Nicholas P. Tatonetti

66 papers A* 1B 1Misc 18Journal 43Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A crisis of overconfidence: Why confidence, not accuracy, is the real risk in clinical AI. BioData Min. Jacob S. Berkowitz, Jake R. Patock, Asma Nawaz, Graciela Gonzalez-Hernandez, Nicholas P. Tatonetti
2025	J	`jnl`	Benchmarking proprietary and open-source language and vision-language models for gastroenterology clinical reasoning. npj Digit. Medicine 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, Aasma Shaukat, Samuel Margolis, Nicholas P. Tatonetti, Girish N. Nadkarni, Bara El Kurdi, Ali Soroush
2025	J	`jnl`	Biomedical text normalization through generative modeling. J. Biomed. Informatics Jacob S. Berkowitz, Apoorva Srinivasan, Jose Miguel Acitores Cortina, Yasaman Fatapour, Nicholas P. Tatonetti
2025	J	`jnl`	Enhancing EHR-based pancreatic cancer prediction with LLM-derived embeddings. npj Digit. Medicine Jiheum Park, Jason Patterson, Jose Miguel Acitores Cortina, Tian Gu, Chin Hur, Nicholas P. Tatonetti
2025	—	`conf`	Evaluating the Reporting Quality of 21,041 Randomized Controlled Trial Articles with Large Language Models: A Large-Scale Transparency Analysis. AIME (1) Apoorva Srinivasan, Sophia Kivelson, Nadine A. Friedrich, Jacob S. Berkowitz, Nicholas P. Tatonetti
2025	J	`jnl`	From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery. BioData Min. Jason H. Moore, Nicholas P. Tatonetti
2025	—	`conf`	Probing Large Language Model Hidden States for Adverse Drug Reaction Knowledge. AIME (1) Jacob S. Berkowitz, Davy Weissenbacher, Apoorva Srinivasan, Nadine A. Friedrich, Jose Miguel Acitores Cortina, Sophia Kivelson, Graciela Gonzalez-Hernandez, Nicholas P. Tatonetti
2025	J	`jnl`	Toward Scalable Early Cancer Detection: Evaluating EHR-Based Predictive Models Against Traditional Screening Criteria. CoRR Jiheum Park, Chao Pang, Tristan Y. Lee, Jeong Yun Yang, Jacob S. Berkowitz, Alexander Z. Wei, Nicholas P. Tatonetti
2025	J	`jnl`	Vibe coding: a new paradigm for biomedical software development. BioData Min. Jason H. Moore, Nicholas P. Tatonetti
2025	J	`jnl`	Vision Language Models versus Machine Learning Models Performance on Polyp Detection and Classification in Colonoscopy Images. CoRR 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, Nicholas Hoerter, Girish N. Nadkarni, Hamid Asadzadeh Aghdaei, Ali Soroush
2024	J	`jnl`	Advancing LGBTQ+ inclusion in STEM education and AI research. Patterns Emily F. Wong, Ryan J. Urbanowicz, Tiffani J. Bright, Nicholas P. Tatonetti, Yi-Wen Hsiao, Xiuzhen Huang, Jason H. Moore, Pei-Chen Peng
2024	J	`jnl`	KG-LIME: predicting individualized risk of adverse drug events for multiple sclerosis disease-modifying therapy. J. Am. Medical Informatics Assoc. Jason Patterson, Nicholas P. Tatonetti
2024	J	`jnl`	TCGA-Reports: A machine-readable pathology report resource for benchmarking text-based AI models. Patterns Jenna Kefeli, Nicholas P. Tatonetti
2024	J	`jnl`	Vision-Language and Large Language Model Performance in Gastroenterology: GPT, Claude, Llama, Phi, Mistral, Gemma, and Quantized Models. CoRR 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, Aasma Shaukat, Samuel Margolis, Nicholas P. Tatonetti, Girish N. Nadkarni, Bara El Kurdi, Ali Soroush
2023	J	`jnl`	ChatGPT and large language models in academia: opportunities and challenges. BioData Min. 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
