Frontiers in Bioinformatics

Original Research

Published on 17 Jul 2025

NfκBin: a machine learning based method for screening TNF-α induced NF-κB inhibitors

in Drug Discovery in Bioinformatics

Shipra Jain
Ritu Tomer
Sumeet Patiyal
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1573744

2,828 views

Original Research

Published on 16 Jul 2025

Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation

in Protein Bioinformatics

Chelsy Chesterman
Thomas Desautels
Luz-Jeannette Sierra
Kathryn T. Arrildt
Adam Zemla
Edmond Y. Lau
Shivshankar Sundaram
Jason Laliberte
Lynn Chen
Aaron Ruby

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1580967

2,969 views

Original Research

Published on 08 Jul 2025

Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data

in Integrative Bioinformatics

Franz Leonard Böge
Helena U. Zacharias
Stefanie C. Becker
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566162

2,070 views

Original Research

Published on 07 Jul 2025

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

in RNA Bioinformatics

Bing He
Teng Xu
Shaowei Xu
Huqiang Fang
Qingshan Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625145

1,556 views
1 citation

Technology and Code

Published on 02 Jul 2025

GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data

in Genomic Analysis

Ryan M. Tobin
Shikha Singh
Sudhir Kumar
Sayaka Miura

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1615834

1,854 views

Original Research

Published on 30 Jun 2025

Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node

in Genomic Analysis

Sandro 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

2,768 views
1 citation

Technology and Code

Published on 26 Jun 2025

ngx-mol-viewers: Angular components for interactive molecular visualization in bioinformatics

in Data Visualization

Damiano Clementel
Alessio Del Conte
Alexander Miguel Monzon
Silvio C. E. Tosatto

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1586744

1,693 views

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

in Integrative Bioinformatics

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

3,194 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

in Protein Bioinformatics

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

3,073 views
1 citation

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

in Integrative Bioinformatics

Mengyao Sha
Jun Chen
Haifeng Hou
Huaihui Dou
Yan Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606284

3,138 views

Editorial

Published on 19 Jun 2025

Editorial: Expert opinions in genomic analysis

in Genomic Analysis

João C. Setubal
Alberto Paccanaro

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641083

1,103 views

Brief Research Report

Published on 19 Jun 2025

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

in Genomic Analysis

Zhaorong Li
Juan I. Fuxman Bass

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1604418

2,155 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

in Genomic Analysis

Qingfang Ba
Heng Zhou
Zheming Yuan
Zhijun Dai

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1607119

1,572 views

Original Research

Published on 18 Jun 2025

Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization

in Integrative Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1602850

3,103 views
1 citation

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

in Genomic Analysis

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1550730

2,217 views
1 citation

Original Research

Published on 11 Jun 2025

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

in Single Cell Bioinformatics

Nicolina Sciaraffa
Antonino Gagliano
Luigi Augugliaro
Claudia Coronnello

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562410

3,546 views
1 citation

Original Research

Published on 09 Jun 2025

TICTAC: target illumination clinical trial analytics with cheminformatics

in Drug Discovery in Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1579865

2,292 views

Brief Research Report

Published on 06 Jun 2025

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

in Data Visualization

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

3,111 views

Technology and Code

Published on 06 Jun 2025

DeepPredict: a state-of-the-art web server for protein secondary structure and relative solvent accessibility prediction

in Protein Bioinformatics

Wafa Alanazi
Di Meng
Gianluca Pollastri

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1607402

3,450 views
1 citation

Perspective

Published on 30 May 2025

Trail-blazing and keeping pace: building, retaining and expanding image analysis expertise

in Computational BioImaging

David Kirchenbuechler
Mariana De Niz
Constadina Arvanitis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613866

1,903 views
1 citation

Original Research

Published on 29 May 2025

In silico analysis of Triphala-derived polyphenols as inhibitors of TIR–TIR homodimerization in the inflammatory pathway

in Drug Discovery in Bioinformatics

Durgadevi Rajendran
Nalini Easwaran

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1565700

24,204 views

Original Research

Published on 29 May 2025

Bridging the gap between hepatocellular carcinoma management guidelines and personalised medicine: a Bayesian network study

in Network Bioinformatics

Yi-Chun Wang
Daniel Bulte
Michael Brady

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1574797

1,939 views

Brief Research Report

Published on 26 May 2025

Quality over quantity: how to get the best results when using docking for repurposing

in Drug Discovery in Bioinformatics

Lenin Domínguez-Ramírez
Maricruz Anaya-Ruiz
Paulina Cortés-Hernández

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1536504

3,996 views
1 citation

Original Research

Published on 26 May 2025

CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines

in RNA Bioinformatics

Shubham Choudhury
Naman Kumar Mehta
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1585794

1,847 views

609 articles

articles

NfκBin: a machine learning based method for screening TNF-α induced NF-κB inhibitors

Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation

Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data

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

GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data

Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node

ngx-mol-viewers: Angular components for interactive molecular visualization in bioinformatics

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

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

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

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

DeepPredict: a state-of-the-art web server for protein secondary structure and relative solvent accessibility prediction

Trail-blazing and keeping pace: building, retaining and expanding image analysis expertise

In silico analysis of Triphala-derived polyphenols as inhibitors of TIR–TIR homodimerization in the inflammatory pathway

Bridging the gap between hepatocellular carcinoma management guidelines and personalised medicine: a Bayesian network study

Quality over quantity: how to get the best results when using docking for repurposing

CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines