Vivek Rudrapatna, MD, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address490 Illinois Street, #21E
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0003-1789-3004 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Harvard University, Cambridge, MAA.B.05/2006Biophysics
    Icahn School of Medicine at Mount Sinai, New York, NYM.D., Ph.D.05/2014Medicine, Cancer Biology
    Baylor College of Medicine, Houston, TXResidency06/2016Internal Medicine
    University of California, San FranciscoFellowship06/2020Gastroenterology, Clinical Data Science
    Collapse Awards and Honors
    2020Vivli Pioneer Award

    Collapse Overview 
    Collapse Overview
    Vivek Rudrapatna is a physician-scientist and Inflammatory Bowel Disease specialist in the Division of Gastroenterology. His research group develops methods for analyzing healthcare data with the goal of improving clinical decision making. Towards these goals, his team draws inspiration from a variety of disciplines within the data sciences, including biostatistics, natural language processing, machine learning, and artificial intelligence.

    Current areas of focus include:
    -Information extraction from clinical notes, particularly using deep learning models like BERT and GPT
    -Methods for integrating data across potentially heterogenous cohorts to reduce bias in individual participant data meta-analyses
    -External control arms using EHR data
    -Methods for improving treatment recommendations to account for patient level factors (precision medicine)
    -Computer vision algorithms for endoscopy photos
    -Reinforcement learning

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    Collapse Featured Publications

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group. BMC Med Res Methodol. 2023 10 03; 23(1):218. Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S. PMID: 37789257; PMCID: PMC10546672.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. S936 Optimizing Treatment Selection in Crohn’s Disease Using Patient-Specific Features: An Individual Participant Data Meta-Analysis of Fifteen Randomized Controlled Trials. The American Journal of Gastroenterology. 2023 Oct 1; 118(10S):s701-s702. Rudrapatna RV, Ravindranath RV, Arneson AD, Mosenia MA, Butte BA, Wang WS. .
      View in: Publisher Site   Mentions:
    3. S1394 NASHDetection: A Natural Language Processing Method for Identifying Patients With Non-alcoholic Steatohepatitis Using Clinical Notes. The American Journal of Gastroenterology. 2023 Oct 1; 118(10S):s1067-s1067. Bhasuran BB, Slatter SS, Fernandes FG, Ru RB, Yang YJ, Zhang ZX, Shankar SR, Ge GJ, Rudrapatna RV. .
      View in: Publisher Site   Mentions:
    4. S1395 Uncontrolled Diabetes and Hypertension Are Associated With the Risk of New-Onset Cirrhosis in Patients With Nonalcoholic Steatohepatitis. The American Journal of Gastroenterology. 2023 Oct 1; 118(10S):s1067-s1067. Bhasuran BB, Slatter SS, Fernandes FG, Ru RB, Yang YJ, Zhang ZX, Shankar SR, Rudrapatna RV, Ge GJ. .
      View in: Publisher Site   Mentions:
    5. S1012 Algorithmic Identification of Treatment-Emergent Adverse Events From Clinical Notes Using Large Language Models: A Pilot Study in Inflammatory Bowel Disease. The American Journal of Gastroenterology. 2023 Oct 1; 118(10S):s768-s768. Silverman SA, Sushil SM, Bhasuran BB, Ludwig LD, Buchanan BJ, Racz RR, Parakala PM, El-Kamary ES, Ahima AO, Belov BA, Choi CL, Billings BM, Li LY, Habal HN, Liu LQ, Tiwari TJ, Butte BA, Rudrapatna RV. .
      View in: Publisher Site   Mentions:
    6. Algorithmic identification of treatment-emergent adverse events from clinical notes using large language models: a pilot study in inflammatory bowel disease. medRxiv. 2023 Sep 08. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. PMID: 37732220; PMCID: PMC10508809.
      View in: PubMed   Mentions:
    7. Reducing diagnostic delays in Acute Hepatic Porphyria using electronic health records data and machine learning: a multicenter development and validation study. medRxiv. 2023 Aug 31. Bhasuran B, Schmolly K, Kapoor Y, Jayakumar NL, Doan R, Amin J, Meninger S, Cheng N, Deering R, Anderson K, Beaven SW, Wang B, Rudrapatna VA. PMID: 37693437; PMCID: PMC10491361.
      View in: PubMed   Mentions:
    8. ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study. Target Oncol. 2023 Jul; 18(4):571-583. Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA. PMID: 37341856; PMCID: PMC10345061.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    9. Assessing the Impact of COVID-19 on IBD Outcomes Among Vulnerable Patient Populations in a Large Metropolitan Center. Inflamm Bowel Dis. 2023 Mar 21. Odufalu FD, Sewell JL, Rudrapatna V, Somsouk M, Mahadevan U. PMID: 36943305.
      View in: PubMed   Mentions:    Fields:    
    10. Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study. PLoS One. 2023; 18(3):e0282267. Rudrapatna VA, Cheng YW, Feuille C, Mosenia A, Shih J, Shi Y, Roberson O, Rubin B, Butte AJ, Mahadevan U, Skomrock N, Erondu N, Chehoud C, Rahim S, Apfel D, Curran M, Khan NS, O'Brien C, Terry N, Martini BD. PMID: 36862717; PMCID: PMC9980824.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    11. Comparative Safety and Effectiveness of Biologic Therapy for Crohn's Disease: A CA-IBD Cohort Study. Clin Gastroenterol Hepatol. 2023 08; 21(9):2359-2369.e5. Singh S, Kim J, Luo J, Paul P, Rudrapatna V, Park S, Zheng K, Syal G, Ha C, Fleshner P, McGovern D, Sauk JS, Limketkai B, Dulai PS, Boland BS, Eisenstein S, Ramamoorthy S, Melmed G, Mahadevan U, Sandborn WJ, Ohno-Machado L. PMID: 36343846.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    12. Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Am J Gastroenterol. 2022 10 01; 117(10):1639-1647. Gu P, Luo J, Kim J, Paul P, Limketkai B, Sauk JS, Park S, Parekh N, Zheng K, Rudrapatna V, Syal G, Ha C, McGovern DP, Melmed GY, Fleshner P, Eisenstein S, Ramamoorthy S, Dulai PS, Boland BS, Grunvald E, Mahadevan U, Ohno-Machado L, Sandborn WJ, Singh S. PMID: 35973139.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    13. Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Clin Gastroenterol Hepatol. 2023 01; 21(1):173-181.e5. Nguyen NH, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk JS, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai PS, Boland BS, Mahadevan U, Sandborn WJ, Ohno-Machado L, McGovern D, Singh S. PMID: 35644340; PMCID: PMC9701245.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    14. 454: OBESITY IS NOT ASSOCIATED WITH INCREASED RISK OF ADVERSE TREATMENT OUTCOMES OR SERIOUS INFECTION IN INFLAMMATORY BOWEL DISEASES PATIENTS (IBD) STARTING NEW BIOLOGIC THERAPY. Gastroenterology. 2022 May 1; 162(7):s-101-s-102. Gu GP, Luo LJ, Paul PP, Limketkai LB, Sauk SJ, Park PS, Parekh PN, Zheng ZK, Rudrapatna RV, Syal SG, Ha HC, Mcgovern MD, Melmed MG, Fleshner FP, Eisenstein ES, Ramamoorthy RS, Dulai DP, Boland BB, Mahadevan MU, Ohno-Machado OL, Sandborn SW, Singh SS. .
      View in: Publisher Site   Mentions:
    15. Su1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBD. Gastroenterology. 2022 May 1; 162(7):s-482-s-483. Nguyen NN, Luo LJ, Paul PP, Kim KJ, Syal SG, Ha HC, Rudrapatna RV, Park PS, Parekh PN, Zheng ZK, Sauk SJ, Limketkai LB, Fleshner FP, Eisenstein ES, Ramamoorthy RS, Melmed MG, Boland BB, Mahadevan MU, Sandborn SW, Ohno-Machado OL, Mcgovern MD, Singh SS. .
      View in: Publisher Site   Mentions:
    16. Su1534: ACCURATE, ROBUST, AND SCALABLE ABSTRACTION OF MAYO ENDOSCOPIC SUBSCORES FROM COLONOSCOPY REPORTS. Gastroenterology. 2022 May 1; 162(7):s-617-s-618. Silverman SA, Bhasuran BB, Mosenia MA, Yasini YF, Gupta GS, Mardirossian MN, Narain NR, Sewell SJ, Butte BA, Rudrapatna RV. .
      View in: Publisher Site   Mentions:
    17. Case-control study of the association of chronic acid suppression and social determinants of health with COVID-19 infection. Sci Rep. 2021 10 25; 11(1):20987. Zhang B, Silverman AL, Bangaru S, Arneson D, Dasharathy S, Nguyen N, Rodden D, Shih J, Butte AJ, El-Nachef WN, Boland BS, Rudrapatna VA. PMID: 34697319; PMCID: PMC8545937.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    18. Fr001 PROTON PUMP INHIBITOR AND RISK OF SARS-COV-2 INFECTION: A MULTI-CENTER EXPERIENCE. Gastroenterology. 2021 May 10; 160(6):s-184. Silverman SA, Arneson AD, Bangaru BS, Zhang ZB, Rodden RD, Dasharathy DS, Shih SJ, Nguyen NN, El-Nachef EW, Boland BB, Rudrapatna RV. .
      View in: Publisher Site   Mentions:
    19. Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib. BMJ Health Care Inform. 2021 May; 28(1). Rudrapatna VA, Glicksberg BS, Butte AJ. PMID: 34011632; PMCID: PMC8141436.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    20. CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties. Sci Data. 2020 11 16; 7(1):405. Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. PMID: 33199721; PMCID: PMC7669883.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsPHPublic Health
    21. S0818 Accurate Machine Classification of Ulcerative Colitis Mayo Subscores From Electronic Health Record Procedure Reports. The American Journal of Gastroenterology. 2020 Oct 1; 115(1):s420-s420. Rudrapatna RV, Gupta GS, Mardirossian MT, Narain NR, Mosenia MA, Butte BA. .
      View in: Publisher Site   Mentions:
    22. S0525 An Electronic Health Records-Based Intervention Improves Appropriate Referrals for Upper Endoscopy: A Prospective, Single Center Study. The American Journal of Gastroenterology. 2020 Oct 1; 115(1):s259-s259. Rudrapatna RV, Ko KM, Mosenia MA, Radhakrishnan RK, Butte BA, Kathpalia KP. .
      View in: Publisher Site   Mentions:
    23. CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties. medRxiv. 2020 May 02. Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. PMID: 32511606; PMCID: PMC7276033.
      View in: PubMed   Mentions:
    24. Sa1851 LOW PREVALENCE OF NONALCOHOLIC FATTY LIVER DISEASE IN ADOLESCENTS WITH INFLAMMATORY BOWEL DISEASE. Gastroenterology. 2020 May 1; 158(6):s-451. Regner RE, Rudrapatna RV, Verstraete VS, Hameed HB, Mahadevan MU. .
      View in: Publisher Site   Mentions:
    25. 518 AN ELECTRONIC MEDICAL RECORDS-BASED INTERVENTION REDUCES UNNECESSARY ENDOSCOPIES FOR HEARTBURN AND DYSPEPSIA. Gastroenterology. 2020 May 1; 158(6):s-101. Ko KM, Rudrapatna RV, Mosenia MA, Radhakrishnan RK, Kathpalia KP. .
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    26. Accuracy of medical billing data against the electronic health record in the measurement of colorectal cancer screening rates. BMJ Open Qual. 2020 03; 9(1). Rudrapatna VA, Glicksberg BS, Avila P, Harding-Theobald E, Wang C, Butte AJ. PMID: 32209595; PMCID: PMC7103821.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansPHPublic Health
    27. Safety of Flexible Sigmoidoscopy in Pregnant Patients with Known or Suspected Inflammatory Bowel Disease. Dig Dis Sci. 2020 10; 65(10):2979-2985. Ko MS, Rudrapatna VA, Avila P, Mahadevan U. PMID: 32034603.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    28. Opportunities and challenges in using real-world data for health care. J Clin Invest. 2020 02 03; 130(2):565-574. Rudrapatna VA, Butte AJ. PMID: 32011317; PMCID: PMC6994109.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    29. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinformatics. 2019 11 01; 35(21):4515-4518. Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna VA, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ. PMID: 31214700; PMCID: PMC6821222.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    30. 302 Increasing Appropriate Referrals to Genetic Counseling at the Time of Endoscopy. The American Journal of Gastroenterology. 2019 Oct 1; 114(1):s177-s177. Feuille FC, Avila AP, Ko KM, Goldberg GD, Rudrapatna RV, Singh SA. .
      View in: Publisher Site   Mentions:
    31. 861 Mind the Gap: A Comparison of the Randomized Clinical Trial Efficacy and Real World Effectiveness of Tofacitinib for the Treatment of Inflammatory Bowel Disease. The American Journal of Gastroenterology. 2019 Oct 1; 114(1):s499-s500. Rudrapatna RV, Butte BA. .
      View in: Publisher Site   Mentions:
    32. Tu1650 – Accuracy of Electronic Health Record Billing Data in the Measurement of Colorectal Cancer Screening Rates. Gastroenterology. 2019 May 1; 156(6):s-1075-s-1076. Rudrapatna RV, Glicksberg GB, Avila AP, Harding-Theobald HE, Wang WC, Butte BA. .
      View in: Publisher Site   Mentions:
    33. 46 – Safety of Flexible Sigmoidoscopy in Pregnant Patients with Inflammatory Bowel Disease – a 10 Year Study. Gastroenterology. 2019 May 1; 156(6):s-18-s-19. Ko KM, Rudrapatna RV, Avila AP, Mahadevan MU. .
      View in: Publisher Site   Mentions:
    34. Biosimilars for the Treatment of Inflammatory Bowel Disease. Pract Gastroenterol. 2019 Apr; 43(4):84-91. Rudrapatna VA, Velayos F. PMID: 31435122; PMCID: PMC6703165.
      View in: PubMed   Mentions: 8  
    35. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. JAMIA Open. 2019 Apr; 2(1):10-14. Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. PMID: 31633087; PMCID: PMC6800657.
      View in: PubMed   Mentions: 6  
    36. Open data informatics and data repurposing for IBD. Nat Rev Gastroenterol Hepatol. 2018 12; 15(12):715-716. Rudrapatna VA, Butte AJ. PMID: 30061595; PMCID: PMC6687058.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    37. Incidence of and Predictors for Early Discontinuation of Biological Therapies in Veteran Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 08; 23(8):1434-1439. Feagins LA, Waljee A, Hou JK, Gu P, Kanjo S, Rudrapatna V, Cipher DJ, Govani S, Gaidos J. PMID: 28570429.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    38. Arterial Thromboses Heralding Cholangiocarcinoma. Am J Med. 2017 Aug; 130(8):e341-e342. Dunn T, Rudrapatna VA, Hesse S, Sargsyan Z. PMID: 28344146.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    39. Sa1885 Incidence of and Predictors for Early Discontinuation of Biologic Therapies in Veteran Patients with Inflammatory Bowel Disease. Gastroenterology. 2016 Apr 1; 150(4):s392. Feagins FL, Waljee WA, Hou HJ, Gu GP, Kanjo KS, Rudrapatna RV, Ellis EA, Govani GS, Gaidos GJ. .
      View in: Publisher Site   Mentions:
    40. A Jnk-Rho-Actin remodeling positive feedback network directs Src-driven invasion. Oncogene. 2014 May 22; 33(21):2801-6. Rudrapatna VA, Bangi E, Cagan RL. PMID: 23831567.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    41. Caspase signalling in the absence of apoptosis drives Jnk-dependent invasion. EMBO Rep. 2013 Feb; 14(2):172-7. Rudrapatna VA, Bangi E, Cagan RL. PMID: 23306653; PMCID: PMC3596137.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    42. Drosophila cancer models. Dev Dyn. 2012 Jan; 241(1):107-18. Rudrapatna VA, Cagan RL, Das TK. PMID: 22038952; PMCID: PMC3677821.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
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