2023	J	`jnl`	Large Language Models for Granularized Barrett's Esophagus Diagnosis Classification. CoRR Jenna Kefeli, Ali Soroush, Courtney J. Diamond, Haley M. Zylberberg, Benjamin L. May, Julian A. Abrams, Chunhua Weng, Nicholas P. Tatonetti
2023	J	`jnl`	Structured deep embedding model to generate composite clinical indices from electronic health records for early detection of pancreatic cancer. Patterns Jiheum Park, Michael G. Artin, Kate E. Lee, Benjamin L. May, Michael Park, Chin Hur, Nicholas P. Tatonetti
2023	J	`jnl`	Using machine learning probabilities to identify effects of COVID-19. Patterns Vijendra Ramlall, Undina Gisladottir, Jenna Kefeli, Yutaro Tanaka, Benjamin L. May, Nicholas P. Tatonetti
2022	J	`jnl`	Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer. J. Biomed. Informatics Jiheum Park, Michael G. Artin, Kate E. Lee, Yoanna S. Pumpalova, Myles A. Ingram, Benjamin L. May, Michael Park, Chin Hur, Nicholas P. Tatonetti
2022	Misc	`conf`	Using Time Series Clustering to Segment and Infer Emergency Department Nursing Shifts from Electronic Health Record Log Files. AMIA Amanda J. Moy, Kenrick Cato, Jennifer Withall, Nicholas P. Tatonetti, Eugene Y. Kim, Sarah Collins Rossetti
2021	Misc	`conf`	Achieving Trustworthy Biomedical Data Solutions. PSB Peter Washington, Serena Yeung, Bethany Percha, Nicholas P. Tatonetti, Jan T. Liphardt, Dennis P. Wall
2021	J	`jnl`	E-Pedigrees: a large-scale automatic family pedigree prediction application. Bioinform. Xiayuan Huang, Nicholas P. Tatonetti, Katie Larow, Brooke Delgoffe, John Mayer, David Page, Scott J. Hebbring
2021	J	`jnl`	Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children. BioData Min. Nicholas Giangreco, Nicholas P. Tatonetti
2021	J	`jnl`	Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 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, Richard A. Dart, Murray H. Brilliant, Eric B. Larson, David S. Carrell, Sarah A. Pendergrass, Shefali Setia Verma, Marylyn D. Ritchie, Barbara Benoit, Vivian S. Gainer, Elizabeth W. Karlson, Adam S. Gordon, Gail P. Jarvik, Ian B. Stanaway, David R. Crosslin, Sumit Mohan, Iuliana Ionita-Laza, Nicholas P. Tatonetti, Ali G. Gharavi, George Hripcsak, Chunhua Weng, Krzysztof Kiryluk
2020	J	`jnl`	Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods. BioData Min. Phyllis M. Thangaraj, Benjamin Kummer, Tal Lorberbaum, Mitchell S. V. Elkind, Nicholas P. Tatonetti
2020	Misc	`conf`	Session Introduction. PSB Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti
2020	J	`jnl`	Using Machine Learning to Identify Adverse Drug Effects Posing Increased Risk to Women. Patterns Payal Chandak, Nicholas P. Tatonetti
2019	Misc	`conf`	Breast Cancer Screening Rates Among Family Members of Affected Relatives. AMIA Fernanda C. Polubriaginof, Silis Y. Jiang, Nicholas P. Tatonetti, David K. Vawdrey
2019	J	`jnl`	Challenges with quality of race and ethnicity data in observational databases. J. Am. Medical Informatics Assoc. 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
2019	Misc	`conf`	Chronic Condition Symptom Enrichment from Electronic Health Records. AMIA Theresa A. Koleck, Suzanne R. Bakken, Nicholas P. Tatonetti
2019	J	`jnl`	Pathway analysis of genomic pathology tests for prognostic cancer subtyping. J. Biomed. Informatics Olga Lyudovyk, Yufeng Shen, Nicholas P. Tatonetti, Susan J. Hsiao, Mahesh M. Mansukhani, Chunhua Weng
2019	J	`jnl`	PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinform. 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, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel T. Dudley, Nicholas P. Tatonetti, Atul J. Butte
2019	J	`jnl`	Translational medicine in the Age of Big Data. Briefings Bioinform. Nicholas P. Tatonetti
2018	Misc	`conf`	Comparison of Electronic Medication Orders Versus Administration Records for Identifying Prevalence of Postoperative Nausea and Vomiting. AMIA Theresa A. Koleck, Suzanne Bakken, Nicholas P. Tatonetti
2018	Misc	`conf`	Low Screening Rates for Diabetes Mellitus Among Family Members of Affected Relatives. AMIA Fernanda C. Polubriaginof, Ning Shang, George Hripcsak, Nicholas P. Tatonetti, David K. Vawdrey
2018	J	`jnl`	Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. BMC Medical Informatics Decis. Mak. Khader Shameer, M. Mercedes Perez-Rodriguez, Roy Bachar, Li Li, Amy Johnson, Kipp W. Johnson, Benjamin S. Glicksberg, Milo R. Smith, Ben Readhead, Joseph Scarpa, Jebakumar Jebakaran, Patricia H. Kovatch, Sabina Lim, Wayne K. Goodman, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Joel T. Dudley
2018	J	`jnl`	Uncovering exposures responsible for birth season - disease effects: a global study. J. Am. Medical Informatics Assoc. Mary Regina Boland, Pradipta Parhi, Li Li, 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, Yu-Chuan (Jack) Li, Rae Woong Park, Joshua C. Denny, Joel T. Dudley, George Hripcsak, Pierre Gentine, Nicholas P. Tatonetti
2018	Misc	`conf`	Using model classifications as quantitative traits to estimate stroke heritability. AMIA 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
2017	—	`conf`	Automated Identification of Families in Electronic Health Records to Support Clinical Research. CRI 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, David K. Vawdrey
2017	Misc	`conf`	Deep recurrent neural networks identify transgender patients. AMIA Joseph D. Romano, Kenrick Cato, Rami Vanguri, Nicholas P. Tatonetti
2017	J	`jnl`	Generative Adversarial Networks for Electronic Health Records: A Framework for Exploring and Evaluating Methods for Predicting Drug-Induced Laboratory Test Trajectories. CoRR Alexandre Yahi, Rami Vanguri, Noémie Elhadad, Nicholas P. Tatonetti
2017	J	`jnl`	Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. J. Biomed. Semant. 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, Sara Dempster, Yongqun He, Anthony G. Sena, Vassilis Koutkias, Pantelis Natsiavas, Patrick B. Ryan
2017	Misc	`conf`	Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. PSB Khader Shameer, Kipp W. Johnson, Alexandre Yahi, Riccardo Miotto, Li Li, Doran Ricks, Jebakumar Jebakaran, Patricia H. Kovatch, Partho P. Sengupta, Annetine Gelijns, Alan Moskovitz, Bruce Darrow, David L. Reich, Andrew Kasarskis, Nicholas P. Tatonetti, Deborah F. Pinney, Joel T. Dudley
2017	J	`jnl`	Procedure prediction from symbolic Electronic Health Records via time intervals analytics. J. Biomed. Informatics Robert Moskovitch, Fernanda Polubriaginof, Aviram Weiss, Patrick B. Ryan, Nicholas P. Tatonetti
2017	J	`jnl`	Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection. IEEE ACM Trans. Comput. Biol. Bioinform. Robert Moskovitch, Hyunmi Choi, George Hripcsak, Nicholas P. Tatonetti
2017	Misc	`conf`	Session Introduction. PSB Konrad J. Karczewski, Nicholas P. Tatonetti, Chirag J. Patel, Arjun K. Manrai, C. Titus Brown, John P. A. Ioannidis
2017	J	`jnl`	Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing. PLoS Comput. Biol. Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti
2017	Misc	`conf`	The Use of Informatics to Reduce Disparities in Transgender Health. AMIA Kenrick Cato, Joseph D. Romano, Rami Vanguri, Nicholas P. Tatonetti
2016	J	`jnl`	Improving condition severity classification with an efficient active learning based framework. J. Biomed. Informatics Nir Nissim, Mary Regina Boland, Nicholas P. Tatonetti, Yuval Elovici, George Hripcsak, Yuval Shahar, Robert Moskovitch
2016	Misc	`conf`	Patient-provided Data Improves Race and Ethnicity Data Quality in Electronic Health Records. AMIA Fernanda Polubriaginof, Hojjat Salmasian, Andrea W. Shapiro, Jennifer E. Prey, George Hripcsak, Adler J. Perotte, Nicholas P. Tatonetti, David K. Vawdrey
2016	J	`jnl`	Predicting G protein-coupled receptor downstream signaling by tissue expression. Bioinform. Yun Hao, Nicholas P. Tatonetti
2016	Misc	`conf`	Session Introduction. PSB Arjun K. Manrai, Chirag J. Patel, Nils Gehlenborg, Nicholas P. Tatonetti, John P. A. Ioannidis, Isaac S. Kohane
2015	B	`conf`	An Active Learning Framework for Efficient Condition Severity Classification. AIME Nir Nissim, Mary Regina Boland, Robert Moskovitch, Nicholas P. Tatonetti, Yuval Elovici, Yuval Shahar, George Hripcsak
2015	Misc	`conf`	An Assessment of Family History Information Captured in an Electronic Health Record. AMIA Fernanda Polubriaginof, Nicholas P. Tatonetti, David K. Vawdrey
2015	J	`jnl`	Birth month affects lifetime disease risk: a phenome-wide method. J. Am. Medical Informatics Assoc. Mary Regina Boland, Zach Shahn, David Madigan, George Hripcsak, Nicholas P. Tatonetti
2015	J	`jnl`	Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PLoS Comput. Biol. Alexandra Jacunski, Scott J. Dixon, Nicholas P. Tatonetti
2015	J	`jnl`	Development and validation of a classification approach for extracting severity automatically from electronic health records. J. Biomed. Semant. Mary Regina Boland, Nicholas P. Tatonetti, George Hripcsak
2015	A*	`conf`	Outcomes Prediction via Time Intervals Related Patterns. ICDM Robert Moskovitch, Colin G. Walsh, Fei Wang, George Hripcsak, Nicholas P. Tatonetti
2015	Misc	`conf`	Recent Advances in Computational Drug Repositioning. AMIA Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang
2015	J	`jnl`	Toward a complete dataset of drug-drug interaction information from publicly available sources. J. Biomed. Informatics Serkan Ayvaz, John R. Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas P. Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, Richard D. Boyce
2013	J	`jnl`	Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden J. Am. Medical Informatics Assoc. Nicholas P. Tatonetti, Joshua C. Denny, Russ B. Altman
2013	J	`jnl`	Web-scale pharmacovigilance: listening to signals from the crowd. J. Am. Medical Informatics Assoc. Ryen W. White, Nicholas P. Tatonetti, Nigam H. Shah, Russ B. Altman, Eric Horvitz
2012	J	`jnl`	A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J. Am. Medical Informatics Assoc. Nicholas P. Tatonetti, Guy Haskin Fernald, Russ B. Altman
2012	Misc	`conf`	Interpretome: A Freely Available, Modular, and Secure Personal Genome Interpretation Engine. Pacific Symposium on Biocomputing Konrad J. Karczewski, Robert P. Tirrell, Pablo Cordero, Nicholas P. Tatonetti, Joel T. Dudley, Keyan Salari, Michael Snyder, Russ B. Altman, Stuart K. Kim
2010	J	`jnl`	An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinform. Nicholas P. Tatonetti, Joel Dudley, Hersh Sagreiya, Atul J. Butte, Russ B. Altman
2010	Misc	`conf`	Improving the Prediction of Pharmacogenes Using Text-Derived Gene-Drug Relationships. Pacific Symposium on Biocomputing Yael Garten, Nicholas P. Tatonetti, Russ B. Altman