Original Research

Published on 08 Feb 2023

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

Harry Bowles
Renata Kabiljo
Ahmad Al Khleifat
Ashley Jones
John P. Quinn
Richard J. B. Dobson
Chad M. Swanson
Ammar Al-Chalabi
Alfredo Iacoangeli

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1062328

4,777 views
2 citations

Original Research

Published on 13 Jan 2023

Interactive extraction of diverse vocal units from a planar embedding without the need for prior sound segmentation

Corinna Lorenz
Xinyu Hao
Tomas Tomka
Linus Rüttimann
Richard H.R. Hahnloser

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.966066

1,899 views
3 citations

Review

Published on 11 Jan 2023

CRISPR genome editing using computational approaches: A survey

Roghayyeh Alipanahi
Leila Safari
Alireza Khanteymoori

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1001131

6,018 views
7 citations

Original Research

Published on 06 Jan 2023

The META tool optimizes metagenomic analyses across sequencing platforms and classifiers

Robert A. Player
Angeline M. Aguinaldo
Brian B. Merritt
Lisa N. Maszkiewicz
Oluwaferanmi E. Adeyemo
Ellen R. Forsyth
Kathleen J. Verratti
Brant W. Chee
Sarah L. Grady
Christopher E. Bradburne

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.969247

3,109 views

Systematic Review

Published on 22 Dec 2022

Algorithms to anonymize structured medical and healthcare data: A systematic review

Ali Sepas
Ali Haider Bangash
Omar Alraoui
Khaled El Emam
Alaa El-Hussuna

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.984807

6,312 views
6 citations

Original Research

Published on 22 Dec 2022

Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models

Daniel V. Olivença
Jacob D. Davis
Eberhard O. Voit

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1021838

1,862 views
3 citations

Perspective

Published on 16 Dec 2022

Machine learning methods for protein-protein binding affinity prediction in protein design

Zhongliang Guo
Rui Yamaguchi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1065703

14,353 views
16 citations

Perspective

Published on 15 Dec 2022

On the choice of negative examples for prediction of host-pathogen protein interactions

Don Neumann
Soumyadip Roy
Fayyaz Ul Amir Afsar Minhas
Asa Ben-Hur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1083292

1,695 views

Brief Research Report

Published on 08 Dec 2022

SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

Renato R. M. Oliveira
Santelmo Vasconcelos
Guilherme Oliveira

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1074802

3,834 views

Original Research

Published on 08 Dec 2022

Molecular cartooning with knowledge graphs

Brook E. Santangelo
Lucas A. Gillenwater
Nourah M. Salem
Lawrence E. Hunter

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1054578

2,125 views
2 citations

Original Research

Published on 05 Dec 2022

Deep learning for MYC binding site recognition

R. Fioresi
P. Demurtas
G. Perini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1015993

2,025 views
2 citations

Original Research

Published on 02 Dec 2022

Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder

Asia Gervits
Roded Sharan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1025783

1,820 views
1 citation

Editorial

Published on 30 Nov 2022

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship

Daniele Raimondi
Gabriele Orlando
Nora Verplaetse
Piero Fariselli
Yves Moreau

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1098941

1,363 views
2 citations

Technology and Code

Published on 21 Nov 2022

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

Ben Murcott
Rebecca J. Pawluk
Anna V. Protasio
Ruth Y. Akinmusola
Dominika Lastik
Vicky L. Hunt

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.994871

2,292 views
1 citation

Original Research

Published on 17 Nov 2022

Nearest neighbor search on embeddings rapidly identifies distant protein relations

Konstantin Schütze
Michael Heinzinger
Martin Steinegger
Burkhard Rost

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1033775

4,730 views
25 citations

Review

Published on 17 Nov 2022

Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells

Bikash Ranjan Samal
Jens Uwe Loers
Vanessa Vermeirssen
Katleen De Preter

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1036963

3,347 views
5 citations

Navigation group

Volumes

An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data

Interactive extraction of diverse vocal units from a planar embedding without the need for prior sound segmentation

CRISPR genome editing using computational approaches: A survey

The META tool optimizes metagenomic analyses across sequencing platforms and classifiers

Algorithms to anonymize structured medical and healthcare data: A systematic review

Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models

Machine learning methods for protein-protein binding affinity prediction in protein design

On the choice of negative examples for prediction of host-pathogen protein interactions

SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

Molecular cartooning with knowledge graphs

Deep learning for MYC binding site recognition

Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

Nearest neighbor search on embeddings rapidly identifies distant protein relations

Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells