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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 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, Ting-Fang 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.
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