Frontiers in Bioinformatics

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

5,429 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

2,005 views
1 citation

Technology and Code

Published on 21 Oct 2024

Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers

in Computational BioImaging

Charlene Z. L. Ong
N. Jannah M. Nasir
Roy E. Welsch
Lisa Tucker-Kellogg
Jagath C. Rajapakse

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1450146

2,017 views

Original Research

Published on 18 Oct 2024

DCMA: faster protein backbone dihedral angle prediction using a dilated convolutional attention-based neural network

in Protein Bioinformatics

Buzhong Zhang
Meili Zheng
Yuzhou Zhang
Lijun Quan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1477909

1,871 views

Original Research

Published on 18 Oct 2024

Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway

in Drug Discovery in Bioinformatics

Narjes Noori Goodarzi
Mahshid Khazani Asforooshani
Behzad Shahbazi
Nayereh Rezaie Rahimi
Farzad Badmasti

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1482338

4,207 views
6 citations

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

2,456 views
2 citations

Editorial

Published on 08 Oct 2024

Editorial: Women in bioinformatics

in Single Cell Bioinformatics

Irma Martínez-Flores
Constanza Cárdenas Carvajal
Viviana Monje-Galvan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1499514

1,857 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

17,270 views
14 citations

Original Research

Published on 04 Oct 2024

Discovery of plasma biomarkers related to blood-brain barrier dysregulation in Alzheimer’s disease

in Integrative Bioinformatics

Yuet Ruh Dan
Keng-Hwee Chiam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1463001

5,116 views
1 citation

Brief Research Report

Published on 02 Oct 2024

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

in Evolutionary Bioinformatics

Júlio C. M. Chaves
Fábio Hepp
Carlos G. Schrago
Beatriz Mello

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1441373

2,704 views

Technology and Code

Published on 27 Sep 2024

SciJava Ops: an improved algorithms framework for Fiji and beyond

in Computational BioImaging

Gabriel J. Selzer
Curtis T. Rueden
Mark C. Hiner
Edward L. Evans
David Kolb
Marcel Wiedenmann
Christian Birkhold
Tim-Oliver Buchholz
Stefan Helfrich
Brian Northan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1435733

3,786 views

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

2,605 views
3 citations

Methods

Published on 23 Sep 2024

QSPRmodeler - An open source application for molecular predictive analytics

in Drug Discovery in Bioinformatics

Rafał A. Bachorz
Damian Nowak
Marcin Ratajewski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1441024

2,568 views
1 citation

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

2,160 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

17,053 views
49 citations

Original Research

Published on 10 Sep 2024

Visual analysis of multi-omics data

in Data Visualization

Austin Swart
Ron Caspi
Suzanne Paley
Peter D. Karp

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1395981

3,550 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

in Drug Discovery in Bioinformatics

Deepasree K
Subhashree Venugopal

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1463750

5,773 views
7 citations

Review

Published on 04 Sep 2024

PhIP-Seq: methods, applications and challenges

in Protein Bioinformatics

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

14,248 views
3 citations

Brief Research Report

Published on 02 Sep 2024

Rvisdiff: An R package for interactive visualization of differential expression

in Data Visualization

David Barrios
Carlos Prieto

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1349205

2,510 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

in Network Bioinformatics

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

3,310 views

Perspective

Published on 21 Aug 2024

Design principles for molecular animation

in Data Visualization

Stuart G. Jantzen
Gaël McGill
Jodie Jenkinson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1353807

4,454 views
1 citation

Technology and Code

Published on 16 Aug 2024

A layout framework for genome-wide multiple sequence alignment graphs

in Network Bioinformatics

Jeremias Schebera
Dirk Zeckzer
Daniel Wiegreffe

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1358374

2,206 views

Original Research

Published on 09 Aug 2024

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

in Drug Discovery in Bioinformatics

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1428539

7,583 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

in Data Visualization

Tim Muruvanda
Hugh Rand
James Pettengill
Arthur Pightling

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1415078

2,103 views
1 citation

579 articles

articles

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

Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers

DCMA: faster protein backbone dihedral angle prediction using a dilated convolutional attention-based neural network

Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway

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

Editorial: Women in bioinformatics

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

Discovery of plasma biomarkers related to blood-brain barrier dysregulation in Alzheimer’s disease

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

SciJava Ops: an improved algorithms framework for Fiji and beyond

Pangenome comparison via ED strings

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