AI Article Synopsis
Article Abstract
Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. The performance of tmap in detecting nonlinear patterns is validated by different scenarios of simulation, which clearly demonstrate its superiority over the most commonly used methods. Application of tmap to several population-scale microbiomes extensively demonstrates its strength in revealing microbiome-associated host or environmental features and in understanding the systematic interrelations among their association patterns. tmap is available at https://github.com/GPZ-Bioinfo/tmap.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927166 | PMC |
| http://dx.doi.org/10.1186/s13059-019-1871-4 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Transdiagnostic neurocognitive deficits in patients with type 2 diabetes mellitus, major depressive disorder, bipolar disorder, and schizophrenia: A 1-year follow-up study.
J Affect Disord
March 2022
Centro Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid 28029, Spain; TMAP - Unidad de Evaluación en Autonomía Personal, Dependencia y Trastornos Mentales Graves, University of Valencia, Valencia 46010, Spain; INCLIVA - Health Research Institute, Valencia 46010, Spain; Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibáñez 17, Valencia 46010, Spain. Electronic address:
Background: Neurocognition impairments are critical factors in patients with major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ), and also in those with somatic diseases such as type 2 diabetes mellitus (T2DM). Intriguingly, these severe mental illnesses are associated with an increased co-occurrence of diabetes (direct comorbidity). This study sought to investigate the neurocognition and social functioning across T2DM, MDD, BD, and SZ using a transdiagnostic and longitudinal approach.
View Article and Find Full Text PDFTopological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome.
Front Artif Intell
August 2021
Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom.
There is growing interest in the connection between the gut microbiome and human health and disease. Conventional approaches to analyse microbiome data typically entail dimensionality reduction and assume linearity of the observed relationships, however, the microbiome is a highly complex ecosystem marked by non-linear relationships. In this study, we use topological data analysis (TDA) to explore differences and similarities between the gut microbiome across several countries.
View Article and Find Full Text PDFA Systematic Protein Turnover Map for Decoding Protein Degradation.
Cell Rep
November 2020
Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Harvard T.H. Chan Advanced Multi-Omics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:
Protein degradation is mediated by an expansive and complex network of protein modification and degradation enzymes. Matching degradation enzymes with their targets and determining globally which proteins are degraded by the proteasome or lysosome/vacuole have been a major challenge. Furthermore, an integrated view of protein degradation for cellular pathways has been lacking.
View Article and Find Full Text PDFtmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.
Genome Biol
December 2019
Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. The performance of tmap in detecting nonlinear patterns is validated by different scenarios of simulation, which clearly demonstrate its superiority over the most commonly used methods.
View Article and Find Full Text PDFMutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.
PLoS One
July 2016
AIT Austrian Institute of Technology, Health and Environment Department, Molecular Diagnostics, Vienna, Austria.
Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!