default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBioinformatics, Volume 41
Volume 41, Number 1, 2025
- Daniel Mechtersheimer
, Wenze Ding, Xiangnan Xu, Sanghyun Kim, Carolyn Sue, Yue Cao, Jean Y. H. Yang:
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits.
Volume 41, Number 3, 2025
- Rawan Shraim, Brian Mooney, Karina L. Conkrite, Amber K. Hamilton, Gregg B. Morin, Poul H. Sorensen, John M. Maris, Sharon J. Diskin, Ahmet Sacan:
ImmunoTar - integrative prioritization of cell surface targets for cancer immunotherapy.
Volume 41, Number 4, 2025
- Zhuoyu Wei, Yongqi Shen, Xiang Tang, Jian Wen, Youyi Song, Mingqiang Wei, Jing Cheng, Xiaolei Zhu:
AVPpred-BWR: antiviral peptides prediction via biological words representation.
Volume 41, Number 7, 2025
- Sicen Liu, Shutao Chen, Tao Bai, Bin Liu:
FusionEncoder: identification of intrinsically disordered regions based on multi-feature fusion. - Meiling Liu, Shuangshuang Wang, Zeyu Luo, Guohua Wang, Yuming Zhao:
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction.
Volume 41, Number 9, 2025
- Asato Yoshinaga, Osamu Maruyama:
CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning. - Tianci Wang, Xin Lai, Shenjie Wang, Yuqian Liu, Xiaoyan Zhu, Jiayin Wang:
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples. - Tong Wang, Zhi-Ping Liu:
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection. - Helena García-Cebollada, Alfonso López, Vladimir Espinosa Angarica, Juan José Galano-Frutos, Javier Sancho:
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins. - Carl M. Kobel, Velma T. E. Aho, Ove Øyås, Niels Nørskov-Lauritsen, Ben J. Woodcroft, Phillip B. Pope:
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. - Shuang Wang, Tianle Ma, Kaiyu Dong, Peifu Han, Xue Li, Junteng Ma, Mao Li, Tao Song:
MVSO-PPIS: a structured objective learning model for protein-protein interaction sites prediction via multi-view graph information integration. - Joseph L. Hellerstein, Lucian P. Smith, Lillian T. Tatka, Steven S. Andrews, Michael A Kochen, Herbert M. Sauro:
Discovering subnetworks in SBML models. - Ryan R. Wick, Benjamin P. Howden, Timothy P. Stinear:
Autocycler: long-read consensus assembly for bacterial genomes. - Johannes Hingerl, Alexander Karollus, Julien Gagneur:
Flashzoi: an enhanced Borzoi for accelerated genomic analysis. - Ke Yan, Shutao Chen, Bin Liu, Hao Wu:
Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework. - Xiang Liu, Yi-Han Tang, James Blachly, Stephen Edge, Yasminka A Jakubek, Martin McCarter, Abdul Rafeh Naqash, Kenneth G. Nepple, Afaf Osman, Matthew J. Reilley, Gregory Riedlinger, Bodour Salhia, Bryan P. Schneider, Craig Shriver, Michelle L. Churchman, Robert J. Rounbehler, Jamie K. Teer, Nancy Gillis, Mingxiang Teng:
qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics. - Sebastian Persson, Fabian Fröhlich, Stephan Grein, Torkel Loman, Damiano Ognissanti, Viktor Hasselgren, Jan Hasenauer, Marija Cvijovic:
PEtab.jl: advancing the efficiency and utility of dynamic modelling. - Seokjun On, Yujin Jeong, Eun-Sol Kim:
Structure-guided sequence representation learning for generalizable protein function prediction.
Volume 41, Number 10, 2025
- Armin Rauschenberger, Petr V. Nazarov, Enrico Glaab:
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation. - Marcos Lopez-De-Castro, Alberto García-Galindo, José González-Gomariz, Rubén Armañanzas:
Conformal inference for reliable single cell RNA-seq annotation. - Daniel Kim, Carissa Chen, Lijia Yu, Jean Yee Hwa Yang, Pengyi Yang:
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data. - Wouter Duverger, Georg Ramer, Nikolaos N. Louros, Joost Schymkowitz, Frederic Rousseau:
AXZ viewer: a web application to visualize unprocessed AFM-IR data. - L. Moritz Blumer, Jeffrey M. Good, Richard Durbin:
WinPCA: a package for windowed principal component analysis. - Chunfeng He, Yue Xu, Yuan Zhou, Jiayao Fan, Chunxiao Cheng, Ran Meng, Lang Wu, Ruiyuan Pan, Ravi V. Shah, Eric R. Gamazon, Dan Zhou:
Integrating population-level and cell-based signatures for drug repositioning. - Qicheng Zhao, Anji Deng, Qihuang Zhang:
DiSTect: a Bayesian model for disease-associated gene discovery and prediction in spatial transcriptomics. - Cem Ata Baykara, Ali Burak Ünal, Nico Pfeifer, Mete Akgün:
Privacy-preserving federated unsupervised domain adaptation with application to age prediction from DNA methylation data. - Austin M. Marcus, Jordan C. Rozum, Herbert Sizek, Luis M. Rocha:
CANA v1.0.0: efficient quantification of canalization in automata networks. - Shengli Zhang, Jingyi Ren, Yunyun Liang:
An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection. - Hongxin Xiang, Mingquan Liu, Linlin Hou, Shuting Jin, Jianmin Wang, Jun Xia, Wenjie Du, Sisi Yuan, Xiangzheng Fu, Xinyu Yang, Li Zeng, Lei Xu:
An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training. - Xinyu Zhou, Yi Yan, Kevin Hu, Haixu Tang, Yijie Wang, Lu Wang, Chi Zhang, Sha Cao:
Predicting the trend of SARS-CoV-2 mutation frequencies using historical data. - Elias Dohmen, Margaux Aubel, Lars A Eicholt, Paul Roginski, Victor Luria, Amir Karger, Anna Grandchamp:
DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation. - Güliz Akkaya, Nesli Erdogmus, Mete Akgün:
PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption. - Hung-Ching Chang, Yusi Fang, Michael T. Gorczyca, Kayhan Batmanghelich, George C. Tseng:
High-dimensional causal mediation analysis by partial sum statistic and sample splitting strategy in imaging genetics application. - Hukam C. Rawal, Qi Chen, Tong Zhou:
FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. - Trevor Schneggenburger, Jaroslaw Zola:
SKiM: accurately classifying metagenomic ONT reads in limited memory. - Daniel E. Schäffer, Samuel Sledzieski, Lenore Cowen, Bonnie Berger:
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT. - Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T. Reddy, Alexander Yermanos:
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests. - Cecilia B. Rodriguez, Ronaldo Romario Tunque Cahui, Nicolás Demitroff, Layla Hirsh, Damien P. Devos, Graciela Boccaccio, Gustavo D. Parisi:
BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins. - Evan Komp, Kristoffer E. Johansson, Nicholas Paul Gauthier, Japheth E. Gado, Kresten Lindorff-Larsen, Gregg T. Beckham:
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE. - Dickson Aruhomukama:
Balancing complexity and clarity - towards clinician-ready antibiotic resistance prediction models. - Jiaqing Xie, Yuqiang Li, Tianfan Fu:
DeepProtein: deep learning library and benchmark for protein sequence learning. - Yue Luo, Lei Deng:
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction. - Suleiman Aminu, Abdulaziz Ascandari, Rachid Benhida, Rachid Daoud:
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk. - Donn Liew, Akesha Dinuli Dharmatilleke, Edwin See, Ee Hou Yong:
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration. - Rok Kogoj, Mauro Petrillo, Samo Zakotnik, Alen Suljic, Misa Korva, Gabriele Leoni:
Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows. - Md Masud Rana, Md. Nurul Haque Mollah, Mohammed H. Albujja, Sibte Syed Hadi, Fan Liu:
ToxAssay: a hierarchical model-driven tool for advanced toxicogenomics biomarker discovery. - Michael L. Sierk, Daniel Danis, Sujay Patil, Nobal Kishor, Rajdeep Mondal, Abhishek Jha, Qingrong Chen, Chunhua Yan, Monica C. Munoz-Torres, Daoud M. Meerzaman, Peter N. Robinson, Justin T. Reese:
Oncopacket: integration of cancer research data using GA4GH phenopackets. - Alexandre Boulay, Emma Cremelie, Clovis Galiez, Yves Briers, Elsa Rousseau, Roberto Vázquez Fernández:
SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains. - Sunjae Lee, Jaebeom Kim, Milot Mirdita, Cameron L. M. Gilchrist, Martin Steinegger:
Easy and interactive taxonomic profiling with Metabuli App. - Melis Gencel, David Gagné-Leroux, Adrian W. R. Serohijos:
Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series. - Wenzhe Xu, Xiaorong Liu, Jie Wang, Fan Zhang, Dongfeng Hu, Liansong Zong:
UAMRL: multi-granularity uncertainty-aware multimodal representation learning for drug-target affinity prediction. - Nigreisy Montalvo, Francisco Requena, Emidio Capriotti, Antonio Rausell:
Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings. - Yurou Wang, Zhixiang Lin, Tao Wang:
InterVelo: a mutually enhancing model for estimating pseudotime and RNA velocity in multi-omic single-cell data. - Xiaoyi Liu, Na Zhang, Chenglong Kang, Chengwei Ai, Hongpeng Yang, Jijun Tang, Fei Guo:
HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning. - Thomas Minotto, Antoine Claessens, Thomas D. Otto:
Exploring homology detection via k-means clustering of proteins embedded with a large language model. - Saba Zerefa, Jesse Cool, Pramesh Singh, Samantha Petti:
An interpretable alphabet for local protein structure search based on amino acid neighborhoods. - Bokeum Cho, Seunggeun Lee:
PTL-PRS: an R package for transfer learning of polygenic risk scores with pseudovalidation. - Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T. Eadon, Qin Ma, Juexin Wang, Dong Xu:
scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data. - Alberto Cattaneo, Stephen Bonner, Thomas Martynec, Edward R. Morrissey, Carlo Luschi, Ian P. Barrett, Daniel Justus:
The role of graph topology in the performance of biomedical Knowledge Graph Completion models. - Nele P. Quast, Charlotte M. Deane, Matthew I. J. Raybould:
STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation. - Mariia Pospelova, Yana Safonova:
PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences. - Zirui Chen, Jiao Hua, Lu Ba, Tianyun He, Boran Yang, Jing Qi, Shuilin Jin:
reDA: differential abundance testing on scATAC-seq data using random walk with restart. - Omri Peleg, Maya Raytan, Elhanan Borenstein:
KADAIF: an anomaly detection method for complex microbiome data. - Pavel P. Kuksa, Matei Ionita, Luke Carter, Jeffrey Cifello, Prabhakaran Gangadharan, Kaylyn Clark, Otto Valladares, Yuk Yee Leung, Li-San Wang:
BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets. - Huiying Jiang, Wenlan Chen, Fei Guo, Cheng Liang:
Cancer survival prediction based on soft-label guided contrastive learning and global feature fusion. - Taushif Khan, Mohammed Toufiq, Marina Yurieva, Nitaya Indrawattana, Akanitt Jittmittraphap, Nathamon Kosoltanapiwat, Pornpan Pumirat, Passanesh Sukphopetch, Muthita Vanaporn, Karolina Palucka, Basirudeen Syed Ahamed Kabeer, Darawan Rinchai, Damien Chaussabel:
Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation. - Shawn T. O'Neil, Brian M. Schilder, Kevin Schaper, Corey Cox, Daniel R. Korn, Sarah Gehrke, Christopher J. Mungall, Melissa A. Haendel:
monarchr: an R package for querying biomedical knowledge graphs.
