NICHOLAS TATONETTI, Ph.D.

Department of Biomedical Informatics,
Department of Systems Biology, &
Department of Medicine
Columbia University
622 West 168th St. PH20
New York, NY 10032
212 305 9104
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
Current
Chief Officer for Cancer Data Science, Herbert Irving Comprehensive Cancer Center, 2022-present
Associate Professor of Biomedical Informatics, 2019-present
Director, Clinical Informatics, Institute for Genomic Medicine, 2017-present
Co-Director, Bioinformatics, Department of Biomedical Informatics, 2017-present

Previous
Director, Clinical Informatics, Herbert Irving Comprehensive Cancer Center, 2013-2022
Herbert Irving Assistant Professor of Biomedical Informatics, 2012-2019

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)

Peer-Reviewed Journal Publications

Google Scholar | NCBI bibliography

2022

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Nicholas Giangreco and Nicholas P Tatonetti A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development Med(In Press)

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Jiheum Park, Michael G Artin, Kate E Lee, Yoanna S Pumpalova, Myles A Ingram, Benjamin L May, Michael Park, Chin Hur, Nicholas P Tatonetti Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer Journal of Biomedical Informatics(2022)

Shen, Tian Huai, Stauber, Jacob, Xu, Katherine, Jacunski, Alexandra, Paragas, Neal, Callahan, Miriam, Banlengchit, Run, Levitman, Abraham D, De Oliveira, Beatriz Desanti, Beenken, Andrew Snapshots of nascent RNA reveal cell-and stimulus-specific responses to acute kidney injury JCI insight, (2022)

Biswas, Saptarshi, Shahriar, Sanjid, Giangreco, Nicholas P, Arvanitis, Panos, Winkler, Markus, Tatonetti, Nicholas P, Brunken, William J, Cutforth, Tyler, Agalliu, Dritan Mural norrin/β-catenin signaling regulates Lama2 expression to promote neurovascular unit assembly bioRxiv, (2022)

Jiwoon Park, Jonathan Foox, T. Hether, D. Danko, S. Warren, Youngmi Kim, J. Reeves, D. Butler, Christopher Mozsary, J. Rosiene, Alon Shaiber, Evan E. Afshin, M. Mackay, André F. Rendeiro, Y. Bram, Vasuretha Chandar, Heather Geiger, A. Craney, P. Velu, A. Melnick, I. Hajirasouliha, A. Beheshti, Deanne M. Taylor, Amanda M. Saravia-Butler, Urminder Singh, E. Wurtele, J. Schisler, S. Fennessey, A. Corvelo, M. Zody, S. Germer, S. Salvatore, Shawn Levy, Shixiu Wu, N. Tatonetti, S. Shapira, M. Salvatore, L. Westblade, M. Cushing, H. Rennert, A. Kriegel, O. Elemento, M. Imieliński, C. Rice, A. Borczuk, Cem Meydan, R. Schwartz, Christopher E. Mason System-wide transcriptome damage and tissue identity loss in COVID-19 patients Cell Reports Medicine, (2022) Vol 3 No 2 Pp 100522

2021

Basile, Anna O, Verma, Anurag, Tang, Leigh Anne, Serper, Marina, Scanga, Andrew, Farrell, Ava, Destin, Brittney, Carr, Rotonya M, Anyanwu-Ofili, Anuli, Rajagopal, Gunaretnam Rapid Identification and Phenotyping of Nonalcoholic Fatty Liver Disease Patients Using an Automated Algorithmic Approach in Diverse, Urban Healthcare Systems medRxiv, (2021)

Xiayuan Huang, N. Tatonetti, Katie LaRow, Brooke Delgoffee, J. Mayer, D. Page, S. Hebbring E-Pedigrees: a large-scale automatic family pedigree prediction application Bioinformatics, (2021) Vol 37 No 21 Pp 3966-3968

N. Giangreco, Sulieman Lina, J. Qian, Aymone Kuoame, V. Subbian, E. Boerwinkle, M. Cicek, Cheryl R. Clark, Elizabeth Cohen, K. Gebo, R. Loperena-Cortes, K. Mayo, S. Mockrin, L. Ohno-Machado, S. Schully, N. Tatonetti, A. Ramirez Pediatric data from the All of Us research program: demonstration of pediatric obesity over time JAMIA Open, (2021) Vol 4 No 4 Pp ooab112

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Hao, Yun, Thangaraj, Phyllis, Tatonetti, Nicholas Predicting the Toxicity of Druggable Proteins to Human Tissues bioRxiv, (2021)

Theresa A. Koleck, M. Topaz, N. Tatonetti, M. George, C. Miaskowski, A. Smaldone, S. Bakken Characterizing shared and distinct symptom clusters in common chronic conditions through natural language processing of nursing notes Research in Nursing & Health, (2021) Vol 44 No 6 Pp 906-919

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S. P. Mcgrath, Mary Lauren Benton, Maryam Tavakoli, N. Tatonetti Predictions, Pivots, and a Pandemic: a Review of 2020's Top Translational Bioinformatics Publications Yearbook of Medical Informatics, (2021) Vol 30 No 01 Pp 219-225

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N. Giangreco, N. Tatonetti A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development Available at SSRN 3898786, (2021)

N. Giangreco, G. Lebreton, S. Restaino, Mary Jane Farr, E. Zorn, P. Colombo, J. Patel, R. Levine, L. Truby, R. Soni, P. Leprince, J. Kobashigawa, N. Tatonetti, B. Fine Plasma kallikrein predicts primary graft dysfunction after heart transplant The Journal of Heart and Lung Transplantation, (2021) Vol 40 No 10 Pp 1199-1211

Kipp W. Johnson, J. Narula, B. Glicksberg, K. Shameer, F. Chaudhry, A. Yahi, Nayaab S. Khan, L. Amadori, C. Krittanawong, B. Readhead, Ross Hagan, C. Becker, F. Chaudhry, Aparna A. Divaraniya, Milo R. Smith, U. Baber, Li Li, Benjamin D McCauley, G. Nadkarni, K. Pak, B. Gray, Deepak A Kaji, B. Percha, Y. Vengrenyuk, Javed Suleman, N. Tatonetti, A. Butte, A. Petrov, E. Arbustini, C. Giannarelli, N. Narula, W. Strauss, J. Dudley, A. Kini Repurposing the atypical antidepressant trazodone for atherosclerotic cardiovascular disease , (2021)

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N. Tatonetti, N. Elhadad Fine-scale genetic ancestry as a potential new tool for precision medicine Nature Medicine, (2021) Vol 27 No 7 Pp 1152-1153

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Tatonetti, Nicholas, Hao, Yun Methods and systems for predicting success rates of clinical trials , (2021)

Wattacheril, J, Basile, AO, Verma, A, Tang, LA, Serper, M, Scanga, A, Farrell, A, Destin, BM, Carr, RM, Anyanwu-Ofili, A Rapid Identification and Phenotyping of Nonalcoholic Fatty Liver Disease Patients Using an Automated Algorithmic Approach in Diverse, Urban Healthcare Systems , (2021)

N. Shang, Atlas Khan, Fernanda C G Polubriaginof, F. Zanoni, Karla Mehl, D. Fasel, P. Drawz, R. J. Carrol, J. Denny, M. Hathcock, A. Arruda-Olson, P. Peissig, R. Dart, M. Brilliant, E. Larson, D. Carrell, S. Pendergrass, S. Verma, M. Ritchie, B. Benoit, V. Gainer, E. Karlson, A. Gordon, G. Jarvik, I. Stanaway, D. Crosslin, S. Mohan, I. Ionita-Laza, N. Tatonetti, A. Gharavi, G. Hripcsak, C. Weng, K. Kiryluk Medical records-based chronic kidney disease phenotype for clinical care and “big data” observational and genetic studies NPJ digital medicine, (2021) Vol 4 No 1 Pp 1-13

D. Butler, Christopher Mozsary, Cem Meydan, Jonathan Foox, J. Rosiene, Alon Shaiber, D. Danko, Ebrahim Afshinnekoo, M. Mackay, F. Sedlazeck, N. A. Ivanov, M. Sierra, D. Pohle, M. Zietz, U. Gisladottir, V. Ramlall, Evan T Sholle, E. Schenck, Craig D. Westover, Ciaran Hassan, Krista A. Ryon, B. Young, Chandrima Bhattacharya, Dianna L. Ng, A. Granados, Yale A Santos, V. Servellita, S. Federman, P. Ruggiero, Arkarachai Fungtammasan, Chen-Shan Chin, N. M. Pearson, B. Langhorst, N. Tanner, Youngmi Kim, J. Reeves, T. Hether, S. Warren, M. Bailey, Justyna Gawrys, D. Meleshko, Dong-Li Xu, M. Couto-Rodriguez, D. Nagy‐Szakal, J. Barrows, H. Wells, N. O’Hara, J. Rosenfeld, Ying Chen, P. Steel Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions Nature communications, (2021) Vol 12 No 1 Pp 1-17

P. Kennel, A. Yahi, Y. Naka, D. Mancini, C. Marboe, K. Max, K. Akat, T. Tuschl, E. Vasilescu, E. Zorn, N. Tatonetti, P. Schulze Longitudinal profiling of circulating miRNA during cardiac allograft rejection: a proof‐of‐concept study ESC heart failure, (2021) Vol 8 No 3 Pp 1840-1849

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N. Giangreco, N. Tatonetti Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children BioData mining, (2021) Vol 14 No 1 Pp 1-17

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Catherine Kim, N. Tatonetti Prediction of adverse drug reactions associated with drug-drug interactions using hierarchical classification bioRxiv, (2021)

E. Spurlin, E. Han, E. Silver, B. May, N. Tatonetti, Myles A Ingram, Zhezhen Jin, C. Hur, A. Advincula, H. Hur Where have all the emergencies gone? The impact of the COVID-19 pandemic on obstetric and gynecologic procedures and consults at a New York City hospital Journal of minimally invasive gynecology, (2021) Vol 28 No 7 Pp 1411-1419. e1

Theresa A. Koleck, N. Tatonetti, S. Bakken, S. Mitha, Morgan Henderson, M. George, C. Miaskowski, A. Smaldone, M. Topaz Identifying symptom information in clinical notes using natural language processing Nursing research, (2021) Vol 70 No 3 Pp 173-183

2020

P. Washington, S. Yeung, B. Percha, N. Tatonetti, Jan Liphardt, D. Wall Achieving trustworthy biomedical data solutions BIOCOMPUTING 2021: Proceedings of the Pacific Symposium, (2020) Pp 1-13

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E. Silver, Han Q Truong, S. Ostvar, C. Hur, N. Tatonetti Association of neighborhood deprivation index with success in cancer care crowdfunding JAMA network open, (2020) Vol 3 No 12 Pp e2026946-e2026946

E. Spurlin, E. Han, E. Silver, B. May, N. Tatonetti, C. Hur, A. Advincula, H. Hur The Impact of the COVID-19 Pandemic on Obstetric and Gynecologic Procedures and Consults at a Metropolitan Hospital in the Epicenter Journal of Minimally Invasive Gynecology, (2020) Vol 27 No 7 Pp S108-S109

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M. Zietz, J. Zucker, N. Tatonetti Associations between blood type and COVID-19 infection, intubation, and death Nature communications, (2020) Vol 11 No 1 Pp 1-6

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Ostvar, Sassan, Truong, Han, Silver, Elisabeth R, Lightdale, Charles J, Hur, Chin, Tatonetti, Nicholas P Transfer learning from simulations improves the classification of OCT images of glandular epithelia bioRxiv, (2020)

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V. Ramlall, J. Zucker, N. Tatonetti Melatonin is significantly associated with survival of intubated COVID-19 patients MedRxiv, (2020)

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N. Giangreco, Jonathan E Elias, N. Tatonetti No population left behind: Improving paediatric drug safety using informatics and systems biology British Journal of Clinical Pharmacology, (2020)

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Payal Chandak, N. Tatonetti Using machine learning to identify adverse drug effects posing increased risk to women Patterns, (2020) Vol 1 No 7 Pp 100108

V. Ramlall, Phyllis M. Thangaraj, Cem Meydan, Jonathan Foox, D. Butler, Jacob Kim, B. May, J. D. De Freitas, B. Glicksberg, C. Mason, N. Tatonetti, S. Shapira Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection Nature medicine, (2020) Vol 26 No 10 Pp 1609-1615

A. Yahi, Paul J. Hoffman, Margot Brandt, P. Mohammadi, N. Tatonetti, T. Lappalainen EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments bioRxiv, (2020)

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A. Yahi, N. Tatonetti Simulating drug effects on blood glucose laboratory test time series with a conditional WGAN medRxiv, (2020)

T. Kapoor, Pooja Mahadeshwar, J. Hui-Yuen, Kayla Quinnies, N. Tatonetti, Y. Gartshteyn, C. Guo, L. Geraldino-Pardilla, A. Askanase Prevalence of progressive multifocal leukoencephalopathy (PML) in adults and children with systemic lupus erythematosus Lupus science & medicine, (2020) Vol 7 No 1 Pp e000388

N. Macesic, Oliver J Bear Don't Walk, I. Pe’er, N. Tatonetti, A. Peleg, A. Uhlemann Predicting phenotypic polymyxin resistance in Klebsiella pneumoniae through machine learning analysis of genomic data Msystems, (2020) Vol 5 No 3 Pp e00656-19

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Phyllis M. Thangaraj, U. Gisladottir, N. Tatonetti Medical data and machine learning improve power of stroke genome-wide association studies bioRxiv, (2020)

2019

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Liu, Zhigang, Wang, Yifan, Huang, Yuhui, Kim, Betty YS, Shan, Hong, Wu, Depei, Jiang, Wen, Basile, Anna O, Yahi, Alexandre, Tatonetti, Nicholas P 608 Max-imizing the Attenuation of Myc Using Small Molecules Science & Society, (2019) Vol 40 No 9 Pp 605-710

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M. Boland, N. Tatonetti Attention deficit-hyperactivity disorder and month of school enrollment The New England journal of medicine, (2019) Vol 380 No 7 Pp 692-693

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Brenner, Steven E, Bulyk, Martha L, Crawford, Dana C, Morgan, Alexander A, Radivojac, Predrag, Tatonetti, Nicholas P Precision Medicine: Addressing the Challenges of Sharing, Analysis, and Privacy at Scale PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020, (2019) Pp 547-550

Zimmerman, Noah, Tatonetti, Nicholas P, Dudley, Joel T AMarketplace FOR HEALTH: OPPORTUNITIES AND CHALLENGES FOR BIOMEDICAL BLOCKCHAINS , (2019)

Basile, Anna, Anyanwu-Ofili, Anuli, Rajagopal, Gunaretnam, Farrell, Ava, Destin, Brittney, Krikhely, Abraham, Bessler, Marc, Tatonetti, Nicholas, Wattacheril, Julia J ELECTRONIC HEALTH RECORD PHENOTYPING ALGORITHM IDENTIFIES PATIENTS WITH ADVANCED FIBROSIS IN A LARGE COHORT WITH NONALCOHOLIC FATTY LIVER DISEASE HEPATOLOGY, (2019) Vol 70 Pp 1137A-1137A

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V. Ramlall, Kayla Quinnies, R. Vanguri, T. Lorberbaum, David Goldstein, N. Tatonetti Predicting the genetic ancestry of 2.6 million New York City patients using clinical data bioRxiv, (2019) Pp 768440

Olga Lyudovyk, Yufeng Shen, N. Tatonetti, S. Hsiao, M. Mansukhani, C. Weng Pathway analysis of genomic pathology tests for prognostic cancer subtyping Journal of biomedical informatics, (2019) Vol 98 Pp 103286

Beatriz Desanti De Oliveira, Katherine Xu, T. Shen, M. Callahan, K. Kiryluk, V. D’Agati, N. Tatonetti, J. Barasch, P. Devarajan Molecular nephrology: types of acute tubular injury Nature Reviews Nephrology, (2019) Vol 15 No 10 Pp 599-612

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Zhouzerui Liu, N. Tatonetti Familial relationships in electronic health records (EHR) v2 bioRxiv, (2019) Pp 731976

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A. Basile, A. Yahi, N. Tatonetti Artificial intelligence for drug toxicity and safety Trends in pharmacological sciences, (2019) Vol 40 No 9 Pp 624-635

Fernanda C G Polubriaginof, P. Ryan, H. Salmasian, Andrea W. Shapiro, A. Perotte, M. Safford, G. Hripcsak, Shaun Smith, N. Tatonetti, D. Vawdrey Challenges with quality of race and ethnicity data in observational databases Journal of the American Medical Informatics Association, (2019) Vol 26 No 8-9 Pp 730-736

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Joseph D. Romano, Hai Li, Ronald B. Realubit, Charles Karan, N. Tatonetti Discovering therapeutic activities from venoms using differential gene expression bioRxiv, (2019) Pp 699280

B. Glicksberg, B. Oskotsky, Phyllis M. Thangaraj, N. Giangreco, M. Badgeley, Kipp W. Johnson, Debajyoti Datta, V. Rudrapatna, N. Rappoport, Mark Shervey, R. Miotto, T. Goldstein, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, B. Percha, Li Li, J. Dudley, N. Tatonetti, A. Butte PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model Bioinformatics, (2019) Vol 35 No 21 Pp 4515-4518

S. Ahalt, C. Chute, K. Fecho, Gustavo Glusman, J. Hadlock, Casey Overby Taylor, E. Pfaff, P. Robinson, H. Solbrig, C. Ta, N. Tatonetti, C. Weng Clinical data: sources and types, regulatory constraints, applications Clinical and translational science, (2019) Vol 12 No 4 Pp 329

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Giangreco, Nicholas P, Fine, Barry, Tatonetti, Nicholas P cohorts: A Python package for clinical ‘omics data management bioRxiv, (2019) Pp 626051

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Joseph D. Romano, N. Tatonetti Informatics and computational methods in natural product drug discovery: a review and perspectives Frontiers in genetics, (2019) Vol 10 Pp 368

Krigel, Anna, Tatonetti, Nicholas, Neugut, Alfred I, Lebwohl, Benjamin Mo1634–No Increased Risk of Colorectal Adenomas in Spouses of Patients with Colorectal Neoplasia Gastroenterology, (2019) Vol 156 No 6 Pp S-810

N. Giangreco, G. Lebreton, S. Restaino, M. Farr, P. Colombo, E. Zorn, N. Tatonetti, P. Leprince, J. Kobashigawa, B. Fine Exosome Proteomics and Machine Learning Identify Novel Biomarkers of Primary Graft Dysfunction The Journal of Heart and Lung Transplantation, (2019) Vol 38 No 4 Pp S137

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Phyllis M. Thangaraj, Benjamin R. Kummer, T. Lorberbaum, Mitchell S. V. Elkind, N. Tatonetti Comparative analysis of EHR-based stroke phenotyping methods, their applications, and interpretation bioRxiv, (2019) Pp 565671

B. Glicksberg, B. Oskotsky, N. Giangreco, Phyllis M. Thangaraj, V. Rudrapatna, Debajyoti Datta, Remi Frazier, Nelson Lee, Rick Larsen, N. Tatonetti, A. Butte ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data JAMIA open, (2019) Vol 2 No 1 Pp 10-14

A. Faye, Fernanda C G Polubriaginof, P. Green, D. Vawdrey, N. Tatonetti, B. Lebwohl Low rates of screening for celiac disease among family members Clinical Gastroenterology and Hepatology, (2019) Vol 17 No 3 Pp 463-468

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N. Tatonetti Translational medicine in the Age of Big Data Briefings in bioinformatics, (2019) Vol 20 No 2 Pp 457-462

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Tatonetti, Nicholas, Altman, Russ B, Fernald, Guy Haskin Signal detection algorithms to identify drug effects and drug interactions , (2019)

2018

Castillero, Estibaliz, Ali, Ziad A, Akashi, Hirokazu, Giangreco, Nicholas, Wang, Catherine, Stöhr, Eric J, Ji, Ruping, Zhang, Xiaokan, Kheysin, Nathaniel, Park, Joo-Eun S Muscle Mechanics and Ventricular Function: Structural and functional cardiac profile after prolonged duration of mechanical unloading: potential implications for myocardial recovery American Journal of Physiology-Heart and Circulatory Physiology, (2018) Vol 315 No 5 Pp H1463

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N. Giangreco, N. Tatonetti Using precision pharmacovigilance to detect and evaluate antiepileptic drug associated adverse reactions in pediatric patients F1000Research, (2018) Vol 7

Fernanda C G Polubriaginof, N. Shang, G. Hripcsak, N. Tatonetti, D. Vawdrey Low screening rates for diabetes mellitus among family members of affected relatives AMIA Annual Symposium Proceedings, (2018) Vol 2018 Pp 1471

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N. Giangreco, N. Tatonetti Using precision pharmacoviglance to detect developmentally-regulated adverse drug reactions: a case study with antiepileptic drugs F1000Research, (2018) Vol 7

N. Giangreco, G. Lebreton, S. Restaino, M. Farr, P. Colombo, E. Zorn, P. Leprince, J. Kobashigawa, N. Tatonetti, B. Fine Standardized and reproducible analysis enables identification of novel primary graft dysfunction biomarkers using exosome proteomics F1000Research, (2018) Vol 7

E. Castillero, Z. Ali, H. Akashi, N. Giangreco, Catherine Wang, E. Stöhr, Ruping Ji, Xiaokan Zhang, Nathaniel Kheysin, Joo-Eun S. Park, Sheetal Hegde, Sanatkumar Patel, Samantha Stein, Carlos Cuenca, Diana Leung, S. Homma, N. Tatonetti, V. Topkara, K. Takeda, P. Colombo, Y. Naka, H. Sweeney, P. Schulze, Isaac J George Structural and functional cardiac profile after prolonged duration of mechanical unloading: potential implications for myocardial recovery American Journal of Physiology-Heart and Circulatory Physiology, (2018) Vol 315 No 5 Pp H1463-H1476

C. Ta, M. Dumontier, G. Hripcsak, N. Tatonetti, C. Weng Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records Scientific data, (2018) Vol 5 No 1 Pp 1-17

A. Faye, Fernanda C G Polubriaginof, P. Green, D. Vawdrey, N. Tatonetti, B. Lebwohl Low Rates of Screening for Celiac Disease Among Family Members Clinical Gastroenterology and Hepatology, (2018) Pp 1

K. Shameer, M. Perez-Rodriguez, Roy Bachar, Li Li, Amy Johnson, Kipp W. Johnson, B. Glicksberg, Milo R. Smith, B. Readhead, Joseph R. Scarpa, Jebakumar Jebakaran, P. Kovatch, Sabina Lim, W. Goodman, D. Reich, A. Kasarskis, N. Tatonetti, J. Dudley Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining BMC Medical Informatics and Decision Making, (2018) Vol 18 No 3 Pp 1-11

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Yun Hao, N. Tatonetti Predicting negative control drugs to support research in drug safety bioRxiv, (2018) Pp 380832

Fabrizio Spagnolo, P. Cristofari, N. Tatonetti, L. Ginzburg, D. Dykhuizen Pathogen population structure can explain hospital outbreaks The ISME journal, (2018) Vol 12 No 12 Pp 2835-2843

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A. Yahi, T. Lappalainen, P. Mohammadi, N. Tatonetti RecNW: a fast pairwise aligner for targeted sequencing bioRxiv, (2018) Pp 371989

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N. Tatonetti Science as a Culinary Art: How Data Science and Informatics Will Change Knowledge Discovery for Everyone Annual Review of Biomedical Data Science, (2018) Vol 1 Pp iv-vi

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Yun Hao, Kayla Quinnies, Ronald B. Realubit, Charles Karan, N. Tatonetti Tissue‐Specific Analysis of Pharmacological Pathways CPT: pharmacometrics & systems pharmacology, (2018) Vol 7 No 7 Pp 453-463

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Fernanda C G Polubriaginof, R. Vanguri, Kayla Quinnies, G. Belbin, A. Yahi, H. Salmasian, T. Lorberbaum, Victor Nwankwo, Li Li, Mark Shervey, P. Glowe, I. Ionita-Laza, M. Simmerling, G. Hripcsak, S. Bakken, David Goldstein, K. Kiryluk, E. Kenny, J. Dudley, D. Vawdrey, N. Tatonetti Disease heritability inferred from familial relationships reported in medical records Cell, (2018) Vol 173 No 7 Pp 1692-1704. e11

Faye, Adam S, Polubriaginof, Fernanda, Green, Peter H, Vawdrey, David K, Tatonetti, Nicholas, Lebwohl, Benjamin Mo1024-Low Rates of Screening for Celiac Disease Among Family Members; Analysis of Algorithm-Identified Familial Relationships Gastroenterology, (2018) Vol 154 No 6 Pp S-674-S-675

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Romano, Joseph D, Nwankwo, Victor, Tatonetti, Nicholas P VenomKB v2. 0: A knowledge repository for computational toxinology bioRxiv, (2018) Pp 295204

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Boland, M, Polubriaginof, F, Tatonetti, NP A MACHINE LEARNING ALGORITHM TO CLASSIFY FDA CATEGORY C DRUGS. CLINICAL PHARMACOLOGY & THERAPEUTICS, (2018) Vol 103 Pp S10-S10

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N. Tatonetti The next generation of drug safety science: coupling detection, corroboration, and validation to discover novel drug effects and drug–drug interactions Clinical Pharmacology & Therapeutics, (2018) Vol 103 No 2 Pp 177-179

P. Kennel, A. Saha, D. Maldonado, R. Givens, D. Brunjes, E. Castillero, Xiaokan Zhang, R. Ji, A. Yahi, Isaac J George, D. Mancini, A. Koller, B. Fine, E. Zorn, P. Colombo, N. Tatonetti, E. Chen, P. Schulze Serum exosomal protein profiling for the non-invasive detection of cardiac allograft rejection The Journal of Heart and Lung Transplantation, (2018) Vol 37 No 3 Pp 409-417

Boland, Mary Regina, Parhi, Pradipta, Li, Li, Miotto, Riccardo, Carroll, Robert, Iqbal, Usman, Nguyen, Phung-Anh, Schuemie, Martijn, You, Seng Chan, Smith, Donahue Uncovering exposures responsible for birth season–disease effects: a global study Journal of the American Medical Informatics Association, (2018) Vol 25 No 3 Pp 275-288

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Fernanda C G Polubriaginof, R. Vanguri, Kayla Quinnies, G. Belbin, A. Yahi, H. Salmasian, T. Lorberbaum, Victor Nwankwo, Li Li, Mark Shervey, P. Glowe, I. Ionita-Laza, M. Simmerling, G. Hripcsak, S. Bakken, David Goldstein, K. Kiryluk, E. Kenny, J. Dudley, D. Vawdrey, N. Tatonetti Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records , (2018)

2017

N. Giangreco, E. Zorn, E. Chen, P. Colombo, N. Tatonetti, B. Fine Identification of novel primary graft dysfunction biomarkers using exosome proteomics Circulation, (2017) Vol 136 No suppl_1 Pp A19311-A19311

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Boland, Mary Regina, Parhi, Pradipta, Gentine, Pierre, Tatonetti, Nicholas P Climate Classification is an Important Factor in Assessing Hospital Performance Metrics AGU Fall Meeting Abstracts, (2017) Vol 2017 Pp IN53A-0079

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A. Yahi, R. Vanguri, Noémie Elhadad, N. Tatonetti Generative adversarial networks for electronic health records: A framework for exploring and evaluating methods for predicting drug-induced laboratory test trajectories arXiv preprint arXiv:1712.00164, (2017)

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M. Boland, Fernanda C G Polubriaginof, N. Tatonetti Development of a machine learning algorithm to classify drugs of unknown fetal effect Scientific reports, (2017) Vol 7 No 1 Pp 1-15

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N. Macesic, Fernanda C G Polubriaginof, N. Tatonetti Machine learning: novel bioinformatics approaches for combating antimicrobial resistance Current opinion in infectious diseases, (2017) Vol 30 No 6 Pp 511-517

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Robert Moskovitch, Fernanda C G Polubriaginof, A. Weiss, P. Ryan, N. Tatonetti Procedure prediction from symbolic Electronic Health Records via time intervals analytics Journal of Biomedical Informatics, (2017) Vol 75 Pp 70-82

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M. Boland, Pradipta Parhi, P. Gentine, N. Tatonetti Climate classification is an important factor in assessing quality-of-care across hospitals Scientific Reports, (2017) Vol 7 No 1 Pp 1-6

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T. Lorberbaum, N. Tatonetti Reply: Combination Therapy With Ceftriaxone and Lansoprazole, Acquired Long QT Syndrome and Torsades de Pointes Risk Journal of the American College of Cardiology, (2017) Vol 69 No 14 Pp 1877-1878

R. Boyce, E. Voss, V. Huser, L. Evans, C. Reich, J. Duke, N. Tatonetti, T. Lorberbaum, M. Dumontier, M. Hauben, M. Wallberg, Lili Peng, S. Dempster, Y. He, A. Sena, V. Koutkias, P. Natsiavas, P. Ryan Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data Journal of biomedical semantics, (2017) Vol 8 Pp 1-15

LA

M. Boland, K. Karczewski, N. Tatonetti Ten simple rules to enable multi-site collaborations through data sharing PLoS Computational Biology, (2017) Vol 13 No 1 Pp e1005278

Katherine Xu, P. Rosenstiel, N. Paragas, C. Hinze, Xiaobo Gao, Tian Huai Shen, Max Werth, C. Forster, R. Deng, E. Bruck, R. W. Boles, A. Tornato, Tejashree Gopal, Madison Jones, Justin Konig, J. Stauber, V. D’Agati, H. Erdjument-Bromage, S. Saggi, G. Wagener, K. Schmidt-Ott, N. Tatonetti, P. Tempst, J. A. Oliver, P. Guarnieri, J. Barasch Unique transcriptional programs identify subtypes of AKI Journal of the American Society of Nephrology, (2017) Vol 28 No 6 Pp 1729-1740

K. Karczewski, N. Tatonetti, A. Manrai, C. Patel, C. Titus Brown, J. Ioannidis Methods to ensure the reproducibility of biomedical research PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017, (2017) Pp 117-119

K. Shameer, Kipp W. Johnson, A. Yahi, R. Miotto, Li Li, D. Ricks, Jebakumar Jebakaran, P. Kovatch, P. Sengupta, A. Gelijns, A. Moskovitz, B. Darrow, D. Reich, A. Kasarskis, N. Tatonetti, D. Pinney, J. Dudley Predictive modeling of hospital readmission rates using electronic medical record-wide machine learning: a case-study using Mount Sinai heart failure cohort Pacific Symposium on Biocomputing 2017, (2017) Pp 276-287

C. Deng, Mark R. Lipstein, L. Scotto, Xavier O Jirau Serrano, M. Mangone, Shirong Li, J. Vendôme, Yun Hao, Xiaomin Xu, S. Deng, Ronald B. Realubit, N. Tatonetti, Charles Karan, S. Lentzsch, D. Fruman, B. Honig, D. Landry, O. O’Connor Silencing c-Myc translation as a therapeutic strategy through targeting PI3Kδ and CK1ε in hematological malignancies Blood, The Journal of the American Society of Hematology, (2017) Vol 129 No 1 Pp 88-99

2016

Mahadeshwar, Pooja, Kapoor, Teja, Quinnies, Kayla, Tatonetti, Nicholas, Hui-Yuen, Joyce, Nguyen, Samantha, Bathon, Joan, Neville, Kayla, Miceli, James, Tanner, Stacy Prevalence of Progressive Multifocal Leukoencephalopathy in Adults and Children with Systemic Lupus Erythematosus ARTHRITIS & RHEUMATOLOGY, (2016) Vol 68

LA

M. Boland, Z. Shahn, D. Madigan, G. Hripcsak, N. Tatonetti Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method HUMAN HEREDITY, (2016) Vol 81 No 2 Pp 52-52

Johnson, Kipp W, Shameer, Khader, Yahi, Alexandre, Miotto, Riccardo, Ricks, Doran, Jebakaran, Jebakumar, Kovatch, Patricia, Sengupta, Partho, Reich, David L, Kasarskis, Andrew Pharmacological factors associated with congestive heart failure hospital readmission: a case-study using 15,768 heart failure patients from two health systems Circulation, (2016) Vol 134 No suppl_1 Pp A19489-A19489

LA

T. Lorberbaum, K. Sampson, Jeremy B. Chang, V. Iyer, R. Woosley, R. Kass, N. Tatonetti Coupling data mining and laboratory experiments to discover drug interactions causing QT prolongation Journal of the American College of Cardiology, (2016) Vol 68 No 16 Pp 1756-1764

LA

Jacunski, Alexandra, Tatonetti, Nicholas Method for identifying synthetic lethality , (2016)

Li Li, M. Boland, R. Miotto, N. Tatonetti, J. Dudley Replicating cardiovascular condition-birth month associations Scientific reports, (2016) Vol 6 No 1 Pp 1-7

LA

Joseph D. Romano, N. Tatonetti Using a novel ontology to inform the discovery of therapeutic peptides from animal venoms AMIA Summits on Translational Science Proceedings, (2016) Vol 2016 Pp 209

LA

Yun Hao, N. Tatonetti Predicting G protein-coupled receptor downstream signaling by tissue expression Bioinformatics, (2016) Vol 32 No 22 Pp 3435-3443

LA

Jeremy B. Chang, Kayla Quinnies, Ronald B. Realubit, Charles Karan, J. Rand, N. Tatonetti A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient Scientific Reports, (2016) Vol 6 No 1 Pp 1-5

LA

Robert Moskovitch, Hyunmi Choi, G. Hripcsak, N. Tatonetti Prognosis of clinical outcomes with temporal patterns and experiences with one class feature selection IEEE/ACM transactions on computational biology and bioinformatics, (2016) Vol 14 No 3 Pp 555-563

LA

M. Boland, N. Tatonetti Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review The pharmacogenomics journal, (2016) Vol 16 No 5 Pp 411-429

Kaitlyn Gayvert, E. Dardenne, C. Cheung, M. Boland, T. Lorberbaum, Jackline Wanjala, Yu Chen, M. Rubin, N. Tatonetti, D. Rickman, O. Elemento A computational drug repositioning approach for targeting oncogenic transcription factors Cell reports, (2016) Vol 15 No 11 Pp 2348-2356

J. Banda, L. Evans, R. Vanguri, N. Tatonetti, P. Ryan, N. Shah A curated and standardized adverse drug event resource to accelerate drug safety research Scientific data, (2016) Vol 3 No 1 Pp 1-11

LA

M. Boland, N. Tatonetti In search of ‘birth month genes’: using existing data repositories to locate genes underlying birth month-disease relationships AMIA Summits on Translational Science Proceedings, (2016) Vol 2016 Pp 189

N. Nissim, M. Boland, N. Tatonetti, Y. Elovici, G. Hripcsak, Yuval Shahar, Robert Moskovitch Improving condition severity classification with an efficient active learning based framework Journal of biomedical informatics, (2016) Vol 61 Pp 44-54

Keith B. Hoffman, M. Dimbil, N. Tatonetti, Robert F Kyle A pharmacovigilance signaling system based on FDA regulatory action and post-marketing adverse event reports Drug safety, (2016) Vol 39 No 6 Pp 561-575

LA

T. Lorberbaum, K. Sampson, R. Woosley, R. Kass, N. Tatonetti An integrative data science pipeline to identify novel drug interactions that prolong the QT interval Drug safety, (2016) Vol 39 No 5 Pp 433-441

A. Manrai, C. Patel, N. Gehlenborg, N. Tatonetti, J. Ioannidis, I. Kohane Methods to enhance the reproducibility of precision medicine Biocomputing 2016: Proceedings of the Pacific Symposium, (2016) Pp 180-182

B. Kidd, A. Wróblewska, M. Boland, J. Agudo, M. Merad, N. Tatonetti, B. Brown, J. Dudley Mapping the effects of drugs on the immune system Nature biotechnology, (2016) Vol 34 No 1 Pp 47-54

LA

M. Boland, A. Jacunski, T. Lorberbaum, Joseph D. Romano, Robert Moskovitch, N. Tatonetti Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms Wiley Interdisciplinary Reviews: Systems Biology and Medicine, (2016) Vol 8 No 2 Pp 104-122

FA

Tatonetti, Nicholas, Altman, Russ B, Fernald, Guy Haskin Signal detection algorithms to identify drug effects and drug interactions , (2016)

2015

LA

S. Vilar, T. Lorberbaum, G. Hripcsak, N. Tatonetti Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling , (2015)

S. Vilar, N. Tatonetti, G. Hripcsak 3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance , (2015)

LA

Chang, JB, Realubit, R, Karan, C, Rand, J, Tatonetti, NP A novel approach to evaluating oral anticoagulants JOURNAL OF THROMBOSIS AND HAEMOSTASIS, (2015) Vol 13 Pp 899-899

C. Deng, Mark R. Lipstein, L. Scotto, Yun Hao, N. Tatonetti, M. Mangone, Shirong Li, S. Lentzsch, Ronald B. Realubit, Charles Karan, O. O’Connor Disruption of the mTOR-eIF4F Axis By Selectively Targeting PI3Kdelta and Proteasome Potently Inhibits Cap Dependent Translation of c-Myc in Aggressive Lymphomas Blood, (2015) Vol 126 No 23 Pp 593

Fernanda C G Polubriaginof, N. Tatonetti, D. Vawdrey An assessment of family history information captured in an electronic health record AMIA Annual Symposium Proceedings, (2015) Vol 2015 Pp 2035

LA

Robert Moskovitch, Colin G. Walsh, Fei Wang, G. Hripcsak, N. Tatonetti Outcomes prediction via time intervals related patterns 2015 IEEE international conference on data mining, (2015) Pp 919-924

Keith B. Hoffman, M. Dimbil, Robert F Kyle, N. Tatonetti, Colin B. Erdman, Andrea Demakas, Dingguo Chen, B. Overstreet A drug safety rating system based on postmarketing costs associated with adverse events and patient outcomes Journal of Managed Care & Specialty Pharmacy, (2015) Vol 21 No 12 Pp 1134-1143c

LA

Joseph D. Romano, N. Tatonetti VenomKB, a new knowledge base for facilitating the validation of putative venom therapies Scientific data, (2015) Vol 2 No 1 Pp 1-9

LA

A. Jacunski, S. Dixon, N. Tatonetti Connectivity homology enables inter-species network models of synthetic lethality PLoS computational biology, (2015) Vol 11 No 10 Pp e1004506

LA

A. Yahi, N. Tatonetti A knowledge-based, automated method for phenotyping in the EHR using only clinical pathology reports AMIA Summits on Translational Science Proceedings, (2015) Vol 2015 Pp 64

LA

T. Lorberbaum, K. Sampson, R. Woosley, R. Kass, N. Tatonetti Data science identifies novel drug interactions that prolong the QT interval bioRxiv, (2015) Pp 024745

LA

S. Vilar, T. Lorberbaum, G. Hripcsak, N. Tatonetti Improving detection of arrhythmia drug-drug interactions in pharmacovigilance data through the implementation of similarity-based modeling PloS one, (2015) Vol 10 No 6 Pp e0129974

N. Nissim, M. Boland, Robert Moskovitch, N. Tatonetti, Y. Elovici, Yuval Shahar, G. Hripcsak An active learning framework for efficient condition severity classification Conference on Artificial Intelligence in Medicine in Europe, (2015) Pp 13-24

LA

M. Boland, Z. Shahn, D. Madigan, G. Hripcsak, N. Tatonetti Birth month affects lifetime disease risk: a phenome-wide method Journal of the American Medical Informatics Association, (2015) Vol 22 No 5 Pp 1042-1053

Ayvaz, Serkan, Horn, John, Hassanzadeh, Oktie, Zhu, Qian, Stan, Johann, Tatonetti, Nicholas P, Vilar, Santiago, Brochhausen, Mathias, Samwald, Matthias, Rastegar-Mojarad, Majid Toward a complete dataset of drug–drug interaction information from publicly available sources Journal of biomedical informatics, (2015) Vol 55 Pp 206-217

LA

M. Boland, N. Tatonetti Are all vaccines created equal? Using electronic health records to discover vaccines associated with clinician-coded adverse events AMIA Summits on Translational Science Proceedings, (2015) Vol 2015 Pp 196

M. Boland, N. Tatonetti, G. Hripcsak Development and validation of a classification approach for extracting severity automatically from electronic health records Journal of biomedical semantics, (2015) Vol 6 No 1 Pp 1-13

S. Vilar, N. Tatonetti, G. Hripcsak 3D pharmacophoric similarity improves multi adverse drug event identification in pharmacovigilance Scientific reports, (2015) Vol 5 No 1 Pp 1-9

LA

T. Lorberbaum, Mavra Nasir, Michael J. Keiser, S. Vilar, G. Hripcsak, N. Tatonetti Systems pharmacology augments drug safety surveillance Clinical Pharmacology & Therapeutics, (2015) Vol 97 No 2 Pp 151-158

2014

Nissim, N, Boland, MR, Moskovitch, R, Tatonetti, NP, Elovici, Y, Shahar, Y An active learning enhancement for conditions severity classification NYC, USA: ACM KDD on Workshop on Connected Health at Big Data Era, (2014)

Karczewski, KJ, Fernald, GH, Martin, AR, Snyder, M, Tatonetti, NP, Dudley, JT STORMSeq: An Open-Source User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud, PlosOne, (2014) Vol 9 No 1

Bockting, Walter, Reame, Nancy, Tatonetti, Nicholas, Arcia, Adriana, Bjarnadottir, Ragnhildur I, Brown III, William, Berkowitz, Bobbie, Bakken, Suzanne Application of Expert-and Informatics-Based Approaches to Understand the Health-Related Needs of LGBT Populations , (2014)

LA

Moskovitch, Robert, Walsh, Colin, Hripcsak, George, Tatonetti, NP Prediction of biomedical events via time intervals mining ACM KDD Workshop on Connected Health in Big Data Era, (2014) Pp 119

LA

S. Vilar, E. Uriarte, L. Santana, C. Friedman, N. Tatonetti State of the art and development of a drug-drug interaction large scale predictor based on 3D pharmacophoric similarity Current Drug Metabolism, (2014) Vol 15 No 5 Pp 490-501

Matos, Maria João, Vilar, Santiago, Kachler, Sonja, Fonseca, André, Santana, Lourdes, Uriarte, Eugenio, Borges, Fernanda, Tatonetti, Nicholas P, Klotz, Karl‐Norbert Back Cover: Insight into the Interactions between Novel Coumarin Derivatives and Human A3 Adenosine Receptors (ChemMedChem 10/2014) ChemMedChem, (2014) Vol 9 No 10 Pp 2392-2392

Vilar, S, Ryan, PB, Madigan, D, Stang, PE, Schuemie, MJ, Friedman, C, Tatonetti, NP, Hripcsak, G Similarity‐based modeling applied to signal detection in pharmacovigilance CPT: pharmacometrics & systems pharmacology, (2014) Vol 3 No 9 Pp 1-9

Keith B. Hoffman, Andrea Demakas, M. Dimbil, N. Tatonetti, Colin B. Erdman Stimulated reporting: the impact of US food and drug administration-issued alerts on the adverse event reporting system (FAERS) Drug safety, (2014) Vol 37 No 11 Pp 971-980

LA

S. Vilar, E. Uriarte, L. Santana, T. Lorberbaum, G. Hripcsak, C. Friedman, N. Tatonetti Similarity-based modeling in large-scale prediction of drug-drug interactions Nature protocols, (2014) Vol 9 No 9 Pp 2147-2163

M. Matos, S. Vilar, S. Kachler, André Fonseca, L. Santana, E. Uriarte, F. Borges, N. Tatonetti, K. Klotz Insight into the interactions between novel coumarin derivatives and human A3 adenosine receptors ChemMedChem, (2014) Vol 9 No 10 Pp 2245-2253

R. Boyce, P. Ryan, G. N. Norén, M. Schuemie, C. Reich, J. Duke, N. Tatonetti, G. Trifirò, R. Harpaz, J. Overhage, A. Hartzema, Mark Khayter, E. Voss, C. Lambert, V. Huser, M. Dumontier Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest Drug safety, (2014) Vol 37 No 8 Pp 557-567

Z. Ali, S. Poludasu, Yasir H. Qureshi, P. Krishnan, Ayyaz A. Ali, N. Tatonetti, Peter Downey, Adrian Zalewski, T. Nazif, I. George, A. Mandava, U. Baber, G. Dangas, R. Mehran, A. Kini, Samin K. 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, (2014) Vol 113 No 9 Pp 1481-1486

Boland, MR, Tatonetti, NP, Hripcsak, G CAESAR: A classification approach for extracting severity automatically from electronic health records Intelligent Systems for Molecular Biology Phenotype Day, (2014) Pp 1-8

S. Dixon, Darpan N. Patel, Matthew E. Welsch, R. Skouta, Eric D. Lee, M. Hayano, A. Thomas, C. Gleason, N. Tatonetti, B. Slusher, B. Stockwell Pharmacological inhibition of cystine–glutamate exchange induces endoplasmic reticulum stress and ferroptosis elife, (2014) Vol 3 Pp e02523

Li Li, D. Ruau, C. Patel, S. Weber, Rong Chen, N. Tatonetti, J. Dudley, A. Butte Disease risk factors identified through shared genetic architecture and electronic medical records Science translational medicine, (2014) Vol 6 No 234 Pp 234ra57-234ra57

G. Delogu, Silvia Serra, E. Quezada, E. Uriarte, S. Vilar, N. Tatonetti, D. Viña Monoamine Oxidase (MAO) Inhibitory Activity: 3‐Phenylcoumarins versus 4‐Hydroxy‐3‐phenylcoumarins ChemMedChem, (2014) Vol 9 No 8 Pp 1672-1676

Matos, Maria João, Vilar, Santiago, García‐Morales, Verónica, Tatonetti, Nicholas P, Uriarte, Eugenio, Santana, Lourdes, Viña, Dolores Insight into the Functional and Structural Properties of 3‐Arylcoumarin as an Interesting Scaffold in Monoamine Oxidase B Inhibition ChemMedChem, (2014) Vol 9 No 7 Pp 1488-1500

Keith B. Hoffman, M. Dimbil, Colin B. Erdman, N. Tatonetti, B. 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 No 4 Pp 283-294

Matos, Maria João, Janeiro, Patricia, Gonzalez Franco, Rosa Maria, Vilar, Santiago, Tatonetti, Nicholas P, Santana, Lourdes, Uriarte, Eugenio, Borges, Fernanda, Fontenla, José Angel, Vina, Dolores 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 No 4 Pp 371-383

LA

K. Karczewski, M. Snyder, R. Altman, N. Tatonetti Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association PLoS genetics, (2014) Vol 10 No 2 Pp e1004122

K. Karczewski, G. Fernald, Alicia R. Martin, M. Snyder, N. Tatonetti, J. Dudley STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud PloS one, (2014) Vol 9 No 1 Pp e84860

2013

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

E. Behr, M. Ritchie, Toshihiro Tanaka, S. Kääb, D. Crawford, P. Nicoletti, A. Floratos, Moritz F. Sinner, P. Kannankeril, A. Wilde, C. Bezzina, E. Schulze-Bahr, S. Zumhagen, P. Guicheney, N. Bishopric, V. Marshall, S. Shakir, C. Dalageorgou, S. Bevan, Y. Jamshidi, R. Bastiaenen, R. Myerburg, J. Schott, A. Camm, G. Steinbeck, Kris J Norris, R. Altman, N. Tatonetti, S. Jeffery, M. Kubo, Yusuke Nakamura, Yufeng Shen, A. George, D. Roden Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes PloS one, (2013) Vol 8 No 11 Pp e78511

LA

Xiaochen Sun, S. Vilar, N. Tatonetti High-throughput methods for combinatorial drug discovery Science translational medicine, (2013) Vol 5 No 205 Pp 205rv1-205rv1

LA

A. Jacunski, N. Tatonetti Connecting the dots: applications of network medicine in pharmacology and disease Clinical Pharmacology & Therapeutics, (2013) Vol 94 No 6 Pp 659-669

M. Matos, S. Vilar, N. 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) Vol 1050 Pp 185-191

M. Perera, L. Cavallari, N. Limdi, E. Gamazon, A. Konkashbaev, R. Daneshjou, A. Pluzhnikov, D. Crawford, Jelai Wang, Nianjun Liu, N. Tatonetti, S. Bourgeois, Harumi Takahashi, Y. Bradford, B. Burkley, R. Desnick, J. Halperin, S. Khalifa, T. Langaee, S. Lubitz, E. Nutescu, M. Oetjens, Mohamed H. Shahin, S. Patel, H. Sagreiya, M. Tector, K. Weck, M. Rieder, S. Scott, A. Wu, J. Burmester, M. Wadelius, P. Deloukas, M. Wagner, T. Mushiroda, M. Kubo, D. Roden, N. Cox, R. Altman, T. Klein, Yusuke Nakamura, Julie A. Johnson Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study The Lancet, (2013) Vol 382 No 9894 Pp 790-796

R. Daneshjou, N. Tatonetti, K. Karczewski, H. Sagreiya, S. Bourgeois, K. Drozda, J. Burmester, T. Tsunoda, Yusuke Nakamura, M. Kubo, M. Tector, N. Limdi, L. Cavallari, M. Perera, Julie A. Johnson, T. Klein, R. Altman Pathway analysis of genome-wide data improves warfarin dose prediction BMC genomics, (2013) Vol 14 No 3 Pp 1-12

Ferino, Giulio, Cadoni, Enzo, Matos, Maria João, Quezada, Elias, Uriarte, Eugenio, Santana, Lourdes, Vilar, Santiago, Tatonetti, Nicholas P, Yáñez, Matilde, Viña, Dolores MAO Inhibitory Activity of 2‐Arylbenzofurans versus 3‐Arylcoumarins: Synthesis, in vitro Study, and Docking Calculations ChemMedChem, (2013) Vol 8 No 6 Pp 956-966

Matos, Maria J, Vilar, Santiago, Gonzalez-Franco, Rosa Mª, Uriarte, Eugenio, Santana, Lourdes, Friedman, Carol, Tatonetti, Nicholas P, Viña, Dolores, Fontenla, Jose A 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, (2013) Vol 63 Pp 151-161

S. Vilar, E. Uriarte, L. Santana, N. Tatonetti, C. Friedman Detection of drug-drug interactions by modeling interaction profile fingerprints PloS one, (2013) Vol 8 No 3 Pp e58321

Ryen W. White, N. Tatonetti, N. Shah, R. Altman, E. Horvitz Web-scale pharmacovigilance: listening to signals from the crowd Journal of the American Medical Informatics Association, (2013) Vol 20 No 3 Pp 404-408

FA

Tatonetti, Nicholas P, Denny, Joshua C, Altman, Russ B Response to ‘Use of an algorithm for identifying hidden drug—drug interactions in adverse event reports’ by Gooden et al Journal of the American Medical Informatics Association, (2013) Vol 20 No 3 Pp 591-591

2012

FA LA

Tatonetti, Nicholas P Data-Driven Detection, Prediction, and Validation of Drug-Drug Interactions , (2012)

FA

N. Tatonetti, P. Ye, R. Daneshjou, R. Altman Data-driven prediction of drug effects and interactions Science translational medicine, (2012) Vol 4 No 125 Pp 125ra31-125ra31

K. Karczewski, Robert P. Tirrell, P. Cordero, N. Tatonetti, J. Dudley, K. Salari, M. Snyder, R. Altman, Stuart K. Kim Interpretome: a freely available, modular, and secure personal genome interpretation engine Biocomputing 2012, (2012) Pp 339-350

2011

FA

N. Tatonetti, G. Fernald, R. Altman A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports Journal of the American Medical Informatics Association, (2011) Vol 19 No 1 Pp 79-85

K. Karczewski, N. Tatonetti, S. Landt, Xinqiong Yang, T. Slifer, R. Altman, M. Snyder Cooperative transcription factor associations discovered using regulatory variation Proceedings of the National Academy of Sciences, (2011) Vol 108 No 32 Pp 13353-13358

FA

N. Tatonetti, J. Denny, S. Murphy, G. Fernald, G. Krishnan, V. Castro, P. Yue, PS Tsau, I. Kohane, D. Roden, R. Altman Detecting drug interactions from adverse‐event reports: interaction between paroxetine and pravastatin increases blood glucose levels Clinical Pharmacology & Therapeutics, (2011) Vol 90 No 1 Pp 133-142

2010

FA

N. Tatonetti, J. Dudley, H. Sagreiya, A. Butte, R. Altman An integrative method for scoring candidate genes from association studies: application to warfarin dosing BMC bioinformatics, (2010) Vol 11 No 9 Pp 1-7

Garten, YAEL, Tatonetti, Nicholas P, Altman, Russ B Improving the prediction of pharmacogenes using text-derived drug-gene relationships Biocomputing 2010, (2010) Pp 305-314

2009

FA

N. Tatonetti, Tianyun Liu, R. Altman Predicting drug side-effects by chemical systems biology Genome biology, (2009) Vol 10 No 9 Pp 1-4

LA

Vanguri, Rami S, Romano, Joseph D, Lorberbaum, Tal, Youn, Choonhan, Nwankwo, Victor, Tatonetti, Nicholas P nSides: An interactive drug–side effect gateway , ()

LA

Moskovitch, Robert, Walsh, Colin, Hripcsak, George, Tatonetti, Nicholas Prediction of Clinical Procedures via Time Intervals Mining , ()

LA

Boland, Mary Regina, Karczewski, Konrad J, Tatonetti, Nicholas P Journal: Ten simple rules to enable multi-site collaborations through data sharing , ()

LA

Boland, MR, Tatonetti, NP Supplemental Appendix for , ()

LA

Lorberbaum, Tal, Sampson, Kevin J, Woosley, Raymond L, Kass, Robert S, Tatonetti, Nicholas P Supplementary Material for An integrative data science pipeline to identify novel drug interactions that prolong the QT interval , ()

LA

Boland, Mary Regina, Hripcsak, George, Ryan, Patrick, Tatonetti, Nicholas P A Climate-Wide Journey to Explore Mechanisms Underlying Birth Month-Disease Risk Associations: A Call for Collaboration Observational Health Data Sciences and Informatics Symposium 2015, ()

Ananiadou, Sophia, Smalheiser, Neil, Nenadic, Goran, Melton-Meaux, Genevieve, Cohen, Trevor, Prabhakaran, Balakrishnan, Jimeno, Antonio, Jiang, Xiaoqian, Torii, Manabu, Shahar, Yuval ICHI 2015 Program Committee , ()

Matos, MJ, Vilar, S, Kachler, S, Fonseca, A, Santana, L, Uriarte, E, Borges, F, Tatonetti, NP, Klotz, KN, Archambault-LØger, V N. Nasheri, CS McKay, K. Fulton, S. Twine, MH Powdrill, AR Sherratt, JP Pezacki* Hydrophobic Triaryl-Substituted b-Lactams as Activity-Based Probes for Profiling Eukaryotic Enzymes and Host–Pathogen Interactions , ()

* Denotes equal contribution.

FA First Author Publication LA Last Author Publication SA Solo Author Publication


Funding Awarded

Data-driven drug discovery: investigating the molecular mechanisms of safety and efficacy R35 GM131905 National Institute for General Medical Sciences ~$2.5 million (PI: Tatonetti)

Clinical and genomic data mining to study pharmacogenomics of drug-induced liver injury Amgen, Inc. (PI: Tatonetti)

Clinical and genomic data mining to study pharmacogenomics of drug-induced liver injury Amgen, Inc. (PI: Tatonetti)

Biomedical Data Translator Technical Feasibility Assessment and Architecture Design OT3 TR002027 National Center for Advancing Translational Research ~$1.8 million (Contact PI: Tatonetti)

Development of an automated clinical informatics system to facilitate genomic discovery AstraZeneca, Inc (PI: Goldstein, Project Lead: Tatonetti)

Genomics of Non-alocholic fatty liver diseae (NAFLD) Janssen Research & Development, LLC (PI: Wattacheril)

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)

Professional Service

External Advisory Panel, Center for Excellence for Natural Product-Drug Interaction Research, 2020-Present

Member, Editorial Board, Annual Reviews of Biomedical Data Science, 2020-Present

Member, International Scientific Advisor Board, UK Biobank, 2019-Present

Special Member, Editorial Board, Annual Reviews of Biomedical Data Science, 2019

National Institute on Aging (NIA) U19 Review Committee, 2018

Chair, AMIA Summit on Translational Bioinformatics, San Francisco, March 2018

Editorial Board Member, Journal of Biomedical Informatics, 2016-2019

Honorary Editorial Board Member, Drug Safety, 2015-

Vice Chair, AMIA Summit on Translational Bioinformatics, San Francisco, March 2017

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: Nature, Science, Cell, NEJM, BMJ, Circulation, Nature Medicine, Science Translational Medicine, Cell Systems, 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

Invited Speaker, American Society for Human Genetics, Houston, October 15-19, 2019

Keynote Speaker, Health Research Symposium 2019, Hong Kong, June 12, 2019

Invited Speaker, ISPE Mid-Year Meeting 2019, Rome, Italy, April 8, 2019

Keynote Speaker, Onassis Health Day, Athens, Greece, February 11, 2019

Keynote Speaker, World Preclinical Congress Europe, Lisbon, November 25-28, 2018

Keynote Speaker, WCP2018 18th Congress on Basic and Clinical Pharmacology, Kyoto, July 1-6, 2018

Invited Speaer, Big Data for Pharmacovigilance, Drug Safety Research Unit, London, June 20-21, 2018

Invited Speaker, Gordon Research Conference on Drug Safety, Boston, June 10-15, 2018

Keynote Speaker, Molecular Medicine Tri-Conference, February 13th, 2018

Distinguished Lecturer, School of Pharmacy, University at Buffalo, February 1st, 2018

Invited Speaker, AI in Healthcare Summit, Boston, January 19th, 2018

Keynote Speaker, Translational Bioinformatics Conference 2017, San Diegeo, September 29th, 2017

Keynote Lecturer, Ben Gurion University, September 12th, 2017

Invited Speaker, Journalism in Science Conference, Dortmund, Germany, August 7th, 2017

Invited Speaker, AI in Healthcare Summit 2017, San Francisco, July 26th, 2017

Keynote Speaker, Biocomputation at Stanford, 2017, April 10th, 2017

Invited Speaker, ASCPT Annual Meeting 2017, March 18th, 2017

European Medicines Agency, London, November 13th, 2016

Invited Speaker, Future directions in medical data science, London October 10th, 2016

Plenary Speaker, American Society for Human Genetics Annual Meeting 2016, Vancouver, October 18th, 2016

New York Academy of Sciences, New York, September 16th, 2016

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 Biostatistics 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

In response to Lorberbaum, et al. JAMIA (2016)

Chicago Tribue, October 10, 2016, "Scientists see progress in identifying deadly drug interactions." link

Live Science, October 10, 2016, "Deadly Mixture: Scientists Uncover Harmful Drug Interactions." link

Cardiology Today, October 20, 2016, "Data mining, lab testing approach reveals ceftriaxone-lansoprazole interaction" link

In response to Boland, et al. JAMIA (2015)

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.

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

Selected Awards and Honors

Mentor for the NIH and NSF 2018 Data Science Innovation Lab, 2018

New Investigator Award, American Medical Informatics Association (AMIA), November 2016

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

Teaching Experience

Instructor, Translational Bioinformatics (BINF G4006), Columbia University, Fall 2015, Fall 2016, Fall 2017, Fall 2019

Instructor, Introduction to Biomedical Informatics, Columbia University, 2014-2019

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

Partner, Woven Sciences, LLC, 2020-Present

Scientific Advisory Board Member, Gilead/Goldfinch Collaboration, 2020-Present

Scientific Advisor, Advera Health, 2012-Present

Scientific Advisor, You Gene, Inc., New York City, NY 2013-2019

Chief Executive 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