Works matching IS 13674803 AND DT 2025 AND VI 41 AND IP 2

Results: 39

PNL: a software to build polygenic risk scores using a super learner approach based on PairNet, a Convolutional Neural Network.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf071

By:

Chen, Ting-Huei;
Lee, Chia-Jung;
Chen, Syue-Pu;
Wu, Shang-Jung;
Fann, Cathy S J

Publication type:

Article

A conditional denoising VAE-based framework for antimicrobial peptides generation with preserving desirable properties.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf069

By:

Zhao, Weizhong;
Hou, Kaijieyi;
Shen, Yiting;
Hu, Xiaohua

Publication type:

Article

NMFProfiler: a multi-omics integration method for samples stratified in groups.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf066

By:

Mercadié, Aurélie;
Gravier, Éléonore;
Josse, Gwendal;
Fournier, Isabelle;
Viodé, Cécile;
Vialaneix, Nathalie;
Brouard, Céline

Publication type:

Article

ESPClust: unsupervised identification of modifiers for the effect size profile in omics association studies.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf065

By:

Pérez-Reche, Francisco J;
Cheetham, Nathan J;
Bowyer, Ruth C E;
Thompson, Ellen J;
Tettamanzi, Francesca;
Menni, Cristina;
Steves, Claire J

Publication type:

Article

SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf057

By:

Chockalingam, Sriram P;
Aluru, Maneesha;
Aluru, Srinivas

Publication type:

Article

COBREXA 2: tidy and scalable construction of complex metabolic models.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf056

By:

Kratochvíl, Miroslav;
Wilken, St Elmo;
Ebenhöh, Oliver;
Schneider, Reinhard;
Satagopam, Venkata P

Publication type:

Article

FoldX force field revisited, an improved version.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf064

By:

Delgado, Javier;
Reche, Raul;
Cianferoni, Damiano;
Orlando, Gabriele;
van der Kant, Rob;
Rousseau, Frederic;
Schymkowitz, Joost;
Serrano, Luis

Publication type:

Article

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf038

By:

Liu, Tiantian;
Xu, Xiangnan;
Wang, Tao;
Xu, Peirong

Publication type:

Article

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf037

By:

Gurbich, Tatiana A;
Beracochea, Martin;
Silva, Nishadi H De;
Finn, Robert D

Publication type:

Article

ParaSurf: a surface-based deep learning approach for paratope–antigen interaction prediction.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf062

By:

Papadopoulos, Angelos-Michael;
Axenopoulos, Apostolos;
Iatrou, Anastasia;
Stamatopoulos, Kostas;
Alvarez, Federico;
Daras, Petros

Publication type:

Article

DNAdesign: feature-aware in silico design of synthetic DNA through mutation.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf052

By:

Wang, Yingfei;
Li, Jinsen;
Chiu, Tsu-Pei;
Gompel, Nicolas;
Rohs, Remo

Publication type:

Article

MolFCL: predicting molecular properties through chemistry-guided contrastive and prompt learning.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf061

By:

Tang, Xiang;
Zhao, Qichang;
Wang, Jianxin;
Duan, Guihua

Publication type:

Article

Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf059

By:

Cui, Haoyu;
Guo, Qinhao;
Xu, Jun;
Wu, Xiaohua;
Cai, Chengfei;
Jiao, Yiping;
Ming, Wenlong;
Wen, Hao;
Wang, Xiangxue

Publication type:

Article

GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf058

By:

Zhang, Zhenmiao;
Gupta, Ishaan;
Pevzner, Pavel A

Publication type:

Article

ipd: an R package for conducting inference on predicted data.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf055

By:

Salerno, Stephen;
Miao, Jiacheng;
Afiaz, Awan;
Hoffman, Kentaro;
Neufeld, Anna;
Lu, Qiongshi;
McCormick, Tyler H;
Leek, Jeffrey T

Publication type:

Article

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf050

By:

Du, Lin;
Farooq, Hammad;
Delafrouz, Pourya;
Liang, Jie

Publication type:

Article

Vistla: identifying influence paths with information theory.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf036

By:

Kursa, Miron B

Publication type:

Article

NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf048

By:

Paton, Victor;
Türei, Denes;
Ivanova, Olga;
Müller-Dott, Sophia;
Rodriguez-Mier, Pablo;
Venafra, Veronica;
Perfetto, Livia;
Garrido-Rodriguez, Martin;
Saez-Rodriguez, Julio

Publication type:

Article

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf049

By:

Brown, Max R;
Rosa, Pablo Manuel Gonzalez de La;
Blaxter, Mark

Publication type:

Article

scatterbar: an R package for visualizing proportional data across spatially resolved coordinates.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf047

By:

Velazquez, Dee;
Fan, Jean

Publication type:

Article

scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf044

By:

Meng, Hua;
Qin, Chuan;
Long, Zhiguo

Publication type:

Article

Multidimensional scaling improves distance-based clustering for microbiome data.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf042

By:

Chen, Guanhua;
Wang, Xinyue;
Sun, Qiang;
Tang, Zheng-Zheng

Publication type:

Article

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf043

By:

Almeida-Silva, Fabricio;
Peer, Yves Van de

Publication type:

Article

Robustly interrogating machine learning-based scoring functions: what are they learning?

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf040

By:

Durant, Guy;
Boyles, Fergus;
Birchall, Kristian;
Marsden, Brian;
Deane, Charlotte M

Publication type:

Article

ELLIPSIS: robust quantification of splicing in scRNA-seq.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf028

By:

Hecke, Marie Van;
Beerenwinkel, Niko;
Lootens, Thibault;
Fostier, Jan;
Raedt, Robrecht;
Marchal, Kathleen

Publication type:

Article

Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf035

By:

Prabakaran, R;
Bromberg, Yana

Publication type:

Article

SSL-VQ: vector-quantized variational autoencoders for semi-supervised prediction of therapeutic targets across diverse diseases.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf039

By:

Namba, Satoko;
Li, Chen;
Otani, Noriko Yuyama;
Yamanishi, Yoshihiro

Publication type:

Article

Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf033

By:

Paul, Niels Benjamin;
Wolber, Jonas Chanrithy;
Sahrhage, Malte Lennart;
Beißbarth, Tim;
Haubrock, Martin

Publication type:

Article

MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf032

By:

Lee, Yujian;
Gao, Peng;
Xu, Yongqi;
Wang, Ziyang;
Li, Shuaicheng;
Chen, Jiaxing

Publication type:

Article

ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf031

By:

Matsumoto, Nicholas;
Choi, Hyunjun;
Moran, Jay;
Hernandez, Miguel E;
Venkatesan, Mythreye;
Li, Xi;
Chang, Jui-Hsuan;
Wang, Paul;
Moore, Jason H

Publication type:

Article

HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf030

By:

Pinchuk, Dmitry;
Chowdhury, H M A Mohit;
Pandeya, Abhishek;
Oluwadare, Oluwatosin

Publication type:

Article

Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf034

By:

Hong, Seokyoung;
Chattaraj, Krishna Gopal;
Guo, Jing;
Trout, Bernhardt L;
Braatz, Richard D

Publication type:

Article

VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf029

By:

Kaiser, Nick Laurenz;
Groschup, Martin H;
Sadeghi, Balal

Publication type:

Article

Trajectory Inference with Cell–Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf027

By:

Fu, Yifeng;
Qu, Hong;
Qu, Dacheng;
Zhao, Min

Publication type:

Article

tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf025

By:

Peulen, Thomas-Otavio;
Hemmen, Katherina;
Greife, Annemarie;
Webb, Benjamin M;
Felekyan, Suren;
Sali, Andrej;
Seidel, Claus A M;
Sanabria, Hugo;
Heinze, Katrin G

Publication type:

Article

PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf014

By:

Jiang, Yifan;
Liao, Disen;
Zhu, Qiyun;
Lu, Yang Young

Publication type:

Article

A comprehensive graph neural network method for predicting triplet motifs in disease–drug–gene interactions.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf023

By:

Kang, Chuanze;
Liu, Zonghuan;
Zhang, Han

Publication type:

Article

CAMIL: channel attention-based multiple instance learning for whole slide image classification.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf024

By:

Mao, Jinyang;
Xu, Junlin;
Tang, Xianfang;
Liu, Yongjin;
Zhao, Heaven;
Tian, Geng;
Yang, Jialiang

Publication type:

Article

tagtango: an application to compare single-cell annotations.

Published in:

Bioinformatics, 2025, v. 41, n. 2, p. 1, doi. 10.1093/bioinformatics/btaf012

By:

Mora, Bernat Bramon;
Lindsay, Helen;
Thiébaut, Antonin;
Stuart, Kenneth D;
Gottardo, Raphael

Publication type:

Article