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Acknowledgments to Reviewers 2018
Publication date: February 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 1Author(s): (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 18, 2019 Category: Bioinformatics Source Type: research

9. 1st before inside back cover-Acknowledgements to Peer Reviewers 2018 E
Publication date: February 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 1Author(s): (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
Publication date: Available online 14 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Valentina Galata, Cédric C. Laczny, Christina Backes, Georg Hemmrich-Stanisak, Susanne Schmolke, Andre Franke, Eckart Meese, Mathias Herrmann, Lutz von Müller, Achim Plum, Rolf Müller, Cord Stähler, Andreas E. Posch, Andreas KellerAbstractEmerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic dat...
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Deep Learning Deepens the Analysis of Alternative Splicing
Publication date: Available online 14 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xudong Zou, Xin Gao, Wei Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name
Publication date: Available online 7 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Huiyan Sun, Liang Chen, Sha Cao, Yanchun Liang, Ying XuAbstractIt has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before startin...
Source: Genomics, Proteomics and Bioinformatics - May 7, 2019 Category: Bioinformatics Source Type: research

GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jiarui Li, Pengcheng Du, Adam Yongxin Ye, Yuanyuan Zhang, Chuan Song, Hui Zeng, Chen ChenAbstractIdentifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic ...
Source: Genomics, Proteomics and Bioinformatics - May 1, 2019 Category: Bioinformatics Source Type: research

The Fast Track for Microbiome Research
Publication date: Available online 26 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Kang Ning, Yigang Tong (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - April 28, 2019 Category: Bioinformatics Source Type: research

Effects of Proton Pump Inhibitors on the Gastrointestinal Microbiota in Gastroesophageal Reflux Disease
We examined the association between the PPI usage and the microbiota present in gastric mucosal and fecal samples from GERD patients and healthy controls (HCs) using 16S rRNA gene sequencing. GERD patients taking PPIs were further divided into short-term and long- term PPI user groups. We showed that PPI administration lowered the relative bacterial diversity of the gastric microbiota in GERD patients. Compared to the non-PPI-user and HC groups, higher abundances of Planococcaceae, Oxalobacteraceae, and Sphingomonadaceae were found in the gastric microbiota from the PPI-user group. In addition, the Methylophilus genus was ...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment
We examined the relationships between gut microbiome profiles of ASD children and those of their mothers, and evaluated the clinical discriminatory power of discovered bacterial biomarkers. Gut microbiome was profiled and evaluated by 16S ribosomal RNA gene sequencing in stool samples of 59 mother–child pairs of ASD children and 30 matched mother–child pairs of healthy children. Significant differences were observed in the gut microbiome composition between ASD and healthy children in our Chinese cohort. Several unique bacterial biomarkers, such as Alcaligenaceae and Acinetobacter, were identified. Mothers of ASD child...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-Related Pathways Mediated by Gut Microbiota
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiaofeng Song, Liang Zhong, Na Lyu, Fei Liu, Boxing Li, Yanan Hao, Yong Xue, Jing Li, Yuqing Feng, Yue Ma, Yongfei Hu, Baoli ZhuAbstractInulin has been used as a prebiotic to alleviate glucose and lipid metabolism disorders in mice and humans by modulating the gut microbiota. However, the mechanism underlying the alleviation of metabolic disorders by inulin through interactions between the gut microbiota and host cells is unclear. We use ob/ob mice as a model to study the effect of inulin on the caecal microbiota by 16S ...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiaoqing Jiang, Xin Li, Longshu Yang, Chunhong Liu, Qi Wang, Weilai Chi, Huaiqiu ZhuAbstractExploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and ...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jiarui Li, Pengcheng Du, Adam Yongxin Ye, Yuanyuan Zhang, Chuan Song, Hui Zeng, Chen ChenAbstractIdentifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic ...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Stereotypes About Enterotype: the Old and New Ideas
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Mingyue Cheng, Kang NingAbstractIn 2011, the term “enterotype” first appeared to the general public on Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view. We firstly illustrated the definition of the enterotype and various influence factors such as diet, administratio...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Maozhen Han, Melissa Dsouza, Chunyu Zhou, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chaofang Zhong, Hao Zhou, Jack A Gilbert, Zhi Wang, Kang NingAbstractAgricultural activities, including stock-farming, planting industry, and fish aquaculture, can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear. Hence, in this work, we selected Honghu lake as a typical lake that is influen...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome
This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota. (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research