Speakers at ICG-13

Speakers at ICG-13

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Biography

Academic Appointments:

July 2009 - Present Department of Biostatistics, Harvard T.H. Chan School of Public Health
April 2013 - Present Associate Professor of Computational Biology and Bioinformatics
July 2009 - March 2013 Assistant Professor of Computational Biology and Bioinformatics

 

Education:

November 2008 - June 2009 Lewis-Sigler Institute for Integrative Genomics, Princeton University
Supervisor: Dr. Olga Troyanskaya

Postdoctoral Researcher

 

August 2004 - November 2008 Computer Science Department, Princeton University
Adviser: Dr. Olga Troyanskaya

Ph.D. in Computer Science, November 2008; M.A., June 2006

 

August 2002 - May 2004 Language Technologies Institute, Carnegie Mellon University
Adviser: Dr. Eric Nyberg

M.S. in Language Technologies, December 2003

 

August 1998 - November 2000 Rose-Hulman Institute of Technology
B.S. summa cum laude, November 2000

Majored in Computer Science, Chemistry, and Math; Minored in Spanish

 

August 1996 - May 1998 Simon's Rock College of Bard

A.A., May 1998

 

Awards, Honors, and Scholarships:
• ISCB Overton Prize (Harvard Chan School, 2015)
• eLife Sponsored Presentation Series early career award (Harvard Chan School, 2014)
• Presidential Early Career Award for Scientists and Engineers (Harvard Chan School, 2012)
• NSF CAREER award (Harvard Chan School, 2010)
• Quantitative and Computational Biology Program Training Fellowship (Princeton University, 2006-2008)
• Association of Princeton Graduate Alumni Teaching Award (Princeton University, 2006)
• Addison-Wesley Computer Science Award (Rose-Hulman Institute of Technology, 2000)
• William Albert Noyes, Sr. Award in Chemistry (Rose-Hulman Institute of Technology, 2000)
• EDS Computer Science Scholarship (Rose-Hulman Institute of Technology, 1998)

• Acceleration to Excellence Program full two-year scholarship (Simon's Rock College of Bard, 1996)

 

Academic Affiliations:
• HMS Systems Biology Program (2011-Present)
• Broad Institute, Associate Member (2010-Present)
• Harvard Microbial Sciences Initiative (2010-Present)
• MGH Center for the Study of Inflammatory Bowel Diseases (2010-Present)
• HSPH Program in Biological Sciences in Public Health (2009-Present)

• Dana-Farber/Harvard Cancer Center (2009-Present)


Abstract

Multi'omics for the microbiome in population health

Jason Lloyd-Price1,2, Cesar Arze2, Ashwin N. Ananthakrishnan3, Melanie Schirmer1, Julian Avila-Pacheco4, Tiffany W. Poon1, Elizabeth Andrews3, Nadim J. Ajami5, Kevin S. Bonham1,2, Colin J. Brislawn6, David Casero7, Antonio Gonzalez8, Thomas G. Graeber9, Brantley Hall1, Kathleen Lake10, Carol J. Landers11, Himel Mallick1,2, Damian R. Plichta1, Mahadev Prasad12, Gholamali Rahnavard1,2, Dmitry Shungin1,13, Yoshiki Vázquez-Baeza8, Richard A. White III6, IBDMDB Investigators, Jonathan Braun7, Lee A. Denson10,16, Janet K. Jansson6, Rob Knight8, Subra Kugathasan12, Dermot P. B. McGovern11, Joseph F. Petrosino5, Thaddeus S. Stappenbeck17, Harland S. Winter14,18, Clary B. Clish4, Eric A. Franzosa2, Hera Vlamakis1, Ramnik J. Xavier1,3,19, Curtis Huttenhower1,2

1Infectious Disease and Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA

2Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, USA

3Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA, USA

4Metabolomics Platform, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA, USA

5Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA, USA

6Earth and Biological Sciences Directorate, Pacific Northwest National Lab, 902 Battelle Blvd, Richland, WA 99354, USA, USA

7Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, 924 Westwood Blvd, Los Angeles, CA 90095, USA, USA

8Molecular Virology and Microbiology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA, USA

9Molecular and Medical Pharmacology, University of California Los Angeles, 570 Westwood Plaza Bldg 114, Los Angeles, CA 90095, USA, USA

10Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA, USA

11F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, 8730 Alden Drive, Los Angeles, CA 90048, USA, USA

12Department of Pediatrics, Emory University, 1599 Clifton Road, Atlanta, GA 30322, USA, USA

13Department of Odontology, Umeå University, Norrlands universitsetssjukhus 1D, Umeå, SE 901 87, Sweden, USA

14Department of Pediatrics, MassGeneral Hospital for Children, 55 Fruit Street, Boston, MA 02114, USA, USA

15Vatche and Tamar manoukian Division of Digestive Diseases, University of California Los Angeles, 100 Medical Plaza Suite 345, Los Angeles, CA 90095, USA, USA

16Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA, USA

17Department of Pathology & Immunology, Washington University, 660 S Euclid Avenue, St. Louis, MO 63110, USA, USA

18Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA, USA

19Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, USA

The human microbiome - the collection of microbial organisms residing in and on the body, mostly in the gut - has been associated with diseases ranging from autism to cancer, but the causative molecular or ecological mechanisms are difficult to discern. In particular, it remains challenging to integrate multiple types of molecular data detailing the microbiome's interaction with human hosts and their environments in large, epidemiology-scale studies, particularly diet, pharmaceuticals, and other biochemical exposures. The Integrative Human Microbiome Project (iHMP or "HMP2") is one of several efforts to better understand microbiome and immune molecular activity as it affects human health. A total of 132 CD patients, UC patients, and non-IBD subjects were followed one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (a total of 2,965 analyzed stool, biopsy, and blood specimens). Together, these provide a comprehensive view of the gut microbiome’s functional dysbiosis during IBD activity, showing a characteristic balance between facultative and obligate anaerobes, as well as molecular disruptions in microbial transcription (e.g. among the clostridia), metabolite pools (e.g. acylcarnitines, bile acids, and short-chain fatty acids), and host serum antibody levels, among others. Other results to date include strain haplotyping and tracking within and among subjects, linking small molecule metabolites to microbial activity, and functional profiling of metatranscriptomes during inflammation. The work suggests future applications and open questions in microbiome functional 'omics, quantitative methods, and epidemiology more broadly in public health.

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