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

Results: 142

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

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

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

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

GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06153-w

By:

Cohen, Shani;
Rokach, Lior;
Veksler-Lublinsky, Isana

Publication type:

Article

scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06147-8

By:

Xie, Qing;
Meng, Wang;
Lin, Shili

Publication type:

Article

The application of compressed sensing on tumor mutation burden calculation from overlapped pooling sequencing data.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06148-7

By:

Cui, Yue;
Qiao, Yi;
An, Rongming;
Pan, Xuan;
Tu, Jing

Publication type:

Article

Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06138-9

By:

Wu, You;
Xu, Li;
Cong, Xiaohong;
Li, Hanxiao;
Li, Yanli

Publication type:

Article

ProTaxoVis—protein taxonomic visualisation of presence.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06146-9

By:

Hsieh, Yin-Chen;
Bockwoldt, Mathias;
Heiland, Ines

Publication type:

Article

RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06145-w

By:

Sen, Samyabrata;
Vairagare, Indraneel;
Gosai, Jitendrapuri;
Shrivastava, Abhishek

Publication type:

Article

Integrating genetic and gene expression data in network-based stratification analysis of cancers.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06143-y

By:

Liou, Kenny;
Wang, Ji-Ping

Publication type:

Article

PCVR: a pre-trained contextualized visual representation for DNA sequence classification.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06136-x

By:

Zhou, Jiarui;
Wu, Hui;
Du, Kang;
Zhou, Wengang;
Zhou, Cong-Zhao;
Li, Houqiang

Publication type:

Article

Sensitivity analysis on protein-protein interaction networks through deep graph networks.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06140-1

By:

Dipalma, Alessandro;
Fontanesi, Michele;
Micheli, Alessio;
Milazzo, Paolo;
Podda, Marco

Publication type:

Article

py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06142-z

By:

Guardado, Miguel;
Perez, Cynthia;
Campana, Sthen;
Chavez Rojas, Berenice;
Magaña, Joaquín;
Jackson, Shalom;
Samperio, Emily;
Hernandez, Selena;
Syas, Kaela;
Hernandez, Ryan D.;
Zavala, Elena I.;
Rohlfs, Rori V.

Publication type:

Article

Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06072-w

By:

Zhang, Kaiwei;
Lin, Yange;
Wu, Guangcheng;
Ren, Yuxiang;
Zhang, Xuecang;
Wang, Bo;
Zhang, Xiao-Yu;
Du, Weitao

Publication type:

Article

Multi-proteins similarity-based sampling to select representative genomes from large databases.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06095-3

By:

Coudert, Rémi-Vinh;
Charrier, Jean-Philippe;
Jauffrit, Frédéric;
Flandrois, Jean-Pierre;
Brochier-Armanet, Céline

Publication type:

Article

M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06131-2

By:

Cui, Xinyue;
Xia, Yuhao;
Hou, Minghua;
Zhao, Xuanfeng;
Wang, Suhui;
Zhang, Guijun

Publication type:

Article

PathNetDRP: a novel biomarker discovery framework using pathway and protein–protein interaction networks for immune checkpoint inhibitor response prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06125-0

By:

Lee, Dohee;
Ahn, Jaegyoon;
Choi, Jonghwan

Publication type:

Article

Fast noisy long read alignment with multi-level parallelism.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06129-w

By:

Xia, Zeyu;
Yang, Canqun;
Peng, Chenchen;
Guo, Yifei;
Guo, Yufei;
Tang, Tao;
Cui, Yingbo

Publication type:

Article

M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06132-1

By:

Schaduangrat, Nalini;
Chuntakaruk, Hathaichanok;
Rungrotmongkol, Thanyada;
Mookdarsanit, Pakpoom;
Shoombuatong, Watshara

Publication type:

Article

PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06139-8

By:

Nakamae, Kazuki;
Ide, Saya;
Ohnuki, Nagaki;
Nakagawa, Yoshiko;
Okuhara, Keisuke;
Bono, Hidemasa

Publication type:

Article

A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06134-z

By:

Munoz Briones, Javier;
Brubaker, Douglas K.

Publication type:

Article

PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06123-2

By:

Xie, Jun;
Zhang, Youli;
Wang, Ziyang;
Jin, Xiaocheng;
Lu, Xiaoli;
Ge, Shengxiang;
Min, Xiaoping

Publication type:

Article

HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06121-4

By:

Liberati, Franco;
Pose Marino, Taiel Maximiliano;
Bottoni, Paolo;
Canestrelli, Daniele;
Castrignanò, Tiziana

Publication type:

Article

FastQTLmapping: an ultra-fast and memory efficient package for mQTL-like analysis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06130-3

By:

Gao, Xingjian;
Li, Jiarui;
Liu, Xinxuan;
Peng, Qianqian;
Jing, Han;
Hadi, Sibte;
Teschendorff, Andrew E.;
Wang, Sijia;
Liu, Fan

Publication type:

Article

metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06137-w

By:

He, Limuxuan;
Zou, Quan;
Wang, Yansu

Publication type:

Article

HPOseq: a deep ensemble model for predicting the protein-phenotype relationships based on protein sequences.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06122-3

By:

Zhao, Kai;
Ji, Zhuocheng;
Zhang, Linlin;
Quan, Na;
Li, Yuheng;
Yu, Guanglei;
Bi, Xuehua

Publication type:

Article

metacp: a versatile software package for combining dependent or independent p-values.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06126-z

By:

Nikolitsa, Evgenia K.;
Kontou, Panagiota I.;
Bagos, Pantelis G.

Publication type:

Article

PRED-LD: efficient imputation of GWAS summary statistics.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06119-y

By:

Manios, Georgios A.;
Michailidi, Aikaterini;
Kontou, Panagiota I.;
Bagos, Pantelis G.

Publication type:

Article

Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06118-z

By:

Guilmineau, Camille;
Tremblay-Franco, Marie;
Vialaneix, Nathalie;
Servien, Rémi

Publication type:

Article

DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06108-1

By:

Ortiz-Martínez, Daniel

Publication type:

Article

Redefining the high variable genes by optimized LOESS regression with positive ratio.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06112-5

By:

Xie, Yue;
Jing, Zehua;
Pan, Hailin;
Xu, Xun;
Fang, Qi

Publication type:

Article

M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06120-5

By:

Sheikholeslami, Mahsa;
Nazari, Mohammad Hasan;
Fassihi, Afshin

Publication type:

Article

Improving data interpretability with new differential sample variance gene set tests.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06117-0

By:

Rahmatallah, Yasir;
Glazko, Galina

Publication type:

Article

DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06113-4

By:

Gomes, Daniel Henrique Ferreira;
Medeiros, Inácio Gomes;
Petta, Tirzah Braz;
Stransky, Beatriz;
de Souza, Jorge Estefano Santana

Publication type:

Article

DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06115-2

By:

Yan, Yuyao;
Chai, Xinyi;
Liu, Jiajun;
Wang, Sijia;
Li, Wenran;
Huang, Tao

Publication type:

Article

Minimum uncertainty as Bayesian network model selection principle.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06104-5

By:

Gogoshin, Grigoriy;
Rodin, Andrei S.

Publication type:

Article