NICHOLAS TATONETTI, Ph.D.Department of Biomedical Informatics,
Columbia Initiative for Systems Biology, &
Department of Medicine
622 West 168th St. PH20
New York, NY 10032
Columbia University, New York, NY
Herbert Irving 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-)
American Society of Human Genetics (2016-)
American Society for Clinical Pharmacology and Therapeutics (2016-)
International Society for Computational Biology (2012-2014)
American Statistical Association (2013-2014)
Lorberbaum T, Sampson KJ, Chang JB, Iyer V, Woosley RL, Kass RS, Tatonetti NP Uncovering drug interactions via data science: the combination of ceftriaxone and lansoprazole is associated with acquired long QT syndrome (LQTS) Journal of the American College of Cardiology (in press)
Hao Y and Tatonetti NP Predicting G Protein-Coupled Recetpor Downstream Signaling by Tissue Expression Bioinformatics (in press)
Chang JB, Quinnies KM, Realubit R, Karan C, Rand JH, Tatonetti NP A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient Scientific Reports 6/29387 doi:10.1038/srep29387
Moskovitch R, Choi H, Hripcsak G, Tatonetti N, Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection IEEE/ACM Transactions on Computational Biology and Bioinformatics 14 July 2016; 10.1109/TCBB.2016.2591539
Boland MR, Tatonetti NP, Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review. The Pharmacogenomics Journal 12 July 2016; doi: 10.1038/tpj.2016.48
Nissim N, Boland MR, Tatonetti NP, Elovici Y, Hripcsak G, Shahar Y, Moskovitch R, Improving Condition Severity Classification with an Efficient Active Learning Based Framework. J Biomed Inform. 2016 Mar 22. pii: S1532-0464(16)30007-7. doi: 10.1016/j.jbi.2016.03.016
Hoffman KB, Dimbil M, Tatonetti NP, Kyle RF, A Pharmacovigilance Signaling System Based on FDA Regulatory Action and Post-Marketing Adverse Event Reports. Drug Safety 2016 Mar 5
T Lorberbaum, KJ Sampson, RL Woosley, RS Kass, NP Tatonetti, An Integrative Data Science Pipeline to Identify Novel Drug Interactions that Prolong the QT Interval Drug Safety pp 1-9 (2016) doi:10.1007/s40264-016-0393-1
BA Kidd, A Wroblewska, MR Boland, J Agudo, M Merad, NP Tatonetti, BD Brown, JT Dudley Mapping the effects of drugs on the immune system Nature biotechnology 34 (1), 47-54 (2016)
KB Hoffman, M Dimbil, RF Kyle, NP Tatonetti, CB Erdman, A Demakas, D Chen, BM Overstreet A Drug Safety Rating System Based on Postmarketing Costs Associated with Adverse Events and Patient Outcomes Journal of managed care & specialty pharmacy (2015)
JD Romano, NP Tatonetti, VenomKB, a new knowledge base for facilitating the validation of putative venom therapies ScientificData 2 (2015) doi:10.1038/sdata.2015.65
MR Boland, A Jacunski, T Lorberbaum, JD Romano, R Moskovitch, NP Tatonetti Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms WIREs Syst Biol Med. (2015) doi: 10.1002/wsbm.1323
A Jacunski, S Dixon, NP Tatonetti, Connectivity homology enables inter-species network models of synthetic lethality PLOS Computational Biology (2015) 11(10): e1004506. doi:10.1371/journal.pcbi.1004506
MR Boland, Z Shahn, D Madigan, G Hripcsak, NP Tatonetti, Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method Journal of the American Medical Informatics Association (2015)
S Vilar, T Lorberbaum, G Hripcsak, NP Tatonetti, Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling PLOS One (2015) 10 (6), e0129974
S Ayvaz, J Horn, O Hassanzadeh, Q Zhu, J Stan, NP Tatonetti, S Vilar, M Brochhausen, M Samwald, M Rastegar-Mojarad, M Dumontier, RD Boyce Toward a complete dataset of drug–drug interaction information from publicly available sources Journal of Biomedical Informatics (2015) 55, 206-217
MR Boland, NP Tatonetti, G Hripcsak, Development and validation of a classification approach for extracting severity automatically from electronic health records Journal of Biomedical Semantics (2015) 6 (1), 14
S Vilar, NP Tatonetti, G Hripcsak, 3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance Scientific Reports (2015) 5
T Lorberbaum, M Nasir, MJ Keiser, S Vilar, G Hripcsak, NP Tatonetti Systems pharmacology augments drug safety surveillance Clinical Pharmacology & Therapeutics (2015) 97 (2), 151-158
KB Hoffman, AR Demakas, M Dimbil, NP Tatonetti, CB Erdman Stimulated Reporting: The Impact of US Food and Drug Administration-Issued Alerts on the Adverse Event Reporting System (FAERS) Drug Safety (2014) 37 (11), 971-980
R Moskovitch, C Walsh, G Hripcsak, N Tatonetti Prediction of biomedical events via time intervals mining ACM KDD Workshop on Connected Health in Big Data Era 2014
R D Boyce, P B Ryan, G N Norén, M J Schuemie, C Reich, J Duke, N P Tatonetti, G Trifiro, R Harpaz, J M Overhage, A G Hartzema, M Khayter, E A Voss, C G Lambert, V Huser, M Dumontier Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest Drug Safety 37 (8), 557-567
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 Drug Metabolism 15 (5), 490-501
S Vilar, E Uriarte, L Santana, T Lorberbaum, G Hripcsak, C Friedman, NP Tatonetti, Similarity-based modeling in large-scale prediction of drug-drug interactions Nature Protocols (2014 Vol 9 Issue 9, 2147-2168)
MJ Matos, S Vilar, S Kachler, A Fonseca, L Santana, E Uriarte, F Borges, NP Tatonetti, KN Klotz. Insight into the Interactions between Novel Coumarin Derivatives and Human A3 Adenosine Receptors. ChemMedChem 2014/7/18
Boyce RD, Ryan PB, Norén GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifirò G, Harpaz R, Overhage JM, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, Dumontier M. Bridging Islands of Information to Establish an Integrated Knowledge Base of Drugs and Health Outcomes of Interest. Drug Safety 2014 Jul 2.
Dixon SJ, Patel DN, Welsch M, Skouta R, Lee ED, Hayano M, Thomas AG, Gleason CE, Tatonetti NP, Slusher BS, Stockwell BR. Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis. eLife 2014 May 20;3:e02523. doi: 10.7554/eLife.02523.
ZA Ali, S Poludasu, YH Qureshi, P Krishnan, AA Ali, N Tatonetti, P Downey, A Zalewski, T Nazif, I George, A Mandava, U Baber, G Dangas, R Mehran, AS Kini, and SK Sharma, Impact of major bleeding on long-term mortality in anemic versus nonanemic patients undergoing percutaneous coronary intervention using bivalirudin, The American journal of cardiology 113, 1481–1486 (2014).
L Li, DJ Ruau, CJ Patel, SC Weber, R Chen, NP Tatonetti, JT Dudley, and AJ Butte, Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records, Science Translational Medicine 6, 234ra57 (2014).
GL Delogu, S Serra, E Quezada, E Uriarte, S Vilar, NP Tatonetti, and D Viña, Monoamine Oxidase (MAO) Inhibitory Activity: 3-Phenylcoumarins versus 4-Hydroxy-3-phenylcoumarins, ChemMedChem (2014), doi:10.1002/cmdc.201402010.
MJ Matos, S Vilar, V Garcia-Morales, NP Tatonetti, E Uriarte, L Santana, D Vina Insight into the Functional and Structural Properties of 3‐Arylcoumarin as an Interesting Scaffold in Monoamine Oxidase B Inhibition. ChemMedChem (2014) Apr 8
KB Hoffman, M Dimbil, CB Erdman, NP Tatonetti, BM Overstreet The Weber Effect and the United States Food and Drug Administration’s Adverse Event Reporting System (FAERS): Analysis of Sixty-Two Drugs Approved from 2006 to 2010. Drug Safety (2014) Vol 37 Iss 4 pp 283-294
MJ Matos, P Janeiro, RM Gonzalez Franco, S Vilar, NP Tatonetti, L Santana, E Uriarte, F Borges, JA Fontenla, D Vina, Synthesis, pharmacological study and docking calculations of new benzo [f] coumarin derivatives as dual inhibitors of enzymatic systems involved in neurodegenerative diseases. Future medicinal chemistry (2014) Vol 6 Iss 4 pp 371-383
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
X Sun, S Vilar, NP Tatonetti, High-Throughput Methods for Combinatorial Drug Discovery. Science Translational Medicine (2013), 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.
Garten Y*, Tatonetti NP*, Altman RB. Improving the prediction of pharmacogenes using
text-derived drug-gene relationships. Pac Symp Biocomput (2010) pp. 305-14.
Tatonetti NP, Liu T, Altman RB. Predicting drug side-effects by chemical systems biology. Genome Biology (2009) vol. 10 (9) pp. 238, PMID:19723347
* Denotes equal contribution.
First Author Publication Last Author Publication
Systems Pharmacology to Predict Adverse Drug Reactions Irving Scholars Program, Irving Institute for Clinical and Translational Research, Columbia University Medical Center. $180,000 (PI: Tatonetti)
Drug Effect Discovery Through Data Mining and Integrative Chemical Biology. R01 GM107145 National Institute for General Medical Sciences. ~$2.5 million (PI: Tatonetti).
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)
Editorial Board Member, Journal of Biomedical Informatics, 2016-2019
Honorary Editorial Board Member, Drug Safety, 2015-
Track Chair, AMIA Summit on Translational Bioinformatics, San Francisco, March 2016
Session Chair, Big Data to Knowledge, AMIA Translational Bioinformatics Meeting, San Francisco, March 2015
Session Chair, Big Data to Knowledge, AMIA Translational Bioinformatics Meeting, San Francisco, March 2014
Chair, Pre-conference on Next Generation Pharmacology, ASCPT Annual Meeting, March 2014
Editorial Board Member, Pharmacology Research & Perspectives, 2013-
Scientific Program Committee Member, AMIA Summit on Translational Bioinformatics, 2013, 2014, 2015, 2016
Reviewer: NEJM, BMJ, Nature Medicine, Science Translational Medicine, Clinical Pharmacology & Therapeutics, CPT:Pharmacometrics & and Systems Pharmacology, PLOS Genetics, PLOS Comp Bio, PLOS One, Molecular Systems Biology, JAMIA, AMIA Symposium, BMC Bioinformatics, Scientific Reports, Journal of Biomedical Informatics, Drug Safety, Database, Allergy, Pacific Symposium on Biocomputing, Bioinformatics,
NIH Peer Reviewer, Special section on Genome-wide Gene by Environment Interactions
Invited Talks and Panels
Drug Safety Conference, Chicago, June 20th, 2016
Department of Biomedical Informatics, Harvard University, Boston, April 6th, 2016
Five Points Lecture, New York Genome Center, New York City, February 3rd, 2016
New York City Genome Data, Rockefeller University, New York City, January 13th, 2016
Department of Biostatitics and Medical Informatics, UW Madison, Madison, December 11th, 2015
Albany College of Pharmacy and Health Sciences, Albany, October 30th, 2015
World Drug Safety Conference, Chicaco, October 27th, 2015
NHLBI Lecture Series, Washington, D.C., October 13th, 2015
Basel Life Sciences Week, Switzerland, September 23rd, 2015
Big Data and Clinical Trials Conference, Philadelphia, August 25th, 2015
Center for Cancer Systems Biology Seminar Series, Stanford University, Stanford, June 19th, 2015
John Jones Surgical Socieity Annual Meeting, Columbia University, May 8th, 2015
Drug Safety Conference, Chicago, April 22th, 2015
Lecture at Mount Sinai Icahn School of Medicine, New York City, December 19th, 2014
Kavli Foundation Symposium, Indonesia, June 19th, 2014
American Diabetes Association Annual Meeting, Section on Data Science, June 17, 2014
IBM Watson Research Center, Seminar Series, June 4, 2014
Cornell University Medical Center, Seminar Series, June 11, 2014
Uppsala Monitoring Centre Research Conference 2014, Risk: Whose Risk? What Risk?, May 2014
ASPET Annual Conference, Session on Data Science, April 2014
University of California, San Francisco, Pharmaceutical Sciences and Pharmacogenomics Seminar Series, February 10, 2014
Joint Statistical Meetings, Montreal, Canada, August 2013.
Food and Drug Administration meeting on Social Medial Data, Washington, DC, September 2013.
Session Keynote, International Conference on Machine Learning, Role of Machine Learning in Transforming Healthcare Workshop, Atlanta, GA, June 2013.
Institute of Medicine workshop on Learning Health Care Systems, Washington, DC April 2013.
Center for Computational Biology and Bioinformatics, IUPUI, Indianapolis, IN March 2013.
Annual Meeting of the Association of Clinical Pharmacology and Therapeutics, Indianapolis, IN March 2013.
Living Well Through Data, New York, NY, October 2012.
3rd Annual Pacific Coast Statisticians and Pharmacometricians Innovation Conference, June 2012.
Journal of the American Medical Informatics Association Editor's Choice Journal Club. November 2011.
IBM Healthcare Lecture Series. November 2011.
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 Magazine, October 2014, Can Big Data Tell Us What Clinical Trials Don’t?, link
Columbia Medicine, June 2014, MiningMedicine Gets Personal, link
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
TIME, June 2015, "See What Diseases You're at Risk For Based on Your Birth Month." link
The Washington Post, June 2015, "Scientists have discovered how the month you're born matters for your health." link
CBS News, June 2015, "Could your birth month indicate your risk of disease?" link
Discover, June 2015, "Your Birth Month Influences Your Risk for Diseases." link
and >200 others.
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
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
Selected Awards and Honors
Irving Scholars Award, Irving Institute for Clinical and Translational Research ($180,000), July 2015
Kavli Foundational Fellow, May 2014
PhRMA Foundation Early Career Award ($100,000), 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
Instructor, Translational Bioinformatics (BINF G4006), Columbia University, Fall 2015
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
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