Medical Computer Science
Resume:
Soumya Raychaudhuri, MD/PhD Curriculum Vitae
Date Prepared: January 30, 2012
Name: Soumya Raychaudhuri, MD, PhD
Office Address: Harvard Medical School
New Research Building, 250D
** ****** ****s Pasteur, Boston MA 02115
Home Address: 26 Gibbs Street, #3
Brookline MA 02446
Work Phone: 617-***-****
Work Email: ******@**************.***
Work
FAX:
Place of Birth: Rochester, NY, USA
Education
1997 B.S., B.A, (summa cum Biophysics ; Mathematics, State University of New
laude, The Outstanding minors in Chemistry and York at Buffalo, Buffalo, NY
Student in Natural Physics
Sciences)
2002 Ph.D. Biomedical Informatics, Stanford University
minor in Computer Science Palo Alto, CA
(Russ Altman)
2004 M.D. Medicine Stanford University,
Palo Alto, CA
Postdoctoral Training
2002-2004 Post-Doctoral Fellow Genetics, and Computer Stanford University, Palo Alto,
Science (Russ Altman) CA
6/2004- House OfficerMedicine Brigham and Women's Hospital,
6/2006 Boston, MA
7/2006- Clinical FellowRheumatology Brigham and Women's Hospital,
6/2010 Boston, MA
12/2006
- Post-Doctoral Fellow Medical and Population Broad Institute of MIT and
6/2010Genetics Group (Mark Daly) Harvard, Cambridge, MA
Faculty Academic Appointments
7/2010 Instructor Division of Rheumatology, Brigham & Women s Hospital,
3/2011Immunology, & Allergy, Harvard Medical SchoolDepartment of Medicine
7/2010 Instructor Division of Genetics, Brigham & Women s Hospital,
3/2011 Department of MedicineHarvard Medical School
4/2011 Assistant Professor Division of Rheumatology, Brigham & Women s Hospital,
Immunology, & Allergy, Harvard Medical School
Department of Medicine
4/2011Assistant Professor Division of Genetics, Brigham & Women s Hospital,
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Soumya Raychaudhuri, MD/PhD Curriculum Vitae
3/2011 Department of Medicine Harvard Medical School
Appointments at Hospitals/Affiliated Institutions
7/2010 - Associate PhysicianRheumatology Brigham & Women s Hospital
7/2010Associate Geneticist Genetics Brigham & Women s Hospital
Professional Societies
2002 American Medical Informatics Association Scientific Advisory Board
Symposium, San Antonio
2008 - American College of Rheumatology Member
2008 - American Society of Human Genetics Member
2008 - International Society of Computational Biology Member
2008 - International Society of Computational Biology Member
2011 AMIA 2011 Summit on Translational Scientific Program Committee
Bioinformatics, San Francisco
Editorial Activities
Ad hoc reviewer Arthritis Research & Therapy
Arthritis & Rheumatism
BMC Bioinformatics
BMC Genomics
Bioinformatics
Circulation: Cardiovascular Genetics
European Journal of Human
Genes and Immunity
Genetics
Genome Biology
Genome Research
Genomics
Human Molecular Genetics
Medical Research Council (UK)
Nature Biotechnology
Pacific Symposium of Biocomputing
Proceedings of the National Academy of Sciences
PLOS One
PLOS Computational Biology
PLOS Genetics
Honors and Prizes
1993 Grace Capen Scholarship SUNY Buffalo
1993 University Honors Scholar SUNY Buffalo
1994 CRC Press Freshman Award SUNY Buffalo Chemistry
Achievement
1994 Summer Life Sciences Training NASA Fellowship
Program
1995 Supercomputing Program for NSF Fellowship
Undergraduates
1995 Barry Goldwater Undergraduate
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Soumya Raychaudhuri, MD/PhD Curriculum Vitae
Scholarship
