MAY 10, 2018 6:00 AM PDT

Differential Abundance Analysis for Microbial Marker-Gene Surveys

Speaker
  • Research Fellow, Dana-Farber Cancer Institute
    Biography
      I am a Research Fellow in the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Department of Biostatistics at the Harvard TH Chan School of Public Health under the guidance of Professor John Quackenbush. Prior to joining Harvard I was a National Science Foundation Graduate Research Fellow at the University of Maryland, College Park where I received my Ph.D. in Applied Mathematics, Statistics and Scientific Computation.
      As a computer scientist and computational biologist, my interests are to develop computational methods for the analysis of high-throughput sequencing data. I also desire to develop software and support these methods as open-source software for the broader scientific community through Bioconductor and popular domain tools such as QIIME and Phyloseq. MetagenomeSeq, is my most popular tool developed and is in the top 5% of all Bioconductor packages downloaded in the last year with over 5,000 unique users. I am excited to leverage statistical and network methodologies in accounting for technological when identifying disease markers.

    Abstract

    We introduce a differential abundance analysis method for the analysis of sparse high-throughput data from large-scale surveys of marker genes for microbial communities. Our approach relies on cumulative sum scaling (CSS) normalization - a count data normalization technique - and the zero-inflated Gaussian (ZIG) model as a statistical method for detecting differential abundance of taxonomic features. ZIG differential abundance detection method accounts for bias introduced by the under-sampling of microbial communities commonly found in large-scale marker gene studies.  We have implemented these methods in the publicly available metagenomeSeq bioconductor package. In addition we highlight the utility of the method in a large scale study characterizing the diarrheal microbiome in young children from developing children. Diarrhea, a major cause of mortality and morbidity in young children from developing countries, leading to as many as 15% of all deaths in children under 5 years of age. While many causes of this disease are already known, conventional diagnostic approaches fail to detect a pathogen in up to 60% of diarrheal cases. Using our novel methodology Streptococci were found in our study to be statistically associated with diarrheal disease in general and more severe forms (such as dysentery) in particular.


    Show Resources
    You May Also Like
    MAY 11, 2021 10:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    MAY 11, 2021 10:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    Date: May 11, 2021 Time: 10:00zm PDT Your samples are some of the most valuable assets in the laboratory. After spending countless hours on extraction and preparation, your conclusions could...
    JUN 09, 2021 7:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    JUN 09, 2021 7:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    Date: June 9, 2021 Time: 09 June 2021, 7am PDT, 10am EDT, 4pm CEST cells with dramatic implications on the validity of past cell culture related research. The fact that at least 509 cell lin...
    DEC 02, 2020 8:00 AM PST
    C.E. CREDITS
    DEC 02, 2020 8:00 AM PST
    DATE: December 2nd, 2020 TIME: 08:00am PDT, 11:00pm EDT Bioreactors and shakers are used to cultivate microorganisms, plant, insect, and mammalian cells in different volumes. Upscaling of pr...
    NOV 16, 2020 8:00 AM PST
    C.E. CREDITS
    NOV 16, 2020 8:00 AM PST
    Date: November 16, 2020 Time: 8:00am (PST), 11:00am (EST) CRISPR screening has become the prime discovery tool in modern biomedical research and drug discovery. At the same time, most screen...
    APR 21, 2021 5:00 PM CEST
    APR 21, 2021 5:00 PM CEST
    Date: April 21, 2021 Time: 8:00am (PDT), 11:00am (EDT), 5:00pm (CEST) Spatial Answers Trilogy - Spatial Answers in Immunology Immunology Researchers share their Spatial Discoveries in SARS-C...
    MAR 16, 2021 10:00 AM PDT
    C.E. CREDITS
    MAR 16, 2021 10:00 AM PDT
    Date: March 16, 2021 Time: 10:00am (PST) Scientific progress and breakthroughs today are often too expensive for most institutions to acquire. Each year, the National Institutes of Health (N...
    MAY 10, 2018 6:00 AM PDT

    Differential Abundance Analysis for Microbial Marker-Gene Surveys


    Specialty

    Genomics

    Molecular Biology

    Immunology

    Molecular Diagnostics

    Microbiology

    Microbiome

    Geography

    Asia100%

    Registration Source

    Website Visitors100%

    Job Title

    Educator/Faculty100%

    Organization

    Government100%


    Show Resources
    Loading Comments...
    Show Resources
    Attendees
    • See more