Frontiers in Bioinformatics

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

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

2,687 views
1 citation

Technology and Code

Published on 26 Jun 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1586744

1,646 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

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

3,145 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

2,993 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

Mengyao Sha
Jun Chen
Haifeng Hou
Huaihui Dou
Yan Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606284

3,096 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

1,096 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

2,118 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

1,546 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

3,050 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1550730

2,162 views
1 citation

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

3,454 views
1 citation

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

2,254 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

3,057 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

Wafa Alanazi
Di Meng
Gianluca Pollastri

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1607402

3,401 views
1 citation

Perspective

Published on 30 May 2025

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

David Kirchenbuechler
Mariana De Niz
Constadina Arvanitis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613866

1,869 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

Durgadevi Rajendran
Nalini Easwaran

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1565700

24,157 views

Original Research

Published on 29 May 2025

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

Yi-Chun Wang
Daniel Bulte
Michael Brady

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1574797

1,898 views

Brief Research Report

Published on 26 May 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1536504

3,900 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

Shubham Choudhury
Naman Kumar Mehta
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1585794

1,826 views

Brief Research Report

Published on 22 May 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1575346

3,262 views

Original Research

Published on 19 May 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1575790

4,076 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

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

3,051 views
1 citation

Technology and Code

Published on 08 May 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1556361

2,887 views
2 citations

Perspective

Published on 08 May 2025

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

Leonora Martínez-Núñez

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1589122

2,985 views

604 Publications

volumes

Volume 5 - 2025

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

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

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

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