Frontiers in Bioinformatics

Technology and Code

Published on 10 Jan 2024

BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier

Suraiya Akhter
John H. Miller

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1284705

5,661 views
13 citations

Perspective

Published on 08 Jan 2024

No-boundary thinking for artificial intelligence in bioinformatics and education

Prajay Patel
Nisha Pillai
Inimary Toby

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1332902

3,813 views
3 citations

Original Research

Published on 05 Jan 2024

Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches

Patricia Soto
Davis T. Thalhuber
Frank Luceri
Jamie Janos
Mason R. Borgman
Noah M. Greenwood
Sofia Acosta
Hunter Stoffel

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1321287

3,017 views

Editorial

Published on 05 Jan 2024

Editorial: Expert opinions in protein bioinformatics: 2022

Daisuke Kihara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1338560

1,688 views
1 citation

Hypothesis and Theory

Published on 05 Jan 2024

RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system

Huyen Le
Ru Chen
Stephen Harris
Hong Fang
Beverly Lyn-Cook
Huixiao Hong
Weigong Ge
Paul Rogers
Weida Tong
Wen Zou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1328613

4,358 views
6 citations

Original Research

Published on 04 Jan 2024

Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank

Yixuan Ye
Jiaqi Hu
Fuyuan Pang
Can Cui
Hongyu Zhao

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1320748

3,656 views
2 citations

Methods

Published on 03 Jan 2024

Identifying epigenetic aging moderators using the epigenetic pacemaker

Colin Farrell
Chanyue Hu
Kalsuda Lapborisuth
Kyle Pu
Sagi Snir
Matteo Pellegrini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1308680

2,659 views
3 citations

Original Research

Published on 22 Dec 2023

Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks

Varun Mannam
Jacob P. Brandt
Cody J. Smith
Xiaotong Yuan
Scott Howard

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1335413

4,027 views
11 citations

Original Research

Published on 18 Dec 2023

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

Kyohei Koyama
Kosuke Hashimoto
Chioko Nagao
Kenji Mizuguchi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1274599

4,463 views
14 citations

Original Research

Published on 15 Dec 2023

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations

Lucas Pagano
Guillaume Thibault
Walid Bousselham
Jessica L. Riesterer
Xubo Song
Joe W. Gray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1308707

2,490 views

Brief Research Report

Published on 15 Dec 2023

Completing a molecular timetree of apes and monkeys

Jack M. Craig
Grace L. Bamba
Jose Barba-Montoya
S. Blair Hedges
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1284744

3,299 views
3 citations

Original Research

Published on 15 Dec 2023

Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning

Archana Machireddy
Guillaume Thibault
Kevin G. Loftis
Kevin Stoltz
Cecilia E. Bueno
Hannah R. Smith
Jessica L. Riesterer
Joe W. Gray
Xubo Song

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1308708

3,785 views
8 citations

Methods

Published on 13 Dec 2023

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs

Paul Klemm
Peter F. Stadler
Marcus Lechner

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1322477

3,439 views
35 citations

Original Research

Published on 11 Dec 2023

Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach

Jan Rothörl
Maarten A. Brems
Tim J. Stevens
Peter Virnau

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1284484

2,525 views
4 citations

Original Research

Published on 07 Dec 2023

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

Annette Lien
Leonardo Pestana Legori
Louis Kraft
Peter Wad Sackett
Gabriel Renaud

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1260486

6,721 views
8 citations

Methods

Published on 04 Dec 2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Joan Segura
Yana Rose
Chunxiao Bi
Jose Duarte
Stephen K. Burley
Sebastian Bittrich

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1311287

5,916 views
14 citations

Original Research

Published on 30 Nov 2023

Real-time open-source FLIM analysis

Kevin K. D. Tan
Mark A. Tsuchida
Jenu V. Chacko
Niklas A. Gahm
Kevin W. Eliceiri

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1286983

5,371 views
9 citations

Mini Review

Published on 24 Nov 2023

Cluster analysis for localisation-based data sets: dos and don’ts when quantifying protein aggregates

Luca Panconi
Dylan M. Owen
Juliette Griffié

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1237551

2,712 views
2 citations

Perspective

Published on 23 Nov 2023

The promises of large language models for protein design and modeling

Giorgio Valentini
Dario Malchiodi
Jessica Gliozzo
Marco Mesiti
Mauricio Soto-Gomez
Alberto Cabri
Justin Reese
Elena Casiraghi
Peter N. Robinson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1304099

14,927 views
32 citations

Technology and Code

Published on 22 Nov 2023

Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

Bela T. L. Vogler
Francesco Reina
Christian Eggeling

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1268899

2,469 views
5 citations

Original Research

Published on 14 Nov 2023

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Suad Algarni
Steven L. Foley
Hailin Tang
Shaohua Zhao
Dereje D. Gudeta
Bijay K. Khajanchi
Steven C. Ricke
Jing Han

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1279359

3,146 views
6 citations

Editorial

Published on 10 Nov 2023

Editorial: Identification of phenotypically important genomic variants

Elizabeth A. Heron
Giorgio Valle
Anna Bernasconi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1328945

1,236 views

Original Research

Published on 09 Nov 2023

An algorithm for drug discovery based on deep learning with an example of developing a drug for the treatment of lung cancer

Dmitrii K. Chebanov
Vsevolod A. Misyurin
Irina Zh. Shubina

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1225149

4,601 views
6 citations

Methods

Published on 07 Nov 2023

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL)

Konstantinos A. Kyritsis
Nikolaos Pechlivanis
Fotis Psomopoulos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1275593

2,901 views

579 Publications

volumes

Volume 3 - 2023

BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier

No-boundary thinking for artificial intelligence in bioinformatics and education

Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches

Editorial: Expert opinions in protein bioinformatics: 2022

RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system

Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank

Identifying epigenetic aging moderators using the epigenetic pacemaker

Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations

Completing a molecular timetree of apes and monkeys

Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs

Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach

Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Real-time open-source FLIM analysis

Cluster analysis for localisation-based data sets: dos and don’ts when quantifying protein aggregates

The promises of large language models for protein design and modeling

Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Editorial: Identification of phenotypically important genomic variants

An algorithm for drug discovery based on deep learning with an example of developing a drug for the treatment of lung cancer

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL)