I am a computer scientist who is passionate about doing research on biomedical informatics, natural language processing, and machine learning. In particular, I am interested in precision phenomics, open domain and clinical information extraction, and phenome-wide association studies. Before joining the Department of Biomedical Informatics at Vanderbilt University, I was involved in research projects in the Department of Biomedical Informatics and Medical Education at the University of Washington, the Institute for Creative Technologies at the University of Southern California, the Human Language Technology Research Institute at the University of Texas at Dallas, and the Faculty of Computer Science at the Alexandru Ioan Cuza University of Iasi, Romania.

2024

• Cost-effective and scalable clonal hematopoiesis assay provides insight into clonal dynamics
  Taralynn Mack, Caitlyn Vlasschaert, Kelly von Beck, Alexander J. Silver, J. Brett Heimlich, Hannah Poisner, Henry Robert Condon, Jessica Ulloa, Andrew L. Sochacki, Travis P. Spaulding, Ashwin Kishtagari, Cosmin A. Bejan, Yaomin Xu, Michael R. Savona, Angela Jones, Alexander Bick
  Journal of Molecular Diagnostics, 2024.
  [ paper ]
• Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis
  Pooja Middha, Rohit Thummalapalli, Michael J. Betti, Lydia Yao, Zoe Quandt, Karmugi Balaratnam, Cosmin A. Bejan, Eduardo Cardenas, Christina J. Falcon, David M. Faleck, Princess Margaret Lung Group, Matthew A. Gubens, Scott Huntsman, Douglas B. Johnson, Linda Kachuri, Khaleeq Khan, Min Li, Christine M. Lovly, Megan H. Murray, Devalben Patel, Kristin Werking, Yaomin Xu, Luna Jia Zhan, Justin M. Balko, Geoffrey Liu, Melinda C. Aldrich, Adam J. Schoenfeld, Elad Ziv
  Nature Communications, 2024.
  [ paper ]
• Interoperability of phenome-wide multimorbidity patterns: a comparative study of two large-scale EHR systems
  Nick Strayer, Tess J Vessels, Karmel W Choi, Siwei Zhang, Yajing Li, Brian Sharber, Ryan S Hsi, Cosmin A Bejan, Alexander G Bick, Justin M Balko, Douglas B Johnson, Lee E Wheless, Quinn S Wells, Ravi V Shah, Elizabeth J Phillips, Wesley H Self, Jill M Pulley, Consuelo H Wilkins, Qingxia Chen, Tina Hartert, Michael R Savona, Yu Shyr, Dan M Roden, Jordan W Smoller, Douglas M Ruderfer, Yaomin Xu
  medRxiv, 2024.
  [ preprint ]
• Evaluation of genetic associations with clinical phenotypes of kidney stone disease
  Ryan S Hsi, Siwei Zhang, Jefferson L Triozzi, Adriana M Hung, Yaomin Xu, Cosmin A Bejan
  medRxiv, 2024.
  [ preprint ]
• Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk
  Ashwin Kishtagari, M. A. Wasay Khan, Yajing Li, Caitlyn Vlasschaert, Naimisha Marneni, Alexander J. Silver, Kelly von Beck, Travis Spaulding, Shannon Stockton, Christina Snider, Andrew Sochacki, Dixon Dorand, Taralynn M. Mack, P. Brent Ferrell Jr, Yaomin Xu, Cosmin A. Bejan, Michael R. Savona, Alexander G. Bick
  Blood Cancer Journal, 2024.
  [ paper ]
• A Natural Language Processing Framework for the Retrospective Identification of Surgical Site Infections
  Parker T. Evans, Cosmin A. Bejan
  American Medical Informatics Association (AMIA) Informatics Summit, Boston, MA, March 2024.
  [ abstract ]
• DrugWAS X PheWAS: A pharmacoepidemiologic framework to investigate the effect of drug exposure during pregnancy on pediatric outcomes
  Cosmin A. Bejan, Leena Choi, Sarah Osmundson, S. Trent Rosenbloom, Elizabeth J. Phillips
  American Medical Informatics Association (AMIA) Informatics Summit, Boston, MA, March 2024.
  [ abstract ]

