Frontiers in Bioinformatics

Original Research

Published on 27 Apr 2022

Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling

Antonios Kioukis
Mohsen Pourjam
Klaus Neuhaus
Ilias Lagkouvardos

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.864597

6,339 views
12 citations

Original Research

Published on 26 Apr 2022

Pathway Tools Management of Pathway/Genome Data for Microbial Communities

Peter D. Karp
Suzanne Paley
Markus Krummenacker
Anamika Kothari
Michael J. Wannemuehler
Gregory J. Phillips

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.869150

8,198 views
15 citations

Methods

Published on 26 Apr 2022

GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data

Christine Tataru
Austin Eaton
Maude M. David

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.828703

4,159 views
5 citations

Technology and Code

Published on 21 Apr 2022

N-Tools-Browser: Web-Based Visualization of Electrocorticography Data for Epilepsy Surgery

Jay Burkhardt
Aaryaman Sharma
Jack Tan
Loraine Franke
Jahnavi Leburu
Jay Jeschke
Sasha Devore
Daniel Friedman
Jingyun Chen
Daniel Haehn

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.857577

3,422 views
1 citation

Perspective

Published on 14 Apr 2022

Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration

Anjalie Schlaeppi
Wilson Adams
Robert Haase
Jan Huisken
Ryan B. MacDonald
Kevin W. Eliceiri
Elisabeth C. Kugler

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.889755

7,680 views
11 citations

Original Research

Published on 13 Apr 2022

MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets

Arnaud Gaudry
Florian Huber
Louis-Félix Nothias
Sylvian Cretton
Marcel Kaiser
Jean-Luc Wolfender
Pierre-Marie Allard

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.842964

6,009 views
16 citations

Methods

Published on 12 Apr 2022

MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions

Michael P. Mariani
Jennifer A. Chen
Ze Zhang
Steven C. Pike
Lucas A. Salas

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.859828

6,877 views
4 citations

Original Research

Published on 12 Apr 2022

Construction and Comprehensive Analysis of ceRNA Networks and Tumor-Infiltrating Immune Cells in Hepatocellular Carcinoma With Vascular Invasion

Shijiao Cai
Renle Du
Yuan Zhang
Zhengyi Yuan
Jie Shang
Yang Yang
Bin Han
Weilong Zhong
Hengjie Yuan
Zhengxiang Li

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.836981

3,019 views
4 citations

Brief Research Report

Published on 11 Apr 2022

Improved Mobilome Delineation in Fragmented Genomes

Catherine M. Mageeney
Gareth Trubl
Kelly P. Williams

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.866850

4,005 views
12 citations

Editorial

Published on 06 Apr 2022

Editorial: Single-Molecule Image Analysis

Thomas Pengo
Siân Culley
Christian Franke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.897938

2,409 views
1 citation

Correction

Published on 06 Apr 2022

Corrigendum: Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge

Paola Lecca

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.888273

2,021 views

Perspective

Published on 06 Apr 2022

A Brave New World: Virtual Reality and Augmented Reality in Systems Biology

Berk Turhan
Zeynep H. Gümüş

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.873478

9,460 views
14 citations

Brief Research Report

Published on 05 Apr 2022

The Importance of Weakly Co-Evolving Residue Networks in Proteins is Revealed by Visual Analytics

Sidharth Mohan
Hatice Gulcin Ozer
William C. Ray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.836526

2,922 views
3 citations

Methods

Published on 25 Mar 2022

OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning

Xiao Wang
Mizuho Kittaka
Yilin He
Yiwei Zhang
Yasuyoshi Ueki
Daisuke Kihara

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.819570

6,558 views
10 citations

Original Research

Published on 24 Mar 2022

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.2022.729902

6,897 views
17 citations

Original Research

Published on 23 Mar 2022

NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction

Ali Al-Fatlawi
Nazia Afrin
Cigdem Ozen
Negin Malekian
Michael Schroeder

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.780229

4,671 views
4 citations

Original Research

Published on 21 Mar 2022

A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures

Shelby Bell-Glenn
Jeffrey A. Thompson
Lucas A. Salas
Devin C. Koestler

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.835591

3,500 views
8 citations

Brief Research Report

Published on 18 Mar 2022

ASPM May be Related to the Malignant Progression of Hepatitis B and is Associated With a Poor Prognosis of Hepatocellular Carcinoma

Siyou Tan
Wenyan Chen
Gaoyin Kong
Lai Wei

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.871027

3,462 views
2 citations

Brief Research Report

Published on 17 Mar 2022

LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images

Mark Winter
Andrew R. Cohen

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.740078

2,239 views
2 citations

Original Research

Published on 17 Mar 2022

Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data

Yubo Wang
Liguan Li
Yu Xia
Tong Zhang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.813771

2,510 views
2 citations

Review

Published on 15 Mar 2022

Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects

Andreas Lardos
Ahmad Aghaebrahimian
Anna Koroleva
Julia Sidorova
Evelyn Wolfram
Maria Anisimova
Manuel Gil

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.827207

5,941 views
10 citations

Technology and Code

Published on 11 Mar 2022

Circr, a Computational Tool to Identify miRNA:circRNA Associations

Martina Dori
Jimmy Caroli
Mattia Forcato

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.852834

9,676 views
14 citations

Methods

Published on 04 Mar 2022

Multi-Dimensional Spectral Single Molecule Localization Microscopy

Corey Butler
G Ezequiel Saraceno
Adel Kechkar
Nathan Bénac
Vincent Studer
Julien P. Dupuis
Laurent Groc
Rémi Galland
Jean-Baptiste Sibarita

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.813494

8,175 views
39 citations

Review

Published on 04 Mar 2022

Don’t Be Fooled by Randomness: Valid p-Values for Single Molecule Microscopy

Magdalena C. Schneider
Gerhard J. Schütz

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.811053

5,547 views
4 citations

602 Publications

volumes

Volume 2 - 2022

Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling

Pathway Tools Management of Pathway/Genome Data for Microbial Communities

GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data

N-Tools-Browser: Web-Based Visualization of Electrocorticography Data for Epilepsy Surgery

Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration

MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets

MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions

Construction and Comprehensive Analysis of ceRNA Networks and Tumor-Infiltrating Immune Cells in Hepatocellular Carcinoma With Vascular Invasion

Improved Mobilome Delineation in Fragmented Genomes

Editorial: Single-Molecule Image Analysis

Corrigendum: Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge

A Brave New World: Virtual Reality and Augmented Reality in Systems Biology

The Importance of Weakly Co-Evolving Residue Networks in Proteins is Revealed by Visual Analytics

OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning

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

NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction

A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures

ASPM May be Related to the Malignant Progression of Hepatitis B and is Associated With a Poor Prognosis of Hepatocellular Carcinoma

LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images

Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data

Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects

Circr, a Computational Tool to Identify miRNA:circRNA Associations

Multi-Dimensional Spectral Single Molecule Localization Microscopy

Don’t Be Fooled by Randomness: Valid p-Values for Single Molecule Microscopy