Frontiers in Bioinformatics | Integrative Bioinformatics

Original Research

Published on 27 Jul 2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

in Integrative Bioinformatics

Ryan S. McClure
Yvonne Rericha
Katrina M. Waters
Robyn L. Tanguay

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1234218

2,920 views
2 citations

Original Research

Published on 27 Jul 2023

Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data

in Integrative Bioinformatics

Saurav Mallik
Soumita Seth
Amalendu Si
Tapas Bhadra
Zhongming Zhao

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1182176

1,833 views
1 citation

Original Research

Published on 05 Jul 2023

Translating theory into practice: assessing the privacy implications of concept-based explanations for biomedical AI

in Integrative Bioinformatics

Adriano Lucieri
Andreas Dengel
Sheraz Ahmed

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1194993

2,531 views
5 citations

Editorial

Published on 04 Jul 2023

Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data

in Integrative Bioinformatics

Diego Mariano
Neli José Da Fonseca Júnior
Lucianna Helene Santos
Raquel Cardoso de Melo-Minardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1246859

1,425 views

Original Research

Published on 20 Jun 2023

Structure-based neural network protein–carbohydrate interaction predictions at the residue level

in Integrative Bioinformatics

Samuel W. Canner
Sudhanshu Shanker
Jeffrey J. Gray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1186531

6,461 views
16 citations

Editorial

Published on 19 May 2023

Editorial: Expert opinions in integrative bioinformatics: 2022

in Integrative Bioinformatics

Tao Zeng
Chuanchao Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1218466

1,423 views

Brief Research Report

Published on 28 Apr 2023

Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy

in Integrative Bioinformatics

Gabriel Wajnberg
Eric P. Allain
Jeremy W. Roy
Shruti Srivastava
Daniel Saucier
Pier Morin
Alier Marrero
Colleen O’Connell
Anirban Ghosh
Stephen M. Lewis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1127661

2,488 views
4 citations

Original Research

Published on 27 Apr 2023

Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning

in Integrative Bioinformatics

Daniele M. Papetti
Simone Spolaor
Iman Nazari
Andrea Tirelli
Tommaso Leonardi
Chiara Caprioli
Daniela Besozzi
Thalia Vlachou
Pier Giuseppe Pelicci
Paolo Cazzaniga

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1067113

4,785 views
7 citations

Original Research

Published on 05 Apr 2023

Adjustments to the reference dataset design improve cell type label transfer

in Integrative Bioinformatics

Carla Mölbert
Laleh Haghverdi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1150099

4,061 views
5 citations

Review

Published on 24 Feb 2023

Enhancer/gene relationships: Need for more reliable genome-wide reference sets

in Integrative Bioinformatics

Tristan Hoellinger
Camille Mestre
Hugues Aschard
Wilfried Le Goff
Sylvain Foissac
Thomas Faraut
Sarah Djebali

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1092853

4,227 views
5 citations

Data Report

Published on 16 Feb 2023

Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures

in Integrative Bioinformatics

Pedro Martins
Diego Mariano
Frederico Chaves Carvalho
Luana Luiza Bastos
Lucas Moraes
Vivian Paixão
Raquel Cardoso de Melo-Minardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1103103

4,931 views
17 citations

Original Research

Published on 15 Feb 2023

Bayesian logical neural networks for human-centered applications in medicine

in Integrative Bioinformatics

Juan G. Diaz Ochoa
Lukas Maier
Orsolya Csiszar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1082941

2,558 views
3 citations

Perspective

Published on 09 Feb 2023

Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study

in Integrative Bioinformatics

Yuexing Liu
Yixue Li
Tao Zeng

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1117271

3,104 views
10 citations

Data Report

Published on 07 Feb 2023

PanViTa: Pan Virulence and resisTance analysis

in Integrative Bioinformatics

Diego Lucas Neres Rodrigues
Juan Carlos Ariute
Francielly Morais Rodrigues da Costa
Ana Maria Benko-Iseppon
Debmalya Barh
Vasco Azevedo
Flávia Aburjaile

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1070406

3,598 views
18 citations

Review

Published on 11 Jan 2023

CRISPR genome editing using computational approaches: A survey

in Integrative Bioinformatics

Roghayyeh Alipanahi
Leila Safari
Alireza Khanteymoori

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1001131

8,362 views
15 citations

Systematic Review

Published on 22 Dec 2022

Algorithms to anonymize structured medical and healthcare data: A systematic review

in Integrative Bioinformatics

Ali Sepas
Ali Haider Bangash
Omar Alraoui
Khaled El Emam
Alaa El-Hussuna

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.984807

8,649 views
10 citations