Frontiers in Bioinformatics

Methods

Published on 23 Sep 2024

QSPRmodeler - An open source application for molecular predictive analytics

Rafał A. Bachorz
Damian Nowak
Marcin Ratajewski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1441024

2,557 views
1 citation

Original Research

Published on 12 Sep 2024

The quantum hypercube as a k-mer graph

Gustavo Becerra-Gavino
Liliana Ibeth Barbosa-Santillan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1401223

2,152 views

Review

Published on 10 Sep 2024

A review of model evaluation metrics for machine learning in genetics and genomics

Catriona Miller
Theo Portlock
Denis M. Nyaga
Justin M. O’Sullivan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1457619

17,034 views
49 citations

Original Research

Published on 10 Sep 2024

Visual analysis of multi-omics data

Austin Swart
Ron Caspi
Suzanne Paley
Peter D. Karp

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1395981

3,541 views
2 citations

Original Research

Published on 06 Sep 2024

Molecular docking and molecular dynamic simulation studies to identify potential terpenes against Internalin A protein of Listeria monocytogenes

Deepasree K
Subhashree Venugopal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1463750

5,766 views
7 citations

Review

Published on 04 Sep 2024

PhIP-Seq: methods, applications and challenges

Ziru Huang
Samarappuli Mudiyanselage Savini Gunarathne
Wenwen Liu
Yuwei Zhou
Yuqing Jiang
Shiqi Li
Jian Huang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1424202

14,240 views
3 citations

Brief Research Report

Published on 02 Sep 2024

Rvisdiff: An R package for interactive visualization of differential expression

David Barrios
Carlos Prieto

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1349205

2,499 views
2 citations

Original Research

Published on 28 Aug 2024

Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis

Hermenegildo Taboada-Castro
Alfredo José Hernández-Álvarez
Juan Miguel Escorcia-Rodríguez
Julio Augusto Freyre-González
Edgardo Galán-Vásquez
Sergio Encarnación-Guevara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1419274

3,306 views

Perspective

Published on 21 Aug 2024

Design principles for molecular animation

Stuart G. Jantzen
Gaël McGill
Jodie Jenkinson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1353807

4,439 views
1 citation

Technology and Code

Published on 16 Aug 2024

A layout framework for genome-wide multiple sequence alignment graphs

Jeremias Schebera
Dirk Zeckzer
Daniel Wiegreffe

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1358374

2,196 views

Original Research

Published on 09 Aug 2024

In silico studies of benzothiazole derivatives as potential inhibitors of Anopheles funestus and Anopheles gambiae trehalase

Temitope A. Ogunnupebi
Gbolahan O. Oduselu
Oluwadunni F. Elebiju
Olayinka O. Ajani
Ezekiel Adebiyi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1428539

7,578 views
3 citations

Technology and Code

Published on 09 Aug 2024

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Tim Muruvanda
Hugh Rand
James Pettengill
Arthur Pightling

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1415078

2,096 views
1 citation

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

1,878 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

3,193 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

4,173 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

3,233 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

2,231 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

3,381 views
4 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

10,459 views
16 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

3,739 views
2 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

4,547 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

2,047 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

2,620 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

4,147 views
1 citation

78 Publications

volumes

QSPRmodeler - An open source application for molecular predictive analytics

The quantum hypercube as a k-mer graph

A review of model evaluation metrics for machine learning in genetics and genomics

Visual analysis of multi-omics data

Molecular docking and molecular dynamic simulation studies to identify potential terpenes against Internalin A protein of Listeria monocytogenes

PhIP-Seq: methods, applications and challenges

Rvisdiff: An R package for interactive visualization of differential expression

Rhizobium etli CFN42 and Sinorhizobium meliloti 1021 bioinformatic transcriptional regulatory networks from culture and symbiosis

Design principles for molecular animation

A layout framework for genome-wide multiple sequence alignment graphs

In silico studies of benzothiazole derivatives as potential inhibitors of Anopheles funestus and Anopheles gambiae trehalase

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

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

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

Network analysis of driver genes in human cancers

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