2023

• Scalable Incident Detection via Natural Language Processing and Probabilistic Language Models
  Colin G. Walsh, Drew Wilimitis, Qingxia Chen, Aileen Wright, Jhansi Kolli, Katelyn Robinson, Michael A. Ripperger, Kevin B. Johnson, David Carrell, Rishi J. Desai, Andrew Mosholder, Sai Dharmarajan, Sruthi Adimadhyam, Daniel Fabbri, Danijela Stojanovic, Michael E. Matheny, Cosmin A. Bejan
  medRxiv, 2023.
  [ preprint ]
• Cost-effective and scalable clonal hematopoiesis assay provides insight into clonal dynamics
  Taralynn Mack, Caitlyn Vlasschaert, Kelly von Beck, Alexander J. Silver, J. Brett Heimlich, Hannah Poisner, Henry Robert Condon, Jessica Ulloa, Andrew L Sochacki, Travis P Spaulding, Ashwin Kishtagari, Cosmin A. Bejan, Yaomin Xu, Michael R. Savona, Angela Jones, Alexander G Bick
  medRxiv, 2023.
  [ preprint ]
• Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis
  Pooja Middha, Rohit Thummalapalli, Michael J Betti, Lydia Yao, Zoe Quandt, Karmugi Balaratnam, Cosmin A Bejan, Eduardo Cardenas, Christina J Falcon, David M Faleck, Princess Margaret Lung Group, Matthew A Gubens, Scott Huntsman, Douglas B Johnson, Linda Kachuri, Khaleeq Khan, Min Li, Christine Lovly, Megan H Murray, Devalben Patel, Kristin Werking, Yaomin Xu, Luna Jia Zhan, Justin M Balko, Geoffrey Liu, Melinda C Aldrich, Adam J Schoenfeld, Elad Ziv
  medRxiv, 2023.
  [ preprint ]
• PheMIME: An Interactive Web App and Knowledge Base for Phenome-Wide, Multi-Institutional Multimorbidity Analysis
  Siwei Zhang, Nick Strayer, Tess Vessels, Karmel Choi, Geoffrey W Wang, Yajing Li, Cosmin Adrian Bejan, Ryan S Hsi, Alexander G Bick, Digna R. Velez Edwards, Michael R Savona, Elizabeth J Philips, Jill Pulley, Wesley H. Self, Wilkins Consuelo Hopkins, Dan M Roden, Jordan Smoller, Douglas M Ruderfer, Yaomin Xu
  medRxiv, 2023.
  [ preprint ]
• Global Trends of Monkeypox-Related Articles: A Bibliometric Analysis Over the Last Five Decades (1964 – July 14, 2022)
  Manar Ahmed Kamal, Ramadan Abdelmoez Farahat, Ahmed K. Awad, Shehroze Tabassum, Fatma Labieb, Cosmin A. Bejan, Jaffar A. Al-Tawfiq, Kuldeep Dhama, Ismail Dergaa
  Journal of Infection and Public Health, 2023.
  [ paper ]
• PI3K Inhibition Restores and Amplifies Response to Ruxolitinib in patients with Myelofibrosis
  Tamara K. Moyo, Ashwin Kishtagari, Matthew Villaume, Brandon McMahon, Sanjay R. Mohan, Tess Stopczynski, Sheau-Chiann Chen, Run Fan, Yuankai Huo, Hyeonsoo Moon, Yucheng Tang, Cosmin A. Bejan, Merrida Childress, Ingrid Anderson, Kyle Rawling, Rhea M. Simons, Ashley Moncrief, Rebekah Caza, Laura Dugger, Aunshka Collins, Channing V. Dudley, P. Brent Ferrell, Michael Byrne, Stephen A. Strickland, Gregory D. Ayers, Bennett A. Landman, Emily F. Mason, Ruben A. Mesa, Jeanne M. Palmer, Laura C. Michaelis, Michael R. Savona
  Clinical Cancer Research, 2023.
  [ paper ]
• Custom Phenotyping in a Deidentified Patient Database Accurately Identifies Large Cohorts of Metastatic Renal Cell Carcinoma Patients
  Joseph Vento, Cosmin A. Bejan
  American Medical Informatics Association (AMIA) 2023 Annual Symposium, New Orleans, LA, November, 2023.
  [ abstract ]
• Reproduction of HLA-A*32:01 and other genetic and ecological factors associated with Vancomycin Drug Reaction With Eosinophilia And Systemic Symptoms in An Electronic Health Record-Based Study
  Matthew Krantz, Jun Qian, Cosmin Bejan, Siwei Zhang, Yoamin Xu, Wei-Qi Wei, Brian Yoon, Jason Trubiano, Elizabeth Phillips
  Journal of Allergy and Clinical Immunology, 2023.
  [ abstract ]

