Works matching IS 13674803 AND DT 2025 AND VI 41 AND IP 4

Results: 51

Gradient matching accelerates mixed-effects inference for biochemical networks Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf154

By:

Oppen, Yulan B van;
Milias-Argeitis, Andreas

Publication type:

Article

Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf153

By:

Hazelett, Dennis J

Publication type:

Article

A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf172

By:

Fu, Yuhan;
Nan, Mengdi;
Ren, Qing;
Chen, Xiang;
Gao, Jie

Publication type:

Article

CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf166

By:

Chivot, Lucas;
Mathieux, Noé;
Cosson, Anna;
Bridier-Nahmias, Antoine;
Favennec, Loïc;
Gelly, Jean-Christophe;
Clain, Jérôme;
Coppée, Romain

Publication type:

Article

adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf168

By:

Fievet, Ghislain;
Broséus, Julien;
Meyre, David;
Hergalant, Sébastien

Publication type:

Article

GSLab: open-source platform for advanced phasor analysis in fluorescence microscopy Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf162

By:

Vallmitjana, Alexander;
Torrado, Belén;
Durkin, Amanda F;
Dvornikov, Alexander;
Rajil, Navid;
Ranjit, Suman;
Balu, Mihaela

Publication type:

Article

GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf160

By:

Jeong, Chang-Uk;
Kim, Jaesik;
Kim, Dokyoon;
Sohn, Kyung-Ah

Publication type:

Article

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf149

By:

Bian, Haiyang;
Chen, Yinxin;
Wei, Lei;
Zhang, Xuegong

Publication type:

Article

PyEvoCell: an LLM-augmented single-cell trajectory analysis dashboard Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf158

By:

Mathur, Sachin;
Beauvais, Mathieu;
Giribet, Arnau;
Barrero, Nicolas Aragon;
Zhang, Chaorui-Tom;
Rahman, Towsif;
Wang, Seqian;
Huang, Jeremy;
Nouri, Nima;
Kurlovs, Andre;
Bar-Joseph, Ziv;
Passban, Peyman

Publication type:

Article

Predicting explainable dementia types with LLM-aided feature engineering Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf156

By:

Kashyap, Aditya M;
Rao, Delip;
Boland, Mary Regina;
Shen, Li;
Callison-Burch, Chris

Publication type:

Article

Approximating edit distances between complex tandem repeats efficiently Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf155

By:

Kawahara, Riki;
Morishita, Shinichi

Publication type:

Article

Realfreq: real-time base modification analysis for nanopore sequencing Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf151

By:

Samarasinghe, Suneth;
Deveson, Ira;
Gamaarachchi, Hasindu

Publication type:

Article

LipidFun: a database of lipid functions Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf110

By:

Lin, Wen-Jen;
Liu, Chia-Hsin;
Huang, Ming-Siang;
Shen, Pei-Chun;
Liu, Hsiu-Cheng;
Tsai, Meng-Hsin;
Lai, Yo-Liang;
Wang, Yu-De;
Hung, Mien-Chie;
Chang, Nai-Wen;
Cheng, Wei-Chung

Publication type:

Article

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf150

By:

Gliozzo, Jessica;
Gomez, Mauricio A Soto;
Bonometti, Arturo;
Patak, Alex;
Casiraghi, Elena;
Valentini, Giorgio

Publication type:

Article

HISSTA: a human in situ single-cell transcriptome atlas Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf142

By:

Yu, Jiwon;
Moon, Jiwoo;
Kim, Minseo;
Han, Gyeol;
Jang, Insu;
Lim, Jinyoung;
Lee, Seungmook;
Yoon, Seok-Hwan;
Park, Woong-Yang;
Lee, Byungwook;
Lee, Sanghyuk

Publication type:

Article

CytoSimplex: visualizing single-cell fates and transitions on a simplex Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf119

By:

Liu, Jialin;
Wang, Yichen;
Li, Chen;
Gu, Yichen;
Ono, Noriaki;
Welch, Joshua

Publication type:

Article

CoverM: read alignment statistics for metagenomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf147

By:

Aroney, Samuel T N;
Newell, Rhys J P;
Nissen, Jakob N;
Camargo, Antonio Pedro;
Tyson, Gene W;
Woodcroft, Ben J

Publication type:

Article

OLTA: Optimizing bait seLection for TArgeted sequencing Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf146

By:

Minbay, Mete Orhun;
Sun, Richard;
Ramachandran, Vijay;
Ay, Ahmet;
Kahveci, Tamer

Publication type:

Article

Marker selection strategies for circulating tumor DNA guided by phylogenetic inference Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf145

By:

Fu, Xuecong;
Luo, Zhicheng;
Deng, Yueqian;
LaFramboise, William;
Bartlett, David;
Schwartz, Russell

Publication type:

Article

CancerTrialMatch: a computational resource for the management of biomarker-based clinical trials at a community cancer center Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf144

By:

Swaminathan, Padmapriya;
Amallraja, Anu;
Kapadia, Shivani;
Williams, Casey B;
Meißner, Tobias

Publication type:

Article

XPRS: a tool for interpretable and explainable polygenic risk score Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf143

By:

Kim, Na Yeon;
Lee, Seunggeun

Publication type:

Article

Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf139

By:

VP, Brintha;
Narayanan, Manikandan

Publication type:

Article

Seed2LP: seed inference in metabolic networks for reverse ecology applications Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf140

By:

Nedjad, Chabname Ghassemi;
Bolteau, Mathieu;
Bourneuf, Lucas;
Paulevé, Loïc;
Frioux, Clémence

Publication type:

Article

Refining Boolean models with the partial most permissive scheme Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf123

By:

Boina, Nadine Ben;
Mossé, Brigitte;
Baudot, Anaïs;
Remy, Elisabeth

Publication type:

Article

Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf136

By:

Saunders, Christopher T;
Holt, James M;
Baker, Daniel N;
Lake, Juniper A;
Belyeu, Jonathan R;
Kronenberg, Zev;
Rowell, William J;
Eberle, Michael A

Publication type:

Article

Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf135

By:

González, Marcelo;
Durán, Roberto E;
Seeger, Michael;
Araya, Mauricio;
Jara, Nicolás

Publication type:

Article

MNMO: discover driver genes from a multi-omics data based-multi-layer network Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf134

By:

Deng, Zheng;
Wu, Jingli;
Chen, Xiaorong;
Li, Gaoshi;
Liu, Jiafei;
Hu, Zhipeng;
Li, Rongyuan;
Deng, Wansu

Publication type:

Article

AlertGS: determining alerts for gene sets Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf133

By:

Kappenberg, Franziska;
Rahnenführer, Jörg

Publication type:

Article

wgatools: an ultrafast toolkit for manipulating whole-genome alignments Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf132

By:

Wei, Wenjie;
Gui, Songtao;
Yang, Jian;
Garrison, Erik;
Yan, Jianbing;
Liu, Hai-Jun

Publication type:

Article

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf131

By:

Chen, Xuanwei;
Ran, Qinghua;
Tang, Junjie;
Chen, Zihao;
Huang, Siyuan;
Shi, Xingjie;
Xi, Ruibin

Publication type:

Article

MR.RGM: an R package for fitting Bayesian multivariate bidirectional Mendelian randomization networks Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf130

By:

Sarkar, Bitan;
Ni, Yang

Publication type:

Article

AI-augmented physics-based docking for antibody-antigen complex prediction Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf129

By:

Gaudreault, Francis;
Sulea, Traian;
Corbeil, Christopher R

Publication type:

Article

Gencube: centralized retrieval and integration of multi-omics resources from leading databases Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf128

By:

Son, Keun Hong;
Cho, Je-Yoel

Publication type:

Article

RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf127

By:

Zeng, Min;
Zhang, Xinyu;
Li, Yiming;
Lu, Chengqian;
Yin, Rui;
Guo, Fei;
Li, Min

Publication type:

Article

AVPpred-BWR: antiviral peptides prediction via biological words representation Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf126

By:

Wei, Zhuoyu;
Shen, Yongqi;
Tang, Xiang;
Wen, Jian;
Song, Youyi;
Wei, Mingqiang;
Cheng, Jing;
Zhu, Xiaolei

Publication type:

Article

MAFin: motif detection in multiple alignment files Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf125

By:

Patsakis, Michail;
Provatas, Kimonas;
Baltoumas, Fotis A;
Chantzi, Nikol;
Mouratidis, Ioannis;
Pavlopoulos, Georgios A;
Georgakopoulos-Soares, Ilias

Publication type:

Article

CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov–Arnold network Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf124

By:

Pratyush, Pawel;
Carrier, Callen;
Pokharel, Suresh;
Ismail, Hamid D;
Chaudhari, Meenal;
KC, Dukka B

Publication type:

Article

H<sup>2</sup>GnnDTI: hierarchical heterogeneous graph neural networks for drug–target interaction prediction Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf117

By:

Jing, Yueying;
Zhang, Dongxue;
Li, Limin

Publication type:

Article

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf122

By:

Li, Zuqi;
Windels, Sam F L;
Malod-Dognin, Noël;
Weinberg, Seth M;
Marazita, Mary L;
Walsh, Susan;
Shriver, Mark D;
Fardo, David W;
Claes, Peter;
Pržulj, Nataša;
Steen, Kristel Van

Publication type:

Article

Exact model-free function inference using uniform marginal counts for null population Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf121

By:

Li, Yiyi;
Song, Mingzhou

Publication type:

Article

Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf111

By:

Samarakoon, Hiruna;
Wan, Yuk Kei;
Parameswaran, Sri;
Göke, Jonathan;
Gamaarachchi, Hasindu;
Deveson, Ira W

Publication type:

Article

PROLONG: penalized regression for outcome guided longitudinal omics analysis with network and group constraints Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf099

By:

Broll, Steven;
Basu, Sumanta;
Lee, Myung Hee;
Wells, Martin T

Publication type:

Article

nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf116

By:

Jain, Tanya;
Clelland, Claire

Publication type:

Article

Lit-OTAR framework for extracting biological evidences from literature Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf113

By:

Tirunagari, Santosh;
Saha, Shyamasree;
Venkatesan, Aravind;
Suveges, Daniel;
Carmona, Miguel;
Buniello, Annalisa;
Ochoa, David;
McEntyre, Johanna;
McDonagh, Ellen;
Harrison, Melissa

Publication type:

Article

PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf102

By:

Leoni, Gabriele;
Petrillo, Mauro;
Ruiz-Serra, Victoria;
Querci, Maddalena;
Coecke, Sandra;
Wiesenthal, Tobias

Publication type:

Article

A framework for analyzing EEG data using high-dimensional tests Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf109

By:

Zhang, Qiuyan;
Xiang, Wenjing;
Yang, Bo;
Yang, Hu

Publication type:

Article

bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf108

By:

Lasher, Brittany;
Hendrix, David A

Publication type:

Article

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf098

By:

Altinkaya, Isin;
Nielsen, Rasmus;
Korneliussen, Thorfinn Sand

Publication type:

Article

Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf095

By:

Jyoti, Jyoti;
Hütt, Marc-Thorsten

Publication type:

Article

Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf070

By:

Cruz-Castillo, Carlos;
Fumis, Luca;
Mehta, Chintan;
Martinez-Osorio, Ricardo Esteban;
Roldan-Romero, Juan Maria;
Cornu, Helena;
Uniyal, Prashant;
Solano-Roman, Antonio;
Carmona, Miguel;
Ochoa, David;
McDonagh, Ellen Mary;
Buniello, Annalisa

Publication type:

Article