Frontiers in Bioinformatics | Genomic Analysis

Technology and Code

Published on 08 May 2025

micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data

in Genomic Analysis

Rachel Griffard-Smith
Emily Schueddig
Diane E. Mahoney
Prabhakar Chalise
Devin C. Koestler
Dong Pei

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1556361

2,406 views
1 citation

Review

Published on 23 Apr 2025

Artificial intelligence in variant calling: a review

in Genomic Analysis

Omar Abdelwahab
Davoud Torkamaneh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1574359

10,069 views
7 citations

Original Research

Published on 16 Apr 2025

Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia

in Genomic Analysis

Mebrie Zemene Kinde
Bizuayehu Kerisew
Tegegne Eshetu
Abebe Tesfaye Gessese

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1572241

3,232 views
1 citation

Perspective

Published on 09 Apr 2025

A cost and community perspective on the barriers to microbiome data reuse

in Genomic Analysis

Julia M. Kelliher
Leah Y. D. Johnson
Francisca E. Rodriguez
Jaclyn K. Saunders
Marie E. Kroeger
Buck Hanson
Aaron J. Robinson
Winston E. Anthony
Marc W. Van Goethem
Anders Kiledal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1585717

4,056 views
2 citations

Brief Research Report

Published on 18 Mar 2025

ORF1ab codon frequency model predicts host-pathogen relationship in orthocoronavirinae

in Genomic Analysis

Phillip E. Davis
Joseph A. Russell

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1562668

1,495 views

Original Research

Published on 17 Mar 2025

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level

in Genomic Analysis

Amy S. Graham
Fadheela Patel
Francesca Little
Andre van der Kouwe
Mamadou Kaba
Martha J. Holmes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1484113

2,773 views
1 citation

Original Research

Published on 10 Mar 2025

Urinary based biomarkers identification and genetic profiling in Parkinson’s disease: a systematic review of metabolomic studies

in Genomic Analysis

Neetu Rani Dhiman
Surbhi Singh
Royana Singh
Anand Kumar
Varun Kumar Singh
Abhishek Pathak
Rameshwar Nath Chaurasia
Vijay Nath Mishra
Niraj Kumar Srivastava
Swati Sahu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1513790

2,908 views
4 citations

Perspective

Published on 10 Mar 2025

A standards perspective on genomic data reusability and reproducibility

in Genomic Analysis

Ishi Keenum
Scott A. Jackson
Emiley Eloe-Fadrosh
Lynn M. Schriml

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1572937

2,332 views
2 citations

Original Research

Published on 03 Mar 2025

MetaComBin: combining abundances and overlaps for binning metagenomics reads

in Genomic Analysis

Francesco Tomasella
Cinzia Pizzi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1504728

1,909 views

Original Research

Published on 04 Feb 2025

Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples

in Genomic Analysis

Sonsiray Álvarez-Narváez
Telvin L. Harrell
Islam Nour
Sujit K. Mohanty
Steven J. Conrad

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1498921

2,137 views
1 citation

Opinion

Published on 16 Dec 2024

Unlocking the future of complex human diseases prediction: multi-omics risk score breakthrough

in Genomic Analysis

Benson R. Kidenya
Gerald Mboowa

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1510352

3,653 views
7 citations

Technology and Code

Published on 15 Nov 2024

Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads

in Genomic Analysis

Lia Obinu
Urmi Trivedi
Andrea Porceddu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1462923

5,237 views
4 citations

Original Research

Published on 13 Nov 2024

Climatic factors, but not geographic distance, promote genetic structure and differentiation of Cleistogenes squarrosa (Trin.) Keng populations

in Genomic Analysis

Ruyan Song
Xueli Zhang
Zhuo Zhang
Chan Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1454689

1,867 views
1 citation

Brief Research Report

Published on 18 Oct 2024

Computational identification and characterization of chitinase 1 and chitinase 2 from neotropical isolates of Beauveria bassiana

in Genomic Analysis

Juan Segura-Vega
Allan González-Herrera
Ramón Molina-Bravo
Stefany Solano-González

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1434442

2,383 views
2 citations

Methods

Published on 07 Oct 2024

In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays

in Genomic Analysis

Ruslan Kalendar
Alexandr Shevtsov
Zhenis Otarbay
Aisulu Ismailova

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1464197

16,851 views
14 citations

Original Research

Published on 26 Sep 2024

Pangenome comparison via ED strings

in Genomic Analysis

Esteban Gabory
Moses Njagi Mwaniki
Nadia Pisanti
Solon P. Pissis
Jakub Radoszewski
Michelle Sweering
Wiktor Zuba

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1397036

2,504 views
3 citations

Original Research

Published on 12 Sep 2024

The quantum hypercube as a k-mer graph

in Genomic Analysis

Gustavo Becerra-Gavino
Liliana Ibeth Barbosa-Santillan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1401223

2,075 views

Review

Published on 10 Sep 2024

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

in Genomic Analysis

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1457619

16,467 views
45 citations

Review

Published on 03 Jul 2024

DNA structural features and variability of complete MHC locus sequences

in Genomic Analysis

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1392613

4,383 views
5 citations

Original Research

Published on 01 Jul 2024

Maximum-scoring path sets on pangenome graphs of constant treewidth

in Genomic Analysis

Broňa Brejová
Travis Gagie
Eva Herencsárová
Tomáš Vinař

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1391086

1,969 views

Original Research

Published on 24 May 2024

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

in Genomic Analysis

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

4,029 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

in Genomic Analysis

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

3,851 views
3 citations

Editorial

Published on 03 May 2024

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

in Genomic Analysis

Pietro Di Lena
Christine Nardini
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1415791

1,518 views

Original Research

Published on 04 Apr 2024

BayesAge: A maximum likelihood algorithm to predict epigenetic age

in Genomic Analysis

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1329144

3,012 views
6 citations

115 articles

articles

micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data

Artificial intelligence in variant calling: a review

Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia

A cost and community perspective on the barriers to microbiome data reuse

ORF1ab codon frequency model predicts host-pathogen relationship in orthocoronavirinae

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level

Urinary based biomarkers identification and genetic profiling in Parkinson’s disease: a systematic review of metabolomic studies

A standards perspective on genomic data reusability and reproducibility

MetaComBin: combining abundances and overlaps for binning metagenomics reads

Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples

Unlocking the future of complex human diseases prediction: multi-omics risk score breakthrough

Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads

Climatic factors, but not geographic distance, promote genetic structure and differentiation of Cleistogenes squarrosa (Trin.) Keng populations

Computational identification and characterization of chitinase 1 and chitinase 2 from neotropical isolates of Beauveria bassiana

In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays

Pangenome comparison via ED strings

The quantum hypercube as a k-mer graph

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

DNA structural features and variability of complete MHC locus sequences

Maximum-scoring path sets on pangenome graphs of constant treewidth

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

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

BayesAge: A maximum likelihood algorithm to predict epigenetic age