Frontiers in Bioinformatics

Technology and Code

Published on 04 Sep 2025

Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

in Protein Bioinformatics

Grigorios Koulouras
Yingrong Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1576317

3,997 views

Brief Research Report

Published on 04 Sep 2025

Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling

in Data Visualization

Tim Breitenbach
Thomas Dandekar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1528515

1,816 views
1 citation

Editorial

Published on 02 Sep 2025

Editorial: Networks and graphs in biological data: current methods, opportunities and challenges

in Network Bioinformatics

Derek L. Thompson
Hsiang-Yun Wu
Christopher W. Bartlett
William C. Ray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1685992

1,445 views
1 citation

Data Report

Published on 02 Sep 2025

Germline mutation profiling of breast cancer patients using a non-BRCA sequencing panel

in Genomic Analysis

Sonar Soni Panigoro
Rafika Indah Paramita
Fadilah Fadilah
Septelia Inawati Wanandi
Aisyah Fitriannisa Prawiningrum
Linda Erlina
Wahyu Dian Utari
Ajeng Megawati Fajrin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1620025

2,059 views

Original Research

Published on 01 Sep 2025

COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices

in Protein Bioinformatics

Rafael Pereira Lemos
Diego Mariano
Sabrina De Azevedo Silveira
Raquel C. de Melo-Minardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1630078

1,979 views
2 citations

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

in Integrative Bioinformatics

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

2,663 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

in Drug Discovery in Bioinformatics

Jingmin Zhang
Tianwei Meng
Weiqi Gao
Xinghua Li
Juan Xu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613985

3,217 views

Original Research

Published on 20 Aug 2025

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

in Genomic Analysis

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

2,309 views

Original Research

Published on 20 Aug 2025

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

in Computational BioImaging

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

4,246 views

Original Research

Published on 18 Aug 2025

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

in Integrative Bioinformatics

Shangyi Luo
Li Liu
Yang Sun
Jian Shi
Yajing Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1669236

2,509 views
1 citation

Brief Research Report

Published on 15 Aug 2025

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

in Genomic Analysis

Christopher Golden
David J. Studholme
Rhys A. Farrer

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1634042

2,727 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

in Drug Discovery in Bioinformatics

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

2,113 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

in Computational BioImaging

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1628724

2,768 views
1 citation

Original Research

Published on 12 Aug 2025

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

in Genomic Analysis

Veronica Remori
Michela Prest
Mauro Fasano

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1657841

1,782 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

in Evolutionary Bioinformatics

Alexandre Pedro Selvatti
Naoko Takezaki

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1563786

2,548 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

in Integrative Bioinformatics

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

2,442 views

Original Research

Published on 01 Aug 2025

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

in RNA Bioinformatics

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

1,842 views

Original Research

Published on 01 Aug 2025

The bacteriostatic regulation of luteolin from honeysuckle by protein network interaction

in Network Bioinformatics

Jianfeng Zhang
Mujun Chen
Dianzeng Yang
Yanjie Jia

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1637479

1,301 views

Original Research

Published on 28 Jul 2025

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

in Drug Discovery in Bioinformatics

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

2,156 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

in Integrative Bioinformatics

Tianle Xue
Yunpeng Chen
Xiaomeng Li
Zhixiang Zhou
Qiyang Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1599098

3,755 views

Original Research

Published on 21 Jul 2025

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

in Integrative Bioinformatics

Delower Hossain
Ehsan Saghapour
Jake Y. Chen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1603133

3,813 views

Original Research

Published on 18 Jul 2025

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

in Protein Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1627836

3,132 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

in Single Cell Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1626153

2,562 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

in Protein Bioinformatics

Yesid Aristizabal
Yamil Liscano
José Oñate-Garzón

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1569480

2,303 views

609 articles

articles

Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides

Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling

Editorial: Networks and graphs in biological data: current methods, opportunities and challenges

Germline mutation profiling of breast cancer patients using a non-BRCA sequencing panel

COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices

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