Frontiers in Bioinformatics

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

3,584 views
1 citation

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

3,505 views
3 citations

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

15,761 views
50 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

3,057 views
6 citations

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

2,740 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

3,645 views
6 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

4,916 views
3 citations

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

3,710 views
4 citations

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

5,288 views
2 citations

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

3,882 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

2,651 views
4 citations

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

2,910 views
3 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

4,131 views
7 citations

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

9,670 views
23 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

2,195 views
7 citations

Editorial

Published on 06 Feb 2024

Editorial: Phasor analysis for fluorescence lifetime data

in Computational BioImaging

Ruofan Cao
Yide Zhang
Jessica Houston

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1375480

1,887 views

Methods

Published on 05 Feb 2024

Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs

in Data Visualization

Jannes Peeters
Daniël M. Bot
Gustavo Rovelo Ruiz
Jan Aerts

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1331043

4,465 views

Brief Research Report

Published on 31 Jan 2024

Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells

in Data Visualization

Aimer Gutierrez-Diaz
Steve Hoffmann
Juan Carlos Gallego-Gómez
Clara Isabel Bermudez-Santana

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1293412

2,622 views
1 citation

Methods

Published on 31 Jan 2024

Making bioinformatics training FAIR: the EMBL-EBI training portal

in Protein Bioinformatics

A. L. Swan
A. Broadbent
P. Singh Gaur
A. Mishra
K. Gurwitz
A. Mithani
S. L. Morgan
G. Malhotra
C. Brooksbank

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1347168

3,304 views
1 citation

Methods

Published on 26 Jan 2024

AlignScape, displaying sequence similarity using self-organizing maps

in Protein Bioinformatics

Isaac Filella-Merce
Vincent Mallet
Eric Durand
Michael Nilges
Guillaume Bouvier
Riccardo Pellarin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1321508

3,610 views

Original Research

Published on 23 Jan 2024

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images

in Computational BioImaging

Grigorios M. Karageorgos
Sanghee Cho
Elizabeth McDonough
Chrystal Chadwick
Soumya Ghose
Jonathan Owens
Kyeong Joo Jung
Raghu Machiraju
Robert West
James D. Brooks

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1296667

4,162 views
5 citations

Original Research

Published on 22 Jan 2024

Assessing 2D visual encoding of 3D spatial connectivity

in Data Visualization

Benedetta F. Baldi
Jenny Vuong
Seán I. O’Donoghue

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1232671

1,872 views

Original Research

Published on 22 Jan 2024

Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct

in Genomic Analysis

Claudia Caudai
Emanuele Salerno

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1287168

2,237 views
2 citations

Original Research

Published on 15 Jan 2024

A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches

in Network Bioinformatics

Anush Karampuri
Shyam Perugu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1328262

5,561 views
10 citations

579 articles

articles

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

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

Editorial: Phasor analysis for fluorescence lifetime data

Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs

Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells

Making bioinformatics training FAIR: the EMBL-EBI training portal

AlignScape, displaying sequence similarity using self-organizing maps

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images

Assessing 2D visual encoding of 3D spatial connectivity

Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct

A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches