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Brett Beaulieu-Jones

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Computational Biomedicine and Biomedical Data Science
AddressChicago IL 60637
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    R00NS114850     (BEAULIEU-JONES, BRETT K)Jun 15, 2023 - May 31, 2026
    NIH
    Characterizing Population Differences between Clinical Trial and Real World Populations
    Role: Principal Investigator
    K99NS114850     (BEAULIEU-JONES, BRETT K)Feb 15, 2021 - Jan 31, 2023
    NIH
    Characterizing Population Differences between Clinical Trial and Real World Populations
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Fitzsimmons L, Undiagnosed Diseases Network, Beaulieu-Jones B, Kobren SN. Phenotypic overlap between rare disease patients and variant carriers in a large population cohort informs biological mechanisms. medRxiv. 2024 Apr 19. PMID: 38699301; PMCID: PMC11064998.
      Citations:    
    2. Beaulieu-Jones BK, Frau F, Bozzi S, Chandross KJ, Peterschmitt MJ, Cohen C, Coulovrat C, Kumar D, Kruger MJ, Lipnick SL, Fitzsimmons L, Kohane IS, Scherzer CR. Disease progression strikingly differs in research and real-world Parkinson's populations. NPJ Parkinsons Dis. 2024 Mar 13; 10(1):58. PMID: 38480700; PMCID: PMC10937726.
      Citations: 1     
    3. Liang WS, Beaulieu-Jones B, Smalley S, Snyder M, Goetz LH, Schork NJ. Emerging therapeutic drug monitoring technologies: considerations and opportunities in precision medicine. Front Pharmacol. 2024; 15:1348112. PMID: 38545548; PMCID: PMC10965556.
      Citations: 3     
    4. Beaulieu-Jones BK, Frau F, Bozzi S, Chandross KJ, Peterschmitt MJ, Cohen C, Coulovrat C, Kumar D, Kruger MJ, Lipnick SL, Fitzsimmons L, Kohane IS, Scherzer CR. Disease progression strikingly differs in research and real-world Parkinson's populations. medRxiv. 2024 Feb 18. PMID: 38405736; PMCID: PMC10889035.
      Citations:    
    5. Beaulieu-Jones BK, Villamar MF, Scordis P, Bartmann AP, Ali W, Wissel BD, Alsentzer E, de Jong J, Patra A, Kohane I. Predicting seizure recurrence after an initial seizure-like episode from routine clinical notes using large language models: a retrospective cohort study. Lancet Digit Health. 2023 12; 5(12):e882-e894. PMID: 38000873; PMCID: PMC10695164.
      Citations: 1     Fields:    Translation:Humans
    6. Alsentzer E, Rasmussen MJ, Fontoura R, Cull AL, Beaulieu-Jones B, Gray KJ, Bates DW, Kovacheva VP. Zero-shot interpretable phenotyping of postpartum hemorrhage using large language models. NPJ Digit Med. 2023 Nov 30; 6(1):212. PMID: 38036723; PMCID: PMC10689487.
      Citations: 11     
    7. Alsentzer E, Rasmussen MJ, Fontoura R, Cull AL, Beaulieu-Jones B, Gray KJ, Bates DW, Kovacheva VP. Zero-shot Interpretable Phenotyping of Postpartum Hemorrhage Using Large Language Models. medRxiv. 2023 Jun 01. PMID: 37398230; PMCID: PMC10312824.
      Citations:    
    8. Hou J, Zhao R, Gronsbell J, Lin Y, Bonzel CL, Zeng Q, Zhang S, Beaulieu-Jones BK, Weber GM, Jemielita T, Wan SS, Hong C, Cai T, Wen J, Ayakulangara Panickan V, Liaw KL, Liao K, Cai T. Generate Analysis-Ready Data for Real-world Evidence: Tutorial for Harnessing Electronic Health Records With Advanced Informatic Technologies. J Med Internet Res. 2023 05 25; 25:e45662. PMID: 37227772; PMCID: PMC10251230.
      Citations: 3     Fields:    Translation:Humans
    9. Sieberts SK, Borzymowski H, Guan Y, Huang Y, Matzner A, Page A, Bar-Gad I, Beaulieu-Jones B, El-Hanani Y, Goschenhofer J, Javidnia M, Keller MS, Li YC, Saqib M, Smith G, Stanescu A, Venuto CS, Zielinski R, BEAT-PD DREAM Challenge Consortium, Jayaraman A, Evers LJW, Foschini L, Mariakakis A, Pandey G, Shawen N, Synder P, Omberg L. Developing better digital health measures of Parkinson's disease using free living data and a crowdsourced data analysis challenge. PLOS Digit Health. 2023 Mar; 2(3):e0000208. PMID: 36976789; PMCID: PMC10047543.
      Citations: 2     
    10. Vaid A, Argulian E, Lerakis S, Beaulieu-Jones BK, Krittanawong C, Klang E, Lampert J, Reddy VY, Narula J, Nadkarni GN, Glicksberg BS. Multi-center retrospective cohort study applying deep learning to electrocardiograms to identify left heart valvular dysfunction. Commun Med (Lond). 2023 Feb 14; 3(1):24. PMID: 36788316; PMCID: PMC9929085.
      Citations: 7     
    11. Villamar MF, Sarkis RA, Pennell P, Kohane I, Beaulieu-Jones BK. Severity of Epilepsy and Response to Antiseizure Medications in Individuals With Multiple Sclerosis: Analysis of a Real-World Dataset. Neurol Clin Pract. 2022 Aug; 12(4):e49-e57. PMID: 36382117; PMCID: PMC9647818.
      Citations: 1     
    12. Hong C, Zhang HG, L'Yi S, Weber G, Avillach P, Tan BWQ, Bonzel CL, Palmer NP, Malovini A, Tibollo V, Luo Y, Hutch MR, Liu M, Bourgeois F, Bellazzi R, Chiovato L, Sanz Vidorreta FJ, Le TT, Wang X, Yuan W, Benoit V, Moal B, Morris M, Hanauer DA, Maidlow S, Wagholikar K, Murphy S, Estiri H, Klann J, Follett RW, Gehlenborg N, Omenn GS, Xia Z, Dagliati A, Visweswaran S, Patel LP, Mowery DL, Schriver ER, Samayamuthu MJ, Kavuluru R, Tan ALM, Tan BWL, Ngiam KY, Holmes JH, Schubert P, Cho K, Ho YL, Beaulieu-Jones BK, Serrano-Balazote P, Kohane I, Consortium for Clinical Characterization of COVID-19 by EHR (4CE), South A, Brat GA, Cai T, Gutiérrez-Sacristán A, Neuraz A, Makoudjou A, Tippmann P, Lozano-Zahonero S, Zöller D, Pedrera-Jiménez M, García-Barrio N. Changes in laboratory value improvement and mortality rates over the course of the pandemic: an international retrospective cohort study of hospitalised patients infected with SARS-CoV-2. BMJ Open. 2022 06 23; 12(6):e057725. PMID: 35738646; PMCID: PMC9226470.
      Citations: 5     Fields:    Translation:HumansCellsPHPublic Health
    13. Weber GM, Hong C, Xia Z, Palmer NP, Avillach P, L'Yi S, Keller MS, Murphy SN, Bonzel CL, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Benoit V, Bourgeois FT, Chiovato L, Cho K, Dagliati A, DuVall SL, Hanauer DA, Ho YL, Holmes JH, Issitt RW, Liu M, Luo Y, Lynch KE, Maidlow SE, Malovini A, Mandl KD, Mao C, Matheny ME, Moore JH, Morris JS, Morris M, Mowery DL, Ngiam KY, Patel LP, Pedrera-Jimenez M, Ramoni RB, Schriver ER, Schubert P, Balazote PS, Spiridou A, Tan ALM, Tan BWL, Tibollo V, Torti C, Trecarichi EM, Wang X, Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Kohane IS, Cai T, Brat GA, Gutiérrez-Sacristán A, Serret-Larmande A, Neuraz A, Barrio NG. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality. NPJ Digit Med. 2022 Jun 13; 5(1):74. PMID: 35697747; PMCID: PMC9192605.
      Citations: 4     
    14. Hou J, Zhao R, Cai T, Beaulieu-Jones B, Seyok T, Dahal K, Yuan Q, Xiong X, Bonzel CL, Fox C, Christiani DC, Jemielita T, Liao KP, Liaw KL, Cai T. Temporal Trends in Clinical Evidence of 5-Year Survival Within Electronic Health Records Among Patients With Early-Stage Colon Cancer Managed With Laparoscopy-Assisted Colectomy vs Open Colectomy. JAMA Netw Open. 2022 06 01; 5(6):e2218371. PMID: 35737384; PMCID: PMC9227003.
      Citations: 3     Fields:    Translation:Humans
    15. Schork NJ, Beaulieu-Jones B, Liang W, Smalley S, Goetz LH. Does Modulation of an Epigenetic Clock Define a Geroprotector? Adv Geriatr Med Res. 2022; 4(1). PMID: 35466328; PMCID: PMC9022671.
      Citations: 6     
    16. Bush WS, Wheeler N, Darabos C, Beaulieu-Jones B. Packaging Biocomputing Software to Maximize Distribution and Reuse. Pac Symp Biocomput. 2022; 27:412-416. PMID: 34890169.
      Citations:    Fields:    Translation:Humans
    17. Marwaha JS, Beaulieu-Jones B, Yuan W, Brat GA. Comment on: Truth and truthiness: evidence, experience and clinical judgement in surgery. Br J Surg. 2021 12 01; 108(12):e417. PMID: 34529769; PMCID: PMC8648077.
      Citations: 1     Fields:    Translation:Humans
    18. Le TT, Son J, Hong C, South AM, Beaulieu-Jones BK, Loh NHW, Luo Y, Morris M, Ngiam KY, Patel LP, Samayamuthu MJ, Schriver E, Tan ALM, Moore J, Cai T, Omenn GS, Avillach P, Kohane IS, Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Visweswaran S, Mowery DL, Xia Z, Gutiérrez-Sacristán A. Multinational characterization of neurological phenotypes in patients hospitalized with COVID-19. Sci Rep. 2021 10 12; 11(1):20238. PMID: 34642371; PMCID: PMC8510999.
      Citations: 9     Fields:    Translation:HumansPHPublic Health
    19. Klann JG, Estiri H, Weber GM, Moal B, Avillach P, Hong C, Tan ALM, Beaulieu-Jones BK, Castro V, Maulhardt T, Geva A, Malovini A, South AM, Visweswaran S, Morris M, Samayamuthu MJ, Omenn GS, Ngiam KY, Mandl KD, Boeker M, Olson KL, Mowery DL, Follett RW, Hanauer DA, Bellazzi R, Moore JH, Loh NW, Bell DS, Wagholikar KB, Chiovato L, Tibollo V, Rieg S, Li ALLJ, Jouhet V, Schriver E, Xia Z, Hutch M, Luo Y, Kohane IS, Consortium for Clinical Characterization of COVID-19 by EHR (4CE) (CONSORTIA AUTHOR), Brat GA, Murphy SN. Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data. J Am Med Inform Assoc. 2021 07 14; 28(7):1411-1420. PMID: 33566082; PMCID: PMC7928835.
      Citations: 25     Fields:    Translation:Humans
    20. Huang Y, Yuan W, Kohane IS, Beaulieu-Jones BK. Illustrating potential effects of alternate control populations on real-world evidence-based statistical analyses. JAMIA Open. 2021 Apr; 4(2):ooab045. PMID: 34142018; PMCID: PMC8206406.
      Citations: 2     
    21. Yuan W, Beaulieu-Jones B, Krolewski R, Palmer N, Veyrat-Follet C, Cohen C, Bozzi S, Cogswell M, Kumar D, Coulouvrat C, Leroy B, Fischer TZ, Sardi SP, Chandross KJ, Rubin LL, Wills AM, Kohane I, Lipnick SL, Frau F. Accelerating diagnosis of Parkinson's disease through risk prediction. BMC Neurol. 2021 May 18; 21(1):201. PMID: 34006233; PMCID: PMC8130278.
      Citations: 9     Fields:    Translation:Humans
    22. Beaulieu-Jones BK, Yuan W, Brat GA, Beam AL, Weber G, Ruffin M, Kohane IS. Machine learning for patient risk stratification: standing on, or looking over, the shoulders of clinicians? NPJ Digit Med. 2021 Mar 30; 4(1):62. PMID: 33785839; PMCID: PMC8010071.
      Citations: 47     
    23. Kohane IS, Aronow BJ, Avillach P, Beaulieu-Jones BK, Bellazzi R, Bradford RL, Brat GA, Cannataro M, Cimino JJ, Gehlenborg N, Ghassemi M, Hanauer DA, Holmes JH, Hong C, Klann JG, Loh NHW, Luo Y, Mandl KD, Daniar M, Moore JH, Murphy SN, Ngiam KY, Omenn GS, Palmer N, Patel LP, Sliz P, South AM, Tan ALM, Taylor DM, Taylor BW, Torti C, Vallejos AK, Wagholikar KB, Consortium For Clinical Characterization Of COVID-19 By EHR (4CE), Weber GM, Cai T, García-Barrio N, Gutiérrez-Sacristán A, Neuraz A, Pedrera-Jiménez M. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask. J Med Internet Res. 2021 03 02; 23(3):e22219. PMID: 33600347; PMCID: PMC7927948.
      Citations: 41     Fields:    Translation:HumansCells
    24. Yuan W, Beaulieu-Jones BK, Yu KH, Lipnick SL, Palmer N, Loscalzo J, Cai T, Kohane IS. Temporal bias in case-control design: preventing reliable predictions of the future. Nat Commun. 2021 02 17; 12(1):1107. PMID: 33597541; PMCID: PMC7889612.
      Citations: 19     Fields:    Translation:Humans
    25. Weber GM, Hong C, Palmer NP, Avillach P, Murphy SN, Xia Z, Neuraz A, Omenn GS, Visweswaran S, Klann JG, South AM, Loh NHW, Cannataro M, Beaulieu-Jones BK, Bellazzi R, Agapito G, Alessiani M, Aronow BJ, Bell DS, Bellasi A, Benoit V, Beraghi M, Boeker M, Booth J, Bosari S, Bourgeois FT, Brown NW, Bucalo M, Chiovato L, Chiudinelli L, Dagliati A, