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

in Integrative Bioinformatics

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

3,082 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

2,908 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

3,054 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

1,092 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

2,088 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

1,527 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

3,008 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

2,117 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

3,369 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

2,218 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

3,034 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

3,354 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

1,856 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

24,115 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

1,881 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

3,844 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

1,794 views

Brief Research Report

Published on 22 May 2025

MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data

in RNA Bioinformatics

Yutaka Nakachi
Jianbin Du
Risa Watanabe
Yutaro Yanagida
Miki Bundo
Kazuya Iwamoto

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1575346

3,212 views

Original Research

Published on 19 May 2025

Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer

in Integrative Bioinformatics

Yizhou Wang
Priyanka Bhandary
Kevin Griffin
Jason H. Moore
Xue Li
Zhiping Paul Wang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1575790

4,031 views
3 citations

Original Research

Published on 13 May 2025

Exploiting subtractive genomics to identify novel drug targets and new immunogenic candidates against Bordetella pertussis: an in silico study

in Drug Discovery in Bioinformatics

Mahshid Khazani Asforooshani
Narjes Noori Goodarzi
Behzad Shahbazi
Nayereh Rezaie Rahimi
Kimia Mahdavian
Mahdi Rohani
Farzad Badmasti

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1570054

3,015 views
1 citation

Perspective

Published on 08 May 2025

Structural biology meets typography: using protein structures to inspire creative expression and connect diverse audiences

in Data Visualization

Leonora Martínez-Núñez

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1589122

2,940 views

Technology and Code

Published on 08 May 2025

micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data

in Genomic Analysis

Rachel Griffard-Smith
Emily Schueddig
Diane E. Mahoney
Prabhakar Chalise
Devin C. Koestler
Dong Pei

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1556361

2,845 views
2 citations

Original Research

Published on 06 May 2025

Computational drug discovery of potential 5α-reductase phytochemical inhibitors and hair growth promotion using in silico techniques

in Drug Discovery in Bioinformatics

Behnam Hasannejad-Asl
Farkhondeh Pooresmaeil
Sareh azadi
Ali Najafi
Ali Esmaeili
Saeid Bagheri-Mohammadi
Bahram Kazemi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1570101

9,581 views
3 citations

Original Research

Published on 06 May 2025

Tumor tissue-of-origin classification using miRNA-mRNA-lncRNA interaction networks and machine learning methods

in RNA Bioinformatics

Ankita Lawarde
Masuma Khatun
Prakash Lingasamy
Andres Salumets
Vijayachitra Modhukur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1571476

4,646 views
2 citations

602 articles

articles

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

MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data

Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer

Exploiting subtractive genomics to identify novel drug targets and new immunogenic candidates against Bordetella pertussis: an in silico study

Structural biology meets typography: using protein structures to inspire creative expression and connect diverse audiences

micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data

Computational drug discovery of potential 5α-reductase phytochemical inhibitors and hair growth promotion using in silico techniques

Tumor tissue-of-origin classification using miRNA-mRNA-lncRNA interaction networks and machine learning methods