Frontiers in Bioinformatics

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

3,317 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

4,118 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

3,091 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

3,031 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

2,939 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

9,914 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

4,716 views
2 citations

Brief Research Report

Published on 06 May 2025

pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context

in Data Visualization

Marina Leer
George A. Soultoukis
Markus Jähnert
Masoome Oveisi
Dirk Walther
Tim J. Schulz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1523184

2,434 views
1 citation

Methods

Published on 30 Apr 2025

Integrating phylogenies with chronology to assemble the tree of life

in Evolutionary Bioinformatics

Jose Barba-Montoya
Jack M. Craig
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1571568

2,933 views
1 citation

Review

Published on 23 Apr 2025

Artificial intelligence in variant calling: a review

in Genomic Analysis

Omar Abdelwahab
Davoud Torkamaneh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1574359

12,395 views
11 citations

Mini Review

Published on 17 Apr 2025

Primer on machine learning applications in brain immunology

in Single Cell Bioinformatics

Niklas Binder
Ashkan Khavaran
Roman Sankowski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1554010

3,532 views
1 citation

Original Research

Published on 17 Apr 2025

Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis

in Computational BioImaging

Natasha N. Kunchur
Joshua J. A. Poole
Jesse Levine
Tillie-Louise Hackett
Rebecca Thornhill
Leila B. Mostaço-Guidolin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1539936

2,663 views

Original Research

Published on 17 Apr 2025

Biomarker-driven drug repurposing for NAFLD-associated hepatocellular carcinoma using machine learning integrated ensemble feature selection

in Drug Discovery in Bioinformatics

Subhajit Ghosh
Sukhen Das Mandal
Subarna Thakur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1522401

4,704 views
1 citation

Original Research

Published on 16 Apr 2025

Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia

in Genomic Analysis

Mebrie Zemene Kinde
Bizuayehu Kerisew
Tegegne Eshetu
Abebe Tesfaye Gessese

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1572241

3,619 views
1 citation

Original Research

Published on 15 Apr 2025

Identification of novel drug targets and small molecule discovery for MRSA infections

in Drug Discovery in Bioinformatics

Nandha Kumar Subramani
Subhashree Venugopal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562596

4,674 views
4 citations

Original Research

Published on 14 Apr 2025

Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio

in Protein Bioinformatics

Ibukun John Abulude
Isabel Cristina Rodríguez Luna
Alejandro Sánchez Varela
Andrew Camilli
Daniel E. Kadouri
Xianwu Guo

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566486

6,681 views
5 citations

Perspective

Published on 09 Apr 2025

A cost and community perspective on the barriers to microbiome data reuse

in Genomic Analysis

Julia M. Kelliher
Leah Y. D. Johnson
Francisca E. Rodriguez
Jaclyn K. Saunders
Marie E. Kroeger
Buck Hanson
Aaron J. Robinson
Winston E. Anthony
Marc W. Van Goethem
Anders Kiledal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1585717

4,618 views
2 citations

Original Research

Published on 09 Apr 2025

Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients

in Evolutionary Bioinformatics

Nicolina Sciaraffa
Daniele Santoni
Andrea Li Greci
Swonild Ilenia Genovese
Claudia Coronnello
Walter Arancio

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1532981

2,380 views
1 citation

Original Research

Published on 04 Apr 2025

Harnessing computational immunology to design targeted subunit vaccines for infectious bursal disease in poultry

in Drug Discovery in Bioinformatics

Elijah Kolawole Oladipo
Stephen Feranmi Adeyemo
Ayomiposi Isaiah Oshoneye
Hannah Blessing Akintola
Bolatito Islam Elegbede
Tobiloba Uren Ayoomoba
Dorcas Ayomide Atilade
Omolara Omoboye Adegboye
Abuoma Elizabeth Ejikeme
Chris Olamide Balogun

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562997

5,401 views
3 citations

Original Research

Published on 28 Mar 2025

Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study

in Integrative Bioinformatics

Kankana Bhattacharjee
Avik Sengupta
Rahul Kumar
Aryya Ghosh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1536783

4,364 views
2 citations

Original Research

Published on 26 Mar 2025

Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment

in Drug Discovery in Bioinformatics

Samina Malik
Mirza Jawad Ul Hasnain
Gul Zaib
Haleema Saadia
Arif Malik
Ayesha Zahid

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1535482

2,150 views
1 citation

Original Research

Published on 26 Mar 2025

Inhibition potential of margolonone and isomargolonone against the dengue virus protease using molecular modeling approaches

in Drug Discovery in Bioinformatics

Gourav Choudhir
Faiza Iram
Israil
Mohammad Shahid
Anas Shamsi
Md Imtaiyaz Hassan
Asimul Islam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1517115

2,252 views

Original Research

Published on 26 Mar 2025

Streptomyces sp. VITGV156 secondary metabolite binds pathogenic protein PBP2a and Beta-lactamase

in Drug Discovery in Bioinformatics

Veilumuthu Pattapulavar
Sathiyabama Ramanujam
Manisha Shah
Muthu Kumar Thirunavukkarasu
Sivakumar Arumugam
Ramanathan Karuppasamy
Antony V. Samrot
K. Deepasree
Subhashree Venugopal
John Godwin Christopher

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1544800

4,134 views
3 citations

Original Research

Published on 25 Mar 2025

Molecular dynamic simulations to assess the structural variability of ClpV from Enterobacter cloacae

in Protein Bioinformatics

Tehrim Motiwala
Babalwa Nyide
Thandeka Khoza

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1498916

2,205 views
2 citations

609 articles

articles

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

pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context

Integrating phylogenies with chronology to assemble the tree of life

Artificial intelligence in variant calling: a review

Primer on machine learning applications in brain immunology

Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis

Biomarker-driven drug repurposing for NAFLD-associated hepatocellular carcinoma using machine learning integrated ensemble feature selection

Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia

Identification of novel drug targets and small molecule discovery for MRSA infections

Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio

A cost and community perspective on the barriers to microbiome data reuse

Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients

Harnessing computational immunology to design targeted subunit vaccines for infectious bursal disease in poultry

Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study

Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment

Inhibition potential of margolonone and isomargolonone against the dengue virus protease using molecular modeling approaches

Streptomyces sp. VITGV156 secondary metabolite binds pathogenic protein PBP2a and Beta-lactamase

Molecular dynamic simulations to assess the structural variability of ClpV from Enterobacter cloacae