2022

• Contraceptive exposure associates with urinary tract infection risk in a cohort of reproductive-age women: a case control study
  Claire Lo, Abin Abraham, Cosmin A. Bejan, Seth A. Reasoner, Mario Davidson, Loren Lipworth, David M. Aronoff
  The European Journal of Contraception and Reproductive Health Care, 2022.
  [ paper ]
• Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs
  Nick Strayer, Siwei Zhang, Lydia Yao, Tess Vessels, Cosmin A Bejan, Ryan S Hsi, Jana K Shirey-Rice, Justin M Balko, Douglas B Johnson, Elizabeth J Phillips, Alex Bick, Todd L Edwards, Digna R Velez Edwards, Jill M Pulley, Quinn S Wells, Michael R Savona, Nancy J Cox, Dan M Roden, Douglas M Ruderfer, Yaomin Xu
  Bioinformatics, 2022.
  [ paper ]
• Kidney stone prevalence based on self-report and Electronic Health Records: insight into the prevalence of active medical care for kidney stones
  Connor M. Forbes, Naren Nimmagadda, Nicholas L. Kavoussi, Yaomin Xu, Cosmin A. Bejan, Nicole L. Miller, Ryan S. Hsi
  Urology, 2022.
  [ paper ]
• Public perspectives of monkeypox in Twitter: A social media analysis using machine learning
  Ramadan Abdelmoez Farahat, Mohammed Abdelwahab Yassin, Jaffar A. Al-Tawfiq, Cosmin A. Bejan, Basel Abdelazeem
  New Microbes and New Infections, 2022.
  [ paper ]
• Improving Methods of Identifying Anaphylaxis for Medical Product Safety Surveillance Using Natural Language Processing and Machine Learning
  David S Carrell, Susan Gruber, James S Floyd, Maralyssa A Bann, Kara L Cushing-Haugen, Ron L Johnson, Vina Graham, David J Cronkite, Brian L Hazlehurst, Andrew H Felcher, Cosmin A Bejan, Adee Kennedy, Mayura Shinde, Sara Karami, Yong Ma, Danijela Stojanovic, Yueqin Zhao, Robert Ball, Jennifer Nelson
  American Journal of Epidemiology, 2022.
  [ paper ]
• Dense phenotyping from electronic health records enables machine learning-based prediction of preterm birth
  Abin Abraham, Brian Le, Idit Kosti, Peter Straub, Digna R. Velez-Edwards, Lea K. Davis, J. M. Newton, Louis J. Muglia, Antonis Rokas, Cosmin A. Bejan, Marina Sirota, John A. Capra
  BMC Medicine, 2022.
  [ paper ]
• Improving ascertainment of suicidal ideation and suicide attempt with natural language processing
  Cosmin A. Bejan, Michael Ripperger, Drew Wilimitis, Ryan Ahmed, JooEun Kang, Katelyn Robinson, Theodore J. Morley, Douglas M. Ruderfer, Colin G. Walsh
  Scientific Reports, 2022.
  [ paper ] [ press ]
• Machine Learning Models to Predict 24 Hour Urinary Abnormalities for Kidney Stone Disease
  Nicholas L Kavoussi, Chase Floyd, Abin Abraham, Wilson Sui, Cosmin Bejan, John A. Capra, Ryan Hsi
  Urology, 2022.
  [ paper ]
• Prediction of Future Health Care Utilization Through Note-extracted Psychosocial Factors
  David A. Dorr, Ana R. Quiñones, Taylor King, Melissa Y. Wei, Kellee White, Cosmin A. Bejan
  Medical Care, 2022.
  [ paper ]
• Kidney stone prevalence based on self-report and Electronic Health Records: insight into the prevalence of active medical care for kidney stones
  Connor M. Forbes, Naren Nimmaggadda, Nicholas L. Kavoussi, Yaomin Xu, Cosmin A. Bejan, Nicole L. Miller, Ryan S. Hsi
  medRxiv, 2022.
  [ preprint ]
• Peripheral blood monocyte abundance predicts outcomes in breast cancer patients
  Margaret L. Axelrod, Yu Wang, Yaomin Xu, Xiaopeng Sun, Cosmin A. Bejan, Paula I. Gonzalez-Ericsson, Sara Nunnery, Riley E. Bergman, Joshua Donaldson, Angel Guerrero-Zotano, Chiara Massa, Barbara Seliger, Melinda Sanders, Ingrid A. Mayer, Justin M. Balko
  Cancer Research Communications, 2022.
  [ paper ] [ press ] [ press ]
• Patient-specific comorbidities as prognostic variables for survival in myelofibrosis
  Andrew L. Sochacki*, Cosmin A. Bejan*, Shilin Zhao, Ameet Patel, Ashwin Kishtagari, Travis P. Spaulding, Alexander J. Silver, Shannon S. Stockton, Kelly Pugh, Rodney Dixon Dorand, Jr, Manasa Ram Bhatta, Nicholas Strayer, Siwei Zhang, Christina A. Snider, Thomas P Stricker, Aziz Nazha, Alexander G. Bick, Yaomin Xu, Michael R Savona
  Blood Advances, 2022.
  [ paper ] (*contributed equally)
• High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster
  Sakshi Jasra, Orsi Giricz, Rachel Zeig-Owens, Kith Pradhan, David G. Goldfarb, Angelica Barreto-Galvez, Alexander J. Silver, Jiahao Chen, Srabani Sahu, Shanisha Gordon-Mitchell, Gaurav S. Choudhary, Srinivas Aluri, Tushar D. Bhagat, Aditi Shastri, Cosmin A. Bejan, Shannon S. Stockton, Travis P. Spaulding, Victor Thiruthuvanathan, Hiroki Goto, Jeannine Gerhardt, Syed Hissam Haider, Arul Veerappan, Matthias Bartenstein, George Nwankwo, Ola Landgren, Michael D. Weiden, Jacqueline Lekostaj, Ryan Bender, Frederick Fletcher, Lee Greenberger, Benjamin L. Ebert, Ulrich Steidl, Britta Will, Anna Nolan, Advaitha Madireddy, Michael R. Savona, David J. Prezant, Amit Verma
  Nature Medicine, 2022.
  [ paper ] [ press ] [ press ] [ press ] [ press ]
• Improving ascertainment of suicidal ideation and suicide attempt with natural language processing
  Cosmin A Bejan, Michael Ripperger, Drew Wilimitis, Ryan Ahmed, JooEun Kang, Katelyn Robinson, Theodore J Morley, Douglas M Ruderfer, Colin G Walsh
  medRxiv, 2022.
  [ preprint ]
• Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs
  Nick Strayer, Siwei Zhang, Lydia Yao, Tess Vessels, Cosmin A Bejan, Ryan S Hsi, Jana K Shirey-Rice, Justin M Balko, Douglas B Johnson, Elizabeth J Philips, Alex Bick, Todd L Edwards, Digna R Velez Edwards, Jill M Pulley, Quinn S Wells, Michael R Savona, Nancy J Cox, Dan M Roden, Douglas M Ruderfer, Yaomin Xu
  medRxiv, 2022.
  [ preprint ]
• Vascular Alterations Impede Fragile Tolerance to Pregnancy in Type 1 Diabetes
  Kelsey L. McNew, Abin Abraham, Daniel E. Sack, Charles Duncan Smart, Yasminye D. Pettway, Alexander Falk, Rolanda L. Lister, Annika B. Faucon, Cosmin A. Bejan, John A. Capra, David M. Aronoff, Kelli L. Boyd, Daniel J. Moore
  F&S Science, 2022.
  [ paper ]
• Integrating Mosaic Chromosomal Alterations and Single-Nucleotide Variants to Predict Evolution of Clonal Hematopoiesis
  Ashwin Kishtagari, Wasay Khan, Yajing Li, Cosmin Bejan, Naimisha Marneni, Alexander J. Silver, Kelly von Beck, Travis Spaulding, Shannon Stockton, Christina A. Snider, Kelly Pugh, Andrew Sochacki, Dixon Dorand, Taralynn Mack, Caitlyn Vlasschaert, Brent Ferrell, Yaomin Xu, Michael R. Savona, Alexander G. Bick
  American Society of Hematology (ASH) Annual Meeting, New Orleans, LA, December 2022.
  [ abstract ]
• Radiation Therapy and Subsequent Clonal Hematopoiesis: An Analysis of a Biorepository of 89,782 Patients
  S.A. Crants, S.S. Olson, Y. Li, C.A. Bejan, A. Bick, L. Lu
  American Society for Radiation Oncology (ASTRO) Annual Meeting, San Antonio, TX, October 2022.
  [ abstract ]
• Mosaic chromosomal alterations increase risk of incident monoclonal gammopathy of undetermined significance and multiple myeloma
  Kelly von Beck, Taralynn Mack, Ashwin Kishtagari, Yajing Li, Cosmin Bejan, Muhamed Baljevic, Michael Savona, Alexander Bick
  Clinical Lymphoma Myeloma and Leukemia, August 2022.
  [ abstract ]
• Ascertaining and Phenotyping Suicidality at Scale Using Electronic Health Records
  Colin Walsh, Michael Ripperger, Drew Wilimitis, Ryan Ahmed, Jooeun Kang, Douglas Ruderfer, Theodore Morley, Cosmin Bejan
  Biological Psychiatry, May 2022.
  [ abstract ]
• Using Natural Language Processing to Identify Laterality of Nephrolithiasis Surgical Procedures
  Cosmin A. Bejan, Siwei Zhang, Yaomin Xu, Ryan S. Hsi
  American Medical Informatics Association (AMIA) Informatics Summit, Chicago, IL, March 2022.
  [ abstract ]
• Improving the Identification of Substance Use from Clinical Notes with BERT
  Stuart J. Waller, Cosmin A. Bejan
  American Medical Informatics Association (AMIA) Informatics Summit, Chicago, IL, March 2022.
  [ abstract ]

2021

• Peripheral Blood Monocyte Abundance Predicts Outcomes in Breast Cancer Patients
  Justin Balko, Margaret Axelrod, Yu Wang, Yaomin Xu, Xiaopeng Sun, Cosmin A. Bejan, Paula González-Ericsson, Sara Nunnery, Riley Berhman, Joshua Donaldson, Angel Guerrero-Zotano, Chiara Massa, Barbara Seliger, Melinda Sanders, Ingrid Mayer
  Research Square, 2021.
  [ preprint ]
• DrugWAS: Drug-wide association studies for COVID-19 drug repurposing
  Cosmin A. Bejan, Katherine N. Cahill, Patrick J. Staso, Leena Choi, Josh F. Peterson, Elizabeth J. Phillips
  Clinical Pharmacology & Therapeutics (CPT), 2021.
  [ paper ][ press ]
• Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features
  Abin Abraham, Nicholas Kavoussi, Wilson Sui, Cosmin A. Bejan, John A Capra, Ryan Hsi
  Journal of Endourology, 2021.
  [ paper ]
• Phenotyping coronavirus disease 2019 during a global health pandemic: lessons learned from the characterization of an early cohort
  Sarah DeLozier, Sarah Bland, Melissa McPheeters, Quinn Wells, Eric Farber-Eger, Cosmin A. Bejan, Daniel Fabbri, Trent Rosenbloom, Dan Roden, Kevin B. Johnson, Wei-Qi Wei, Josh Peterson, Lisa Bastarache
  Journal of Biomedical Informatics (JBI), 2021.
  [ paper ]
• Leveraging Machine Learning to Characterize the Role of Socio-economic Determinants on Physical Health and Well-being Among Veterans
  Christos Makridis, David Zhao, Cosmin A. Bejan, Gil Alterovitz
  Computers in Biology and Medicine, 2021.
  [ paper ] [ press ]
• DrugWAS: Leveraging drug-wide association studies to facilitate drug repurposing for COVID-19
  Cosmin A Bejan, Katherine N Cahill, Patrick J Staso, Leena Choi, Josh F Peterson, Elizabeth J Phillips
  medRxiv, 2021.
  [ preprint ] [ press ]
• Peripheral immunity predicts therapeutic outcomes in breast cancer patients
  Margaret L Axelrod, Yu Wang, Yaomin Xu, Cosmin A Bejan, Xiaopeng Sun, Paula I Gonzalez-Ericsson, Riley E Bergman, Joshua Donaldson, Sara Nunnery, Melinda Sanders, Chiara Massa, Barbara Seliger, Ingrid A Mayer, Justin M Balko
  San Antonio Breast Cancer Symposium (SABCS), San Antonio, TX, December 2021.
  [ abstract ]
• A genome-wide association study of nephrolithiasis identified from electronic health records
  Ryan Hsi, Siwei Zhang, Yaomin Xu, Cosmin A Bejan
  American Urological Association (AUA) Annual Meeting, Las Vegas, NV, September 2021.
  [ abstract ]
• Machine learning models to predict 24-hour urine abnormalities from electronic health record-derived features
  Nicholas Kavoussi, Abin Abraham, Wilson Sui, Cosmin Bejan, John Capra, Ryan Hsi
  American Urological Association (AUA) Annual Meeting, Las Vegas, NV, September 2021.
  [ abstract ]
• Improving Methods of Identifying Anaphylaxis for Medical Product Safety Surveillance Using Natural Language Processing and Machine Learning
  David S. Carrell, Susan Gruber, James S. Floyd, Maralyssa Bann, Kara Cushing-Haugen, Ron Johnson, Vina Graham, David Cronkite, Brian Hazlehurst, Andrew H. Felcher, Cosmin A. Bejan, Adee Kennedy, Mayura Shinde, Sara Karami, Yong Ma, Danijela Stojanovic, Yueqin Zhao, Robert Ball, Jennifer Nelson
  The 37th International Conference on Pharmacoepidemiology (ICPE), Virtual Meeting, August 2021.
  [ abstract ]

2020

• Building longitudinal medication dose data using medication information extracted from clinical notes in electronic health records
  Elizabeth McNeer, Cole Beck, Hannah L Weeks, Michael L Williams, Nathan T James, Cosmin A Bejan, Leena Choi
  Journal of the American Medical Informatics Association (JAMIA), 2020.
  [ paper ]
• Leveraging Machine Learning to Characterize the Role of Socio-economic Determinants of Physical Health and Well-being Among Veterans
  Christos Makridis, David Zhao, Cosmin A. Bejan, Gil Alterovitz
  SSRN, 2020.
  [ preprint ]
• Dense phenotyping from electronic health records enables machine-learning-based prediction of preterm birth
  Abin Abraham, Brian Le, Idit Kosti, Peter Straub, Digna R. Velez-Edwards, Lea K. Davis, Louis J. Muglia, Antonis Rokas, Cosmin A. Bejan, Marina Sirota, John A. Capra
  medRxiv, 2020.
  [ preprint ]
• Association of chronic kidney disease stage with 24-hour urine values among patients with nephrolithiasis
  Wilson Sui, Joshua Calvert, Nicholas Kavoussi, Edward R Gould, Nicole Miller, Cosmin Bejan, Ryan Hsi
  Journal of Endourology, 2020.
  [ paper ]
• Development of a System for Post‐marketing Population Pharmacokinetic and Pharmacodynamic Studies using Real‐World Data from Electronic Health Records
  Leena Choi, Cole Beck, Elizabeth McNeer, Hannah L. Weeks, Michael L. Williams, Nathan T. James, Xinnan Niu, Bassel W. Abou‐Khalil, Kelly A. Birdwell, Dan M. Roden, C. Michael Stein, Cosmin A. Bejan, Joshua C. Denny, Sara L. Van Driest
  Clinical Pharmacology & Therapeutics (CPT), 2020.
  [ paper ]
• medExtractR: A targeted, customizable approach to medication extraction from electronic health records
  Hannah L Weeks, Cole Beck, Elizabeth McNeer, Michael L Williams, Cosmin A Bejan, Joshua C Denny, Leena Choi
  Journal of the American Medical Informatics Association (JAMIA), 2020.
  [ paper ]
• Accurate and reproducible machine learning prediction of preterm birth from electronic health records linked to a genetic biobank
  A. Abraham, B. L. Le, I. Kosti, P. Straub, D. Velez-Edwards, L. K. Davis, C. Bejan, L. Muglia, M. Sirota, J. A. Capra
  American Society of Human Genetics (ASHG) 2020 Annual Meeting, Virtual Meeting, September 2020.
  [ abstract ]
• Improving Identification of Anaphylaxis
  James S. Floyd, David S. Carrell, Maralyssa A. Bann, Susan Gruber, Ron L. Johnson, Vina F. Graham, Cosmin A. Bejan, Yong Ma, Adee Kennedy, Mayura Shinde, Robert Ball, Jennifer C. Nelson
  The 36th International Conference on Pharmacoepidemiology (ICPE), Virtual Meeting, September 2020.
  [ abstract ]
• Feasibility and Validation of Large-Scale Data Acquisition from the Electronic Health Record to a Secure Research Database for Nephrolithiasis
  Wilson Sui, Joshua K Calvert, Nicholas L Kavoussi, Adam Lewis, Nicole L Miller, Cosmin A Bejan, Ryan S Hsi
  American Urological Association (AUA) Annual Virtual Meeting, May 2020.
  [ abstract ]
• Machine Learning Models to Predict Kidney Stone Composition and 24-hour Urine Abnormalities from Electronic Health Record-Derived Features
  Chi Le, Nicholas Kavoussi, Wilson Sui, Cosmin Bejan, Nicole Miller, Ryan Hsi
  American Urological Association (AUA) Annual Virtual Meeting, May 2020.
  [ abstract ]
• Urinary Citrate Wasting among Nephrolithiasis Patients Associates with Obesity and Diabetes Mellitus
  Wilson Sui, Joshua K Calvert, Nicholas L Kavoussi, John Asplin, Nicole L Miller, Cosmin A Bejan, Ryan S Hsi
  American Urological Association (AUA) Annual Virtual Meeting, May 2020.
  [ abstract ]

