Frontiers in Bioinformatics

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

1,234 views
1 citation

Editorial

Published on 03 May 2024

Editorial: Computational methods for analysis of DNA methylation data, volume II

in Genomic Analysis

Pietro Di Lena
Christine Nardini
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1415791

825 views

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

1,828 views

Review

Published on 11 Apr 2024

From complex data to clear insights: visualizing molecular dynamics trajectories

in Data Visualization

Hayet Belghit
Mariano Spivak
Manuel Dauchez
Marc Baaden
Jessica Jonquet-Prevoteau

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1356659

3,707 views
5 citations

Original Research

Published on 08 Apr 2024

Prediction of polyspecificity from antibody sequence data by machine learning

in Drug Discovery in Bioinformatics

Szabolcs Éliás
Clemens Wrzodek
Charlotte M. Deane
Alain C. Tissot
Stefan Klostermann
Francesca Ros

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1286883

3,678 views
2 citations

Original Research

Published on 04 Apr 2024

BayesAge: A maximum likelihood algorithm to predict epigenetic age

in Genomic Analysis

Lajoyce Mboning
Liudmilla Rubbi
Michael Thompson
Louis-S. Bouchard
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1329144

1,677 views
3 citations

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

1,600 views
2 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

3,385 views
1 citation

Opinion

Published on 19 Mar 2024

Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research

in Genomic Analysis

Michael Olbrich
Lennart Bartels
Inken Wohlers

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1384497

1,652 views

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

2,124 views
1 citation

Review

Published on 15 Mar 2024

Ten common issues with reference sequence databases and how to mitigate them

in Genomic Analysis

Samuel D. Chorlton

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1278228

4,736 views
7 citations

Technology and Code

Published on 12 Mar 2024

ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data

in Evolutionary Bioinformatics

Gennaro Calendo
Dara Kusic
Jozef Madzo
Neda Gharani
Laura Scheinfeldt

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1351620

1,428 views
1 citation

Methods

Published on 08 Mar 2024

A network-based method for associating genes with autism spectrum disorder

in Drug Discovery in Bioinformatics

Neta Zadok
Gil Ast
Roded Sharan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1295600

1,336 views

Original Research

Published on 04 Mar 2024

Where are we in the implementation of tissue-specific epigenetic clocks?

in Genomic Analysis

Claudia Sala
Pietro Di Lena
Danielle Fernandes Durso
Italo Faria do Valle
Maria Giulia Bacalini
Daniele Dall’Olio
Claudio Franceschi
Gastone Castellani
Paolo Garagnani
Christine Nardini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1306244

1,941 views
3 citations

Original Research

Published on 04 Mar 2024

Predicting cell population-specific gene expression from genomic sequence

in Single Cell Bioinformatics

Lieke Michielsen
Marcel J. T. Reinders
Ahmed Mahfouz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1347276

2,828 views
1 citation

Original Research

Published on 04 Mar 2024

Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network

in Single Cell Bioinformatics

Marin Truchi
Caroline Lacoux
Cyprien Gille
Julien Fassy
Virginie Magnone
Rafael Lopes Goncalves
Cédric Girard-Riboulleau
Iris Manosalva-Pena
Marine Gautier-Isola
Kevin Lebrigand

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1340339

1,784 views

Navigation group

Articles

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

Editorial: Computational methods for analysis of DNA methylation data, volume II

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

From complex data to clear insights: visualizing molecular dynamics trajectories

Prediction of polyspecificity from antibody sequence data by machine learning

BayesAge: A maximum likelihood algorithm to predict epigenetic age

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

Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research

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

Ten common issues with reference sequence databases and how to mitigate them

ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data

A network-based method for associating genes with autism spectrum disorder

Where are we in the implementation of tissue-specific epigenetic clocks?

Predicting cell population-specific gene expression from genomic sequence

Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network