1997 Phi Beta Kappa
1997 The Outstanding Student in SUNY Buffalo
Natural Science
1997 Honors Department of Mathematics, SUNY
Buffalo
1997 Medical Scientist Training NIH Pre-Doctoral
Program Fellowship
2006 University Citation for Teaching Tufts University
Excellence
2007 Clinical Fellow Teaching Award Brigham and Women s Hospital
2006-2008 Travel Fellowship American College of Rheumatology
2008 Outstanding Poster American College of Rheumatology
Presentation
2008 Travel Fellowship American College of Rheumatology
2009 Within Our Reach American College of Rheumatology
Travel Scholarship
2009 Distinguished Fellow Award American College of Rheumatology
2010 Trainee Research Semifinalist American Society of Human
Award Genetics
2011 Harvard Medical School Harvard Medical School
Excellence in Tutoring Award
(ETA)
Report of Funded and Unfunded Projects
Funding Information
Past
2008 Bridge to Career Development Award
ACR/REF
PI ($75,000)
Bioinformatics and Population Genetics to Identify Rheumatoid Arthritis Genes
2009 - 2011 KAR055688A-S
NIAMS-NIH, ARRA Supplemental Funding
PI ($100,000)
Bioinformatics and Population Genetics to Identify Rheumatoid Arthritis Genes
Current
2008 - 2013 KAR055688A
NIAMS-NIH
PI ($570,439)
Bioinformatics and Population Genetics to Identify Rheumatoid Arthritis Genes
2011-2012 Pilot Feasibility Grant (Raychaudhuri)
Harvard Digestive Diseases Center
PI ($25,000)
Correlating Natural Killer T cell function and Crohn's susceptibility.
2011 William F. Milton Fund
3
Soumya Raychaudhuri, MD
/PhD Curriculum Vitae
Harvard University
PI ($40,000)
Using rheumatoid arthritis risk loci to identify and investigate pathogenic immune cell
subsets
2011-2012 Innovative Research Grant
Arthritis Foundation
PI ($184,000)
RA risk alleles influence function of CD4 positive effector memory cells.
Report of Local Teaching and Training
Teaching of Students in Courses
2000 CS 274 (BMI 214) Algorithms and Stanford University
Representations in Molecular Biology
Undergraduate and graduate students Teaching Assistant
2000 CS 272 (BMI 212) Biomedical Informatics Stanford University
Project Course.
Graduate students Teaching Assistant
2005, 2007 Longitudinal Course in Clinical Medicine Harvard University School of Medicine
MD/PhD Students Clinical Preceptor
2006-2009 Medical Residency Program in Primary The Brigham and Women s Hospital
Care Core Rotation, Rheumatology
Elective, and Genetics Elective
Residents Lecturer and Preceptor
2006-2009 IN708.0f, Human Systems Rheumatology Harvard University School of Medicine
Course for Harvard
Medical Students Tutor
2009-2011 IN755.0: Human Genetics Harvard University School of Medicine
Medical Students Tutor
Formal Teaching of Residents, Clinical Fellows and Research Fellows (post-docs)
Clinical Supervisory and Training Responsibilities
2010 - Rheumatology Clinic Preceptor / Brigham & One session per two months
Women s Hospital
Laboratory and Other Research Supervisory and Training Responsibilities
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Soumya Raychaudhuri, MD/PhD Curriculum Vitae
Formally Supervised Trainees
2002-2003 Nipun Mehra, Computer Science MS Student / now MBA student at Wharton/U Penn
2009- Elizabeth Rossin, Harvard HST MD student / now a Harvard BBS PhD Student
Co-authored two manuscripts, received funding through Harvard-MIT Health Sciences
2
and Technology IDEA grant program.
2010- Xinli Hu, Harvard HST MD Student
Trainee in the laboratory
Received a Harvard Medical School Fellowship for Summer 2010
2
Received IDEA dellowship for 2010-2011 through Harvard-MIT s Health Sciences and
Technology Division
2010- Aleksandar Kostic, Harvard BBS PhD student
Dissertation Advisory Committee
2011- Cynthia Sandor, PhD, Postdoctoral fellow
Trainee in the laboratory
2011 Problems in Quantitative Genetics, Stellar Abstract Award, Boston, MA
Received the European Union Marie Curie Fellowship (2012-2015)
2011- Vineeta Agarwala, Harvard BBS PhD student
Dissertation Advisory Committee
2012- Gosia Trynka
Received The Rubicon Fellowship, The Netherlands (2012-2013)
Received the European Union Marie Curie Fellowship (2012-2015)
Formal Teaching of Peers (e.g., CME and other continuing education courses)
Local Invited Presentations2/15/2002 Literature based assessment of the functional coherence of a group of genes
Department of Genetics, Stanford University, Stanford CA
4/11/2002 Using biological text in genomic scale analysis
The Arabidopsis Information Resource, Carnegie Institution of Washington, Stanford, CA
10/15/2007 Computational Biology to Enhance Analysis of Rheumatoid Arthritis Genome
Scans
Rheumatology, Immunology, and Allergy Retreat, Brigham and Women s Hospital, Beth
Israel Deaconess Hospital, and Joslin Diabetes Center
11/6/2007 A Meta-Analysis of Three Whole Genome Analysis Scans in Rheumatoid Arthritis
Inflammatory Disease Group Meeting, Broad Institute, Cambridge, MA
11/8/2007 A Meta-Analysis of Three Whole Genome Analysis Scans in Rheumatoid Arthritis
Medical and Population Genetics Seminar, Broad Institute, Cambridge, MA
11/27/2007 A Meta-analysis of Genome-Wide Association Studies in RA
Division of Rheumatology-Centocor Symposium, Brigham and Women s Hospital
(Centecor)
10/15/2008 Txt-Mining to Identify Functional Relationships Between Disease Associated
Genetic
Regions
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Soumya Raychaudhuri, MD/PhD Curriculum Vitae
The Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA
10/21/2008 Using Functional Information in Published Text to Interpret and Predict
Genome-Wide
Association Resuls
Bioinformatics Core Forum, Harvard School of Public Heath, Boston, MA
11/4/2008 Using a Text-Based Approach to Find Shared Function Among Associated Variants
Broad Institute Annual Retreat, Boston, MA
12/11/2008 Using Functional Genomics to Understand the Underpinnings of Complex Disease
Medical and Population Genetics Seminar, Broad Institute, Cambridge, MA
12/16/2008 Genetic Studies in Rheumatology
Division of Rheumatology-Centocor Symposium, Brigham and Women s Hospital
2/18/2009 GRAIL: A Text-based Method to Find Common Function within Disease Regions
Computational Biology and Bioinformatics Seminar, Broad Institute, Cambridge, MA
5/22/2009 Genetics of Rheumatoid Arthritis
Rheumatology Grand Rounds, Beth Israel Deaconess Medical Center, Boston, MA
11/2/2009 Pathway Analyses of CNVs in Neuropsychiatric Diseases are Confounded by Gene
Size
Broad Institute Annual Retreat, Boston, MA
11/12/2009
Applying Pathway Analyses to Disease Loci
Conference in Quantitative Genomics,
Harvard School of Public Health, Boston, MA
12/8/2009 Genomic Screens to Function: Translating Disease-Associated Genetic Variants
Into
Pathways
Center for Systems Biology Science Talks Series, Massachusetts General Hospital,
Boston, MA
1/19/2010 Genomic Screens to Function: Translating Disease-Associated Genetic Variants
Into
Pathways
Center for Biomedical Informatics, Harvard University Medical School, Boston, MA
1/28/2010Applying Text-Mining to Understand Genomic Screens
Functional Jamboree, Broad Institute, Cambridge, MA
2/23/2010 Genomic Screens to Function: Translating Rheumatoid Arthritis Genetic Variants
into
Pathways
Division of Genetics Seminar Series,
Brigham and Women s Hospital, Boston, MA
2/25/2010 Analyzing large genomic data sets to understand rheumatic disease
Brigham- Harvard International Rheumatology Symposium, Boston, MA
5/20/2010 Fine-Mapping the CFH region in Age Related Macular Degeneration
Snapshots of Genome Wide Analysis in Human Disease, Broad Institute, Cambridge, MA
6/10/2010 Translating genetic loci into pathogenic processes and pathways
Kinome Meeting, Broad Institute, Cambridge, MA
6/22/2010 From Genetic Variants to Disease Pathogenesis
Rheumatology Grand Rounds, Brigham & Women s Hospital, Boston, MA
3/16/2011 Translating genetic loci into pathogenic processes and pathways
Systems-based Consortium for Organ Design & Engineering Seminar, Boston, MA
5/17/2011 Fine Mapping Inflammatory loci
Rheumatology Grand Rounds, Brigham & Women s Hospital, Boston, MA
9/28/2011 Genetics and Functional Genomics to Understand Human Disease
BBS Faculty Seminar Series
1/18/2012 The cutting edge in Medical Research Bioinformatics and Genetics
BWH Rheumatology Symposium
2/01/2012 Imputation and Fine-mapping of the Major Histocompatiblity Complex in
Rheumatoid
Arthritis
Harvard School of Public Health, Epidemiology Seminar Series
2/07/2012 Fine mapping the CFH locus in age-related macular degeneration
Harvard School of Public Health Program in Quantitative Genomics: Short Course For
Analyzing Quantitative 'Omic Data
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Soumya Raychaudhuri, MD/PhD Curriculum Vitae
Report of Regional, National and International Invited Teaching
and Presentations
Invited Presentations and Courses
No presentations below were sponsored by outside entities
Regional
12/15/2005 Computational Analysis of Text in Genomics
Bioinformatics Program, Boston University, Boston, MA
3/09/2012 Using genetic risk factors to identify pathogenic cell-types in autoimmune
diseases.
Seminar at Vertex Pharmaceuticals
National
6/24/1995 Mathematical Analysis of the Transformation of Micronuclei into Decompression-
Sickness Bubbles. Undersea and Hyperbaric Medicine / Plenary Talk (Abstract)
Undersea and Hyperbaric Medical Society, Palm Beach, FL
1/6/2000 Principal Components Analysis to Summarize Microarray Experiments: Application
to
Sporulation Time Series / Platform Talk (Abstract)
Pacific Symposium on Biocomputing, Waikiki, HI
1/13/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Department of Computer Science and Engineering, Pennsylvania State University. State
College, PA
1/14/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Department of Computer Science, Cornell University. Ithaca, NY.
2/13/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
School of Information and Computer Science, University of California, Irvine. Irvine, CA
2/18/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Center for Bioinformatics, University of Pennsylvania. Philadelphia, PA
2/21/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Institute for Research in the Cognitive Science, University of Pennsylvania.
Philadelphia,
PA
2/25/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Department of Biomolecular Engineering, University of California, Santa Cruz. Santa
Cruz, CA
1/15/2003 Memorial Sloan Kettering Cancer Center
New York, NY
3/24/2003 Integrating Background Knowledge into Bioinformatics Algorithms
Bioinformatics Program, Boston University
4/16/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Department of Computer Science, University of Southern California.
5/16/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Almaden Research Center. International Business Machines, Almaden, CA
6/9/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Department of Biochemistry and Molecular Biology, Pennsylvania State University. State
College, PA
8/6/2003 Statistical Methods to Explain Biological Data by Automatic Interpretation of
Text /
Platform Talk (Abstract)
Joint Statistical Meeting, San Francisco, CA
7
Soumya Raychaudhuri, MD/PhD Curriculum Vitae
10/27/2008 Common Variants At CD40 and Other Loci Confer Risk Of Rheumatoid Arthritis /
Platform Talk (Abstract)
American College of Rheumatology Annual Meeting, San Francisco, CA
6/8/2009 Mining Prior Knowledge to find Shared Function Among Associated Variants
ENDGAMe (Enhancing Development of Genome-Wide Association Methods) Symposium
and NCI Workshop, Ann Arbor, MI
6/18/2009 A Text-Based Strategy to Identify Disease Variants: Looking for Gene
Relationships
Across Implicated Loci (GRAIL) / Plenary Talk (Abstract)
Summit on Systems Biology, Richmond, VA
7/26/2009 Using A Text-Mining Algorithm to Identify Novel RA Risk Variants
Feinstein Institute for Medical Research, Manhasset, NY
8/14/2009
Using Gene Function to Identify Disease Genes : Rheumatoid Arthritis
Biomarkers Group, South San Francisco, CA
10/16/2009
Using Gene Function to Identify Novel Rheumatoid Arthritis Risk Loci /
Platform Talk
(Abstract)
American College of Rheumatology Annual Meeting, Philadelphia, PA
12/9/2009 Genomic Screens to Function: Translating Disease-Associated Genetic Variants
Into
Pathways
Bioinformatics Seminar Series, University of Michigan, Ann Arbor, MI
1/27/2010 Genomic Screens to Function: Translating Rheumatoid Arthritis Genetic Variants
into
Pathways
Vanderbilt Informatics Seminar Series, Vanderbilt University, Nashville, TN
1/29/2010 Genomic Screens to Function: Translating Rheumatoid Arthritis Genetic Variants
into
Pathways
Hospital for Special Surgery Division of Rheumatology Seminar Series, New York, NY
2/17/2010 Genomic Screens to Function: Translating Rheumatoid Arthritis Genetic Variants
into
Pathways
Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY
4/29/2010 Genomic Screens to Function: Translating Rheumatoid Arthritis Genetic Variants
into
Pathways
Center for Biomedical Medical Informatics Research, Stanford University, Palo Alto, CA
11/4/2010 Accurately assessing the risk of schizophrenia conferred by rare copy-number
variation
affecting genes with brain function / Platform Talk (Abstract)
American Society of Human Genetics Annual Meeting, Washington, DC
2/3/2011 Using Complex Disease Genetics to Identify Key Disease Mechanisms in Autoimmune
Disease
Rheumatology Grand Rounds, University of Alabama, Birmingham, AL
7/20/2011 A rare penetrant mutation in CFH confers high risk of age-related macular
degeneration.
/ Plenary Talk (Abstract)
Gordon Research Conference on Human Genetics & Genomics, Newport RI
11/7/2011 Histocompatibility complex association to rheumatoid arthritis Is explained by
polymorphic amino acids In the binding grooves of HLA-DRB1, HLA-B, and HLA-
DPB1 / Platform Talk (Abstract)
American College of Rheumatology Annual Meeting, Chicago, IL
1/22/2012 Five Amino Acids in Three HLA Proteins Explain Rheumatoid Arthritis Risk in
the MHC /
Invited Plenary Talk
Keystone Symposium: Rheumatoid Arthritis: Molecular and Clinical Insights, Santa Fe,
NM
2/20/2012 Using Complex Disease Genetics to Identify Pathogenic Mechanisms in
Inflammatory
Diseases
Genome Science Seminar Series, University of Virginia, Charlottesville, VA
2/22/2012 Genetics to Identify Key Mechanisms in Autoimmune Disease
8
Soumya Raychaudhuri, MD/PhD Curriculum Vitae
Cincinnati Children's Hospital Medical Center, Cincinnati, OH
International
8/20/2000 Pattern Recognition of Genomic Features with Microarrays : Site Typing of M.
