Frontiers in Bioinformatics

Perspective

Published on 29 Aug 2025

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

Patricia Agudelo-Romero
Talya Conradie
Jose Antonio Caparros-Martin
David Jimmy Martino
Anthony Kicic
Stephen Michael Stick
Christopher Hakkaart
Abhinav Sharma
the Theme Collaboration Group

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1610015

2,610 views

Original Research

Published on 26 Aug 2025

Identifying novel therapeutic targets for non-alcoholic fatty liver disease using bioinformatics approaches: from drug repositioning to traditional Chinese medicine

Jingmin Zhang
Tianwei Meng
Weiqi Gao
Xinghua Li
Juan Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613985

3,174 views

Original Research

Published on 20 Aug 2025

Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler

Kleber Padovani
Rafael Cabral Borges
Roberto Xavier
André Carlos Carvalho
Anna Reali
Annie Chateau
Ronnie Alves

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1633623

2,238 views

Original Research

Published on 20 Aug 2025

Novel deep learning for multi-class classification of Alzheimer’s in disability using MRI datasets

Sumaiya Binte Shahid
Maleeha Kaikaus
Md. Hasanul Kabir
Mohammad Abu Yousuf
A. K. M. Azad
A. S. Al-Moisheer
Naif Alotaibi
Salem A. Alyami
Touhid Bhuiyan
Mohammad Ali Moni

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1567219

4,168 views

Original Research

Published on 18 Aug 2025

Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma

Shangyi Luo
Li Liu
Yang Sun
Jian Shi
Yajing Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1669236

2,474 views
1 citation

Brief Research Report

Published on 15 Aug 2025

DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics

Christopher Golden
David J. Studholme
Rhys A. Farrer

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1634042

2,683 views
1 citation

Brief Research Report

Published on 14 Aug 2025

Precision medicine on a budget in Africa: using existing genetic data to mitigate adverse drug reactions to conventional cancer drugs

Alexandra Lindsey Djomkam Zune
Charles Ochieng’ Olwal
Emmanuel Agbeli
Abdoulaye Baniré Diallo
Emmanuella Amoako
Yaw Bediako
Lily Paemka

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1555637

2,059 views
1 citation

Original Research

Published on 14 Aug 2025

Stain-free artificial intelligence-assisted light microscopy for the identification of blood cells in microfluidic flow

Alexander Hunt
Holger Schulze
Kay Samuel
Robert B. Fisher
Till T. Bachmann

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1628724

2,710 views
1 citation

Original Research

Published on 12 Aug 2025

Sequence-based prioritization of i-Motif candidates in the human genome

Veronica Remori
Michela Prest
Mauro Fasano

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1657841

1,748 views

Original Research

Published on 07 Aug 2025

Internal fossil constraints have more effect on the age estimates of crown Palaeognathae than different phylogenomic data type

Alexandre Pedro Selvatti
Naoko Takezaki

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1563786

2,487 views

Original Research

Published on 05 Aug 2025

In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes

Raghad Alshelaiel
Abdulmohsen Alkushi
Lolwah Abdullah Alriyees
Abir Abdullah Alamro
Humidah Alanazi
Areej Alhareeri
Bader AlMuzzaini
Mamoon Rashid

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1606828

2,385 views

Original Research

Published on 01 Aug 2025

Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer

Xiaohua An
Xiaoxue Huang
Qiujie Yu
Yiyue Tang
Yan Wang
Huasu Chen
Yafei Zhang
Qianhao Huang
Yudi Rao
Guomei Hu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1605681

1,812 views

Original Research

Published on 01 Aug 2025

The bacteriostatic regulation of luteolin from honeysuckle by protein network interaction

Jianfeng Zhang
Mujun Chen
Dianzeng Yang
Yanjie Jia

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1637479

1,283 views

Original Research

Published on 28 Jul 2025

Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase

Riya Nalwa
Anis Ahmad Chaudhary
Mandeep Chouhan
Prashant Kumar Tiwari
Saurabh Gupta
Hassan Ahmed Rudayni
Vivek Dhar Dwivedi
Sanjay Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1637207

2,112 views
1 citation

Original Research

Published on 28 Jul 2025

Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

Tianle Xue
Yunpeng Chen
Xiaomeng Li
Zhixiang Zhou
Qiyang Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1599098

3,721 views

Original Research

Published on 21 Jul 2025

NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach

Delower Hossain
Ehsan Saghapour
Jake Y. Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1603133

3,771 views

Original Research

Published on 18 Jul 2025

IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions

Clara Shionyu-Mitusyama
Satoshi Ohmori
Subaru Hirata
Hirokazu Ishida
Tsuyoshi Shirai

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1627836

3,073 views

Original Research

Published on 18 Jul 2025

Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data

Qiu Wang
Hong Yang
Fang Li
Song Ge
Ling Ji
Xiaofeng Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1626153

2,509 views

Original Research

Published on 17 Jul 2025

Understanding the selectivity in silico of colistin and daptomycin toward gram-negative and gram-positive bacteria, respectively, from the interaction with membrane phospholipids

Yesid Aristizabal
Yamil Liscano
José Oñate-Garzón

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1569480

2,266 views

Original Research

Published on 17 Jul 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1573744

2,763 views

Original Research

Published on 16 Jul 2025

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

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

2,928 views

Original Research

Published on 08 Jul 2025

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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566162

2,040 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

Bing He
Teng Xu
Shaowei Xu
Huqiang Fang
Qingshan Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625145

1,521 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

Ryan M. Tobin
Shikha Singh
Sudhir Kumar
Sayaka Miura

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1615834

1,825 views

604 Publications

volumes

Volume 5 - 2025

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

Identifying novel therapeutic targets for non-alcoholic fatty liver disease using bioinformatics approaches: from drug repositioning to traditional Chinese medicine

Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler

Novel deep learning for multi-class classification of Alzheimer’s in disability using MRI datasets

Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma

DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics

Precision medicine on a budget in Africa: using existing genetic data to mitigate adverse drug reactions to conventional cancer drugs

Stain-free artificial intelligence-assisted light microscopy for the identification of blood cells in microfluidic flow

Sequence-based prioritization of i-Motif candidates in the human genome

Internal fossil constraints have more effect on the age estimates of crown Palaeognathae than different phylogenomic data type

In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes

Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer

The bacteriostatic regulation of luteolin from honeysuckle by protein network interaction

Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase

Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer

NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach

IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions

Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data

Understanding the selectivity in silico of colistin and daptomycin toward gram-negative and gram-positive bacteria, respectively, from the interaction with membrane phospholipids

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