Frontiers in Bioinformatics

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

6,911 views
6 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

2,842 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

10,844 views
17 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

5,093 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

10,913 views
14 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

3,711 views
8 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

22,796 views
33 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

3,131 views
2 citations

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

6,431 views
2 citations

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

3,542 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

3,576 views
3 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

2,876 views
3 citations

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

2,445 views
7 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

3,689 views
3 citations

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

8,559 views
38 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

5,341 views
11 citations

Mini Review

Published on 26 Oct 2022

A brief survey of tools for genomic regions enrichment analysis

Davide Chicco
Giuseppe Jurman

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.968327

9,392 views
24 citations

Methods

Published on 24 Oct 2022

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

Zachary S. Wallace
James Davis
Anna Maria Niewiadomska
Robert D. Olson
Maulik Shukla
Rick Stevens
Yun Zhang
Christian M. Zmasek
Richard H. Scheuermann

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1020189

3,150 views
9 citations

Perspective

Published on 21 Oct 2022

Towards rational computational peptide design

Liwei Chang
Arup Mondal
Alberto Perez

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1046493

11,774 views
33 citations

Review

Published on 20 Oct 2022

Advances in antibody discovery from human BCR repertoires

Zichang Xu
Hendra S. Ismanto
Hao Zhou
Dianita S. Saputri
Fuminori Sugihara
Daron M. Standley

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1044975

13,478 views
9 citations

Perspective

Published on 19 Oct 2022

Integration of multi-omics technologies for crop improvement: Status and prospects

Ru Zhang
Cuiping Zhang
Chengyu Yu
Jungang Dong
Jihong Hu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1027457

9,577 views
52 citations

Mini Review

Published on 19 Oct 2022

Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks

Francesco Petrizzelli
Tommaso Biagini
Salvatore Daniele Bianco
Niccolò Liorni
Alessandro Napoli
Stefano Castellana
Tommaso Mazza

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1045368

4,026 views
7 citations

Methods

Published on 12 Oct 2022

Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images

Edgar Lefevre
Emmanuel Bouilhol
Antoine Chauvière
Wilfried Souleyreau
Marie-Alix Derieppe
Aurélien J. Trotier
Sylvain Miraux
Andreas Bikfalvi
Emeline J. Ribot
Macha Nikolski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.999700

3,310 views
4 citations

Original Research

Published on 10 Oct 2022

SETH predicts nuances of residue disorder from protein embeddings

Dagmar Ilzhöfer
Michael Heinzinger
Burkhard Rost

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.1019597

6,668 views
45 citations

115 Publications

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

A brief survey of tools for genomic regions enrichment analysis

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

Towards rational computational peptide design

Advances in antibody discovery from human BCR repertoires

Integration of multi-omics technologies for crop improvement: Status and prospects

Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks

Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images

SETH predicts nuances of residue disorder from protein embeddings