Frontiers in Bioinformatics

Original Research

Published on 23 Oct 2023

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

Famke Bäuerle
Gwendolyn O. Döbel
Laura Camus
Simon Heilbronner
Andreas Dräger

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1214074

6,162 views
1 citation

Original Research

Published on 19 Oct 2023

3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding

Erik Burlingame
Luke Ternes
Jia-Ren Lin
Yu-An Chen
Eun Na Kim
Joe W. Gray
Young Hwan Chang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1275402

5,283 views
12 citations

Methods

Published on 17 Oct 2023

Protein quality assessment with a loss function designed for high-quality decoys

Soumyadip Roy
Asa Ben-Hur

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1198218

3,399 views
4 citations

Original Research

Published on 12 Oct 2023

Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage

Xu Yang
Langwen Lai
Xiaoli Qiang
Ming Deng
Yuhao Xie
Xiaolong Shi
Zheng Kou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1276934

3,531 views
1 citation

Methods

Published on 12 Oct 2023

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

Kejue Jia
Mesih Kilinc
Robert L. Jernigan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1227193

4,607 views
2 citations

Original Research

Published on 11 Oct 2023

VariantSurvival: a tool to identify genotype–treatment response

Thomas Krannich
Marina Herrera Sarrias
Hiba Ben Aribi
Moustafa Shokrof
Alfredo Iacoangeli
Ammar Al-Chalabi
Fritz J. Sedlazeck
Ben Busby
Ahmad Al Khleifat

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1277923

2,630 views

Original Research

Published on 10 Oct 2023

DeepRaccess: high-speed RNA accessibility prediction using deep learning

Kaisei Hara
Natsuki Iwano
Tsukasa Fukunaga
Michiaki Hamada

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1275787

3,788 views
3 citations

Opinion

Published on 09 Oct 2023

Artificial intelligence in imaging flow cytometry

Paolo Pozzi
Alessia Candeo
Petra Paiè
Francesca Bragheri
Andrea Bassi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1229052

6,462 views
4 citations

Original Research

Published on 20 Sep 2023

NeighborNet: improved algorithms and implementation

David Bryant
Daniel H. Huson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1178600

6,476 views
46 citations

Data Report

Published on 19 Sep 2023

VariBench, new variation benchmark categories and data sets

Niloofar Shirvanizadeh
Mauno Vihinen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1248732

2,807 views
4 citations

Correction

Published on 13 Sep 2023

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis

Mohammed Zidane
Ahmad Makky
Matthias Bruhns
Alexander Rochwarger
Sepideh Babaei
Manfred Claassen
Christian M. Schürch

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1287407

1,745 views
1 citation

Editorial

Published on 12 Sep 2023

Editorial: Recent advances in peptide informatics: challenges and opportunities

Rahul Kumar
Kumardeep Chaudhary
Sandeep Kumar Dhanda

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1271932

2,189 views

Original Research

Published on 01 Sep 2023

The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen

Jack M. Craig
Sudhir Kumar
S. Blair Hedges

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1233281

10,742 views
18 citations

Editorial

Published on 21 Aug 2023

Editorial: Insights in integrative bioinformatics–2021

Zhi-Ping Liu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1267370

1,731 views

Original Research

Published on 17 Aug 2023

Improved prediction of MHC-peptide binding using protein language models

Nasser Hashemi
Boran Hao
Mikhail Ignatov
Ioannis Ch. Paschalidis
Pirooz Vakili
Sandor Vajda
Dima Kozakov

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1207380

9,735 views
16 citations

Methods

Published on 10 Aug 2023

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

Wanxin Li
Jules Mirone
Ashok Prasad
Nina Miolane
Carine Legrand
Khanh Dao Duc

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1211819

2,851 views
1 citation

Review

Published on 04 Aug 2023

Omics data integration in computational biology viewed through the prism of machine learning paradigms

Aziz Fouché
Andrei Zinovyev

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1191961

6,845 views
15 citations

Editorial

Published on 04 Aug 2023

Editorial: Transparent machine learning in bio-medicine

Juan G. Diaz Ochoa
André Marquardt

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1264803

2,311 views
1 citation

Methods

Published on 04 Aug 2023

Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range

Florian Levet

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1249291

3,965 views
5 citations

Opinion

Published on 04 Aug 2023

Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering

Joran Deschamps
Damian Dalle Nogare
Florian Jug

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1255159

3,096 views
7 citations

Methods

Published on 03 Aug 2023

Molecular timetrees using relaxed clocks and uncertain phylogenies

Jose Barba-Montoya
Sudip Sharma
Sudhir Kumar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1225807

4,009 views
4 citations

Original Research

Published on 02 Aug 2023

XMR: an explainable multimodal neural network for drug response prediction

Zihao Wang
Yun Zhou
Yu Zhang
Yu K. Mo
Yijie Wang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1164482

5,276 views
11 citations

Original Research

Published on 27 Jul 2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

Ryan S. McClure
Yvonne Rericha
Katrina M. Waters
Robyn L. Tanguay

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1234218

3,959 views
2 citations

Perspective

Published on 27 Jul 2023

Current successes and remaining challenges in protein function prediction

Constance J. Jeffery

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1222182

7,587 views
22 citations

602 Publications

volumes

Volume 3 - 2023

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding

Protein quality assessment with a loss function designed for high-quality decoys

Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

VariantSurvival: a tool to identify genotype–treatment response

DeepRaccess: high-speed RNA accessibility prediction using deep learning

Artificial intelligence in imaging flow cytometry

NeighborNet: improved algorithms and implementation

VariBench, new variation benchmark categories and data sets

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis

Editorial: Recent advances in peptide informatics: challenges and opportunities

The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen

Editorial: Insights in integrative bioinformatics–2021

Improved prediction of MHC-peptide binding using protein language models

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

Omics data integration in computational biology viewed through the prism of machine learning paradigms

Editorial: Transparent machine learning in bio-medicine

Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range

Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering

Molecular timetrees using relaxed clocks and uncertain phylogenies

XMR: an explainable multimodal neural network for drug response prediction

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

Current successes and remaining challenges in protein function prediction