Frontiers in Bioinformatics | Genomic Analysis

Original Research

Accepted on 11 Feb 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

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

232 views

Original Research

Accepted on 27 Jan 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
Abhishek Pathak
Rameshwar Nath Chaurasia
Vijaya Nath Mishra
Anand Kumar
Varun Kumar Singh
Niraj kumar Srivastava
Swati Sahu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1513790

Original Research

Accepted on 27 Jan 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

123 views

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

933 views

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

1,371 views

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

472 views

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

932 views

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

4,084 views
2 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

901 views

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

749 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

3,167 views

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

1,614 views

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

815 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

2,207 views

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

2,150 views
1 citation

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Articles

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

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

Urinary based biomarkers identification and genetic profiling in Parkinson's Disease: A systematic review of metabolomic studies

MetaComBin: combining abundances and overlaps for binning metagenomics reads

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