Tuberculosis Strains. / Plenary Talk (Abstract)
Intelligent Systems in Molecular Biology, San Diego, CA
7/21/2001 Towards incorporating text into biological algorithms / Tutorial
Intelligent Systems in Molecular Biology, Copenhagen, Denmark
8/1/2002 Text analysis of scientific literature can automatically determine if a group
of genes share
common biological function / Plenary Talk (Abstract)
Intelligent Systems in Molecular Biology SIG Text Mining, Edmonton, Canada
2/13/2003 Algorithms that use Biological Literature in the Analysis of Gene Expression
Data
EMBO Practical Course on Functional Genomics, University of Milano, Bicocca, Milan,
Italy
6/16/2003 Scientific Literature as a Knowledge Source in Bioinformatics Algorithms
Sanger Center, Cambridge, England
7/14/2010 Discerning key pathogenic biological processes from genetic disease loci /
Tutorial
Workshop, MGED 13 conference, Boston, MA
3/11/2011 Translating genetic loci into pathogenic processes and pathways / Invited
Plenary Talk
International Conference: From DNA to phenotype. Molecular Medicine Postgraduate
School, Erasmus Medical College, Rotterdam, The Netherlands
11/30/2011 The Genetics of Rheumatoid Arthritis / Invited Plenary Talk
th
27 Annual Conference of Indian Rheumatology Association, Vellore, India
12/3/2011 Genomic Medicine in Rheumatology / Invited Plenary Talk
th
27 Annual Conference of Indian Rheumatology Association, Vellore, India
Report of Clinical Activities and Innovations
Current Licensure and Certification
2006 - Massachusetts Medical Board License #230263
1/17/2007- American Board of Internal Medicine Certification in Internal Medicine
10/08/2009 American Board of Internal Medicine Certification in Rheumatology
Practice Activities
2006- Rheumatology Outpatient Clinic
Report of Education of Patients and Service to the Community
Activities
Report of Scholarship
Publications
9
Soumya Raychaudhuri, MD/PhD Curriculum Vitae
*Co/corresponding author.
**Equal contributor.
Narrative Report (limit to 500 words)
I am a researcher in computational biology, human genetics, and rheumatology. I have been
engaged in
computational biology since 2000 when I started as a graduate student in the
interpretation of large
genomic data sets, including gene expression data, biological text, and data generated by
human
genetic studies. I have also contributed to discovering key pathogenic loci in rheumatoid
arthritis, cancer,
age-related macular degeneration, and multiple sclerosis. I am clinically trained as a
rheumatologist and
spend ~10% of my time actively involved in clinical care. I spend the remainder of his
effort doing
research in genetics and genomics.
My research has ranged broadly from structural biology to human genetics. My current
efforts emphasize
discovering novel RA risk loci and devising novel algorithms to understand key processes
sugges ted by
human genetic loci. In 2008-2010 I have described twelve novel RA risk loci in two
separate first-
14
Soumya Raychaudhuri, MD/PhD Curriculum Vitae
authored Nature Genetics papers. I have also developed a novel statistical method, Gene
Relationships
Among Implicated Loci (GRAIL),that takes a list of disease regions and automatically
assesses the
degree of relatedness of implicated genes using 400,000 PubMed abstracts. Currently GRAIL
has over
600 users worldwide and has been used to interpret the significance of genetic
discoveries in Cancer,
height, Crohn s disease, and rheumatoid arthritis. It is rapidly emerging as the standard
pathway -tool to
interpret human genetic results. Currently, I am also trying to understand the
significance of copy number
variation in neuropsychiatric disease and age-related macular degeneration with first-
authored papers in
on both of these subjects. I have additionally made substantial contributions to the
field of text mining in
biology, where I have written the seminal textbook, and whole transcriptome profiling
where I described
the first application of dimensional reduction in a highly cited (>400) conference
publication.I have also demonstrated clinical excellence. As a resident and fellow I have received
multiple local
teaching awards, and also have been recognized at the national level by the American
College of
Rheumatology as a Distinguished Fellow in 2009.
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