Works matching IS 14712105 AND DT 2025 AND VI 26 AND IP 1

Results: 175

A novel machine learning architecture to improve classification of intermediate cases in health: workflow and case study for public health.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06228-8

By:

Hammoud, Bassel;
Semaan, Aline;
Benova, Lenka;
Elhajj, Imad H.

Publication type:

Article

SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06195-0

By:

Zhang, Qiaosheng;
Sun, Zhenyu;
Zhong, Zhaoman;
Yang, Huihui;
Wei, Yalong;
Xu, Junjie

Publication type:

Article

Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06186-1

By:

Xiong, Jiaqi;
Yin, Nan;
Liang, Shiyang;
Li, Haoyang;
Wang, Yingxu;
Ai, Duo;
Wang, Jingjie

Publication type:

Article

LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06212-2

By:

Li, Luna Xingyu;
Aguilar, Boris;
Gennari, John;
Qin, Guangrong

Publication type:

Article

MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06211-3

By:

Chigira, Koki;
Yamasaki, Masanori;
Ookawa, Taiichiro

Publication type:

Article

RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA–protein binding sites prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06197-y

By:

Zhang, Jiangbo;
Peng, Yunhui;
Cui, Feifei;
Zhang, Zilong;
Yan, Shankai;
Zhang, Qingchen

Publication type:

Article

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06194-1

By:

Strobel, Michael;
Gil-de-la-Fuente, Alberto;
Zare Shahneh, Mohammad Reza;
Abiead, Yasin El;
Bushuiev, Roman;
Bushuiev, Anton;
Pluskal, Tomáš;
Wang, Mingxun

Publication type:

Article

Rprot-Vec: a deep learning approach for fast protein structure similarity calculation.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06213-1

By:

Zhang, Yichuan;
Zhang, Wen

Publication type:

Article

PhyloScape: interactive and scalable visualization platform for phylogenetic trees.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06203-3

By:

Wang, Jiajia;
Zhang, Bo;
Zheng, Linglu;
Chen, Yan;
Zhang, Chunyang;
Lin, Guojiao;
Meng, Zhen;
Wang, Xuezhi;
Zhou, Yuanchun

Publication type:

Article

EDRMM: enhancing drug recommendation via multi-granularity and multi-attribute representation.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06167-4

By:

Liu, Feiyan;
Wang, Wenhao;
Zheng, Jiawei;
Xie, Yibo;
Wang, Xiaoli;
Zhang, Dongxiang

Publication type:

Article

A new alignment-free method: K-mer Subsequence Natural Vector (K-mer SNV) for classification of fungi.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06152-x

By:

He, Lily;
Huang, Mochao;
Yiming, Gulinisha;
Zhu, Yi;
Liu, Ruowei;
Chen, Jinghan;
Yau, Stephen S. T.

Publication type:

Article

HIVGenoPipe: a nextflow pipeline for the detection of HIV-1 drug resistance using a real-time sample-specific reference sequence.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06201-5

By:

Dotrang, Thoai;
Sherman, Brad T.;
Dai, Lisheng;
Khan, Muhammad Ayub;
Highbarger, Helene C.;
Bruchey, Whitney;
Laverdure, Sylvain;
Baseler, Michael W.;
Imamichi, Tomozumi;
Dewar, Robin L.;
Chang, Weizhong

Publication type:

Article

DiscMycoVir: a user-friendly platform for discovering mycoviruses in fungal transcriptomes.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06196-z

By:

Bompotas, Agorakis;
Kalogeropoulos, Nikitas-Rigas;
Giachali, Maria;
Kotta-Loizou, Ioly;
Makris, Christos

Publication type:

Article

Multi-task genomic prediction using gated residual variable selection neural networks.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06188-z

By:

Fan, Yuhua;
Waldmann, Patrik

Publication type:

Article

Automated sparse feature selection in high-dimensional proteomics data via 1-bit compressed sensing and K-Medoids clustering.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06193-2

By:

Wen, FuDong;
Su, Yue;
Liu, Dan;
Wang, YuPeng;
Liu, MeiNa

Publication type:

Article

Adaptive gradient scaling: integrating Adam and landscape modification for protein structure prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06185-2

By:

Kapitan, Vitalii;
Choi, Michael

Publication type:

Article

2dSpAn-Auto: an automated tool for analysis of two-dimensional dendritic spine images.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06179-0

By:

Paul, Shauvik;
Pramanick, Rahul;
Das, Nirmal;
Baczynska, Ewa;
Bedrood, Zeinab;
Chakraborti, Tapabrata;
Basu, Subhadip;
Wlodarczyk, Jakub

Publication type:

Article

Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06177-2

By:

McGovern, Kyle C.;
Silverman, Justin D.

Publication type:

Article

Coconut: covariate-assisted composite null hypothesis testing with applications to replicability analysis of high-throughput experimental data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06163-8

By:

Li, Yan;
Li, Yanmei;
Ma, Han;
Yue, Zitong;
Zhang, Xin

Publication type:

Article

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06151-y

By:

Elnahas, Osama;
Ead, Waleed M.;
Qiu, Yushan;
Lu, Jian

Publication type:

Article

SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-024-06019-7

By:

Eremeyeva, M.;
Din, Y.;
Shirokii, N.;
Serov, N.

