Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships. - Yael Garten; Nicholas P. Tatonetti; Russ B. Altman (Pacific Symposium on Biocomputing, 2010)

An integrative method for scoring candidate genes from association studies: application to warfarin dosing. - Nicholas P. Tatonetti; Joel Dudley; Hersh Sagreiya; Atul J. Butte; Russ B. Altman (BMC Bioinform., 2010)

Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. - Konrad J. Karczewski; Robert P. Tirrell; Pablo Cordero; Nicholas P. Tatonetti; Joel T. Dudley; Keyan Salari; Michael Snyder 001; Russ B. Altman; Stuart K. Kim (Pacific Symposium on Biocomputing, 2012)

A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. - Nicholas P. Tatonetti; Guy Haskin Fernald; Russ B. Altman (J. Am. Medical Informatics Assoc., 2012)

Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al. - Nicholas P. Tatonetti; Joshua C. Denny; Russ B. Altman (J. Am. Medical Informatics Assoc., 2013)

Web-scale pharmacovigilance: listening to signals from the crowd. - Ryen W. White; Nicholas P. Tatonetti; Nigam H. Shah; Russ B. Altman; Eric Horvitz (J. Am. Medical Informatics Assoc., 2013)

An Active Learning Framework for Efficient Condition Severity Classification. - Nir Nissim; Mary Regina Boland; Robert Moskovitch; Nicholas P. Tatonetti; Yuval Elovici; Yuval Shahar; George Hripcsak (AIME, 2015)

Recent Advances in Computational Drug Repositioning. - Atul J. Butte; Nigam Shah; Nicholas P. Tatonetti; Hua Xu 001; Ping Zhang (AMIA, 2015)

An Assessment of Family History Information Captured in an Electronic Health Record. - Fernanda Polubriaginof; Nicholas P. Tatonetti; David K. Vawdrey (AMIA, 2015)

Outcomes Prediction via Time Intervals Related Patterns. - Robert Moskovitch; Colin G. Walsh; Fei Wang 001; George Hripcsak; Nicholas P. Tatonetti (ICDM, 2015)

Development and validation of a classification approach for extracting severity automatically from electronic health records. - Mary Regina Boland; Nicholas P. Tatonetti; George Hripcsak (J. Biomed. Semant., 2015)

Birth month affects lifetime disease risk: a phenome-wide method. - Mary Regina Boland; Zach Shahn; David Madigan; George Hripcsak; Nicholas P. Tatonetti (J. Am. Medical Informatics Assoc., 2015)

Toward a complete dataset of drug-drug interaction information from publicly available sources. - Serkan Ayvaz; John R. Horn; Oktie Hassanzadeh; Qian Zhu 003; Johann Stan; Nicholas P. Tatonetti; Santiago Vilar; Mathias Brochhausen; Matthias Samwald; Majid Rastegar-Mojarad; Michel Dumontier; Richard D. Boyce (J. Biomed. Informatics, 2015)

Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. - Alexandra Jacunski; Scott J. Dixon; Nicholas P. Tatonetti (PLoS Comput. Biol., 2015)

Patient-provided Data Improves Race and Ethnicity Data Quality in Electronic Health Records. - Fernanda Polubriaginof; Hojjat Salmasian; Andrea W. Shapiro; Jennifer E. Prey; George Hripcsak; Adler J. Perotte; Nicholas P. Tatonetti; David K. Vawdrey (AMIA, 2016)

Session Introduction. - Arjun K. Manrai; Chirag J. Patel; Nils Gehlenborg; Nicholas P. Tatonetti; John P. A. Ioannidis; Isaac S. Kohane (PSB, 2016)

Predicting G protein-coupled receptor downstream signaling by tissue expression. - Yun Hao; Nicholas P. Tatonetti (Bioinform., 2016)

Improving condition severity classification with an efficient active learning based framework. - Nir Nissim; Mary Regina Boland; Nicholas P. Tatonetti; Yuval Elovici; George Hripcsak; Yuval Shahar; Robert Moskovitch (J. Biomed. Informatics, 2016)

The Use of Informatics to Reduce Disparities in Transgender Health. - Kenrick Cato; Joseph D. Romano; Rami Vanguri; Nicholas P. Tatonetti (AMIA, 2017)

Deep recurrent neural networks identify transgender patients. - Joseph D. Romano; Kenrick Cato; Rami Vanguri; Nicholas P. Tatonetti (AMIA, 2017)

Automated Identification of Families in Electronic Health Records to Support Clinical Research. - Fernanda Polubriaginof; Kayla Quinnies; Rami Vanguri; Alexandre Yahi; Mary Simmerling; Iuliana Ionita-Laza; Hojjat Salmasian; Suzanne Bakken; George Hripcsak; Krzysztof Kiryluk; David Goldstein; Nicholas P. Tatonetti; et al. (CRI, 2017)

Session Introduction. - Konrad J. Karczewski; Nicholas P. Tatonetti; Chirag J. Patel; Arjun K. Manrai; C. Titus Brown; John P. A. Ioannidis (PSB, 2017)

Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. - Khader Shameer; Kipp W. Johnson; Alexandre Yahi; Riccardo Miotto; Li Li 062; Doran Ricks; Jebakumar Jebakaran; Patricia H. Kovatch; Partho P. Sengupta; Annetine Gelijns; Alan Moskovitz; Bruce Darrow; et al. (PSB, 2017)

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. - Richard D. Boyce; Erica A. Voss; Vojtech Huser; Lee Evans; Christian G. Reich; Jon D. Duke; Nicholas P. Tatonetti; Tal Lorberbaum; Michel Dumontier; Manfred Hauben; Magnus Wallberg; Lili Peng; et al. (J. Biomed. Semant., 2017)

Generative Adversarial Networks for Electronic Health Records: A Framework for Exploring and Evaluating Methods for Predicting Drug-Induced Laboratory Test Trajectories. - Alexandre Yahi; Rami Vanguri; Noémie Elhadad; Nicholas P. Tatonetti (CoRR, 2017)

Procedure prediction from symbolic Electronic Health Records via time intervals analytics. - Robert Moskovitch; Fernanda Polubriaginof; Aviram Weiss; Patrick B. Ryan; Nicholas P. Tatonetti (J. Biomed. Informatics, 2017)

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing. - Mary Regina Boland; Konrad J. Karczewski; Nicholas P. Tatonetti (PLoS Comput. Biol., 2017)

Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection. - Robert Moskovitch; Hyunmi Choi; George Hripcsak; Nicholas P. Tatonetti (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Comparison of Electronic Medication Orders Versus Administration Records for Identifying Prevalence of Postoperative Nausea and Vomiting. - Theresa A. Koleck; Suzanne Bakken; Nicholas P. Tatonetti (AMIA, 2018)

Low Screening Rates for Diabetes Mellitus Among Family Members of Affected Relatives. - Fernanda C. Polubriaginof; Ning Shang; George Hripcsak; Nicholas P. Tatonetti; David K. Vawdrey (AMIA, 2018)

Using model classifications as quantitative traits to estimate stroke heritability. - Phyllis M. Thangaraj; Fernanda C. Polubriaginof; Benjamin Kummer; Rami Vanguri; Tal Lorberbaum; Joseph D. Romano; Kayla Quinnies; Alexandre Yahi; Mitchell S. V. Elkind; Nicholas P. Tatonetti (AMIA, 2018)

Uncovering exposures responsible for birth season - disease effects: a global study. - Mary Regina Boland; Pradipta Parhi; Li Li 062; Riccardo Miotto; Robert J. Carroll; Usman Iqbal; Phung-Anh (Alex) Nguyen; Martijn J. Schuemie; Seng Chan You; Donahue Smith; Sean D. Mooney; Patrick B. Ryan; et al. (J. Am. Medical Informatics Assoc., 2018)

Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. - Khader Shameer; M. Mercedes Perez-Rodriguez; Roy Bachar; Li Li 062; Amy Johnson; Kipp W. Johnson; Benjamin S. Glicksberg; Milo R. Smith; Ben Readhead; Joseph Scarpa; Jebakumar Jebakaran; Patricia H. Kovatch; et al. (BMC Medical Informatics Decis. Mak., 2018)

Chronic Condition Symptom Enrichment from Electronic Health Records. - Theresa A. Koleck; Suzanne R. Bakken; Nicholas P. Tatonetti (AMIA, 2019)

Breast Cancer Screening Rates Among Family Members of Affected Relatives. - Fernanda C. Polubriaginof; Silis Y. Jiang; Nicholas P. Tatonetti; David K. Vawdrey (AMIA, 2019)

Translational medicine in the Age of Big Data. - Nicholas P. Tatonetti (Briefings Bioinform., 2019)

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. - Benjamin S. Glicksberg; Boris Oskotsky; Phyllis M. Thangaraj; Nicholas Giangreco; Marcus A. Badgeley; Kipp W. Johnson; Debajyoti Datta; Vivek A. Rudrapatna; Nadav Rappoport; Mark M. Shervey; Riccardo Miotto; Theodore C. Goldstein; et al. (Bioinform., 2019)

Challenges with quality of race and ethnicity data in observational databases. - Fernanda C. Polubriaginof; Patrick B. Ryan; Hojjat Salmasian; Andrea W. Shapiro; Adler J. Perotte; Monika M. Safford; George Hripcsak; Shaun Smith; Nicholas P. Tatonetti; David K. Vawdrey (J. Am. Medical Informatics Assoc., 2019)

Pathway analysis of genomic pathology tests for prognostic cancer subtyping. - Olga Lyudovyk; Yufeng Shen; Nicholas P. Tatonetti; Susan J. Hsiao; Mahesh M. Mansukhani; Chunhua Weng (J. Biomed. Informatics, 2019)

Session Introduction. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Alexander A. Morgan; Predrag Radivojac; Nicholas P. Tatonetti (PSB, 2020)

Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods. - Phyllis M. Thangaraj; Benjamin Kummer; Tal Lorberbaum; Mitchell S. V. Elkind; Nicholas P. Tatonetti (BioData Min., 2020)

Using Machine Learning to Identify Adverse Drug Effects Posing Increased Risk to Women. - Payal Chandak; Nicholas P. Tatonetti (Patterns, 2020)

Achieving Trustworthy Biomedical Data Solutions. - Peter Washington 001; Serena Yeung; Bethany Percha; Nicholas P. Tatonetti; Jan T. Liphardt; Dennis P. Wall (PSB, 2021)

Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children. - Nicholas Giangreco; Nicholas P. Tatonetti (BioData Min., 2021)

E-Pedigrees: a large-scale automatic family pedigree prediction application. - Xiayuan Huang; Nicholas P. Tatonetti; Katie Larow; Brooke Delgoffe; John Mayer; David Page; Scott J. Hebbring (Bioinform., 2021)

Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. - Ning Shang; Atlas Khan; Fernanda Polubriaginof; Francesca Zanoni; Karla Mehl; David Fasel; Paul E. Drawz; Robert J. Carroll; Joshua C. Denny; Matthew A. Hathcock; Adelaide M. Arruda-Olson; Peggy L. Peissig; et al. (npj Digit. Medicine, 2021)

Using Time Series Clustering to Segment and Infer Emergency Department Nursing Shifts from Electronic Health Record Log Files. - Amanda J. Moy; Kenrick Cato; Jennifer Withall; Nicholas P. Tatonetti; Eugene Y. Kim; Sarah Collins Rossetti (AMIA, 2022)

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

Large Language Models for Granularized Barrett's Esophagus Diagnosis Classification. - Jenna Kefeli; Ali Soroush; Courtney J. Diamond; Haley M. Zylberberg; Benjamin L. May; Julian A. Abrams; Chunhua Weng; Nicholas P. Tatonetti (CoRR, 2023)

ChatGPT and large language models in academia: opportunities and challenges. - Jesse G. Meyer; Ryan J. Urbanowicz; Patrick C. N. Martin; Karen O'Connor; Ruowang Li; Pei-Chen Peng; Tiffani J. Bright; Nicholas P. Tatonetti; Kyoung-Jae Won; Graciela Gonzalez-Hernandez; Jason H. Moore (BioData Min., 2023)

Structured deep embedding model to generate composite clinical indices from electronic health records for early detection of pancreatic cancer. - Jiheum Park; Michael G. Artin; Kate E. Lee; Benjamin L. May; Michael Park; Chin Hur; Nicholas P. Tatonetti (Patterns, 2023)

Using machine learning probabilities to identify effects of COVID-19. - Vijendra Ramlall; Undina Gisladottir; Jenna Kefeli; Yutaro Tanaka; Benjamin L. May; Nicholas P. Tatonetti (Patterns, 2023)

Vision-Language and Large Language Model Performance in Gastroenterology: GPT, Claude, Llama, Phi, Mistral, Gemma, and Quantized Models. - Seyed Amir Ahmad Safavi-Naini; Shuhaib Ali; Omer Shahab; Zahra Shahhoseini; Thomas Savage; Sara Rafiee; Jamil S. Samaan; Reem Al Shabeeb; Farah Ladak; Jamie O. Yang; Juan Echavarria; Sumbal Babar; et al. (CoRR, 2024)

KG-LIME: predicting individualized risk of adverse drug events for multiple sclerosis disease-modifying therapy. - Jason Patterson; Nicholas P. Tatonetti (J. Am. Medical Informatics Assoc., 2024)

Advancing LGBTQ+ inclusion in STEM education and AI research. - Emily Wong; Ryan J. Urbanowicz; Tiffani J. Bright; Nicholas P. Tatonetti; Yi-Wen Hsiao; Xiuzhen Huang; Jason H. Moore; Pei-Chen Peng (Patterns, 2024)

TCGA-Reports: A machine-readable pathology report resource for benchmarking text-based AI models. - Jenna Kefeli; Nicholas P. Tatonetti (Patterns, 2024)

Probing Large Language Model Hidden States for Adverse Drug Reaction Knowledge. - Jacob S. Berkowitz; Davy Weissenbacher; Apoorva Srinivasan; Nadine A. Friedrich; Jose Miguel Acitores Cortina; Sophia Kivelson; Graciela Gonzalez-Hernandez; Nicholas P. Tatonetti (AIME (1), 2025)

Evaluating the Reporting Quality of 21,041 Randomized Controlled Trial Articles with Large Language Models: A Large-Scale Transparency Analysis. - Apoorva Srinivasan; Sophia Kivelson; Nadine A. Friedrich; Jacob S. Berkowitz; Nicholas P. Tatonetti (AIME (1), 2025)

Vibe coding: a new paradigm for biomedical software development. - Jason H. Moore; Nicholas P. Tatonetti (BioData Min., 2025)

Biomedical text normalization through generative modeling. - Jacob S. Berkowitz; Apoorva Srinivasan; Jose Miguel Acitores Cortina; Yasaman Fatapour; Nicholas P. Tatonetti (J. Biomed. Informatics, 2025)

Enhancing EHR-based pancreatic cancer prediction with LLM-derived embeddings. - Jiheum Park; Jason Patterson; Jose Miguel Acitores Cortina; Tian Gu; Chin Hur; Nicholas P. Tatonetti (npj Digit. Medicine, 2025)

Vision Language Models versus Machine Learning Models Performance on Polyp Detection and Classification in Colonoscopy Images. - Mohammad Amin Khalafi; Seyed Amir Ahmad Safavi-Naini; Ameneh Salehi; Nariman Naderi; Dorsa Alijanzadeh; Pardis Ketabi Moghadam; Kaveh Kavosi; Negar Golestani; Shabnam Shahrokh; Soltanali Fallah; Jamil S. Samaan; Nicholas P. Tatonetti; et al. (CoRR, 2025)