Frontiers in Bioinformatics

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

4,059 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

2,449 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

2,574 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

2,025 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

2,629 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

1,700 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

2,428 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

2,303 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

1,781 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

1,251 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

2,071 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

3,671 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

3,726 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

3,010 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

2,479 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

2,212 views

Original Research

Published on 17 Jul 2025

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

in Drug Discovery in Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1573744

2,706 views

Original Research

Published on 16 Jul 2025

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

in Protein Bioinformatics

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

2,881 views

Original Research

Published on 08 Jul 2025

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

in Integrative Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1566162

1,994 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

in RNA Bioinformatics

Bing He
Teng Xu
Shaowei Xu
Huqiang Fang
Qingshan Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1625145

1,479 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

in Genomic Analysis

Ryan M. Tobin
Shikha Singh
Sudhir Kumar
Sayaka Miura

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1615834

1,800 views

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

in Genomic Analysis

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

2,618 views
1 citation

Technology and Code

Published on 26 Jun 2025

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

in Data Visualization

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1586744

1,621 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

in Integrative Bioinformatics

Yuyun Jia
Yanping Cao
Qin Yin
Xueqian Li
Xiu Wen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1594971

3,068 views

601 articles

articles

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

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