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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.
Volume 42, Number 2, 2026
- 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.
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