Frontiers in Bioinformatics

Perspective

Published on 07 Oct 2022

Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy

Priscila S. F. C. Gomes
Diego E. B. Gomes
Rafael C. Bernardi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.983306

13,252 views
32 citations

Original Research

Published on 30 Sep 2022

In silico discovery of biomarkers for the accurate and sensitive detection of Fusarium solani

Olalekan Olanrewaju Bakare
Arun Gokul
Muhali Olaide Jimoh
Ashwil Klein
Marshall Keyster

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.972529

3,523 views
1 citation

Perspective

Published on 30 Sep 2022

The druggable genome: Twenty years later

Chris J. Radoux
Francesca Vianello
Jake McGreig
Nikita Desai
Anthony R. Bradley

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.958378

17,136 views
19 citations

Review

Published on 27 Sep 2022

Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review

Shihao Zheng
Tianyu Xue
Bin Wang
Haolin Guo
Qiquan Liu

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.928116

9,839 views
24 citations

Original Research

Published on 27 Sep 2022

Predicting liver cancer on epigenomics data using machine learning

Vishalkumar Vekariya
Kalpdrum Passi
Chakresh Kumar Jain

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.954529

3,817 views
6 citations

Original Research

Published on 26 Sep 2022

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

Isak Johansson-Åkhe
Björn Wallner

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.959160

35,701 views
143 citations

Technology and Code

Published on 21 Sep 2022

Assessing equivalent and inverse change in genes between diverse experiments

Lisa Neums
Devin C. Koestler
Qing Xia
Jinxiang Hu
Shachi Patel
Shelby Bell-Glenn
Dong Pei
Bo Zhang
Samuel Boyd
Prabhakar Chalise

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.893032

2,784 views
2 citations

Original Research

Published on 16 Sep 2022

In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

Kenny da Costa Pinheiro
Bruna Verônica Azevedo Gois
Wylerson Guimarães Nogueira
Fabrício Almeida Araújo
Ana Lídia Cavalcante Queiroz
Oscar Cardenas-Alegria
Artur Luiz da Costa da Silva
Antônio Márcio Gomes Martins Júnior
Rommel Thiago Jucá Ramos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.931583

2,490 views
4 citations

Perspective

Published on 13 Sep 2022

Challenges of intracellular visualization using virtual and augmented reality

Cesar Augusto Valades-Cruz
Ludovic Leconte
Gwendal Fouche
Thomas Blanc
Nathan Van Hille
Kevin Fournier
Tao Laurent
Benjamin Gallean
Francois Deslandes
Bassam Hajj

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.997082

5,131 views
4 citations

Original Research

Published on 13 Sep 2022

Investigating the molecular mechanism of iguratimod act on SLE using network pharmacology and molecular docking analysis

Huiqiong Zeng
Shuai Chen
Xiaoping Lu
Zhenbo Yan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.932114

4,188 views
5 citations

Original Research

Published on 31 Aug 2022

Sparse bayesian learning for genomic selection in yeast

Maryam Ayat
Mike Domaratzki

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.960889

2,053 views

Original Research

Published on 10 Aug 2022

Functional networks of the human bromodomain-containing proteins

Cong Gao
Karen C. Glass
Seth Frietze

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.835892

4,942 views
1 citation

Original Research

Published on 09 Aug 2022

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

Aristeidis Litos
Evangelia Intze
Pavlos Pavlidis
Ilias Lagkouvardos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.866902

4,152 views
3 citations

Original Research

Published on 03 Aug 2022

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences

Yu-Peng Hsieh
Yuan-Mao Hung
Mong-Hsun Tsai
Liang-Chuan Lai
Eric Y. Chuang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.905489

20,160 views
27 citations

Technology and Code

Published on 25 Jul 2022

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.835805

3,421 views
4 citations

Methods

Published on 22 Jul 2022

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Ulas Karaoz
Eoin L. Brodie

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.918853

19,565 views
69 citations

Correction

Published on 20 Jul 2022

Corrigendum: Increased Expression of INHBA Is Correlated With Poor Prognosis and High Immune Infiltrating Level in Breast Cancer

Zeying Yu
Li Cheng
Xinlian Liu
Lushun Zhang
Hui Cao

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.974000

1,044 views

Technology and Code

Published on 18 Jul 2022

genomeSidekick: A user-friendly epigenomics data analysis tool

Junjie Chen
Ashley J. Zhu
René R. S. Packard
Thomas M. Vondriska
Douglas J. Chapski

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.831025

6,028 views
2 citations

Original Research

Published on 14 Jul 2022

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning

Cristiano Galletti
Joaquim Aguirre-Plans
Baldo Oliva
Narcis Fernandez-Fuentes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.906644

6,335 views
9 citations

Original Research

Published on 13 Jul 2022

Bacteriophage Genetic Edition Using LSTM

Shabnam Ataee
Xavier Brochet
Carlos Andrés Peña-Reyes

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.932319

6,949 views
6 citations

Original Research

Published on 11 Jul 2022

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

Christoph Flamm
Julia Wielach
Michael T. Wolfinger
Stefan Badelt
Ronny Lorenz
Ivo L. Hofacker

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.835422

6,596 views
30 citations

Original Research

Published on 08 Jul 2022

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

Vivek Ruhela
Anubha Gupta
K. Sriram
Gaurav Ahuja
Gurvinder Kaur
Ritu Gupta

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.842051

5,487 views
2 citations

Review

Published on 05 Jul 2022

Open-Source Biomedical Image Analysis Models: A Meta-Analysis and Continuous Survey

Rui Li
Vaibhav Sharma
Subasini Thangamani
Artur Yakimovich

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.912809

8,934 views
4 citations

Methods

Published on 04 Jul 2022

ShapoGraphy: A User-Friendly Web Application for Creating Bespoke and Intuitive Visualisation of Biomedical Data

Muhammed Khawatmi
Yoann Steux
Saddam Zourob
Heba Z. Sailem

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.788607

5,505 views
4 citations

115 Publications

volumes

Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy

In silico discovery of biomarkers for the accurate and sensitive detection of Fusarium solani

The druggable genome: Twenty years later

Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review

Predicting liver cancer on epigenomics data using machine learning

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

Assessing equivalent and inverse change in genes between diverse experiments

In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

Challenges of intracellular visualization using virtual and augmented reality

Investigating the molecular mechanism of iguratimod act on SLE using network pharmacology and molecular docking analysis

Sparse bayesian learning for genomic selection in yeast

Functional networks of the human bromodomain-containing proteins

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time

16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences

ChanFAD: A Functional Annotation Database for Ion Channels

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Corrigendum: Increased Expression of INHBA Is Correlated With Poor Prognosis and High Immune Infiltrating Level in Breast Cancer

genomeSidekick: A user-friendly epigenomics data analysis tool

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning

Bacteriophage Genetic Edition Using LSTM

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data

Open-Source Biomedical Image Analysis Models: A Meta-Analysis and Continuous Survey

ShapoGraphy: A User-Friendly Web Application for Creating Bespoke and Intuitive Visualisation of Biomedical Data