2019

• medExtractR: A medication extraction algorithm for electronic health records using the R programming language
  Hannah L Weeks, Cole Beck, Elizabeth McNeer, Cosmin A Bejan, Joshua C Denny, Leena Choi
  medRxiv, 2019.
  [ preprint ]
• Performance of a Natural Language Processing Method to Extract Stone Composition From the Electronic Health Record
  Cosmin A. Bejan, Daniel J. Lee, Yaomin Xu, Ryan S. Hsi
  Urology, 2019.
  [ paper ]
• HLA-A*32:01 is strongly associated with vancomycin-induced drug reaction with eosinophilia and systemic symptoms
  Katherine C Konvinse, Jason A Trubiano, Rebecca Pavlos, Ian James, Christian M Shaffer, Cosmin A Bejan, Ryan J Schutte, David A Ostrov, Mark A Pilkinton, Misha Rosenbach, Jeffrey P Zwerner, Kristina B Williams, Jack Bourke, Patricia Martinez, Francois Rwandamuriye, Abha Chopra, Mark Watson, Alec J Redwood, Katie D White, Simon A Mallal, Elizabeth J Phillips
  Journal of Allergy and Clinical Immunology (JACI), 2019.
  [ paper ] [ press ]
• JAK2^V617F Clonal Hematopoiesis Stratifies By Peripheral Blood Counts
  Andrew Sochacki, Shilin Zhao, Cosmin Adrian Bejan, Travis Spaulding, Shannon Stockton, Alexander Silver, Dixon Dorand, Siwei Zhang, Thomas Stricker, Yaomin Xu, Michael R. Savona
  American Society of Hematology (ASH) Annual Meeting, Orlando, FL, December 2019.
  [ abstract ]
• Patient Specific Comorbidities Impact Overall Survival in Myelofibrosis
  Andrew Sochacki, Cosmin Adrian Bejan, Shilin Zhao, Travis Spaulding, Shannon Stockton, Alexander Silver, Dixon Dorand, Siwei Zhang, Thomas Stricker, Yaomin Xu, Michael R. Savona
  American Society of Hematology (ASH) Annual Meeting, Orlando, FL, December 2019.
  [ abstract ]
• medExtractR: A medication extraction algorithm for electronic health records using the R programming language
  Hannah Weeks, Cole Beck, Elizabeth McNeer, Cosmin A. Bejan, Joshua C. Denny, Leena Choi
  American Medical Informatics Association (AMIA) Annual Symposium, Washington DC, November 2019.
  [ abstract ]
• Evaluation of non-linear comorbidity structure and genetic risk for classification of preterm birth from electronic health records
  Abin Abraham, Cosmin A. Bejan, Digna R. Velez-Edwards, John Capra
  American Society of Human Genetics (ASHG) 2019 Annual Meeting, Houston, TX, October, 2019.
  [ abstract ]
• Identifying Patients with Significant Problems Related to Social Determinants of Health with Natural Language Processing
  David Dorr, Cosmin A. Bejan, Christie Pizzimenti, Sumeet Singh, Matt Storer, Ana Quinones
  The 17th World Congress of Medical and Health Informatics (MedInfo), Lyon, France, August 2019.
  [ abstract ]
• A Natural Language Processing Algorithm for Medication Extraction from Electronic Health Records Using the R Programming Language: MedExtractR
  Hannah L Weeks, Cole Beck, Elizabeth McNeer, Joshua C Denny, Cosmin A Bejan, Leena Choi
  The 2019 Joint Statistical Meetings (JSM), Denver, CO, July 2019.
  [ abstract ]
• Resolving the Preterm Birth Phenotype Using Electronic Health Records and Genomic Biobanks
  Abin Abraham, Cosmin A. Bejan, Digna Edwards, John Capra
  The 67th Annual Clinical and Scientific Meeting of the American College of Obstetricians and Gynecologists (ACOG), Nashville, TN, May 2019.
  [ abstract ]
• Validation of a Natural Language Processing Method for Phenotyping Kidney Stone Composition from Large-Scale Electronic Health Records
  Ryan S. Hsi, Daniel J. Lee, Yaomin Xu, Cosmin A. Bejan
  American Urological Association (AUA) Annual Meeting, Chicago, IL, May 2019.
  [ abstract ]
• A Text Mining Approach for Obstetric History Identification in Electronic Health Records
  Cosmin A. Bejan, Joshua C. Denny
  American Medical Informatics Association (AMIA) Informatics Summit, San Francisco, CA, March 2019.
  [ abstract ]
• Using Clinical Notes to Assess the Exposure of Tobacco and Alcohol Use in the Electronic Health Record
  Jessica Chen, Abel Ermias, Cosmin A. Bejan
  American Medical Informatics Association (AMIA) Informatics Summit, San Francisco, CA, March 2019.
  [ abstract ]
• Validation of a Natural Language Processing System to Identify Peripheral Artery Disease Cases from Clinical Narratives in 3 eMERGE sites
  Sungrim Moon, Uriel Sanchez Rangel, Naveed Afzal, Cosmin A. Bejan, Ning Shang, Sungwhan Sohn, Joshua C. Denny, George Hripcsak, Iftikhar J. Kullo, Hongfang Liu, Adelaide M. Arruda-Olson
  American Medical Informatics Association (AMIA) Informatics Summit, San Francisco, CA, March 2019.
  [ abstract ]
• Medication Data Extraction Algorithms: A Foundation for Post-Marketing Population Pharmacokinetic and Pharmacodynamic Studies Using Electronic Health Records
  L Choi, HL Weeks, C Beck, CA Bejan, X Niu, RJ Carroll, SL Van Driest, KA Birdwell, CM Stein, JC Denny
  American Society for Clinical Pharmacology & Therapeutics (ASCPT) Annual Meeting, Washington DC, March 2019.
  [ abstract ]

2018

• Next Generation Myelofibrosis Risk Analysis in the Electronic Health Record
  Andrew Sochacki*, Cosmin Adrian Bejan*, Shilin Zhao, Travis Spaulding, Thomas Stricker, Yaomin Xu, Michael R. Savona
  American Society of Hematology (ASH) Annual Meeting, San Diego, CA, December, 2018.
  [ abstract ] (*contributed equally)
• Leveraging electronic health records to map the genetic and phenotypic complexity of preterm birth
  Abin Abraham, Cosmin Bejan, John Capra
  American Society of Human Genetics (ASHG) 2018 Annual Meeting, San Diego, CA, October, 2018.
  [ abstract ]
• Large-scale text mining of kidney stone composition from electronic health records
  Ryan S. Hsi, Daniel J. Lee, Cosmin A. Bejan
  36th World Congress of Endourology (WCE), Paris, France, September, 2018.
  [ abstract ]
• Mining kidney stone composition from millions of clinical notes within the electronic health record
  Ryan S. Hsi, Daniel J. Lee, Cosmin A. Bejan
  American Urological Association (AUA) Annual Meeting, San Francisco, CA, May, 2018.
  [ abstract ]
• Identification of myelofibrosis from electronic health records with novel algorithms and JAKextractor
  Cosmin A. Bejan*, Andrew Sochacki*, Shilin Zhao, Yaomin Xu, Michael Savona
  American Association for Cancer Research (AACR) Annual Meeting, Chicago, IL, April, 2018.
  [ abstract ] (*contributed equally)
• Phenome-Wide Associations of Homelessness in Electronic Health Records
  Jared M. Hendrickson, Joshua C. Denny, Cosmin A. Bejan
  American Medical Informatics Association (AMIA) Informatics Summit, San Francisco, CA, March, 2018.
  [ abstract ]

2017

• Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records
  Cosmin A. Bejan, John Angiolillo, Douglas Conway, Robertson Nash, Jana K. Shirey-Rice, Loren Lipworth, Robert M. Cronin, Jill Pulley, Sunil Kripalani, Shari Barkin, Kevin B. Johnson, Joshua C. Denny
  Journal of the American Medical Informatics Association (JAMIA), 2017.
  [ paper ]
• Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences
  Cosmin A. Bejan, John Angiolillo, Douglas Conway, Robertson Nash, Jana K. Shirey-Rice, Loren Lipworth, Robert M. Cronin, Jill Pulley, Sunil Kripalani, Shari Barkin, Kevin B. Johnson, Joshua C. Denny
  American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2017.
  [ podium abstract ]
• A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects
  Cosmin A. Bejan, Joshua C. Denny
  American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2017.
  [ abstract ]
• Development of Specific Electronic Phenotypes for Severe Cutaneous Adverse Drug Reactions Facilitates Genetic Discovery
  Sarah Garon, Lincoln Shade, Michael I Derrick, Cosmin A. Bejan, Elizabeth J. Phillips
  Journal of Allergy and Clinical Immunology, 2017.
  [ abstract ]

2015

• Desiderata for computable representations of electronic health records-driven phenotype algorithms
  Huan Mo, William K Thompson, Luke V Rasmussen, Jennifer A Pacheco, Guoqian Jiang, Richard Kiefer, Qian Zhu, Jie Xu, Enid Montague, David S Carrell, Todd Lingren, Frank D Mentch, Yizhao Ni, Firas H Wehbe, Peggy L Peissig, Gerard Tromp, Eric B Larson, Christopher G Chute, Jyotishman Pathak, Joshua C Denny, Peter Speltz, Abel N Kho, Gail P Jarvik, Cosmin A Bejan, Marc S Williams, Kenneth Borthwick, Terrie E Kitchner, Dan M Roden, Paul A Harris
  Journal of the American Medical Informatics Association (JAMIA), 2015.
  [ paper ]
• Building bridges across electronic health record systems through inferred phenotypic topics
  You Chen, Joydeep Ghosh, Cosmin Adrian Bejan, Carl A. Gunter, Siddharth Gupta, Abel Kho, David Liebovitz, Jimeng Sun, Joshua Denny, Bradley Malin
  Journal of Biomedical Informatics (JBI), 2015.
  [ paper ]
• Mining phenotypic keywords from a large collection of clinical narratives
  Cosmin Adrian Bejan, Robertson Nash, Douglas Conway, Erica A. Bowton, Kevin B. Johnson, Joshua C. Denny
  AMIA Summit on Clinical Research Informatics (AMIA-CRI), San Francisco, CA, USA, March 2015.
  [ podium abstract ]

2014

• Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
  Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text [ PMID: 25336593 ]
  Journal of the American Medical Informatics Association (JAMIA), 2014.
• Cosmin Adrian Bejan, Joshua C. Denny
  Learning to Identify Treatment Relations in Clinical Text [ pdf ]
  American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2014.
• Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
  Using SemRep and a medication indication resource to extract treatment relations from clinical notes [ pdf ] (Podium Abstract)
  AMIA Summit on Translational Bioinformatics (AMIA-TBI), San Francisco, CA, USA, April 2014.
• Cosmin Adrian Bejan, Sanda Harabagiu
  Unsupervised Event Coreference Resolution [ pdf | data ]
  Computational Linguistics, 2014.

2013

• Cosmin Adrian Bejan, Lucy Vanderwende, Heather L. Evans, Mark M. Wurfel, Meliha Yetisgen-Yildiz
  On-time clinical phenotype prediction based on narrative reports [ PMID: 24551325 ]
  American Medical Informatics Association Fall Symposium (AMIA) , Washington DC, November, 2013.
  Distinguished Paper Award
• Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Mark M. Wurfel
  Identification of Patients with Acute Lung Injury from Free-Text Chest X-ray Reports [ pdf ]
  ACL workshop on Biomedical Natural Language Processing (BioNLP), Sofia, Bulgaria, August 2013.
• Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Heather L. Evans, Mark M. Wurfel
  Automated Tools for Phenotype Extraction from Medical Records (Abstract) [ PMID: 24303281 ]
  AMIA Summit on Clinical Research Informatics (AMIA-CRI), San Francisco, CA, USA, March 2013.
• Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Meliha Yetisgen-Yildiz
  Assertion modeling and its role in clinical phenotype identification [ code | PMID: 23000479 ]
  Journal of Biomedical Informatics (JBI), 2013.

2012

• Cosmin Adrian Bejan, Lucy Vanderwende, Mark M. Wurfel, Meliha Yetisgen-Yildiz
  Assessing Pneumonia Identification from Time-Ordered Narrative Reports [ PMID: 23304388 ]
  American Medical Informatics Association Fall Symposium (AMIA) , Chicago, IL, USA, November 2012.
• Cosmin Adrian Bejan, Lucy Vanderwende, Mark M Wurfel, Meliha Yetisgen-Yildiz
  Assessing Pneumonia Identification from Time-Ordered Narrative Reports (Poster)
  Pacific Northwest Regional NLP Workshop (NW-NLP), Microsoft Research, Redmond, WA, USA, May 2012.
• Cosmin Adrian Bejan, Fei Xia, Lucy Vanderwende, Mark M Wurfel, Meliha Yetisgen-Yildiz
  Pneumonia identification using statistical feature selection [ PMID: 22539080 ]
  Journal of the American Medical Informatics Association (JAMIA), 2012.
• Heather Evans, Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Keir Warner, Robert Black, Ronald Maier, Mark M. Wurfel
  Chest X-ray Report Language is Incongruous with Quantitative Culture Results in Ventilator-Associated Pneumonia (Abstract)
  Annual Meeting of the Surgical Infection Society (SIS), Dallas, TX, USA, April 2012.

2011

• Andrew S. Gordon, Cosmin Adrian Bejan, Kenji Sagae
  Commonsense Causal Reasoning Using Millions of Personal Stories [ pdf ]
  AAAI Conference on Artificial Intelligence (AAAI), San Francisco, CA, USA, August 2011.
• Melissa Roemmele, Cosmin Adrian Bejan, Andrew S. Gordon
  Choice of Plausible Alternatives: An Evaluation of Commonsense Causal Reasoning [ pdf ]
  AAAI Spring Symposium on Logical Formalizations of Commonsense Reasoning (Commonsense), Stanford University, Palo Alto, CA, USA, March 2011.
• Kirk Roberts, Cosmin Adrian Bejan, Sanda Harabagiu
  Using Event Semantics for Toponym Disambiguation
  Applied Natural Language Processing: Identification, Investigation and Resolution, Philip M. McCarthy and Chutima Boonthum-Denecke (Eds.), IGI Global, 2011.
• Bryan Rink, Cosmin Adrian Bejan, Sanda Harabagiu
  The Role of Textual Graph Patterns in Discovering Event Causality
  Applied Natural Language Processing: Identification, Investigation and Resolution, Philip M. McCarthy and Chutima Boonthum-Denecke (Eds.), IGI Global, 2011.

2010

• Cosmin Adrian Bejan, Sanda Harabagiu
  Unsupervised Event Coreference Resolution with Rich Linguistic Features [ pdf | data ]
  Annual Meeting of the Association for Computational Linguistics (ACL), Uppsala, Sweden, July 2010.
• Kirk Roberts, Srikanth Gullapalli, Cosmin Adrian Bejan, Sanda Harabagiu
  A Linguistic Resource for Semantic Parsing of Motion Events [ pdf ]
  International Conference on Language Resources and Evaluation (LREC), Valletta, Malta, May 2010.
• Bryan Rink, Cosmin Adrian Bejan, Sanda Harabagiu
  Learning Textual Graph Patterns to Detect Causal Event Relations [ pdf ]
  Florida Artificial Intelligence Research Society International Conference (FLAIRS), Daytona Beach, FL, USA, May 2010.
  Best Paper in Track Award
• Kirk Roberts, Cosmin Adrian Bejan, Sanda Harabagiu
  Toponym Disambiguation Using Events [ pdf ]
  Florida Artificial Intelligence Research Society International Conference (FLAIRS), Daytona Beach, FL, USA, May 2010.
• Sanda Harabagiu, Cosmin Adrian Bejan
  A Knowledge Extraction Framework for Biomedical Pathways [ pdf | PMID: 21347132 ]
  AMIA Summit on Translational Bioinformatics (AMIA-STB), San Francisco, CA, USA, March 2010.

2009

• Cosmin Adrian Bejan
  Learning Event Structures from Text [ pdf ]
  PhD Dissertation, The University of Texas at Dallas, December 2009.
• Cosmin Adrian Bejan, Matthew Titsworth, Andy Hickl, Sanda Harabagiu
  Nonparametric Bayesian Models for Unsupervised Event Coreference Resolution [ pdf | data ]
  Advances in Neural Information Processing Systems 23 (NIPS), Vancouver, Canada, December 2009.

2008

• Cosmin Adrian Bejan, Sanda Harabagiu
  Using Clustering Methods for Discovering Event Structures (Abstract) [ pdf ]
  AAAI Conference on Artificial Intelligence (AAAI), Chicago, IL, USA, July 2008.
• Cosmin Adrian Bejan, Sanda Harabagiu
  A Linguistic Resource for Discovering Event Structures and Resolving Event Coreference [ pdf ]
  International Conference on Language Resources and Evaluation (LREC), Marrakech, Morocco, 2008.
• Cosmin Adrian Bejan
  Unsupervised Discovery of Event Scenarios from Texts [ pdf ]
  Florida Artificial Intelligence Research Society International Conference (FLAIRS), Coconut Grove, FL, USA, May 2008.
  Best Paper in Track Award
  Best Student Paper Award

2007

• Cosmin Adrian Bejan, Chris Hathaway
  UTD-SRL: A Pipeline Architecture for Extracting Frame Semantic Structures [ pdf ]
  ACL workshop on on Semantic Evaluations (SemEval ), Prague, Czech Republic, June 2007.
• Cosmin Adrian Bejan
  Deriving Chronological Information from Texts through a Graph-based Algorithm (Poster) [ pdf ]
  Florida Artificial Intelligence Research Society International Conference (FLAIRS), Key West, FL, USA, May 2007.

2006

• Sanda Harabagiu, Cosmin Adrian Bejan
  An Answer Bank for Temporal Inference [ pdf ]
  International Conference on Language Resources and Evaluation (LREC), Genoa, Italy, 2006.

2005

• Sanda Harabagiu, Cosmin Adrian Bejan, Paul Morarescu
  Shallow Semantics for Relation Extraction [ pdf ]
  International Joint Conference on Artificial Intelligence (IJCAI), Edinburgh, Scotland, 2005.
• Sanda Harabagiu, Cosmin Adrian Bejan
  Question Answering Based on Temporal Inference [ pdf ]
  AAAI Workshop on Inference for Textual Question Answering, Pittsburgh, PA, USA, 2005.

2004

• Cosmin Adrian Bejan, Alessandro Moschitti, Paul Morarescu, Gabriel Nicolae, Sanda Harabagiu
  Semantic Parsing Based on FrameNet [ pdf ]
  ACL workshop on the Evaluation of Systems for the Semantic Analysis of Text (SENSEVAL3), Barcelona, Spain, 2004.
  Best System of the Automatic Labeling of Semantic Roles Challenge
• Alessandro Moschitti, Cosmin Adrian Bejan
  A Semantic Kernel for Predicate Argument Classification [ pdf ]
  Conference on Computational Natural Language Learning (CoNLL), Boston, MA, USA, 2004.
• Sanda Harabagiu, Steven Maiorano, Alessandro Moschitti, Cosmin Adrian Bejan
  Intentions, Implicatures and Processing of Complex Questions [ pdf ]
  HLT-NAACL Workshop on Pragmatics of Question Answering, Boston, MA, USA, 2004.