JAN 30, 2018 09:00 AM PST

WEBINAR: Metagenomics and base modifications from long, short, and linked-reads

SPONSORED BY: Zymo Research
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  • Associate Professor, Department of Physiology and Biophysics, WorldQuant (WQ) Scholar, Director, WQ Init. for Quantitative Prediction, Weill Cornell Medicine
      Dr. Christopher Mason completed his dual B.S. in Genetics and Biochemistry (2001) from University of Wisconsin-Madison, his Ph.D. in Genetics (2006) from Yale University, and then completed post-doctoral training in clinical genetics (2009) at Yale Medical School, and a joint post-doctoral Fellow of Genomics, Ethics, and Law at Yale Law School (2009). He is currently an Associate Professor at Weill Cornell Medicine, with appointments at the Tri-Institutional Program on Computational Biology and Medicine, the Meyer Cancer Center, and the Feil Family Brain and Mind Research Institute.
      The Mason laboratory develops and deploys new biochemical and computational methods in functional genomics to elucidate the genetic basis of human disease and human physiology. We create and explore novel techniques in next-generation sequencing and algorithms for: tumor evolution, genome evolution, DNA and RNA modifications, and genome/epigenome engineering. We also work closely with NIST/FDA to build international standards for these methods, to ensure clinical-quality genome measurements/editing. We also work with NASA to build integrated molecular portraits of genomes, epigenomes, transcriptomes, and metagenomes for astronauts, which establish the molecular foundations and genetic defenses for enabling long-term human space travel.
      He has won the NIH's Transformative R01 Award, the NASA Group Achievement Award, the Pershing Square Sohn Cancer Research Alliance Young Investigator award, the Hirschl-Weill-Caulier Career Scientist Award, the Vallee Scholar Award, the CDC Honor Award for Standardization of Clinical Testing, and the WorldQuant Foundation Scholar Award. He has >130 peer-reviewed papers that have been featured on the covers of Nature, Science, Cell Host and Microbe, Nature Biotechnology, Nature Microbiology, and many others.He was named as one of the "Brilliant Ten" Scientists by Popular Science, featured as a TEDMED speaker, and called "The Genius of Genetics".
    • Scientist, Zymo Research Corp.
        Dr. Shuiquan Tang is currently a research scientist at Zymo Research. He received his Ph.D. in the Department of Chemical Engineering and Applied Chemistry from the University of Toronto. Dr. Tang joined Zymo Research in 2014, and has since been instrumental in the research and development of Zymo's microbiomics and metagenomics programs. His past experiences include work in the fields of environmental microbiology and biological process engineering, with an emphasis on bioinformatics, metagenomics and anaerobic cultivation. Most recently, Dr. Tang has been involved in the development of Zymo Research's microbiomics portfolio. He has multiple publications in different journals, including Frontiers in Microbiology, Applied & Environmental Microbiology and Philosophical Transactions of the Royal Society of London, Series B, Biological Science.


      DATE: January 30, 2018
      TIME: 9:00AM PST, 12:00PM EST

      Infectious disease surveillance and monitoring is critical in settings where disease outbreaks and antibiotic resistance can dramatically impact human health.  Rapid and accurate detection of human pathogens between closely related strains and across phylogenetic kingdoms is paramount to mitigate disease outbreaks and to diagnose affected individuals.  Here, we use demonstrate cross-kingdom species detection by simultaneously sequencing DNA from 8 bacteria and 2 fungi in the ZymoBIOMICS control.  We test this on long-read (PacBio, oxford nanopore), short read (Illumina), and linked, long-read (10x Genomics) platforms.  We also show that these standard aliquots can be used for benchmarking a variety of tools and also characterize their epigenetic changes (base modifications).  These standards are now being used internationally as part of a large-scale effort and improving metagenomics use in the clinic, or “precision metagenomics.” 

      Learning Objectives:

      • Describe the impact of a sickness on the proportion of natural flora.

      • List tools implemented for microbiome and metagenome data analysis and species detection, such as BLAST, MetaPhlAn, and CLARK

      • Describe the utility of metagenome standards and benchmarking measures

      • List the most prevalent bacteria of the skin, gastrointestinal (GI) tract, oral cavity, and urogenital tract

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