Frontiers in Bioinformatics

Editorial

Published on 09 Aug 2024

Editorial: Big data and artificial intelligence for genomics and therapeutics – Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS)

Huixiao Hong
Inimary Toby-Ogundeji
Robert J. Doerksen
Zhaohui Steve Qin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1470107

1,887 views

Editorial

Published on 09 Aug 2024

Editorial: Machine learning approaches to antimicrobials: discovery and resistance

Shira L. Broschat
Shirley W. I. Siu
Cesar de la Fuente-Nunez

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1458237

3,204 views
2 citations

Original Research

Published on 26 Jul 2024

Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences

Abdullahi Tunde Aborode
Neeraj Kumar
Christopher Busayo Olowosoke
Tope Abraham Ibisanmi
Islamiyyah Ayoade
Haruna Isiyaku Umar
Abdullahi Temitope Jamiu
Basit Bolarinwa
Zainab Olapade
Abidemi Ruth Idowu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1411935

4,183 views
6 citations

Original Research

Published on 25 Jul 2024

A hybrid approach for predicting transcription factors

Sumeet Patiyal
Palak Tiwari
Mohit Ghai
Aman Dhapola
Anjali Dhall
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1425419

3,242 views
3 citations

Original Research

Published on 15 Jul 2024

CAEM-GBDT: a cancer subtype identifying method using multi-omics data and convolutional autoencoder network

Jiquan Shen
Xuanhui Guo
Hanwen Bai
Junwei Luo

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1403826

2,238 views
2 citations

Original Research

Published on 10 Jul 2024

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters

Steven Weaver
Vanessa M. Dávila Conn
Daniel Ji
Hannah Verdonk
Santiago Ávila-Ríos
Andrew J. Leigh Brown
Joel O. Wertheim
Sergei L. Kosakovsky Pond

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1400003

3,385 views
4 citations

Original Research

Published on 08 Jul 2024

Network analysis of driver genes in human cancers

Shruti S. Patil
Steven A. Roberts
Assefaw H. Gebremedhin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1365200

3,755 views
2 citations

Mini Review

Published on 08 Jul 2024

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations

Mahnoor N. Gondal
Saad Ur Rehman Shah
Arul M. Chinnaiyan
Marcin Cieslik

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1417428

10,479 views
16 citations

Review

Published on 03 Jul 2024

DNA structural features and variability of complete MHC locus sequences

Trudy M. Wassenaar
Terry Harville
Jonathan Chastain
Visanu Wanchai
David W. Ussery

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1392613

4,559 views
5 citations

Original Research

Published on 01 Jul 2024

Maximum-scoring path sets on pangenome graphs of constant treewidth

Broňa Brejová
Travis Gagie
Eva Herencsárová
Tomáš Vinař

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1391086

2,057 views

Original Research

Published on 24 Jun 2024

The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders

Alexander G. Lucaci
William E. Brew
Jason Lamanna
Avery Selberg
Vincenzo Carnevale
Anna R. Moore
Sergei L. Kosakovsky Pond

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1381540

2,631 views
1 citation

Perspective

Published on 20 Jun 2024

Bioinformatics proficiency among African students

Ashraf Akintayo Akintola
Abdullahi Tunde Aborode
Muhammed Taofiq Hamza
Augustine Amakiri
Benjamin Moore
Suliat Abdulai
Oluyinka Ajibola Iyiola
Lateef Adegboyega Sulaimon
Effiong Effiong
Adedeji Ogunyemi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1328714

4,160 views
1 citation

Original Research

Published on 19 Jun 2024

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

Michael Vacher
Rodrigo Canovas
Simon M. Laws
James D. Doecke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1390607

5,943 views
12 citations

Original Research

Published on 24 May 2024

Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

Phillip J. Tomezsko
Colby T. Ford
Avery E. Meyer
Adam M. Michaleas
Rafael Jaimes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1397968

4,062 views
12 citations

Original Research

Published on 24 May 2024

Effects of highly active antiretroviral therapy initiation on epigenomic DNA methylation in persons living with HIV

Joshua Zhang
Mary E. Sehl
Roger Shih
Elizabeth Crabb Breen
Fengxue Li
Ake T. Lu
Jay H. Bream
Priya Duggal
Jeremy Martinson
Steven M. Wolinsky

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1357889

4,146 views
3 citations

Original Research

Published on 24 May 2024

Decreased but persistent epigenetic age acceleration is associated with changes in T-cell subsets after initiation of highly active antiretroviral therapy in persons living with HIV

Mary E. Sehl
Elizabeth Crabb Breen
Roger Shih
Fengxue Li
Joshua Zhang
Peter Langfelder
Steve Horvath
Jay H. Bream
Priya Duggal
Jeremy Martinson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1356509

3,956 views
3 citations

Original Research

Published on 14 May 2024

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

Xihaier Luo
Seyednami Niyakan
Patrick Johnstone
Sean McCorkle
Gilchan Park
Vanessa López-Marrero
Shinjae Yoo
Edward R. Dougherty
Xiaoning Qian
Francis J. Alexander

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1280971

5,025 views
3 citations

Editorial

Published on 03 May 2024

Editorial: Computational methods for analysis of DNA methylation data, volume II

Pietro Di Lena
Christine Nardini
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1415791

1,571 views

Original Research

Published on 16 Apr 2024

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

Fengyuan Huang
Robert S. Welner
Jake Y. Chen
Zongliang Yue

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1336135

3,175 views
1 citation

Review

Published on 11 Apr 2024

From complex data to clear insights: visualizing molecular dynamics trajectories

Hayet Belghit
Mariano Spivak
Manuel Dauchez
Marc Baaden
Jessica Jonquet-Prevoteau

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1356659

10,445 views
8 citations

Original Research

Published on 04 Apr 2024

BayesAge: A maximum likelihood algorithm to predict epigenetic age

Lajoyce Mboning
Liudmilla Rubbi
Michael Thompson
Louis-S. Bouchard
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1329144

3,110 views
6 citations

Original Research

Published on 03 Apr 2024

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

Shamini Hemandhar Kumar
Ines Tapken
Daniela Kuhn
Peter Claus
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1380928

3,273 views
3 citations

Brief Research Report

Published on 27 Mar 2024

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease

Alban Obel Slabowska
Charles Pyke
Henning Hvid
Leon Eyrich Jessen
Simon Baumgart
Vivek Das

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1352594

6,470 views
9 citations

579 Publications

volumes

Volume 4 - 2024

Editorial: Big data and artificial intelligence for genomics and therapeutics – Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS)

Editorial: Machine learning approaches to antimicrobials: discovery and resistance

Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences

A hybrid approach for predicting transcription factors

CAEM-GBDT: a cancer subtype identifying method using multi-omics data and convolutional autoencoder network

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters

Network analysis of driver genes in human cancers

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations

DNA structural features and variability of complete MHC locus sequences

Maximum-scoring path sets on pangenome graphs of constant treewidth

The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders

Bioinformatics proficiency among African students

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens

Effects of highly active antiretroviral therapy initiation on epigenomic DNA methylation in persons living with HIV

Decreased but persistent epigenetic age acceleration is associated with changes in T-cell subsets after initiation of highly active antiretroviral therapy in persons living with HIV

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

Editorial: Computational methods for analysis of DNA methylation data, volume II

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

From complex data to clear insights: visualizing molecular dynamics trajectories

BayesAge: A maximum likelihood algorithm to predict epigenetic age

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease

Volume 3 - 2023

Prediction of polyspecificity from antibody sequence data by machine learning