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

1,324 views
1 citation

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

2,822 views

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

1,371 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

1,733 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

3,696 views
5 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

1,204 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

1,189 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

1,714 views
2 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

2,485 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

1,432 views

Original Research

Published on 23 Feb 2024

Computational identification of antibody-binding epitopes from mimotope datasets

in Protein Bioinformatics

Rang Li
Sabrina Wilderotter
Madison Stoddard
Debra Van Egeren
Arijit Chakravarty
Diane Joseph-McCarthy

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1295972

2,249 views

Methods

Published on 22 Feb 2024

Posterior inference of Hi-C contact frequency through sampling

in Genomic Analysis

Yanlin Zhang
Christopher J. F. Cameron
Mathieu Blanchette

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1285828

1,461 views

Opinion

Published on 22 Feb 2024

Limits of experimental evidence in RNA secondary structure prediction

in Genomic Analysis

Sarah von Löhneysen
Mario Mörl
Peter F. Stadler

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1346779

1,169 views
1 citation

Perspective

Published on 09 Feb 2024

A perspective on FAIR quality control in multiplexed imaging data processing

in Computational BioImaging

Wouter-Michiel A. M. Vierdag
Sinem K. Saka

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1336257

1,174 views
2 citations

Technology and Code

Published on 09 Feb 2024

MARTin—an open-source platform for microarray analysis

in Protein Bioinformatics

Kai O. Kreissner
Benjamin Faller
Ivan Talucci
Hans M. Maric

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1329062

1,805 views
1 citation

Technology and Code

Published on 08 Feb 2024

MetaWin 3: open-source software for meta-analysis

in Evolutionary Bioinformatics

Michael S. Rosenberg

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1305969

3,417 views
7 citations

Navigation group

Articles

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

Computational identification of antibody-binding epitopes from mimotope datasets

Posterior inference of Hi-C contact frequency through sampling

Limits of experimental evidence in RNA secondary structure prediction

A perspective on FAIR quality control in multiplexed imaging data processing

MARTin—an open-source platform for microarray analysis

MetaWin 3: open-source software for meta-analysis