Frontiers in Bioinformatics

Brief Research Report

Published on 29 Jan 2025

End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN

Gabriel David
Emmanuel Faure

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1497539

2,850 views
1 citation

Methods

Published on 23 Jan 2025

A novel lossless encoding algorithm for data compression–genomics data as an exemplar

Anas Al-okaily
Abdelghani Tbakhi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1489704

2,858 views
1 citation

Original Research

Published on 17 Jan 2025

Innovative CDR grafting and computational methods for PD-1 specific nanobody design

Jagadeeswara Reddy Devasani
Girijasankar Guntuku
Nalini Panatula
Murali Krishna Kumar Muthyala
Mary Sulakshana Palla
Teruna J. Siahaan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1488331

4,223 views
2 citations

Original Research

Published on 15 Jan 2025

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

Wang Wenlun
Yu Chaohang
Huang Yan
Li Wenbin
Zhou Nanqing
Hu Qianmin
Wu Shengcai
Yuan Qing
Yu Shirui
Zhang Feng

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1494717

3,919 views
2 citations

Original Research

Published on 14 Jan 2025

hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family

H. W. Cayatineto
S. T. Hakim

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1487292

2,041 views

Brief Research Report

Published on 09 Jan 2025

Detection of reproducible liver cancer specific ligand-receptor signaling in blood

Aram Safrastyan
Damian Wollny

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1332782

1,972 views

Editorial

Published on 07 Jan 2025

Editorial: Multi-omics approaches in the study of human disease mechanisms

Dapeng Wang
Giuseppe Agapito

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1546680

2,839 views
3 citations

Original Research

Published on 06 Jan 2025

In silico identification of chilli genome encoded MicroRNAs targeting the 16S rRNA and secA genes of “Candidatus phytoplasma trifolii”

Vineeta Pandey
Aarshi Srivastava
Ramwant Gupta
Haitham E. M. Zaki
Muhammad Shafiq Shahid
Rajarshi K. Gaur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1493712

2,328 views
1 citation

Technology and Code

Published on 20 Dec 2024

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

Benjamin Dubois
Mathieu Delitte
Salomé Lengrand
Claude Bragard
Anne Legrève
Frédéric Debode

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1483255

7,660 views
8 citations

Opinion

Published on 16 Dec 2024

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

Benson R. Kidenya
Gerald Mboowa

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1510352

3,770 views
7 citations

Brief Research Report

Published on 16 Dec 2024

Completing a molecular timetree of primates

Jack M. Craig
S. Blair Hedges
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1495417

7,942 views
4 citations

Original Research

Published on 06 Dec 2024

Time-calibrated phylogeny of neotropical freshwater fishes

Victor A. Tagliacollo
Milton Tan
Roberto E. Reis
Ronielson Gaia
Virgilio Carrijo
Marcelo Ranuzi
Jack M. Craig
James S. Albert

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1433995

7,677 views
3 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

Lia Obinu
Urmi Trivedi
Andrea Porceddu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1462923

5,401 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

Ruyan Song
Xueli Zhang
Zhuo Zhang
Chan Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1454689

1,984 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

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

1,995 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1434442

2,450 views
2 citations

Original Research

Published on 18 Oct 2024

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

Buzhong Zhang
Meili Zheng
Yuzhou Zhang
Lijun Quan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1477909

1,862 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1482338

4,173 views
6 citations

Editorial

Published on 08 Oct 2024

Editorial: Women in bioinformatics

Irma Martínez-Flores
Constanza Cárdenas Carvajal
Viviana Monje-Galvan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1499514

1,844 views

Methods

Published on 07 Oct 2024

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

Ruslan Kalendar
Alexandr Shevtsov
Zhenis Otarbay
Aisulu Ismailova

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1464197

17,219 views
14 citations

Original Research

Published on 04 Oct 2024

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

Yuet Ruh Dan
Keng-Hwee Chiam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1463001

5,083 views
1 citation

Brief Research Report

Published on 02 Oct 2024

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1441373

2,677 views

Technology and Code

Published on 27 Sep 2024

SciJava Ops: an improved algorithms framework for Fiji and beyond

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

3,778 views

Original Research

Published on 26 Sep 2024

Pangenome comparison via ED strings

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

2,575 views
3 citations

78 Publications

volumes

End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN

A novel lossless encoding algorithm for data compression–genomics data as an exemplar

Innovative CDR grafting and computational methods for PD-1 specific nanobody design

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family

Detection of reproducible liver cancer specific ligand-receptor signaling in blood

Editorial: Multi-omics approaches in the study of human disease mechanisms

In silico identification of chilli genome encoded MicroRNAs targeting the 16S rRNA and secA genes of “Candidatus phytoplasma trifolii”

PRONAME: a user-friendly pipeline to process long-read nanopore metabarcoding data by generating high-quality consensus sequences

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

Completing a molecular timetree of primates

Time-calibrated phylogeny of neotropical freshwater fishes

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

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

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

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