiber, Ruth Hamilton, Gaynor McKenzie, Susan McCallum, Benjamin Kilian, Alan Humphries, Loi Huu Nguyen, Tin Huynh Quang, Akanksha Singh, Shivali Sharma, Sarah Trinder, Manuel Feser, Paul D. Shaw:
Beyond the clipboard: data collection with GridScore NEXT. 44 - Hyotae Kim, Nazema Y. Siddiqui, Lisa Karstens, Li Ma:
A negative binomial latent factor model for paired microbiome sequencing data. 45 - Artem Ershov, Renpeng Ding, Qian Fu, Ivan Kozlov, Ekaterina Fadeeva, Evgeniy Mozheiko, Ming Ni, Yong Hou, Yan Zhou:
zDUR: reference-free FASTQ compressor with high compression ratio and speed. 46 - Simone Montalbano, G. Bragi Walters, Gudbjorn F. Jonsson, Jesper R. Gådin, Thomas Werge, Daniel Fannar Gudbjartsson, Hreinn Stefansson, Andrés Ingason:
CNValidatron: accurate and efficient validation of PennCNV calls using computer vision. 47 - Blaz Brence, Josephine Brummer, Vincent J. Dercksen, Mehmet Neset Özel, Abhishek Kulkarni, Neele Wolterhoff, Steffen Prohaska, Peter Robin Hiesinger, Daniel Baum:
Semi-automatic geometrical reconstruction and analysis of filopodia dynamics in 4D two-photon microscopy images. 48 - Hamdiye Uzuner, Felix Wiegand, Sven Schrinner, David Laehnemann, Dirk Schadendorf, Johannes Köster:
Virus variant quantification with Orthanq. 49 - Abdulraheem Arome Musa, Norbert Reinsch:
PyMSQ: a Python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection. 50 - Charlie Bayne, Brianna Hurysz, David J. Gonzalez, Anthony O'Donoghue:
mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry. 51 - Thi Van Nguyen, Van Hoan Do, Vu-Linh Nguyen:
Srnc: semi-supervised learning for robust novel cell-type identification in single cell RNA sequencing data. 52 - Scott Silvey, Amy Olex, Shaojun Tang, Jinze Liu:
Sample size requirements for machine learning classification of binary outcomes in bulk RNA-Seq data. 53 - Dominik Robak, Guillem Ylla:
piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs. 54 - Yongqing Zhang, Le Chen, Hong Luo, Tianhao Li, Shuwen Xiong, Zixuan Wang, Quan Zou, Wenqian Zhang:
Contrastive learning in both structure and function spaces improve drug-target interaction prediction. 55 - Simo Iisakki Inkala, Michele Fratello, Giusy del Giudice, Giorgia Migliaccio, Angela Serra, Dario Greco, Antonio Federico:
MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration. 56 - John Stephen Malamon:
DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants. 57 - Guojing Cong, Robert M. Patton, Frank Chao, Daniel L. Svoboda, Jeremy N. Erickson, Michele R. Balik-Meisner, Deepak Mav, Dhiral P. Phadke, Elizabeth H. Scholl, Ruchir R. Shah, Scott S. Auerbach:
Transplatformer: translating toxicogenomic profiles between generations of platforms. 58 - Samuel Hamilton, Gaurav Gadhvi, Tyler Therron, Deborah R. Winter:
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples. 59 - Niccolò Bianchi, Armel E. J. L. Lefebvre, Katherine J. Wolstencroft, Marco Spruit:
Design and evaluation of semantically-valid negative samples integration techniques for scalable semi-automated drug repurposing prediction pipelines in rare disease research. 60 - Muhaiminur Hossain, Anik Mojumder, S. M. Mahbubur Rashid, Abul Bashar Mir Md Khademul Islam:
ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species. 61 - Yi Zhao, Xuteng Ye, Jun Cheng, Li Yin, Danyu Shen, Daolong Dou, Jinding Liu:
YamOmics: a comprehensive data resource on yam multi-omics. 62 - Xuan Wang, Zhengao Mo, Fuwei Li, Fa Zhang, Xiaohua Wan:
Point cloud deformation modeling for particle selection following cryo-EM 2D classification. 63 - Gabriel Victor Pina Rodrigues, Lucas Yago Melo Ferreira, Eric Roberto Guimarães Rocha Aguiar:
ViralQuest: a user-friendly interactive pipeline for viral-sequences analysis and curation. 64 - Daehee Kim, Seongjun Byun, Jaehyun Park, Soo-Jin Jang, Yongku Kim, Seung Yeop Yang, Myungjin Kim, Semin Oh, Jieun Lee, Kee-Beom Kim, Dong Kyu Choi, Samuel Beck, Jun-Yeong Lee:
hStouffer: the enhanced meta-analysis method for the comprehensive analysis of large-scale RNA-seq data. 65 - Zeyu Chen, Yuqi Liu, Jia Meng, Jiaming Huang, Xuan Wang, Xiangyu Yin, Wei Zhong, Gang Tu, Yongshuang Xiao:
Domain-derived knowledge enabled machine learning and functional characterization of cancer-associated RNA methylation sites. 66 - Evelin Aasna, Simon Gottlieb, Marcel Ehrhardt, Knut Reinert:
DREAM-Stellar: parallel and space efficient exact local alignment. 67 - Ugochukwu O. Ugwu, Richard A. Slayden, Michael Kirby:
Transfer learning models for bacterial strain dissemination biomarkers using weighted non-parallel proximal support vector machines. 68 - Soumya Nayak, Dheemanth Reddy Regati, Murugavel Pavalam, Ramanathan Sowdhamini:
Cascade PSI-BLAST 2.0: a fast-searching parallelized remote homology detection tool and development of Cascade web server 2.0. 69 - Rui Geng, Benjamin L. Kidder:
ColonyQuant: automated quantification and morphometric analysis of pluripotent stem cell colonies. 70 - Awais Qureshi, Abdul Wahid, Shams Qazi, Muhammad K. Shahzad, Hashir Moheed Kiani, Muhammad Daud Abdullah Asif:
DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models. 71 - Nesma Lotfy:
Transformation to estimate the causal effect in Mendelian randomization study with binary risk factor and outcome. 72
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