Frontiers in Bioinformatics | Integrative Bioinformatics

Original Research

Published on 19 Jun 2024

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

in Integrative Bioinformatics

Michael Vacher
Rodrigo Canovas
Simon M. Laws
James D. Doecke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1390607

6,433 views
13 citations

Original Research

Published on 14 May 2024

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

in Integrative Bioinformatics

Xihaier Luo
Seyednami Niyakan
Patrick Johnstone
Sean McCorkle
Gilchan Park
Vanessa López-Marrero
Shinjae Yoo
Edward R. Dougherty
Xiaoning Qian
Francis J. Alexander

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1280971

5,912 views
3 citations

Original Research

Published on 16 Apr 2024

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

in Integrative Bioinformatics

Fengyuan Huang
Robert S. Welner
Jake Y. Chen
Zongliang Yue

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1336135

3,367 views
1 citation

Original Research

Published on 03 Apr 2024

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

in Integrative Bioinformatics

Shamini Hemandhar Kumar
Ines Tapken
Daniela Kuhn
Peter Claus
Klaus Jung

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1380928

3,575 views
3 citations

Brief Research Report

Published on 27 Mar 2024

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease

in Integrative Bioinformatics

Alban Obel Slabowska
Charles Pyke
Henning Hvid
Leon Eyrich Jessen
Simon Baumgart
Vivek Das

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1352594

6,804 views
9 citations

Original Research

Published on 15 Mar 2024

An interactive visualization tool for educational outreach in protein contact map overlap analysis

in Integrative Bioinformatics

Kevan Baker
Nathaniel Hughes
Sutanu Bhattacharya

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1358550

3,710 views
4 citations

Original Research

Published on 06 Feb 2024

MRSLpred—a hybrid approach for predicting multi-label subcellular localization of mRNA at the genome scale

in Integrative Bioinformatics

Shubham Choudhury
Nisha Bajiya
Sumeet Patiyal
Gajendra P. S. Raghava

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1341479

2,310 views
7 citations

Perspective

Published on 08 Jan 2024

No-boundary thinking for artificial intelligence in bioinformatics and education

in Integrative Bioinformatics

Prajay Patel
Nisha Pillai
Inimary Toby

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1332902

4,069 views
3 citations

Hypothesis and Theory

Published on 05 Jan 2024

RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system

in Integrative Bioinformatics

Huyen Le
Ru Chen
Stephen Harris
Hong Fang
Beverly Lyn-Cook
Huixiao Hong
Weigong Ge
Paul Rogers
Weida Tong
Wen Zou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1328613

4,803 views
6 citations

Original Research

Published on 14 Nov 2023

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

in Integrative Bioinformatics

Suad Algarni
Steven L. Foley
Hailin Tang
Shaohua Zhao
Dereje D. Gudeta
Bijay K. Khajanchi
Steven C. Ricke
Jing Han

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1279359

3,362 views
6 citations

Original Research

Published on 11 Oct 2023

VariantSurvival: a tool to identify genotype–treatment response

in Integrative Bioinformatics

Thomas Krannich
Marina Herrera Sarrias
Hiba Ben Aribi
Moustafa Shokrof
Alfredo Iacoangeli
Ammar Al-Chalabi
Fritz J. Sedlazeck
Ben Busby
Ahmad Al Khleifat

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1277923

2,630 views

Editorial

Published on 21 Aug 2023

Editorial: Insights in integrative bioinformatics–2021

in Integrative Bioinformatics

Zhi-Ping Liu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1267370

1,731 views

Review

Published on 04 Aug 2023

Omics data integration in computational biology viewed through the prism of machine learning paradigms

in Integrative Bioinformatics

Aziz Fouché
Andrei Zinovyev

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1191961

6,845 views
15 citations

Editorial

Published on 04 Aug 2023

Editorial: Transparent machine learning in bio-medicine

in Integrative Bioinformatics

Juan G. Diaz Ochoa
André Marquardt

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1264803

2,311 views
1 citation

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

3,959 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

2,782 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

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

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

2,138 views
1 citation

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

8,222 views
19 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

1,902 views
2 citations

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

3,576 views
5 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

5,940 views
12 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

5,656 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

5,869 views
7 citations

90 articles

articles

A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer’s disease

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation

PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

A systematic evaluation of state-of-the-art deconvolution methods in spatial transcriptomics: insights from cardiovascular disease and chronic kidney disease

An interactive visualization tool for educational outreach in protein contact map overlap analysis

MRSLpred—a hybrid approach for predicting multi-label subcellular localization of mRNA at the genome scale

No-boundary thinking for artificial intelligence in bioinformatics and education

RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

VariantSurvival: a tool to identify genotype–treatment response

Editorial: Insights in integrative bioinformatics–2021

Omics data integration in computational biology viewed through the prism of machine learning paradigms

Editorial: Transparent machine learning in bio-medicine

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

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

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

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

Editorial: Expert opinions in integrative bioinformatics: 2022

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

Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning

Adjustments to the reference dataset design improve cell type label transfer

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