NICHOLAS TATONETTI, Ph.D.
Department of Computational Biomedicine, &Cedars-Sinai Cancer
Cedars-Sinai Medical Center
700 N. San Vicente Blvd., Suite 540
West Hollywood, CA 90069
nicholas.tatonetti@cshs.org
tatonettilab.org
Education
Professional Experience
Cedars-Sinai Medical Center, Los Angeles, CA
Professor of of Computational Biomedicine, 2023-Current
Vice Chair, Operations, Department of Computational Biomedicine, 2022-Current
Associate Director, Data Science, Samuel Oschin Cancer Center, 2022-Current
Columbia University, New York, NY
Chief Officer for Cancer Data Science, Herbert Irving Comprehensive Cancer Center, 2022
Associate Professor of Biomedical Informatics, 2019-2022
Director, Clinical Informatics, Institute for Genomic Medicine, 2017-2022
Co-Director, Bioinformatics, Department of Biomedical Informatics, 2017-2022
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
2022
A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development Med(In Press)
Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer Journal of Biomedical Informatics(2022)
Snapshots of nascent RNA reveal cell-and stimulus-specific responses to acute kidney injury JCI insight, (2022)
Mural norrin/β-catenin signaling regulates Lama2 expression to promote neurovascular unit assembly bioRxiv, (2022)
System-wide transcriptome damage and tissue identity loss in COVID-19 patients Cell Reports Medicine, (2022) Vol 3 No 2 Pp 100522
2021
Rapid Identification and Phenotyping of Nonalcoholic Fatty Liver Disease Patients Using an Automated Algorithmic Approach in Diverse, Urban Healthcare Systems medRxiv, (2021)
E-Pedigrees: a large-scale automatic family pedigree prediction application Bioinformatics, (2021) Vol 37 No 21 Pp 3966-3968
Pediatric data from the All of Us research program: demonstration of pediatric obesity over time JAMIA Open, (2021) Vol 4 No 4 Pp ooab112
Predicting the Toxicity of Druggable Proteins to Human Tissues bioRxiv, (2021)
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
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
A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development Available at SSRN 3898786, (2021)
Plasma kallikrein predicts primary graft dysfunction after heart transplant The Journal of Heart and Lung Transplantation, (2021) Vol 40 No 10 Pp 1199-1211
Repurposing the atypical antidepressant trazodone for atherosclerotic cardiovascular disease , (2021)
Fine-scale genetic ancestry as a potential new tool for precision medicine Nature Medicine, (2021) Vol 27 No 7 Pp 1152-1153
Methods and systems for predicting success rates of clinical trials , (2021)
Rapid Identification and Phenotyping of Nonalcoholic Fatty Liver Disease Patients Using an Automated Algorithmic Approach in Diverse, Urban Healthcare Systems , (2021)
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
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
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
Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children BioData mining, (2021) Vol 14 No 1 Pp 1-17
Prediction of adverse drug reactions associated with drug-drug interactions using hierarchical classification bioRxiv, (2021)
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
Identifying symptom information in clinical notes using natural language processing Nursing research, (2021) Vol 70 No 3 Pp 173-183
2020
Achieving trustworthy biomedical data solutions BIOCOMPUTING 2021: Proceedings of the Pacific Symposium, (2020) Pp 1-13
Association of neighborhood deprivation index with success in cancer care crowdfunding JAMA network open, (2020) Vol 3 No 12 Pp e2026946-e2026946
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
Associations between blood type and COVID-19 infection, intubation, and death Nature communications, (2020) Vol 11 No 1 Pp 1-6
Transfer learning from simulations improves the classification of OCT images of glandular epithelia bioRxiv, (2020)
Melatonin is significantly associated with survival of intubated COVID-19 patients MedRxiv, (2020)
No population left behind: Improving paediatric drug safety using informatics and systems biology British Journal of Clinical Pharmacology, (2020)
Using machine learning to identify adverse drug effects posing increased risk to women Patterns, (2020) Vol 1 No 7 Pp 100108
Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection Nature medicine, (2020) Vol 26 No 10 Pp 1609-1615
EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments bioRxiv, (2020)
Simulating drug effects on blood glucose laboratory test time series with a conditional WGAN medRxiv, (2020)
Prevalence of progressive multifocal leukoencephalopathy (PML) in adults and children with systemic lupus erythematosus Lupus science & medicine, (2020) Vol 7 No 1 Pp e000388
Predicting phenotypic polymyxin resistance in Klebsiella pneumoniae through machine learning analysis of genomic data Msystems, (2020) Vol 5 No 3 Pp e00656-19
Medical data and machine learning improve power of stroke genome-wide association studies bioRxiv, (2020)
2019
608 Max-imizing the Attenuation of Myc Using Small Molecules Science & Society, (2019) Vol 40 No 9 Pp 605-710
