Frontiers in Bioinformatics

Original Research

Published on 26 Jun 2025

Identification of immune and major depressive disorder-related diagnostic markers for early nonalcoholic fatty liver disease by WGCNA and machine learning

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

125 views

Original Research

Published on 25 Jun 2025

In-silico molecular analysis and blocking of the viral G protein of Nipah virus interacting with ephrin B2 and B3 receptor by using peptide mass fingerprinting

Ayesha Sajjad
Ihteshamul Haq
Rabia Syed
Faheem Anwar
Muhammad Hamza
Muhammad Musharaf
Tehmina Kiani
Faisal Nouroz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1526566

354 views

Original Research

Published on 25 Jun 2025

Integrated single-cell and bulk RNA dequencing to identify and validate prognostic genes related to T Cell senescence in acute myeloid leukemia

Mengyao Sha
Jun Chen
Haifeng Hou
Huaihui Dou
Yan Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606284

182 views

Original Research

Accepted on 24 Jun 2025

Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins

bing he
teng xu
shaowei xu
huqiang fang
Qingshan Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625145

Original Research

Accepted on 23 Jun 2025

Understanding the selectivity in silico of colistin and daptomycin toward Gram-negative and Gram-positive bacteria, respectively, from the interaction with membrane phospholipids

Jose Oñate
Yamil Liscano
Yesid Aristizabal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1569480

Technology and Code

Accepted on 19 Jun 2025

Frontiers in Bioinformatics Genomic Analysis Technology and Code GenoPath: A pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data

Ryan M Tobin
Shikha Singh
Sudhir Kumar
Sayaka Miura

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1615834

292 views

Editorial

Published on 19 Jun 2025

Editorial: Expert opinions in genomic analysis

João C. Setubal
Alberto Paccanaro

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641083

236 views

Brief Research Report

Published on 19 Jun 2025

ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets

Zhaorong Li
Juan I. Fuxman Bass

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1604418

402 views

Methods

Published on 18 Jun 2025

Enhancing genomic prediction in Arabidopsis thaliana with optimized SNP subset by leveraging gene ontology priors and bin-based combinatorial optimization

Qingfang Ba
Heng Zhou
Zheming Yuan
Zhijun Dai

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1607119

280 views

Original Research

Published on 18 Jun 2025

Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization

Ehsan Saghapour
Rahul Sharma
Delower Hossain
Kevin Song
Zhandos Sembay
Jake Y. Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1602850

624 views

Original Research

Accepted on 17 Jun 2025

Using Deep Neural Networks and LASSO Regression to Predict miRNA Expression Changes Based on mRNA Data

Franz Leonard Böge
Helena U Zacharias
Stefanie Christine Becker
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566162

198 views

Original Research

Published on 17 Jun 2025

Utility of regional STR marker variations in Tunisian and sub-Saharan populations: insights into forensic and population genetics

Asma Attaoui
Hajer Foddha
Houcemeddine Othman
Hassen Ben Abdennebi
Amel Haj Khelil

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1550730

388 views

Original Research

Accepted on 13 Jun 2025

Long-Read Microbial Genome Assembly, Gene Prediction and Functional Annotation: A Service of the MIRRI ERIC Italian Node

Sandro Gepiro Gepiro Contaldo
Antonio d'Acierno
Lorenzo Bosio
Francesco Venice
Elisa Li Perottino
Janneth Estefania Hoyos Rea
Giovanna Cristina Varese
Francesca Cordero
Marco Beccuti

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1632189

150 views

Original Research

Published on 11 Jun 2025

Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics

Nicolina Sciaraffa
Antonino Gagliano
Luigi Augugliaro
Claudia Coronnello

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562410

615 views

Original Research

Published on 09 Jun 2025

TICTAC: target illumination clinical trial analytics with cheminformatics

Jeremiah I. Abok
Jeremy S. Edwards
Jeremy J. Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1579865

662 views

Brief Research Report

Published on 06 Jun 2025

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

Maxime Maria
Valentin Guillaume
Simon Guionnière
Nicolas Dacquay
Cyprien Plateau–Holleville
Vincent Larroque
Jean Lardé
Yassine Naimi
Jean-Philip Piquemal
Guillaume Levieux

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1588661

1,114 views

466 Publications

Volume 5 - 2025

Identification of immune and major depressive disorder-related diagnostic markers for early nonalcoholic fatty liver disease by WGCNA and machine learning

In-silico molecular analysis and blocking of the viral G protein of Nipah virus interacting with ephrin B2 and B3 receptor by using peptide mass fingerprinting

Integrated single-cell and bulk RNA dequencing to identify and validate prognostic genes related to T Cell senescence in acute myeloid leukemia

Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins

Understanding the selectivity in silico of colistin and daptomycin toward Gram-negative and Gram-positive bacteria, respectively, from the interaction with membrane phospholipids

Frontiers in Bioinformatics Genomic Analysis Technology and Code GenoPath: A pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data

Editorial: Expert opinions in genomic analysis

ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets

Enhancing genomic prediction in Arabidopsis thaliana with optimized SNP subset by leveraging gene ontology priors and bin-based combinatorial optimization

Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization

Using Deep Neural Networks and LASSO Regression to Predict miRNA Expression Changes Based on mRNA Data

Utility of regional STR marker variations in Tunisian and sub-Saharan populations: insights into forensic and population genetics

Long-Read Microbial Genome Assembly, Gene Prediction and Functional Annotation: A Service of the MIRRI ERIC Italian Node

Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics

TICTAC: target illumination clinical trial analytics with cheminformatics

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model