Works matching IS 13674803 AND DT 2025 AND VI 41 AND IP 3

Results: 51

AlphaPulldown2—a general pipeline for high-throughput structural modeling.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf115

By:

Molodenskiy, Dmitry;
Maurer, Valentin J;
Yu, Dingquan;
Chojnowski, Grzegorz;
Bienert, Stefan;
Tauriello, Gerardo;
Gilep, Konstantin;
Schwede, Torsten;
Kosinski, Jan

Publication type:

Article

QuickEd: high-performance exact sequence alignment based on bound-and-align.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf112

By:

Doblas, Max;
Lostes-Cazorla, Oscar;
Aguado-Puig, Quim;
Iñiguez, Cristian;
Moreto, Miquel;
Marco-Sola, Santiago

Publication type:

Article

actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf107

By:

Varga, Julia K;
Ovchinnikov, Sergey;
Schueler-Furman, Ora

Publication type:

Article

mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf114

By:

Chen, Jinjin;
Mohamed, Ahmed;
Bhuva, Dharmesh D;
Davis, Melissa J;
Tan, Chin Wee

Publication type:

Article

VisionMol: a novel virtual reality tool for protein molecular structure visualization and manipulation.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf118

By:

Wang, Xin;
Zhuang, Yicheng;
Liang, Wenrui;
Wen, Haoyang;
Cai, Zhencong;
He, Yujia;
Su, Yuxi;
Qin, Wei;
Cai, Yuanzhe;
Liang, Lixin;
Huang, Bingding

Publication type:

Article

BioArchLinux: community-driven fresh reproducible software repository for life sciences.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf106

By:

Zhang, Guoyi;
Ristola, Pekka;
Su, Han;
Kumar, Bipin;
Zhang, Boyu;
Hu, Yujin;
Elliot, Michael G;
Drobot, Viktor;
Zhu, Jie;
Staal, Jens;
Larralde, Martin;
Wang, Shun;
Yi, Yun;
Yu, Haoran

Publication type:

Article

PopGLen—a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf105

By:

Nolen, Zachary J

Publication type:

Article

Generating multiple alignments on a pangenomic scale.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf104

By:

Olbrich, Jannik;
Büchler, Thomas;
Ohlebusch, Enno

Publication type:

Article

UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf103

By:

Aucello, Riccardo;
Pernice, Simone;
Tortarolo, Dora;
Calogero, Raffaele A;
Herrera-Rincon, Celia;
Ronchi, Giulia;
Geuna, Stefano;
Cordero, Francesca;
Lió, Pietro;
Beccuti, Marco

Publication type:

Article

PgRC2: engineering the compression of sequencing reads.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf101

By:

Kowalski, Tomasz M;
Grabowski, Szymon

Publication type:

Article

GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf100

By:

Taylor, Avigail;
Macaulay, Valentine M;
Miossec, Matthieu J;
Maurya, Anand K;
Buffa, Francesca M

Publication type:

Article

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf097

By:

Pedersen, Brent S;
Quinlan, Aaron R

Publication type:

Article

AJGM: joint learning of heterogeneous gene networks with adaptive graphical model.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf096

By:

Yang, Shunqi;
Hu, Lingyi;
Chen, Pengzhou;
Zeng, Xiangxiang;
Mao, Shanjun

Publication type:

Article

ENACT: End-to-End Analysis of Visium High Definition (HD) Data.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf094

By:

Kamel, Mena;
Song, Yiwen;
Solbas, Ana;
Villordo, Sergio;
Sarangi, Amrut;
Senin, Pavel;
Sunaal, Mathew;
Ayestas, Luis Cano;
Levin, Clement;
Wang, Seqian;
Classe, Marion;
Bar-Joseph, Ziv;
Planas, Albert Pla

Publication type:

Article

ORCO: Ollivier-Ricci Curvature-Omics—an unsupervised method for analyzing robustness in biological systems.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf093

By:

Simhal, Anish K;
Weistuch, Corey;
Murgas, Kevin;
Grange, Daniel;
Zhu, Jiening;
Oh, Jung Hun;
Elkin, Rena;
Deasy, Joseph O

Publication type:

Article

CryoTEN: efficiently enhancing cryo-EM density maps using transformers.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf092

By:

Selvaraj, Joel;
Wang, Liguo;
Cheng, Jianlin

Publication type:

Article

Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf091

By:

Lavikka, Kari;
Maarala, Altti Ilari;
Oikkonen, Jaana;
Hautaniemi, Sampsa

Publication type:

Article

Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf090

By:

Liu, Wendao;
Zhao, Zhongming

Publication type:

Article

NanoASV: a snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data analysis.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf089

By:

Cousson, Arthur;
Mahé, Frédéric;
Guyet, Ulysse;
Razafimahafaly, Damase;
Bernard, Laetitia

Publication type:

Article

Predicting circRNA–disease associations with shared units and multi-channel attention mechanisms.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf088

By:

Zhang, Xue;
Zou, Quan;
Niu, Mengting;
Wang, Chunyu

Publication type:

Article

AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf087

By:

Hamraoui, Ali;
Jourdren, Laurent;
Thomas-Chollier, Morgane

Publication type:

Article

SpectroPipeR—a streamlining post Spectronaut<sup>®</sup> DIA-MS data analysis R package.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf086

By:

Michalik, Stephan;
Hammer, Elke;
Steil, Leif;
Salazar, Manuela Gesell;
Hentschker, Christian;
Surmann, Kristin;
Busch, Larissa M;
Sura, Thomas;
Völker, Uwe

Publication type:

Article

PharaCon: a new framework for identifying bacteriophages via conditional representation learning.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf085

By:

Bai, Zeheng;
Zhang, Yao-zhong;
Pang, Yuxuan;
Imoto, Seiya

Publication type:

Article

NPM: latent batch effects correction of omics data by nearest-pair matching.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf084

By:

Zito, Antonino;
Martinelli, Axel;
Masiero, Mauro;
Akhmedov, Murodzhon;
Kwee, Ivo

Publication type:

Article

COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf083

By:

Wei, Xindian;
Chen, Tianyi;
Wang, Xibiao;
Shen, Wenjun;
Liu, Cheng;
Wu, Si;
Wong, Hau-San

Publication type:

Article

Tribus: semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic data.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf082

By:

Kang, Ziqi;
Szabo, Angela;
Farago, Teodora;
Perez-Villatoro, Fernando;
Junquera, Ada;
Shah, Saundarya;
Launonen, Inga-Maria;
Anttila, Ella;
Casado, Julia;
Elias, Kevin;
Virtanen, Anni;
Haltia, Ulla-Maija;
Färkkilä, Anniina

Publication type:

Article

SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf081

By:

Onoprishvili, Tornike;
Yuan, Jui-Hung;
Petrov, Kamen;
Ingalalli, Vijay;
Khederlarian, Lila;
Leuchtenmuller, Niklas;
Chandra, Sona;
Duarte, Aurelien;
Bender, Andreas;
Gloaguen, Yoann

Publication type:

Article

TrAGEDy—trajectory alignment of gene expression dynamics.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf073

By:

Laidlaw, Ross F;
Briggs, Emma M;
Matthews, Keith R;
Mamlouk, Amir Madany;
McCulloch, Richard;
Otto, Thomas D

Publication type:

Article

Single-cell copy number calling and event history reconstruction.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf072

By:

Kuipers, Jack;
Tuncel, Mustafa Anıl;
Ferreira, Pedro F;
Jahn, Katharina;
Beerenwinkel, Niko

Publication type:

Article

TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf068

By:

Jiao, Yanxin;
Li, Hongjia;
Xue, Yang;
Yang, Guoliang;
Qi, Lei;
Zhang, Fa;
Zang, Dawei;
Han, Renmin

Publication type:

Article

Efficient storage and regression computation for population-scale genome sequencing studies.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf067

By:

Rivas, Manuel A;
Chang, Christopher

Publication type:

Article

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf063

By:

Gavriilidis, George I;
Vasileiou, Vasileios;
Dimitsaki, Stella;
Karakatsoulis, Georgios;
Giannakakis, Antonis;
Pavlopoulos, Georgios A;
Psomopoulos, Fotis

Publication type:

Article

EpicPred: predicting phenotypes driven by epitope-binding TCRs using attention-based multiple instance learning.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf080

By:

Jeon, Jaemin;
Yu, Suwan;
Lee, Sangam;
Kim, Sang Cheol;
Jo, Hye-Yeong;
Jung, Inuk;
Kim, Kwangsoo

Publication type:

Article

AskBeacon—performing genomic data exchange and analytics with natural language.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf079

By:

Wickramarachchi, Anuradha;
Tonni, Shakila;
Majumdar, Sonali;
Karimi, Sarvnaz;
Kõks, Sulev;
Hosking, Brendan;
Rambla, Jordi;
Twine, Natalie A;
Jain, Yatish;
Bauer, Denis C

Publication type:

Article

Sul-BertGRU: an ensemble deep learning method integrating information entropy-enhanced BERT and directional multi-GRU for S-sulfhydration sites prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf078

By:

Wei, Xirun;
Ning, Qiao;
Che, Kuiyang;
Liu, Zhaowei;
Li, Hui;
Guo, Shikai

Publication type:

Article

MiNEApy: enhancing enrichment network analysis in metabolic networks.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf077

By:

Pandey, Vikash

Publication type:

Article

HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf076

By:

Balajti, Máté;
Kandhari, Rohan;
Jurič, Boris;
Zavolan, Mihaela;
Kanitz, Alexander

Publication type:

Article

MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf075

By:

Zou, Wei;
Ji, Yongxin;
Guan, Jiaojiao;
Sun, Yanni

Publication type:

Article

GCLink: a graph contrastive link prediction framework for gene regulatory network inference.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf074

By:

Yu, Weiming;
Lin, Zerun;
Lan, Miaofang;
Ou-Yang, Le

Publication type:

Article

ImmunoTar—integrative prioritization of cell surface targets for cancer immunotherapy.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf060

By:

Shraim, Rawan;
Mooney, Brian;
Conkrite, Karina L;
Hamilton, Amber K;
Morin, Gregg B;
Sorensen, Poul H;
Maris, John M;
Diskin, Sharon J;
Sacan, Ahmet

Publication type:

Article

MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf054

By:

Vicedomini, Riccardo;
Andreace, Francesco;
Dufresne, Yoann;
Chikhi, Rayan;
González, Camila Duitama

Publication type:

Article

DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf053

By:

Hirota, Keisuke;
Salim, Felix;
Yamada, Takuji

Publication type:

Article

MMnc: multi-modal interpretable representation for non-coding RNA classification and class annotation.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf051

By:

Creux, Constance;
Zehraoui, Farida;
Radvanyi, François;
Tahi, Fariza

Publication type:

Article

Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf046

By:

Staniak, Mateusz;
Huang, Ting;
Figueroa-Navedo, Amanda M;
Kohler, Devon;
Choi, Meena;
Hinkle, Trent;
Kleinheinz, Tracy;
Blake, Robert;
Rose, Christopher M;
Xu, Yingrong;
Beltran, Pierre M Jean;
Xue, Liang;
Bogdan, Małgorzata;
Vitek, Olga

Publication type:

Article

MetAssimulo 2.0: a web app for simulating realistic 1D and 2D metabolomic <sup>1</sup>H NMR spectra.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf045

By:

Yan, Yan;
Jiménez, Beatriz;
Judge, Michael T;
Athersuch, Toby;
Iorio, Maria De;
Ebbels, Timothy M D

Publication type:

Article

Embed-Search-Align: DNA sequence alignment using Transformer models.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf041

By:

Holur, Pavan;
Enevoldsen, K C;
Rajesh, Shreyas;
Mboning, Lajoyce;
Georgiou, Thalia;
Bouchard, Louis-S;
Pellegrini, Matteo;
Roychowdhury, Vwani

Publication type:

Article

Significance in scale space for Hi-C data.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf026

By:

Liu, Rui;
Zhang, Zhengwu;
Won, Hyejung;
Marron, J S

Publication type:

Article

SP-DTI: subpocket-informed transformer for drug–target interaction prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf011

By:

Liu, Sizhe;
Liu, Yuchen;
Xu, Haofeng;
Xia, Jun;
Li, Stan Z

Publication type:

Article

FlowPacker: protein side-chain packing with torsional flow matching.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btaf010

By:

Lee, Jin Sub;
Kim, Philip M

Publication type:

Article

Privacy-preserving framework for genomic computations via multi-key homomorphic encryption.

Published in:

Bioinformatics, 2025, v. 41, n. 3, p. 1, doi. 10.1093/bioinformatics/btae754

By:

Namazi, Mina;
Farahpoor, Mohammadali;
Ayday, Erman;
Pérez-González, Fernando

Publication type:

Article