Frontiers in Bioinformatics

Original Research

Published on 10 Dec 2025

Neurogenic locus notch homolog protein 1 (NOTCH 1) SNP informatics coupled with intrinsically disordered regions and post-translational modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD)

Pearl John
C. Sudandiradoss

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1641521

656 views

Review

Accepted on 08 Dec 2025

Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges

Boris Tchatchoua Ngassam
Huilin Niu
Valeryia Shydlouskaya
Tallulah Suzanne Andrews

Frontiers in Bioinformatics

339 views

Original Research

Accepted on 05 Dec 2025

Visualizing Stability: A Sensitivity Analysis Framework for t-SNE Embeddings

Susanne Zabel
Philipp Hennig
Kay Katja Nieselt

Frontiers in Bioinformatics

218 views

Original Research

Published on 05 Dec 2025

Uncovering human kinase substrates in nipah proteome

Vineetha Shaji
Akash Anil
Ayisha A. Jabbar
Althaf Mahin
Ahmad Rafi
Amjesh Revikumar
Sowmya Soman
Ganesh Prasad
Sneha M. Pinto
Yashwanth Subbannayya

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1678189

1,514 views

Original Research

Published on 04 Dec 2025

Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data

Arsenij Ustjanzew
Federico Marini
Saskia Wagner
Arthur Wingerter
Roger Sandhoff
Jörg Faber
Claudia Paret

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1705930

1,002 views

Original Research

Published on 03 Dec 2025

Subtractive genomic approach to uncover novel drug targets in Salmonella typhimurium and computational screening of food-based polyphenols as inhibitors

Mohammed Naveez Valathoor
Subhashree Venugopal
Anand Prem Rajan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1695217

1,004 views

Correction

Published on 03 Dec 2025

Correction: 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.2025.1750582

506 views

Original Research

Accepted on 02 Dec 2025

KG2ML: Integrating Knowledge Graphs and Positive Unlabeled Learning for Identifying Disease-Associated Genes

Praveen Kumar
Vincent T. Metzger
Swastika T. Purushotham
Priyansh Kedia
Cristian G Bologa
Christophe G. Lambert
Jeremy J Yang

Frontiers in Bioinformatics

183 views

Original Research

Published on 02 Dec 2025

Genomics-driven drug repurposing and novel targets identification for sickle cell disease in Saudi patients

Ali Alghubayshi
Mohammad A. Alshabeeb
Dayanjan Wijesinghe
Mohammed AlAwadh
Suad Alshammari
Khalifa Alrajeh
Mona A. Alkhairi
Imadul Islam
Ahmed Alaskar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1671626

1,361 views

Original Research

Published on 02 Dec 2025

Functional and structural impacts of oncogenic missense variants on human polo-like kinase 1 protein

Gayatri Munieswaran
Venkatraman Manickam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1680578

986 views

Original Research

Accepted on 01 Dec 2025

Altered circRNAs: A novel potential mechanism for the functions of extracellular vesicles derived from platelet-rich plasma

Lifeng Niu
Yanli Wang
Yao Gao
Jun Zhang

Frontiers in Bioinformatics

166 views

Original Research

Published on 28 Nov 2025

Beyond Tanimoto: a learned bioactivity similarity index enhances ligand discovery

Gustavo Schottlender
Juan Manuel Prieto
Marcelo A. Marti
Dario Fernández Do Porto

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1695353

976 views

Review

Accepted on 27 Nov 2025

Advances in Protein-Protein Interaction Prediction: A Deep Learning Perspective

Noor Alkhateeb
Mamoun Awad

Frontiers in Bioinformatics

370 views

Brief Research Report

Published on 27 Nov 2025

Higher frequency of prokaryotic low complexity regions in core and orthologous genes

Vineet Saravanan
Alexander Kravetz
Fabia Ursula Battistuzzi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1673480

556 views

Technology and Code

Published on 25 Nov 2025

Bacteriocin prediction through cross-validation-based and hypergraph-based feature evaluation approaches

Suraiya Akhter
John H. Miller

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1694009

890 views

Original Research

Accepted on 24 Nov 2025

Stain-free artificial intelligence-assisted light microscopy for the identification of leukocyte morphology change in presence of bacteria

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

Frontiers in Bioinformatics

200 views

Original Research

Accepted on 21 Nov 2025

Identification of Key Genes in Phosgene-induced Acute Lung Injury Using Bioinformatics Methods

