Frontiers in Bioinformatics

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

Saurav Mallik
Soumita Seth
Amalendu Si
Tapas Bhadra
Zhongming Zhao

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1182176

2,782 views
1 citation

Perspective

Published on 26 Jul 2023

Digital staining facilitates biomedical microscopy

Michael John Fanous
Nir Pillar
Aydogan Ozcan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1243663

4,898 views
8 citations

Review

Published on 26 Jul 2023

A review on deep learning applications in highly multiplexed tissue imaging data analysis

Mohammed Zidane
Ahmad Makky
Matthias Bruhns
Alexander Rochwarger
Sepideh Babaei
Manfred Claassen
Christian M. Schürch

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1159381

10,604 views
27 citations

Perspective

Published on 25 Jul 2023

Moving beyond the desktop: prospects for practical bioimage analysis via the web

Wei Ouyang
Kevin W. Eliceiri
Beth A. Cimini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1233748

4,138 views
8 citations

Editorial

Published on 19 Jul 2023

Editorial: Expert Opinions in Network bioinformatics: 2022

Paola Lecca

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1254668

1,840 views

Methods

Published on 14 Jul 2023

CardIAP: calcium transients confocal image analysis tool

Ana Julia Velez Rueda
Luis Alberto Gonano
Agustín García Smith
Gustavo Parisi
María Silvina Fornasari
Leandro Matías Sommese

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1137815

4,261 views
5 citations

Perspective

Published on 14 Jul 2023

Machine learning enhanced cell tracking

Christopher J. Soelistyo
Kristina Ulicna
Alan R. Lowe

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1228989

7,796 views
11 citations

Mini Review

Published on 13 Jul 2023

Geometric deep learning as a potential tool for antimicrobial peptide prediction

Fabiano C. Fernandes
Marlon H. Cardoso
Abel Gil-Ley
Lívia V. Luchi
Maria G. L. da Silva
Maria L. R. Macedo
Cesar de la Fuente-Nunez
Octavio L. Franco

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1216362

11,707 views
29 citations

Original Research

Published on 12 Jul 2023

Visualization of automatically combined disease maps and pathway diagrams for rare diseases

Piotr Gawron
David Hoksza
Janet Piñero
Maria Peña-Chilet
Marina Esteban-Medina
Jose Luis Fernandez-Rueda
Vincenza Colonna
Ewa Smula
Laurent Heirendt
François Ancien

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1101505

4,141 views
3 citations

Original Research

Published on 05 Jul 2023

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

Adriano Lucieri
Andreas Dengel
Sheraz Ahmed

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1194993

3,342 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

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

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1246859

2,138 views
1 citation

Original Research

Published on 29 Jun 2023

Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes

Linghao Hu
Blanche Ter Hofstede
Dhavan Sharma
Feng Zhao
Alex J. Walsh

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1210157

4,503 views
7 citations

Methods

Published on 22 Jun 2023

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

Alexander Mazein
Marcio Luis Acencio
Irina Balaur
Adrien Rougny
Danielle Welter
Anna Niarakis
Diana Ramirez Ardila
Ugur Dogrusoz
Piotr Gawron
Venkata Satagopam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1197310

4,914 views
19 citations

Original Research

Published on 20 Jun 2023

Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode

Nour Nissan
Julia Hooker
Eric Arezza
Kevin Dick
Ashkan Golshani
Benjamin Mimee
Elroy Cober
James Green
Bahram Samanfar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1199675

3,169 views
3 citations

Original Research

Published on 20 Jun 2023

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

Samuel W. Canner
Sudhanshu Shanker
Jeffrey J. Gray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1186531

8,222 views
19 citations

Original Research

Published on 19 Jun 2023

Microbiome maps: Hilbert curve visualizations of metagenomic profiles

Camilo Valdes
Vitalii Stebliankin
Daniel Ruiz-Perez
Ji In Park
Hajeong Lee
Giri Narasimhan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1154588

4,466 views
4 citations

Editorial

Published on 09 Jun 2023

Editorial: Graph representation learning in biological network

Swarup Roy
Pietro Hiram Guzzi
Jugal Kalita

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1222711

2,266 views
4 citations

Original Research

Published on 07 Jun 2023

Human adenovirus DNA polymerase is evolutionarily and functionally associated with human telomerase reverse transcriptase based on in silico molecular characterization that implicate abacavir and zidovudine

Toluwase Hezekiah Fatoki

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1123307

4,507 views
13 citations

Original Research

Published on 01 Jun 2023

Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses

Ahmed Abdelmonem Hemedan
Reinhard Schneider
Marek Ostaszewski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1189723

4,742 views
11 citations

Original Research

Published on 01 Jun 2023

Visualizing incompatibilities in phylogenetic trees using consensus outlines

Daniel H. Huson
Banu Cetinkaya

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1155286

4,967 views
7 citations

Original Research

Published on 26 May 2023

Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs

Haruki Yamane
Takashi Ishida

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1193025

3,108 views
3 citations

Methods

Published on 25 May 2023

ModEx: a general purpose computer model exploration system

Hamid Younesy
Joseph Pober
Torsten Möller
Mohammad M. Karimi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1153800

3,271 views

Original Research

Published on 24 May 2023

Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk

T. Waddell
A. I. L. Namburete
P. Duckworth
N. Eichert
H. Thomaides-Brears
D. J. Cuthbertson
J. P. Despres
M. Brady

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1163430

2,924 views
1 citation

Perspective

Published on 24 May 2023

Network medicine: facilitating a new view on complex diseases

Marija Cvijovic
Annikka Polster

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1163445

3,110 views
6 citations

602 Publications

volumes

Volume 3 - 2023

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

Digital staining facilitates biomedical microscopy

A review on deep learning applications in highly multiplexed tissue imaging data analysis

Moving beyond the desktop: prospects for practical bioimage analysis via the web

Editorial: Expert Opinions in Network bioinformatics: 2022

CardIAP: calcium transients confocal image analysis tool

Machine learning enhanced cell tracking

Geometric deep learning as a potential tool for antimicrobial peptide prediction

Visualization of automatically combined disease maps and pathway diagrams for rare diseases

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

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

Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode

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

Microbiome maps: Hilbert curve visualizations of metagenomic profiles

Editorial: Graph representation learning in biological network

Human adenovirus DNA polymerase is evolutionarily and functionally associated with human telomerase reverse transcriptase based on in silico molecular characterization that implicate abacavir and zidovudine

Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses

Visualizing incompatibilities in phylogenetic trees using consensus outlines

Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs

ModEx: a general purpose computer model exploration system

Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk

Network medicine: facilitating a new view on complex diseases