Frontiers in Bioinformatics

Original Research

Published on 06 May 2025

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

Ankita Lawarde
Masuma Khatun
Prakash Lingasamy
Andres Salumets
Vijayachitra Modhukur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1571476

4,177 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1523184

2,205 views
1 citation

Methods

Published on 30 Apr 2025

Integrating phylogenies with chronology to assemble the tree of life

Jose Barba-Montoya
Jack M. Craig
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1571568

2,596 views
1 citation

Review

Published on 23 Apr 2025

Artificial intelligence in variant calling: a review

Omar Abdelwahab
Davoud Torkamaneh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1574359

10,632 views
7 citations

Mini Review

Published on 17 Apr 2025

Primer on machine learning applications in brain immunology

Niklas Binder
Ashkan Khavaran
Roman Sankowski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1554010

3,152 views
1 citation

Original Research

Published on 17 Apr 2025

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

Subhajit Ghosh
Sukhen Das Mandal
Subarna Thakur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1522401

4,318 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

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

2,303 views

Original Research

Published on 16 Apr 2025

Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia

Mebrie Zemene Kinde
Bizuayehu Kerisew
Tegegne Eshetu
Abebe Tesfaye Gessese

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1572241

3,331 views
1 citation

Original Research

Published on 15 Apr 2025

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

Nandha Kumar Subramani
Subhashree Venugopal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562596

4,177 views
1 citation

Original Research

Published on 14 Apr 2025

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

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

5,867 views
4 citations

Perspective

Published on 09 Apr 2025

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

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

4,179 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1532981

2,138 views

Original Research

Published on 04 Apr 2025

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

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

4,935 views
2 citations

Original Research

Published on 28 Mar 2025

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

Kankana Bhattacharjee
Avik Sengupta
Rahul Kumar
Aryya Ghosh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1536783

3,788 views

Original Research

Published on 26 Mar 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1535482

1,880 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1517115

1,891 views

Original Research

Published on 26 Mar 2025

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

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

3,593 views
3 citations

Original Research

Published on 25 Mar 2025

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

Tehrim Motiwala
Babalwa Nyide
Thandeka Khoza

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1498916

1,876 views
2 citations

Original Research

Published on 20 Mar 2025

Divergent evolution of low-complexity regions in the vertebrate CPEB protein family

Serena Vaglietti
Stefania Boggio Bozzo
Mirella Ghirardi
Ferdinando Fiumara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1491735

3,915 views
1 citation

Brief Research Report

Published on 18 Mar 2025

ORF1ab codon frequency model predicts host-pathogen relationship in orthocoronavirinae

Phillip E. Davis
Joseph A. Russell

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562668

1,542 views

Original Research

Published on 17 Mar 2025

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level

Amy S. Graham
Fadheela Patel
Francesca Little
Andre van der Kouwe
Mamadou Kaba
Martha J. Holmes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1484113

2,927 views
1 citation

Brief Research Report

Published on 11 Mar 2025

Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer

Dawei Jiang
Zixi Chen
Hongli Du

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566174

5,133 views

Original Research

Published on 10 Mar 2025

Urinary based biomarkers identification and genetic profiling in Parkinson’s disease: a systematic review of metabolomic studies

Neetu Rani Dhiman
Surbhi Singh
Royana Singh
Anand Kumar
Varun Kumar Singh
Abhishek Pathak
Rameshwar Nath Chaurasia
Vijay Nath Mishra
Niraj Kumar Srivastava
Swati Sahu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1513790

3,051 views
5 citations

Data Report

Published on 10 Mar 2025

An extended miRNA repertoire in Rattus norvegicus

Julienne Lehmann
Ali Yazbeck
Jörg Hackermüller
Sebastian Canzler

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1545680

1,326 views
1 citation

180 Publications

volumes

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

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

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

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

Divergent evolution of low-complexity regions in the vertebrate CPEB protein family

ORF1ab codon frequency model predicts host-pathogen relationship in orthocoronavirinae

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level

Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer

Urinary based biomarkers identification and genetic profiling in Parkinson’s disease: a systematic review of metabolomic studies

An extended miRNA repertoire in Rattus norvegicus