Works matching IS 13674803 AND DT 2025 AND VI 41 AND IP 5

Results: 44

Missense variants pathogenicity annotation from homologous proteins Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf305

By:

Ruiz-Alías, Gabriel;
Soldevila, Sergi;
Altafaj, Xavier;
Cordomí, Arnau;
Olivella, Mireia

Publication type:

Article

KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf300

By:

Aman, Javed M;
Zhu, Audrey W;
Wühr, Martin;
Shvartsman, Stanislav Y;
Singh, Mona

Publication type:

Article

Nonparametric IPSS: fast, flexible feature selection with false discovery control Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf299

By:

Melikechi, Omar;
Dunson, David B;
Miller, Jeffrey W

Publication type:

Article

MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf297

By:

Mehdiabadi, Mahta;
Blum, Matthias;
Tesei, Giulio;
Bülow, Sören von;
Lindorff-Larsen, Kresten;
Tosatto, Silvio C E;
Piovesan, Damiano

Publication type:

Article

CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf296

By:

Liu, Zhe;
He, Bintao;
Zhang, Tian;
Feng, Chenjie;
Zhang, Fa;
Yang, Zhongjun;
Han, Renmin

Publication type:

Article

scACCorDiON: a clustering approach for explainable patient level cell–cell communication graph analysis Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf288

By:

Nagai, James S;
Maié, Tiago;
Schaub, Michael T;
Costa, Ivan G

Publication type:

Article

MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf285

By:

Wang, Beibei;
Cui, Boyue;
Chen, Shiqu;
Wang, Xuan;
Wang, Yadong;
Li, Junyi

Publication type:

Article

Correction to: Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment Open Access.

Published in:: 2025
Publication type:: Correction Notice

Mapping the attractor landscape of Boolean networks with biobalm Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf280

By:

Trinh, Van-Giang;
Park, Kyu Hyong;
Pastva, Samuel;
Rozum, Jordan C

Publication type:

Article

OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf279

By:

McLaughlin, James;
Lagrimas, Josh;
Iqbal, Haider;
Parkinson, Helen;
Harmse, Henriette

Publication type:

Article

Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf277

By:

Kandathil, Shaun M;
Lau, Andy M;
Buchan, Daniel W A;
Jones, David T

Publication type:

Article

SimSon: simple contrastive learning of SMILES for molecular property prediction Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf275

By:

Lee, Chae Eun;
Kim, Jin Sob;
Min, Jin Hong;
Han, Sung Won

Publication type:

Article

A noise-robust classification method for cryo-ET subtomograms with out-of-distribution detection Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf274

By:

Meng, Wenjia;
Yu, Xueshi;
Zhang, Tingting;
Han, Renmin

Publication type:

Article

Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf272

By:

Wagner, Naama;
Baumer, Ella;
Lyubman, Iris;
Shimony, Yair;
Bracha, Noam;
Martins, Leonor;
Potnis, Neha;
Chang, Jeff H;
Teper, Doron;
Koebnik, Ralf;
Pupko, Tal

Publication type:

Article

ProBASS—a language model with sequence and structural features for predicting the effect of mutations on binding affinity Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf270

By:

Gurusinghe, Sagara N S;
Wu, Yibing;
DeGrado, William;
Shifman, Julia M

Publication type:

Article

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2 Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf269

By:

Wright, Robyn J;
Langille, Morgan G I

Publication type:

Article

High-dimensional biomarker identification for interpretable disease prediction via machine learning models Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf266

By:

Dai, Yifan;
Wu, Di;
Carroll, Ian;
Zou, Fei;
Zou, Baiming

Publication type:

Article

Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf250

By:

Kyrouz, Alison;
Liu, Lian;
Qin, Lixin;
Tjaden, Brian

Publication type:

Article

RabbitSketch: a high-performance sketching library for genome analysis Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf249

By:

Zhang, Tong;
Yin, Zekun;
Xu, Xiaoming;
Yan, Lifeng;
Zhu, Fangjin;
Duan, Xiaohui;
Schmidt, Bertil;
Liu, Weiguo

Publication type:

Article

Co-design protein sequence and structure in discrete space via generative flow Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf248

By:

Yang, Sen;
Ju, Lingli;
Cheng, Peng;
Zhou, JiangLin;
Cai, Yamin;
Feng, Dawei

Publication type:

Article

Preserving full spectrum information in imaging mass spectrometry data reduction Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf247

By:

Moens, Roger A R;
Migas, Lukasz G;
Ardenne, Jacqueline M Van;
Skaar, Eric P;
Spraggins, Jeffrey M;
Plas, Raf Van de

Publication type:

Article

TissueViewer: a web-based multiplexed image viewer Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf246

By:

IJzendoorn, David Gerardus Pieter van;
Matusiak, Magdalena;
West, Rob;
van de Rijn, Matt

Publication type:

Article

m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf221

By:

Zhang, Wei;
Zhang, Ziqi;
Yang, Hailong;
Zhang, Te;
Jiang, Shu;
Qiao, Ning;
Deng, Zhaohong;
Pan, Xiaoyong;
Shen, Hong-Bin;
Yu, Dong-Jun;
Wang, Shitong

Publication type:

Article

VSOT: volume-surface optimization for accurate ultrastructure analysis of dendritic spines Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf220

By:

Lyu, Boyu;
Wang, Jiangxiong;
Risher, William Christopher;
Yu, Guoqiang

Publication type:

Article

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf219

By:

Marin, Maximillian G;
Quinones-Olvera, Natalia;
Wippel, Christoph;
Behruznia, Mahboobeh;
Jeffrey, Brendan M;
Harris, Michael;
Mann, Brendon C;
Rosenthal, Alex;
Jacobson, Karen R;
Warren, Robin M;
Li, Heng;
Meehan, Conor J;
Farhat, Maha R

Publication type:

Article

De novo clustering of large long-read transcriptome datasets with isONclust3 Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf207

By:

Petri, Alexander J;
Sahlin, Kristoffer

Publication type:

Article

JAX-RNAfold: scalable differentiable folding Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf203

By:

Krueger, Ryan K;
Ward, Max

Publication type:

Article

Functional protein biomarkers based on distributions of expression levels in single-cell imaging data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf182

By:

Yi, Misung;
Zhan, Tingting;
Rui, Hallgeir;
Chervoneva, Inna

Publication type:

Article

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf175

By:

Obinu, Lia;
Booth, Timothy;
Weerd, Heleen De;
Trivedi, Urmi;
Porceddu, Andrea

Publication type:

Article

MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf174

By:

Fontanarrosa, Pedro;
Clare, Chania;
Fedorec, Alex J H;
Barnes, Chris P

Publication type:

Article

argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf173

By:

Perovic, Svetlana Ugarcina;
Ramji, Vedanth;
Chong, Hui;
Duan, Yiqian;
Maguire, Finlay;
Coelho, Luis Pedro

Publication type:

Article

ProtNote: a multimodal method for protein–function annotation Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf170

By:

Char, Samir;
Corley, Nathaniel;
Alamdari, Sarah;
Yang, Kevin K;
Amini, Ava P

Publication type:

Article

ROICellTrack: a deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf152

By:

Song, Xiaofei;
Yu, Xiaoqing;
Moran-Segura, Carlos M;
Xu, Hongzhi;
Li, Tingyi;
Davis, Joshua T;
Vosoughi, Aram;
Grass, G Daniel;
Li, Roger;
Wang, Xuefeng

Publication type:

Article

Charting the structure-sequence landscape of light chain amyloids Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf167

By:

Orlando, Gabriele;
Gallardo, Rodrigo;
Colla, Alicia;
Schymkowitz, Joost;
Rousseau, Frederic

Publication type:

Article

MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf161

By:

Shi, Ruibing;
Klawonn, Frank;
Brönstrup, Mark;
Franke, Raimo

Publication type:

Article

Automatic biomarker discovery and enrichment with BRAD Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf159

By:

Pickard, Joshua;
Prakash, Ram;
Choi, Marc Andrew;
Oliven, Natalie;
Stansbury, Cooper;
Cwycyshyn, Jillian;
Galioto, Nicholas;
Gorodetsky, Alex;
Velasquez, Alvaro;
Rajapakse, Indika

Publication type:

Article

Finding antibodies in cryo-EM maps with CrAIOpen Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf157

By:

Mallet, Vincent;
Rapisarda, Chiara;
Minoux, Hervé;
Ovsjanikov, Maks

Publication type:

Article

In silico identification of archaeal DNA-binding proteins Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf169

By:

Donvil, Linus;
Housmans, Joëlle A J;
Peeters, Eveline;
Vranken, Wim;
Orlando, Gabriele

Publication type:

Article

Topology-driven negative sampling enhances generalizability in protein–protein interaction prediction Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf148

By:

Chatterjee, Ayan;
Ravandi, Babak;
Haddadi, Parham;
Philip, Naomi H;
Abdelmessih, Mario;
Mowrey, William R;
Ricchiuto, Piero;
Liang, Yupu;
Ding, Wei;
Mobarec, Juan Carlos;
Eliassi-Rad, Tina

Publication type:

Article

Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf138

By:

Mahajan, Mayank;
Hemberg, Martin

Publication type:

Article

scMUSCL: multi-source transfer learning for clustering scRNA-seq data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf137

By:

Khoeini, Arash;
Sar, Funda;
Lin, Yen-Yi;
Collins, Colin;
Ester, Martin

Publication type:

Article

Topology-based metrics for finding the optimal sparsity in gene regulatory network inference Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf120

By:

Lundqvist, Nils;
Garbulowski, Mateusz;
Hillerton, Thomas;
Sonnhammer, Erik L L

Publication type:

Article

EPIPDLF: a pretrained deep learning framework for predicting enhancer–promoter interactions Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btae716

By:

Xiao, Zhichao;
Li, Yan;
Ding, Yijie;
Yu, Liang

Publication type:

Article

MVSF-AB: accurate antibody–antigen binding affinity prediction via multi-view sequence feature learning Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btae579

By:

Li, Minghui;
Shi, Yao;
Hu, Shengqing;
Hu, Shengshan;
Guo, Peijin;
Wan, Wei;
Zhang, Leo Yu;
Pan, Shirui;
Li, Jizhou;
Sun, Lichao;
Lan, Xiaoli

Publication type:

Article