Frontiers in Bioinformatics | Genomic Analysis

Methods

Published on 12 Oct 2023

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

in Genomic Analysis

Kejue Jia
Mesih Kilinc
Robert L. Jernigan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1227193

2,377 views
2 citations

Original Research

Published on 10 Oct 2023

DeepRaccess: high-speed RNA accessibility prediction using deep learning

in Genomic Analysis

Kaisei Hara
Natsuki Iwano
Tsukasa Fukunaga
Michiaki Hamada

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1275787

2,320 views

Data Report

Published on 19 Sep 2023

VariBench, new variation benchmark categories and data sets

in Genomic Analysis

Niloofar Shirvanizadeh
Mauno Vihinen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1248732

1,659 views
1 citation

Original Research

Published on 16 May 2023

Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data

in Genomic Analysis

Jared Huzar
Madelyn Shenoy
Maxwell D. Sanderford
Sudhir Kumar
Sayaka Miura

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1090730

1,608 views
1 citation

Technology and Code

Published on 30 Mar 2023

EGAsubmitter: A software to automate submission of nucleic acid sequencing data to the European Genome-phenome Archive

in Genomic Analysis

Marco Viviani
Marilisa Montemurro
Livio Trusolino
Andrea Bertotti
Gianvito Urgese
Elena Grassi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1143014

2,232 views

Brief Research Report

Published on 28 Mar 2023

Leveraging primate-specific genomic information for genetic studies of complex diseases

in Genomic Analysis

Wen-Hua Wei
Hui Guo

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1161167

1,328 views
1 citation

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

7,880 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

2,393 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

2,036 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

5,121 views
3 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

2,284 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

1,505 views
3 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

2,493 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

2,069 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

1,995 views
2 citations

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

1,842 views
4 citations

Navigation group

Articles

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

DeepRaccess: high-speed RNA accessibility prediction using deep learning

VariBench, new variation benchmark categories and data sets

Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data

EGAsubmitter: A software to automate submission of nucleic acid sequencing data to the European Genome-phenome Archive

Leveraging primate-specific genomic information for genetic studies of complex diseases

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