Attention deficit-hyperactivity disorder and month of school enrollment The New England journal of medicine, (2019) Vol 380 No 7 Pp 692-693
Precision Medicine: Addressing the Challenges of Sharing, Analysis, and Privacy at Scale PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020, (2019) Pp 547-550
AMarketplace FOR HEALTH: OPPORTUNITIES AND CHALLENGES FOR BIOMEDICAL BLOCKCHAINS , (2019)
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
Predicting the genetic ancestry of 2.6 million New York City patients using clinical data bioRxiv, (2019) Pp 768440
Pathway analysis of genomic pathology tests for prognostic cancer subtyping Journal of biomedical informatics, (2019) Vol 98 Pp 103286
Molecular nephrology: types of acute tubular injury Nature Reviews Nephrology, (2019) Vol 15 No 10 Pp 599-612
Familial relationships in electronic health records (EHR) v2 bioRxiv, (2019) Pp 731976
Artificial intelligence for drug toxicity and safety Trends in pharmacological sciences, (2019) Vol 40 No 9 Pp 624-635
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
Discovering therapeutic activities from venoms using differential gene expression bioRxiv, (2019) Pp 699280
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
Clinical data: sources and types, regulatory constraints, applications Clinical and translational science, (2019) Vol 12 No 4 Pp 329
cohorts: A Python package for clinical ‘omics data management bioRxiv, (2019) Pp 626051
Informatics and computational methods in natural product drug discovery: a review and perspectives Frontiers in genetics, (2019) Vol 10 Pp 368
Mo1634–No Increased Risk of Colorectal Adenomas in Spouses of Patients with Colorectal Neoplasia Gastroenterology, (2019) Vol 156 No 6 Pp S-810
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
Comparative analysis of EHR-based stroke phenotyping methods, their applications, and interpretation bioRxiv, (2019) Pp 565671
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
Low rates of screening for celiac disease among family members Clinical Gastroenterology and Hepatology, (2019) Vol 17 No 3 Pp 463-468
Translational medicine in the Age of Big Data Briefings in bioinformatics, (2019) Vol 20 No 2 Pp 457-462
Signal detection algorithms to identify drug effects and drug interactions , (2019)
2018
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
Using precision pharmacovigilance to detect and evaluate antiepileptic drug associated adverse reactions in pediatric patients F1000Research, (2018) Vol 7
Low screening rates for diabetes mellitus among family members of affected relatives AMIA Annual Symposium Proceedings, (2018) Vol 2018 Pp 1471
Using precision pharmacoviglance to detect developmentally-regulated adverse drug reactions: a case study with antiepileptic drugs F1000Research, (2018) Vol 7
Standardized and reproducible analysis enables identification of novel primary graft dysfunction biomarkers using exosome proteomics F1000Research, (2018) Vol 7
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
Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records Scientific data, (2018) Vol 5 No 1 Pp 1-17
Low Rates of Screening for Celiac Disease Among Family Members Clinical Gastroenterology and Hepatology, (2018) Pp 1
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
Predicting negative control drugs to support research in drug safety bioRxiv, (2018) Pp 380832
Pathogen population structure can explain hospital outbreaks The ISME journal, (2018) Vol 12 No 12 Pp 2835-2843
RecNW: a fast pairwise aligner for targeted sequencing bioRxiv, (2018) Pp 371989
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
Tissue‐Specific Analysis of Pharmacological Pathways CPT: pharmacometrics & systems pharmacology, (2018) Vol 7 No 7 Pp 453-463
Disease heritability inferred from familial relationships reported in medical records Cell, (2018) Vol 173 No 7 Pp 1692-1704. e11
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
VenomKB v2. 0: A knowledge repository for computational toxinology bioRxiv, (2018) Pp 295204
A MACHINE LEARNING ALGORITHM TO CLASSIFY FDA CATEGORY C DRUGS. CLINICAL PHARMACOLOGY & THERAPEUTICS, (2018) Vol 103 Pp S10-S10
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
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
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
Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records , (2018)
2017
Identification of novel primary graft dysfunction biomarkers using exosome proteomics Circulation, (2017) Vol 136 No suppl_1 Pp A19311-A19311
Climate Classification is an Important Factor in Assessing Hospital Performance Metrics AGU Fall Meeting Abstracts, (2017) Vol 2017 Pp IN53A-0079
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)
Development of a machine learning algorithm to classify drugs of unknown fetal effect Scientific reports, (2017) Vol 7 No 1 Pp 1-15
Machine learning: novel bioinformatics approaches for combating antimicrobial resistance Current opinion in infectious diseases, (2017) Vol 30 No 6 Pp 511-517
Procedure prediction from symbolic Electronic Health Records via time intervals analytics Journal of Biomedical Informatics, (2017) Vol 75 Pp 70-82
Climate classification is an important factor in assessing quality-of-care across hospitals Scientific Reports, (2017) Vol 7 No 1 Pp 1-6
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
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
Ten simple rules to enable multi-site collaborations through data sharing PLoS Computational Biology, (2017) Vol 13 No 1 Pp e1005278
Unique transcriptional programs identify subtypes of AKI Journal of the American Society of Nephrology, (2017) Vol 28 No 6 Pp 1729-1740
Methods to ensure the reproducibility of biomedical research PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017, (2017) Pp 117-119
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
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
Prevalence of Progressive Multifocal Leukoencephalopathy in Adults and Children with Systemic Lupus Erythematosus ARTHRITIS & RHEUMATOLOGY, (2016) Vol 68
Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method HUMAN HEREDITY, (2016) Vol 81 No 2 Pp 52-52
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
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
Method for identifying synthetic lethality , (2016)
Replicating cardiovascular condition-birth month associations Scientific reports, (2016) Vol 6 No 1 Pp 1-7
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
Predicting G protein-coupled receptor downstream signaling by tissue expression Bioinformatics, (2016) Vol 32 No 22 Pp 3435-3443
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
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
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
A computational drug repositioning approach for targeting oncogenic transcription factors Cell reports, (2016) Vol 15 No 11 Pp 2348-2356
A curated and standardized adverse drug event resource to accelerate drug safety research Scientific data, (2016) Vol 3 No 1 Pp 1-11
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
Improving condition severity classification with an efficient active learning based framework Journal of biomedical informatics, (2016) Vol 61 Pp 44-54
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
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
Methods to enhance the reproducibility of precision medicine Biocomputing 2016: Proceedings of the Pacific Symposium, (2016) Pp 180-182
Mapping the effects of drugs on the immune system Nature biotechnology, (2016) Vol 34 No 1 Pp 47-54
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
Signal detection algorithms to identify drug effects and drug interactions , (2016)
2015
Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling , (2015)
3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance , (2015)
A novel approach to evaluating oral anticoagulants JOURNAL OF THROMBOSIS AND HAEMOSTASIS, (2015) Vol 13 Pp 899-899
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
An assessment of family history information captured in an electronic health record AMIA Annual Symposium Proceedings, (2015) Vol 2015 Pp 2035
Outcomes prediction via time intervals related patterns 2015 IEEE international conference on data mining, (2015) Pp 919-924
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
VenomKB, a new knowledge base for facilitating the validation of putative venom therapies Scientific data, (2015) Vol 2 No 1 Pp 1-9
Connectivity homology enables inter-species network models of synthetic lethality PLoS computational biology, (2015) Vol 11 No 10 Pp e1004506
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
Data science identifies novel drug interactions that prolong the QT interval bioRxiv, (2015) Pp 024745
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
An active learning framework for efficient condition severity classification Conference on Artificial Intelligence in Medicine in Europe, (2015) Pp 13-24
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
Toward a complete dataset of drug–drug interaction information from publicly available sources Journal of biomedical informatics, (2015) Vol 55 Pp 206-217
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
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
3D pharmacophoric similarity improves multi adverse drug event identification in pharmacovigilance Scientific reports, (2015) Vol 5 No 1 Pp 1-9
Systems pharmacology augments drug safety surveillance Clinical Pharmacology & Therapeutics, (2015) Vol 97 No 2 Pp 151-158
2014
An active learning enhancement for conditions severity classification NYC, USA: ACM KDD on Workshop on Connected Health at Big Data Era, (2014)
STORMSeq: An Open-Source User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud, PlosOne, (2014) Vol 9 No 1
Application of Expert-and Informatics-Based Approaches to Understand the Health-Related Needs of LGBT Populations , (2014)
Prediction of biomedical events via time intervals mining ACM KDD Workshop on Connected Health in Big Data Era, (2014) Pp 119
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
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
Similarity‐based modeling applied to signal detection in pharmacovigilance CPT: pharmacometrics & systems pharmacology, (2014) Vol 3 No 9 Pp 1-9
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
Similarity-based modeling in large-scale prediction of drug-drug interactions Nature protocols, (2014) Vol 9 No 9 Pp 2147-2163
Insight into the interactions between novel coumarin derivatives and human A3 adenosine receptors ChemMedChem, (2014) Vol 9 No 10 Pp 2245-2253
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
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
CAESAR: A classification approach for extracting severity automatically from electronic health records Intelligent Systems for Molecular Biology Phenotype Day, (2014) Pp 1-8
Pharmacological inhibition of cystine–glutamate exchange induces endoplasmic reticulum stress and ferroptosis elife, (2014) Vol 3 Pp e02523
Disease risk factors identified through shared genetic architecture and electronic medical records Science translational medicine, (2014) Vol 6 No 234 Pp 234ra57-234ra57
Monoamine Oxidase (MAO) Inhibitory Activity: 3‐Phenylcoumarins versus 4‐Hydroxy‐3‐phenylcoumarins ChemMedChem, (2014) Vol 9 No 8 Pp 1672-1676
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
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
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
Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association PLoS genetics, (2014) Vol 10 No 2 Pp e1004122
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
Detection of drug-drug interactions by modeling interaction profile fingerprints , (2013)
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
High-throughput methods for combinatorial drug discovery Science translational medicine, (2013) Vol 5 No 205 Pp 205rv1-205rv1
Connecting the dots: applications of network medicine in pharmacology and disease Clinical Pharmacology & Therapeutics, (2013) Vol 94 No 6 Pp 659-669
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
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
Pathway analysis of genome-wide data improves warfarin dose prediction BMC genomics, (2013) Vol 14 No 3 Pp 1-12
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
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
Detection of drug-drug interactions by modeling interaction profile fingerprints PloS one, (2013) Vol 8 No 3 Pp e58321
Web-scale pharmacovigilance: listening to signals from the crowd Journal of the American Medical Informatics Association, (2013) Vol 20 No 3 Pp 404-408
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
Data-Driven Detection, Prediction, and Validation of Drug-Drug Interactions , (2012)
Data-driven prediction of drug effects and interactions Science translational medicine, (2012) Vol 4 No 125 Pp 125ra31-125ra31
Interpretome: a freely available, modular, and secure personal genome interpretation engine Biocomputing 2012, (2012) Pp 339-350
2011
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
Cooperative transcription factor associations discovered using regulatory variation Proceedings of the National Academy of Sciences, (2011) Vol 108 No 32 Pp 13353-13358
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
An integrative method for scoring candidate genes from association studies: application to warfarin dosing BMC bioinformatics, (2010) Vol 11 No 9 Pp 1-7
Improving the prediction of pharmacogenes using text-derived drug-gene relationships Biocomputing 2010, (2010) Pp 305-314
2009
Predicting drug side-effects by chemical systems biology Genome biology, (2009) Vol 10 No 9 Pp 1-4
nSides: An interactive drug–side effect gateway , ()
Prediction of Clinical Procedures via Time Intervals Mining , ()
Journal: Ten simple rules to enable multi-site collaborations through data sharing , ()
Supplemental Appendix for , ()
Supplementary Material for An integrative data science pipeline to identify novel drug interactions that prolong the QT interval , ()
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, ()
ICHI 2015 Program Committee , ()
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.
First Author Publication Last Author Publication 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 Advisor Board Member, University of Alabama, Birmingham Informatics Institute, 2022
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
Keynote Speaker, AMIA Translational Bioinformatics Year-in-Review, Seattle, March 13-16, 2023
Invited Speaker, American Society of Health-System Pharmacists, Las Vegas, December 6-7, 2022
Invited Speaker, American Heart Association, San Diego, September 12-13, 2022
Invited Speaker, Science, Society, and the Legacy of Donald A.B. Lindberg M.D., Washington DC/Virtual, September 1, 2022
Invited Speaker, American Society of Health-System Pharmacists Summer Meeting, June 11-13, 2022
Host, Symposium for Artificial Intelligence in Learning Health System (SAIL), May 23-27, 2022
Invited Speaker, United Kingdom's Drug Safety Symposium, London, UK/Virtual, May 10-11, 2022
Keynote Speaker, AMIA Translational Bioinformatics Year-in-Review, Chicago, March 19-22, 2022
Keynote Speaker, AMIA Translational Bioinformatics Year-in-Review, Virtual, March 23, 2021
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
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
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
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