Publication type:

Article

Differential expression analysis with inmoose, the integrated multi-omic open-source environment in Python.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06180-7

By:

Colange, Maximilien;
Appé, Guillaume;
Meunier, Léa;
Weill, Solène;
Nordor, Akpéli;
Behdenna, Abdelkader

Publication type:

Article

PRCFX-DT: a new graph-based approach for feature selection and classification of genomic sequences.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06183-4

By:

Khodaei, Amin;
Eskandari, Sania;
Sharifi, Hadi;
Mozaffari-Tazehkand, Behzad

Publication type:

Article

Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06144-x

By:

Smeriglio, Riccardo;
Bardini, Roberta;
Savino, Alessandro;
Di Carlo, Stefano

Publication type:

Article

SCATrans: semantic cross-attention transformer for drug–drug interaction predication through multimodal biomedical data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06165-6

By:

Zhang, Shanwen;
Yu, Changqing;
Zhang, Chuanlei

Publication type:

Article

SEQSIM: A novel bioinformatics tool for comparisons of promoter regions—a case study of calcium binding protein spermatid associated 1 (CABS1).

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06160-x

By:

Santos, Joy Ramielle L.;
Sun, Weijie;
Befus, A. Dean;
Marcet-Palacios, Marcelo

Publication type:

Article

Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06043-1

By:

Oles, Vladyslav;
Dash, Sajal;
Anandakrishnan, Ramu

Publication type:

Article

'gitana' (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06178-1

By:

Galisteo, Cristina;
de la Haba, Rafael R.

Publication type:

Article

Pytrf: a python package for finding tandem repeats from genomic sequences.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06168-3

By:

Du, Lianming;
Sun, Dalin;
Chen, Jiahao;
Zhou, Xinyi;
Zhao, Kelei;
Zeng, Qianglin;
Yang, Nan

Publication type:

Article

HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06157-6

By:

Luo, Yue;
Deng, Lei;
Huang, Zhijian

Publication type:

Article

GNNMutation: a heterogeneous graph-based framework for cancer detection.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06133-0

By:

Özcan Şimşek, Nuriye Özlem;
Özgür, Arzucan;
Gürgen, Fikret

Publication type:

Article

Pytrf: a python package for finding tandem repeats from genomic sequences.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06168-3

By:

Du, Lianming;
Sun, Dalin;
Chen, Jiahao;
Zhou, Xinyi;
Zhao, Kelei;
Zeng, Qianglin;
Yang, Nan

Publication type:

Article

Efficient structure learning of gene regulatory networks with Bayesian active learning.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06149-6

By:

Sándor, Dániel;
Antal, Péter

Publication type:

Article

MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06176-3

By:

Kwek, Jes Hui Min;
Fullwood, Melissa Jane

Publication type:

Article

Blastn2dotplots: multiple dot-plot visualizer for genome comparisons.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06175-4

By:

Okuno, Miki;
Yamamoto, Takeshi;
Ogura, Yoshitoshi

Publication type:

Article

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06174-5

By:

Yousefian, Maryam;
Frank, Anna-Simone;
Weber, Marcus;
Röblitz, Susanna

Publication type:

Article

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06173-6

By:

Liao, Linbu;
Madan, Esha;
Palma, António M.;
Kim, Hyobin;
Kumar, Amit;
Bhoopathi, Praveen;
Winn, Robert;
Trevino, Jose;
Fisher, Paul;
Brakebusch, Cord Herbert;
Kim, Gahyun;
Kim, Junil;
Gogna, Rajan;
Won, Kyoung Jae

Publication type:

Article

Class-balanced negative training sets for improving classifier model predictions of enhancer-promoter interactions.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06171-8

By:

Maruyama, Osamu;
Koga, Tsukasa

Publication type:

Article

Universal multilayer network embedding reveals a causal link between GABA neurotransmitter and cancer.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06158-5

By:

Pio-Lopez, Léo;
Levin, Michael

Publication type:

Article

One-sample missing DNA-methylation value imputation.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06154-9

By:

Kemda Ngueda, Christelle;
Palm, Julia;
Remo, Flavia;
Scherag, André;
Leistritz, Lutz

Publication type:

Article

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06172-7

By:

Patsakis, Michail;
Provatas, Kimonas;
Karatzikos, Aris;
Koilakos, Charalampos;
Mouratidis, Ioannis;
Georgakopoulos-Soares, Ilias

Publication type:

Article

RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06166-5

By:

Maździarz, Mateusz;
Zając, Sebastian;
Paukszto, Łukasz;
Sawicki, Jakub

Publication type:

Article

Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06159-4

By:

Edelman, Brice;
Skolnick, Jeffrey

Publication type:

Article

FunFEA: an R package for fungal functional enrichment analysis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06164-7

By:

Charest, Julien;
Loebenstein, Paul;
Mach, Robert L.;
Mach-Aigner, Astrid R.

Publication type:

Article

Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06161-w

By:

Anuarbekov, Alikhan;
Kléma, Jiří

Publication type:

Article

DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06162-9

By:

Delgado-Chaves, Fernando M.;
Spurny, Ferdinand;
Laske, Tanja;
Oubounyt, Mhaned;
Baumbach, Jan

Publication type:

Article

TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06156-7

By:

Shen, Qingrong;
Fan, Xiaoqian;
Sun, Yangyang;
Gao, Hao;
Su, Xiaoquan

Publication type:

Article

CRISP: correlation-refined image segmentation process.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06150-z

By:

Briggs, Jennifer K.;
Jin, Erli;
Merrins, Matthew J.;
Benninger, Richard K. P.

Publication type:

Article

Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06128-x

By:

Zeng, Xin;
Liu, Shu;
Liu, Bowen;
Zhang, Weihang;
Xu, Wanzhe;
Toriumi, Fujio;
Nakai, Kenta

Publication type:

Article

KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06127-y

By:

Kim, Dongin;
Sohn, Ji Yeon;
Cho, Jin Hee;
Choi, Ji-Hye;
Oh, Gwi-young;
Woo, Hyun Goo

Publication type:

Article