Bioinformatics in Microbiota

Editorial

05 February 2020

Editorial: Bioinformatics in Microbiota

Xing Chen

Hongsheng Liu

and

Qi Zhao

4,659 views

5 citations

Editors

University of Science and Technology Liaoning

Impact

Correction

08 January 2021

Corrigendum: Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations

Bhusan K. Kuntal

, 1 more and

Sharmila S. Mande

1,624 views

1 citations

Original Research

17 October 2019

Cross-Regional View of Functional and Taxonomic Microbiota Composition in Obesity and Post-obesity Treatment Shows Country Specific Microbial Contribution

Daniel A. Medina

, 4 more and

Andrés Moya

7,259 views

18 citations

Original Research

13 September 2019

Incorporating Statistical Test and Machine Intelligence Into Strain Typing of Staphylococcus haemolyticus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Chia-Ru Chung

, 7 more and

Jang-Jih Lu

3,611 views

24 citations

Relative abundance of genera in the AB group. Each column represents a sample in the AB group. The genera were sorted in descending order of average abundance in abscess samples. Different bacterial taxonomies at the genus level are shown in different colors on the bottom. Abundance cutoff in this bar graph was set at 1%; some below 1% were shown as “others.”

Original Research

30 July 2019

Microbiota in Human Periodontal Abscess Revealed by 16S rDNA Sequencing

Jiazhen Chen

, 5 more and

Wenhong Zhang

7,615 views

18 citations

Original Research

10 July 2019

RWHMDA: Random Walk on Hypergraph for Microbe-Disease Association Prediction

Ya-Wei Niu

, 2 more and

Gui-Ying Yan

4,963 views

22 citations

Original Research

04 June 2019

Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis

Die Dai

, 3 more and

Wei-Hua Chen

5,287 views

15 citations

Methods

16 May 2019

Evaluating the Effect of QIIME Balanced Default Parameters on Metataxonomic Analysis Workflows With a Mock Community

Dimitrios Kioroglou

, 1 more and

Maria del Carmen Portillo

4,467 views

8 citations

Original Research

03 July 2019

Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection

Guanshu Yin

and

Yao Xia

2,262 views

1 citations

Review

18 April 2019

Application of Machine Learning in Microbiology

Kaiyang Qu

, 3 more and

Quan Zou

56,583 views

172 citations

Differences in intestinal microbiome at the genus and species level among samples of different states. Green represents a healthy sample, and red represents a colorectal cancer sample. (A) The top nine microbial genera with significant differences in abundance. (B) The top five microbial strains with significant differences in abundance.

Original Research

24 April 2019

Identifying Gut Microbiota Associated With Colorectal Cancer Using a Zero-Inflated Lognormal Model

Dongmei Ai

, 4 more and

Li C. Xia

11,792 views

153 citations

S. aureus KUB7 detection with qPCR in organs as decomposition progresses. The log genomic units are plotted on the y-axis and postmortem time on the x-axis. Each circle represents a sample and the line represents the mean (±SE) log genomic units of S. aureus KUB7 during decomposition in the (A) lungs, (B) intestines, (C) heart, and (D) bone marrow.

Original Research

18 April 2019

Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model

Zachary M. Burcham

, 5 more and

Heather R. Jordan

7,292 views

32 citations

Original Research

09 April 2019

A Novel Human Microbe-Disease Association Prediction Method Based on the Bidirectional Weighted Network

Hao Li

, 5 more and

Lei Wang

3,473 views

24 citations

Two-two combination process of amino acids. (A) Two-two combination of residues. (B) Three-dimensional heat map of amino acid frequency. (C) Heat map of amino acid frequency.

Original Research

26 March 2019

Identification of Phage Viral Proteins With Hybrid Sequence Features

Xiaoqing Ru

, 1 more and

Chunyu Wang

3,553 views

14 citations

Methods

12 March 2019

DMSC: A Dynamic Multi-Seeds Method for Clustering 16S rRNA Sequences Into OTUs

Ze-Gang Wei

and

Shao-Wu Zhang

3,500 views

14 citations

Neural network structure of MTB dataset where dataset was categorized into three categories input, hidden, and output layers. “W” represent weight parameter with layer node, “B” represent bias unit.

Original Research

04 March 2019

Artificial Neural Networks for Prediction of Tuberculosis Disease

Muhammad Tahir Khan

, 4 more and

Dong-Qing Wei

11,001 views

67 citations

Flowchart of the calculation model of MDLPHMDA: We first enforced matrix decomposition to eliminate the noise of original known microbe-disease associations and gained a new adjacency matrix. Then LPA was implemented based on the created new adjacency matrix for the identification of the potential microbe-disease associations.

Original Research

26 February 2019

Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation

Jia Qu

, 1 more and

Jun Yin

3,785 views

41 citations

Technology Report

22 February 2019

Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations

Bhusan K. Kuntal

, 1 more and

Sharmila S. Mande

14,023 views

37 citations

Original Research

22 February 2019

Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles

Lianwei Li

and

Zhanshan (Sam) Ma

10,342 views

25 citations

Fifteen genera experienced maximum temporal fluctuations in abundance levels at different stages of diabetes development. These 15 genera (A–O) depict highly dynamic variations. P-values (P < 0.5) are shown on plot corners. Box plots display the following values: the Y-axis represents relative abundance of the genus, the X-axis represents time grouping; middle box line, represents the median; the upper and lower whiskers represent 1.5 times IQR beyond the upper and lower quartiles, respectively; and dots represent outlier values. Genera Bilophila, Proteus, Rothia, and Streptococcus have low abundance levels. For better inspection, these plots have been divided into three parts (red, green, and blue) that reflect their relative abundances.

Original Research

14 February 2019

Dynamic Development of Fecal Microbiome During the Progression of Diabetes Mellitus in Zucker Diabetic Fatty Rats

Wen Zhou

, 3 more and

Lijing Zhang

6,260 views

75 citations

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