Works matching IS 13674803 AND DT 2025 AND VI 41 AND IP 1

Results: 60

nipalsMCIA: flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf015

By:

Mattessich, Max;
Reyna, Joaquin;
Aron, Edel;
Ay, Ferhat;
Kilmer, Misha;
Kleinstein, Steven H;
Konstorum, Anna

Publication type:

Article

PredCMB: predicting changes in microbial metabolites based on the gene–metabolite network analysis of shotgun metagenome data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf020

By:

Ji, Jungyong;
Jung, Sungwon

Publication type:

Article

DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf019

By:

Savojardo, Castrense;
Manfredi, Matteo;
Martelli, Pier Luigi;
Casadio, Rita

Publication type:

Article

Bayesian gene set benchmark dose estimation for "omic" responses.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf008

By:

Zilber, Daniel;
Messier, Kyle P;
House, John;
Parham, Fred;
Auerbach, Scott S;
Wheeler, Matthew W

Publication type:

Article

PHIStruct: improving phage–host interaction prediction at low sequence similarity settings using structure-aware protein embeddings.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf016

By:

Gonzales, Mark Edward M;
Ureta, Jennifer C;
Shrestha, Anish M S

Publication type:

Article

TPepRet: a deep learning model for characterizing T-cell receptors–antigen binding patterns.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf022

By:

Wang, Meng;
Fan, Wei;
Wu, Tianrui;
Li, Min

Publication type:

Article

FlexLMM: a Nextflow linear mixed model framework for GWAS.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf021

By:

Pierotti, Saul;
Fitzgerald, Tomas;
Birney, Ewan

Publication type:

Article

A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf013

By:

Zhou, Yanfeng;
Zhong, Liqun;
Wang, Zichen;
Ge, Yang

Publication type:

Article

BetaAlign: a deep learning approach for multiple sequence alignment.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf009

By:

Dotan, Edo;
Wygoda, Elya;
Ecker, Noa;
Alburquerque, Michael;
Avram, Oren;
Belinkov, Yonatan;
Pupko, Tal

Publication type:

Article

EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf018

By:

Wang, Yubo;
Zhu, Haoran;
Wang, Yansong;
Yang, Yuning;
Huang, Yujian;
Zhang, Jian;
Wong, Ka-chun;
Li, Xiangtao

Publication type:

Article

Funmap: integrating high-dimensional functional annotations to improve fine-mapping.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf017

By:

Li, Yuekai;
Xiao, Jiashun;
Ming, Jingsi;
Zeng, Yicheng;
Cai, Mingxuan

Publication type:

Article

Nanopore decoding with speed and versatility for data storage.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf006

By:

Volkel, Kevin D;
Hook, Paul W;
Keung, Albert;
Timp, Winston;
Tuck, James M

Publication type:

Article

Proteoform identification and quantification based on alignment graphs.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf007

By:

Zhan, Zhaohui;
Wang, Lusheng

Publication type:

Article

PCA-based spatial domain identification with state-of-the-art performance.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf005

By:

Schaub, Darius P;
Yousefi, Behnam;
Kaiser, Nico;
Khatri, Robin;
Puelles, Victor G;
Krebs, Christian F;
Panzer, Ulf;
Bonn, Stefan

Publication type:

Article

Semblans: automated assembly and processing of RNA-seq data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf003

By:

Woodcock-Girard, Miles D;
Bretz, Eric C;
Robertson, Holly M;
Ramanauskas, Karolis;
Hampton-Marcell, Jarrad T;
Walker, Joseph F

Publication type:

Article

Rnalib: a Python library for custom transcriptomics analyses.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae751

By:

Popitsch, Niko;
Ameres, Stefan L

Publication type:

Article

Heterogeneous entity representation for medicinal synergy prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae750

By:

Wu, Jiawei;
Wen, Jun;
Yan, Mingyuan;
Dong, Anqi;
Gao, Shuai;
Wang, Ren;
Chen, Can

Publication type:

Article

Ligand identification in CryoEM and X-ray maps using deep learning.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae749

By:

Karolczak, Jacek;
Przybyłowska, Anna;
Szewczyk, Konrad;
Taisner, Witold;
Heumann, John M;
Stowell, Michael H B;
Nowicki, Michał;
Brzezinski, Dariusz

Publication type:

Article

CParty: hierarchically constrained partition function of RNA pseudoknots.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae748

By:

Gray, Mateo;
Trinity, Luke;
Stege, Ulrike;
Ponty, Yann;
Will, Sebastian;
Jabbari, Hosna

Publication type:

Article

RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf004

By:

Bernard, Clément;
Postic, Guillaume;
Ghannay, Sahar;
Tahi, Fariza

Publication type:

Article

Improving generalizability of drug–target binding prediction by pre-trained multi-view molecular representations.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btaf002

By:

Ouyang, Xike;
Feng, Yannuo;
Cui, Chen;
Li, Yunhe;
Zhang, Li;
Wang, Han

Publication type:

Article

Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset.

Published in:: 2025
Publication type:: Correction Notice

Transcription factor prediction using protein 3D secondary structures.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae762

By:

Liebold, Jeanine;
Neuhaus, Fabian;
Geiser, Janina;
Kurtz, Stefan;
Baumbach, Jan;
Newaz, Khalique

Publication type:

Article

Crypt4GH-JS: securely storing sensitive data online with client-side encryption.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae763

By:

Thelen, Fabienne;
Hochmuth, Jannis;
Griep, Sven;
Schwab, Benedikt;
Goesmann, Alexander;
Förster, Frank

Publication type:

Article

Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae761

By:

Faubert, Andre C;
Wang, Shang

Publication type:

Article

NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae747

By:

Chen, Yunlu;
Ruan, Feng;
Wang, Ji-Ping

Publication type:

Article

MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae760

By:

Chaabane, Farid;
Pillonel, Trestan;
Bertelli, Claire

Publication type:

Article

SampleExplorer: using language models to discover relevant transcriptome data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae759

By:

Chin, Wee Loong;
Lassmann, Timo

Publication type:

Article

VarNMF: non-negative probabilistic factorization with source variation.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae758

By:

Fallik, Ela;
Friedman, Nir

Publication type:

Article

Fast and exact gap-affine partial order alignment with POASTA.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae757

By:

Dijk, Lucas R van;
Manson, Abigail L;
Earl, Ashlee M;
Garimella, Kiran V;
Abeel, Thomas

Publication type:

Article

FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme–substrate interactions from published manuscripts.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae756

By:

Smith, Nathaniel;
Yuan, Xinyu;
Melissinos, Chesney;
Moghe, Gaurav

Publication type:

Article

Gretl—variation GRaph Evaluation TooLkit.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae755

By:

Vorbrugg, Sebastian;
Bezrukov, Ilja;
Bao, Zhigui;
Weigel, Detlef

Publication type:

Article

Correction to: Damsel: analysis and visualisation of DamID sequencing in R.

Published in:: Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae753
Publication type:: Article

QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae752

By:

Li, Manci;
Bryant, Damani N;
Gresch, Sarah;
Milstein, Marissa S;
Christenson, Peter R;
Lichtenberg, Stuart S;
Larsen, Peter A;
Oh, Sang-Hyun

Publication type:

Article

The scalable variant call representation: enabling genetic analysis beyond one million genomes.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae746

By:

Poterba, Timothy;
Vittal, Christopher;
King, Daniel;
Goldstein, Daniel;
Goldstein, Jacqueline I;
Schultz, Patrick;
Karczewski, Konrad J;
Seed, Cotton;
Neale, Benjamin M

Publication type:

Article

CryptoBench: cryptic protein–ligand binding sites dataset and benchmark.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae745

By:

Škrhák, Vít;
Novotný, Marian;
Feidakis, Christos P;
Krivák, Radoslav;
Hoksza, David

Publication type:

Article

End-to-end simulation of nanopore sequencing signals with feed-forward transformers.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae744

By:

Beslic, Denis;
Kucklick, Martin;
Engelmann, Susanne;
Fuchs, Stephan;
Renard, Bernhard Y;
Körber, Nils

Publication type:

Article

The Naïve Bayes classifier++ for metagenomic taxonomic classification—query evaluation.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae743

By:

Duan, Haozhe (Neil);
Hearne, Gavin;
Polikar, Robi;
Rosen, Gail L

Publication type:

Article

CrossIsoFun: predicting isoform functions using the integration of multi-omics data.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae742

By:

Liu, Yiwei;
Li, Hong-Dong;
Wang, Jianxin

Publication type:

Article

MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae741

By:

Newell, Nicholas E

Publication type:

Article

DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae740

By:

Durham, Jesse;
Zhang, Jing;
Schaeffer, Richard D;
Cong, Qian

Publication type:

Article

The FunCoup Cytoscape App: multi-species network analysis and visualization.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae739

By:

Buzzao, Davide;
Steininger, Lukas;
Guala, Dimitri;
Sonnhammer, Erik L L

Publication type:

Article

DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae738

By:

Lupo, Umberto;
Sgarbossa, Damiano;
Milighetti, Martina;
Bitbol, Anne-Florence

Publication type:

Article

Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae732

By:

Sergouniotis, Panagiotis I;
Diakite, Adam;
Gaurav, Kumar;
Consortium, UK Biobank Eye and Vision;
Birney, Ewan;
Fitzgerald, Tomas

Publication type:

Article

Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae728

By:

Xi, Duo;
Zhang, Minjianan;
Shang, Muheng;
Du, Lei;
Han, Junwei;
Initiative, Alzheimer's Disease Neuroimaging

Publication type:

Article

A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae737

By:

Johnston, Iain G;
Diaz-Uriarte, Ramon

Publication type:

Article

Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae727

By:

Yin, Danqing;
Cao, Yue;
Chen, Junyi;
Mak, Candice L Y;
Yu, Ken H O;
Zhang, Jiaxuan;
Li, Jia;
Lin, Yingxin;
Ho, Joshua W K;
Yang, Jean Y H

Publication type:

Article

A near-tight lower bound on the density of forward sampling schemes.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae736

By:

Kille, Bryce;
Koerkamp, Ragnar Groot;
McAdams, Drake;
Liu, Alan;
Treangen, Todd J

Publication type:

Article

SuperSpot: coarse graining spatial transcriptomics data into metaspots.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae734

By:

Teleman, Matei;
Gabriel, Aurélie A G;
Hérault, Léonard;
Gfeller, David

Publication type:

Article

SCARAP: scalable cross-species comparative genomics of prokaryotes.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae735

By:

Wittouck, Stijn;
Eilers, Tom;
Noort, Vera van;
Lebeer, Sarah

Publication type:

Article