Lina Wang
Yuntao Wang
Daikun He

Frontiers in Bioinformatics

241 views

Technology and Code

Published on 21 Nov 2025

inDAGO: a user-friendly interface for seamless dual and bulk RNA-Seq analysis

Gaetano Aufiero
Carmine Fruggiero
Nunzio D’Agostino

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1696823

904 views

Brief Research Report

Published on 19 Nov 2025

Computational analysis of transcriptome data and mapping of functional networks in Parkinson’s disease

Konstantinos Perperidis
Themis P. Exarchos
Aristidis G. Vrahatis
Panagiotis Vlamos
Marios G. Krokidis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1690229

1,197 views

Methods

Published on 19 Nov 2025

Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling

Hiba Orsud
Sumaya Zoughbor
Fatima AlDhaheri
Khalid Hajissa
Manar Refaey
Suad Ajab
Khaled Alswaider
Nora Mohamed
Obaid Alkaabi
Zakeya Al Rasbi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1690766

909 views

Brief Research Report

Published on 19 Nov 2025

Completing a molecular timetree of Afrotheria

Jack M. Craig
Whitney L. Fisher
Allan S. Thomas
S. Blair Hedges
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1710926

1,320 views

Original Research

Published on 18 Nov 2025

Food-derived linear vs. rationally designed cyclic peptides as potent TNF-alpha inhibitors: an integrative computational study

Manisha Shah
Sivakumar Arumugam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1716375

1,081 views

Original Research

Published on 18 Nov 2025

Role of histone-lysine N-methyltransferase 2D (KMT2D) in MEK-ERK signaling-mediated epigenetic regulation: a phosphoproteomics perspective

Sreeshma Ravindran Kammarambath
Leona Dcunha
Athira Perunelly Gopalakrishnan
Amal Fahma
Neelam Krishna
Altaf Mahin
Samseera Ummar
Prathik Basthikoppa Shivamurthy
Inamul Hasan Madar
Rajesh Raju

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1683469

1,310 views

Original Research

Published on 17 Nov 2025

QSAR-guided discovery of novel KRAS inhibitors for lung cancer therapy

Osasan Stephen Adebayo
George Oche Ambrose
Daramola Olusola
Adefolalu Oluwafemi
Hind A. Alzahrani
Abdulkarim Hasan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1663846

968 views
1 citation

180 Publications

volumes

Neurogenic locus notch homolog protein 1 (NOTCH 1) SNP informatics coupled with intrinsically disordered regions and post-translational modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD)

Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges

Visualizing Stability: A Sensitivity Analysis Framework for t-SNE Embeddings

Uncovering human kinase substrates in nipah proteome

Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data

Subtractive genomic approach to uncover novel drug targets in Salmonella typhimurium and computational screening of food-based polyphenols as inhibitors

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

KG2ML: Integrating Knowledge Graphs and Positive Unlabeled Learning for Identifying Disease-Associated Genes

Genomics-driven drug repurposing and novel targets identification for sickle cell disease in Saudi patients

Functional and structural impacts of oncogenic missense variants on human polo-like kinase 1 protein

Altered circRNAs: A novel potential mechanism for the functions of extracellular vesicles derived from platelet-rich plasma

Beyond Tanimoto: a learned bioactivity similarity index enhances ligand discovery

Advances in Protein-Protein Interaction Prediction: A Deep Learning Perspective

Higher frequency of prokaryotic low complexity regions in core and orthologous genes

Bacteriocin prediction through cross-validation-based and hypergraph-based feature evaluation approaches

Stain-free artificial intelligence-assisted light microscopy for the identification of leukocyte morphology change in presence of bacteria

Identification of Key Genes in Phosgene-induced Acute Lung Injury Using Bioinformatics Methods

inDAGO: a user-friendly interface for seamless dual and bulk RNA-Seq analysis

Computational analysis of transcriptome data and mapping of functional networks in Parkinson’s disease

Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling

Completing a molecular timetree of Afrotheria

Food-derived linear vs. rationally designed cyclic peptides as potent TNF-alpha inhibitors: an integrative computational study

Role of histone-lysine N-methyltransferase 2D (KMT2D) in MEK-ERK signaling-mediated epigenetic regulation: a phosphoproteomics perspective

QSAR-guided discovery of novel KRAS inhibitors for lung cancer therapy