NICHOLAS TATONETTI, Ph.D.

Department of Biomedical Informatics,
Columbia Initiative for Systems Biology, &
Department of Medicine
Columbia University
622 West 168th St. VC5
New York, NY 10032
nick.tatonetti@columbia.edu
tatonettilab.org

Education

Stanford University, Stanford, CA 2008-2012
Ph.D. in Biomedical Informatics, June 2012
M.S. in Biomedical Informatics, December 2011
Arizona State University, Tempe, AZ 2005-2008
B.S. Summa Cum Laude in Computational Mathematics, May 2008
B.S. Summa Cum Laude in Molecular Biosciences/Biotechnology, May 2008

Professional Experience

Columbia University, New York, NY
Assistant Professor of Biomedical Informatics (in the Departments of Biomedical Informatics, Systems Biology, and Medicine), 2012-present
Director, Clinical Informatics, Herbert Irving Comprehensive Cancer Center, 2013-present

Stanford University, Stanford, CA
Department of Energy Office of Science Graduate Fellow in the Biomedical Informatics Training Program, 2008-2012.
Doctoral Advisor: Russ Altman,
Doctoral Committee: Atul Butte, Trevor Hastie, and Phillip Tsao,
Dissertation Title: "Data-driven Detection, Prediction, and Validation of Drug-Drug Interactions."

Professional Society Memberships
American Medical Informatics Association (2011-)
International Society for Computational Biology (2012-2014)
American Statistical Association (2013-2014)

Publications

KJ Karczewski, M Snyder, RB Altman, NP Tatonetti, Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association. PLOS Genetics (2014) 10(2): e1004122. doi:10.1371/journal.pgen.1004122

KJ Karczewski, GH Fernald, AR Martin, M Snyder, NP Tatonetti, JT Dudley, STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud. PLOS One (2014) 9 (1), e84860

S Vilar, E Uriarte, L Santana, C Friedman, NP Tatonetti, State of the Art and Development of a New Drug-Drug Interaction Large Scale Predictor Based on 3D Pharmacophoric Similarity Current Topics in Drug Metabolism (In press)

X Sun, S Vilar, NP Tatonetti, High-Throughput Methods for Combinatorial Drug Discovery. Science Translational Medicine 5 (205), 205rv1-205rv1.

A Jacunski, NP Tatonetti, Connecting the Dots: Applications of Network Medicine in Pharmacology and Disease. Clinical Pharmacology & Therapeutics (2013).

MJ Matos, S Vilar, NP Tatonetti, L Santana, E Uriarte, Comparative study of the 3-phenylcoumarin scaffold: synthesis, X-ray structural analysis and semiempirical calculations of a selected series of compounds. Journal of Molecular Structure (2013).

M A Perera, L Cavallari, N Limdi, E Gamazon, A Konkashbaev, R Daneshjou, A Pluzhnikov, D C Crawford, J Wang, N Liu, NP Tatonetti, S Bourgeois, H Takahashi, Y Bradford, B M Burkley, R J Desnick, J L Halperin, S I Khalifa, T Y Langaee, S A Lubitz, E A Nutescu, M Oetjens, M H Shahin, S R Patel, H Sagreiya, M Tector, K E Weck, M J Rieder, S A Scott, A HB Wu, J K Burmester, M Wadelius, P Deloukas, M J Wagner, T Mushiroda, M Kubo, D M Roden, N J Cox, R B Altman, T E Klein, Y Nakamura, J A Johnson, Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study. The Lancet (2013).

Ferino G, Cadoni E, Matos MJ, Quezada E, Uriarte E, Santana L, Vilar S, Tatonetti NP, Yanez M, Vina D, Picciau C, Serra S, Delogu G, MAO Inhibitory Activity of 2‐Arylbenzofurans versus 3‐Arylcoumarins: Synthesis, in vitro Study, and Docking Calculations. ChemMedChem (2013).

S Vilar, E Uriarte, L Santana, NP Tatonetti, C Friedman. Detection of Drug-Drug Interactions by Modeling Interaction Profile Fingerprints. PLoS One 8 (3), e58321.

White RW, Tatonetti NP, Shah NH, Altman RB, Horvitz E, Web-scale pharmacovigilance: listening to signals from the crowd. J Am Med Inform Assoc (2013).

Matos MJ, Vilar S, Gonzalez-Franco RM, Uriarte E, Santana L, Friedman C, Tatonetti NP, Viña D, Fontenla JA, Novel (coumarin-3-yl)carbamates as selective MAO-B inhibitors: Synthesis, in vitro and in vivo assays, theoretical evaluation of ADME properties and docking study. European Journal of Medicinal Chemistry 63, 151-161 (2013).

Tatonetti NP, Denny JC, Altman RB, Response to "Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports" by Gooden et al, J Am Med Inform Assoc (2013), doi:10.1136/amiajnl-2012-001603.

Vilar S, Uriarte E, Santana L, Tatonetti NP, Friedman C, Detection of drug-drug interactions by modeling interaction profile fingerprints. PLoS ONE 8, e58321 (2013).

Tatonetti NP, Ye PP, Daneshjou R, Altman RB, Data-driven prediction of drug effects and interactions. Science Translational Medicine 4, 125ra31 (2012).

Karczewski, KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK. Interpretome: A freely available, modular, and secure personal genome interpretation engine. Pac Symp Biocomput 17:339-350(2012)

Karczewski, K.J. Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci USA 108, 13353–13358 (2011).

Tatonetti, N.P., Fernald, G.H. & Altman, R.B. A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J Am Med Inform Assoc (2011) DOI:10.1136/amiajnl-2011-000214

Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, P Yue, PS Tsao, Kohane I, Roden DM, and Altman RB. Detecting Drug Interactions From Adverse-Event Reports: Interaction Between Paroxetine and Pravastatin Increases Blood Glucose Levels Clinical Pharmacology & Therapeutics 2011 DOI:10.1038/clpt.2011.83

Tatonetti NP*, Dudley JT*, Sagreiya H, Butte AJ, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics 2010 11(Suppl 9):S9. PMID:21044367

Garten Y*, Tatonetti NP*, Altman RB. Improving the prediction of pharmacogenes using text-derived drug-gene relationships. Pac Symp Biocomput (2010) pp. 305-14. PMID:19908383

Tatonetti NP, Liu T, Altman RB. Predicting drug side-effects by chemical systems biology. Genome Biol (2009) vol. 10 (9) pp. 238, PMID:19723347

* Denotes equal contribution.

Invited Talks and Panels

Data-driven Prediction of Drug Effects and Interactions.
Joint Statistical Meetings, Montreal, Canada, August 2013.

Enhancing observational data mining through chemical systems biology.
Food and Drug Administration meeting on Social Medial Data, Washington, DC, September 2013.

Observational data for biomedical Discovery.
Session Keynote, International Conference on Machine Learning, Role of Machine Learning in Transforming Healthcare Workshop, Atlanta, GA, June 2013.

Drug-drug interaction detection in Observational Clinical Data.
Institute of Medicine workshop on Learning Health Care Systems, Washington, DC April 2013.

Hypothesis generation in large-scale Observational Data.
Center for Computational Biology and Bioinformatics, IUPUI, Indianapolis, IN March 2013.

Mining for adverse drug-drug interactions in large observational data sets.
Annual Meeting of the Association of Clinical Pharmacology and Therapeutics, Indianapolis, IN March 2013.

Leveraging clinical data for biological discovery.
Living Well Through Data, New York, NY, October 2012.

Mining for adverse drug-drug interactions in large observational data sets.
3rd Annual Pacific Coast Statisticians and Pharmacometricians Innovation Conference, June 2012.

Detecting hidden drug-drug interactions in Adverse Event Reports
Journal of the American Medical Informatics Association Editor's Choice Journal Club. November 2011.

Hypothesis generation in large-scale Observational Data
IBM Healthcare Lecture Series. November 2011.

Observational Analysis in a PetaByte World
SFSU Center for Computing for Life Sciences Panel on Data Mining and Predictive Analysis: Research Applications. October 2011.

Popular and Scientific Press

New York Times, January 2013, Mining Electronic Health Records for Revealing Health Data, link

Genome Web, December 2012, "Seventh Annual Young Investigators." link

Science Careers, April 2012, "Computational Biologists: The Next Pharma Scientists?" link

In response to Tatonetti, et al. Science Transl Med (2012)

Communications of the ACM, October 2012, "Digging for Drug Facts." link

Nature, March 2012, "Drug data reveal sneaky side effects." link

Gizmodo, March 2012, "Drugs Cause About Five Times More Side Effects Than We Realized." link

GenomeWeb, March 2012, "Good Apart, Bad Together." link

ABC News SLC, March 2012, "Drugs may cause five times more side effects than previously believed." link

In response to Tatonetti, et al. Clinical Pharm & Therap (2011)

DrugTopics, August 2011, "Data-mining uncovers hyperglycemic drug-drug interaction between paroxetine and pravastatin." link

Journal of the American Medical Association, July 2011, "Data Mining Approach Shows Promise in Detecting Unexpected Drug Interactions." link

NewScientist, May 2011, "Common drug combo increases diabetes risk." link

US News, May 25, 2011, "Combo of Paxil, Pravachol May Raise Blood Sugar." link

NPR Shots Health Blog, May 25, 2011, "How A MacBook Pro Found Unexpected Drug Side Effects." link

Funding Awarded

Leveraging Big-Data for Drug Discovery in Diseases of Metabolism. PhRMA Foundation Research Starter Award. $100,000 (PI: Tatonetti).

WICER 4 U To develop integrative informatics approaches to investigate genetic determinants of clinical outcomes in a longitudinal electronic health records of a community health center. (PI: Bakken, Pilot-Project PI: Tatonetti)

High-throughput and computational drug screening. CPS Ignition Grant Application (PIs: Ali and Tatonetti)

Novel Statistical Methods for Observational Clinical Studies Innovation awards in population medicine research pilot grant. $25,000. (PI: Altman)

Selected Awards

PhRMA Foundation Early Career Award, January 2014

Featured by Genome Web in the Seventh Annual Young Investigator Profiles, December 2012

Highlighted Research in the IMIA Yearbook of Medical Informatics, 2012

Top Podium Presentation Award - AMIA Summit on Translational Bioinformatics, March 2011

Best Presentation (Runner Up) - Biomedical Computation at Stanford, November 2010

Outstanding Paper Award - AMIA Summit on Translational Bioinformatics, March 2010

Department of Energy Graduate Fellowship ($150,000), September 2010

National Library of Medicine Training Grant Recipient, September 2008

Phi Beta Kappa Lifetime Member, November 2007

Beckman Scholar Award ($17,600), May 2007 - October 2008

Goldwater Scholar Honorable Mention, April 2007

ASU SOLUR Researcher Award, August 2006 - May 2007

1997 Pinto Horse Association of America National Champion, All Around-Year End Youth High Point Award

1997 Pinto Horse Association of America National Youth Reining Horse Champion

Teaching Experience

Director, Biomedical Informatics Research Seminar, Columbia University, 2013-2014

Guest Lecturer, Medical Genetics, Columbia University, December 2013

Guest Lecturer, Introduction to Biomedical Informatics, Columbia University, December 2012, November 2013

Teaching Assistant for Course Design, Methods in Healthcare Informatics (BIOMEDIN215), Stanford University, March 2011

Teaching Assistant, Genomics and Personalized Medicine (GENE210), Stanford University, March 2011 - June 2011

Guest Lecturer, Statistical Genetics (GENE244), Stanford University, February 2011

Teaching Assistant, Representations and Algorithms for Computational Molecular Biology (BIOMEDIN214), Stanford University, March 2010 - June 2010

Teaching Assistant, Modeling biomedical systems: ontology, terminology, problem solving (BIOMEDIN210), Stanford University, September 2009 - December 2009

Related and Professional Experience

Chief Execute Officer, Stimulomics, Inc., Portola Valley, CA 2009-2012

Chief Science Officer, Mophilia, Inc., Mountain View, CA 2009-2010

Co-Founder (volunteer), The CHERUB Foundation, Tempe, AZ 2006-2008

Chief Technical Officier (volunteer), The Triple Helix, Inc., Ithica, NY 2006-2007

Vice President/Co-Founder (volunteer), The Triple Helix at ASU, Tempe, AZ 2006

Founder/Owner, Tatonetti Web_Construction, Tempe, AZ 2003 - 2008