Volume 41, Number 11, 2025
- Leo Hermet, Leo Laoubi, Martial Scavino, Anne-Claire Doffin, Alexia Gazeu, Justine Berthet, Berenice Pillat, Stephanie Tissot, Sylvie Rusakiewicz, Marie-Cécile Michallet, Nathalie Bendriss-Vermare, Jenny Valladeau-Guilemond, Jean Hausser, Christophe Caux, Margaux Hubert:
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment. - Tiberiu Totu, Rafael Riudavets Puig, Lukas Jonathan Häuser, Mattia Tomasoni, Hella Anna Bolck, Marija Buljan:
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline. - Amir Hassan Shariatmadari, Alireza Jafari, Sikun Guo, Sneha Srinivasan, Nathan C. Sheffield, Aidong Zhang, Kishlay Jha:
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation. - Yu Xu, Chonghao Wang, Ke Xu, Yi Ding, Aiping Lyu, Lu Zhang:
TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction. - Oscar Rojas Labra, Carla M. Martinez-Garcia, Nelly Beatriz Santoyo-Rivera, Daniel Montiel-Garcia, Vijay S. Reddy:
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs. - Enzo Battistella, Nick Jiang, Chris Rohlicek, Ilya Shlyakhter, Victoria Popic:
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement. - Stefaan Verwimp, Rob Lavigne, Cédric Lood, Vera van Noort:
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures. - Yanli Wang, Frimpong Boadu, Jianlin Cheng:
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs. - Ryuichiro Nakato, Luis Augusto Eijy Nagai:
ShortCake: an integrated platform for efficient and reproducible single-cell analysis. - William Gilpin:
The cell as a token: high-dimensional geometry in language models and cell embeddings. - Melissa Van Norden, William Mangione, Zackary Falls, Ram Samudrala:
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. - Charles Tapley Hoyt, Klas Karis, Benjamin M. Gyori:
Assembly and reasoning over semantic mappings at scale for biomedical data integration. - Kangsheng Qi, Can Cenik:
Topological and functional characterization of human translation efficiency covariation network. - Feng Chen, Chunhe Li:
Reconstructing gene network structure and dynamics from single cell data. - Florestan De Moor, Olivier Boulle, Dominique Lavenier:
De-Bruijn graph partitioning for scalable and accurate DNA storage processing. - Philip Hartout, Dexiong Chen, Paolo Pellizzoni, Carlos G. Oliver, Karsten M. Borgwardt:
Endowing protein language models with structural knowledge. - Yangyang Chen, Zixu Wang, Pengyong Li, Li Zeng, Xiangxiang Zeng, Lei Xu:
ZeroGEN: leveraging language models for zero-shot ligand design from protein sequences. - Andrew J. Bass, David J. Cutler, Michael P. Epstein:
A powerful framework for differential co-expression analysis of general risk factors. - Jan Pielesiak, Maciej Antczak, Marta Szachniuk, Tomasz Zok:
RNAtive to recognize native-like structure in a set of RNA 3D models. - Mark Chernyshev, Aron Stålmarck, Martin Corcoran, Gunilla B. Karlsson Hedestam, Ben Murrell:
Detection of PCR chimeras in adaptive immune receptor repertoire sequences. - Ana Laura Chenoweth Galaz, Nadia Tahiri:
aPhyloGeo: a Python application for correlating genetic and climatic conditions. - Yicong Mao, Zhiwen Jiang, Tianying Wang, Yijuan Hu, Xiang Zhan:
TCVS: tree-guided compositional variable selection analysis of microbiome data. - Yinan Zheng, Feng Gao, Lifang Hou:
PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework. - Minsoo Kim, Hanjin Bae, Gyeongpil Jo, Kunwoo Kim, Sung Jong Lee, Jejoong Yoo, Keehyoung Joo:
DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models. - Michael B. Hall, Chenxi Zhou, Lachlan J. M. Coin:
Genome size estimation from long read overlaps. - Jacqueline M. Boccacino, Martin Del Castillo Velasco-Herrera, Mathew A Beale, Jamie Billington, Ian Vermes, Sofia Obolenski, Kim Wong, Laura Torrens, Sarah J. Moody, Sandra Perdomo, Saamin Cheema, Bailey Francis, Victoria Offord, Adam P. Butler, David J. Adams:
SPARKI: a tool for the statistical analysis of pathogen identification results.
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2025-12-02 23:30 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
