Review

Published on 03 Mar 2023

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

in Genomic Analysis

Fotis A. Baltoumas
Evangelos Karatzas
David Paez-Espino
Nefeli K. Venetsianou
Eleni Aplakidou
Anastasis Oulas
Robert D. Finn
Sergey Ovchinnikov
Evangelos Pafilis
Nikos C. Kyrpides

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1157956

7,364 views
5 citations

Original Research

Published on 21 Feb 2023

Protein domains provide a new layer of information for classifying human variations in rare diseases

in Genomic Analysis

Mélanie Corcuff
Marc Garibal
Jean-Pierre Desvignes
Céline Guien
Coralie Grattepanche
Gwenaëlle Collod-Béroud
Estelle Ménoret
David Salgado
Christophe Béroud

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1127341

2,222 views
2 citations

Original Research

Published on 08 Feb 2023

Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae

in Genomic Analysis

Flemming Damgaard Nielsen
Jakob Møller-Jensen
Mikkel Girke Jørgensen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1074212

1,864 views
2 citations

Original Research

Published on 08 Feb 2023

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

in Genomic Analysis

Harry Bowles
Renata Kabiljo
Ahmad Al Khleifat
Ashley Jones
John P. Quinn
Richard J. B. Dobson
Chad M. Swanson
Ammar Al-Chalabi
Alfredo Iacoangeli

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1062328

4,777 views
2 citations

Original Research

Published on 05 Dec 2022

Deep learning for MYC binding site recognition

in Genomic Analysis

R. Fioresi
P. Demurtas
G. Perini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1015993

2,025 views
2 citations

Editorial

Published on 30 Nov 2022

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship

in Genomic Analysis

Daniele Raimondi
Gabriele Orlando
Nora Verplaetse
Piero Fariselli
Yves Moreau

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1098941

1,363 views
2 citations

Technology and Code

Published on 21 Nov 2022

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

in Genomic Analysis

Ben Murcott
Rebecca J. Pawluk
Anna V. Protasio
Ruth Y. Akinmusola
Dominika Lastik
Vicky L. Hunt

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.994871

2,292 views
1 citation

Methods

Published on 24 Oct 2022

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

in Genomic Analysis

Zachary S. Wallace
James Davis
Anna Maria Niewiadomska
Robert D. Olson
Maulik Shukla
Rick Stevens
Yun Zhang
Christian M. Zmasek
Richard H. Scheuermann

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1020189

1,913 views
9 citations

Technology and Code

Published on 21 Sep 2022

Assessing equivalent and inverse change in genes between diverse experiments

in Genomic Analysis

Lisa Neums
Devin C. Koestler
Qing Xia
Jinxiang Hu
Shachi Patel
Shelby Bell-Glenn
Dong Pei
Bo Zhang
Samuel Boyd
Prabhakar Chalise

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.893032

1,857 views
1 citation

Original Research

Published on 16 Sep 2022

In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

in Genomic Analysis

Kenny da Costa Pinheiro
Bruna Verônica Azevedo Gois
Wylerson Guimarães Nogueira
Fabrício Almeida Araújo
Ana Lídia Cavalcante Queiroz
Oscar Cardenas-Alegria
Artur Luiz da Costa da Silva
Antônio Márcio Gomes Martins Júnior
Rommel Thiago Jucá Ramos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.931583

1,676 views
2 citations

Original Research

Published on 31 Aug 2022

Sparse bayesian learning for genomic selection in yeast

in Genomic Analysis

Maryam Ayat
Mike Domaratzki

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.960889

1,271 views

Original Research

Published on 09 Aug 2022

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

in Genomic Analysis

Aristeidis Litos
Evangelia Intze
Pavlos Pavlidis
Ilias Lagkouvardos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.866902

2,925 views
2 citations

Original Research

Published on 03 Aug 2022

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences

in Genomic Analysis

Yu-Peng Hsieh
Yuan-Mao Hung
Mong-Hsun Tsai
Liang-Chuan Lai
Eric Y. Chuang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.905489

15,311 views
10 citations

Methods

Published on 22 Jul 2022

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

in Genomic Analysis

Ulas Karaoz
Eoin L. Brodie

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.918853

11,246 views
24 citations

Original Research

Published on 08 Jul 2022

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

in Genomic Analysis

Vivek Ruhela
Anubha Gupta
K. Sriram
Gaurav Ahuja
Gurvinder Kaur
Ritu Gupta

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.842051

3,746 views
1 citation

Technology and Code

Published on 01 Jul 2022

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

in Genomic Analysis

Attayeb Mohsen
Yi-An Chen
Rodolfo S. Allendes Osorio
Chihiro Higuchi
Kenji Mizuguchi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.893933

7,691 views
4 citations

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Articles

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

Protein domains provide a new layer of information for classifying human variations in rare diseases

Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

Deep learning for MYC binding site recognition

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

Assessing equivalent and inverse change in genes between diverse experiments

In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

Sparse bayesian learning for genomic selection in yeast

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2