Frontiers in Bioinformatics

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

2,275 views
1 citation

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

3,290 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

2,689 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

1,563 views
2 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

1,754 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

2,781 views
3 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

5,690 views
14 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

1,213 views

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

1,540 views
4 citations

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

2,485 views

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

2,114 views
1 citation

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

1,678 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

2,745 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

2,466 views
3 citations

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

1,183 views

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

1,264 views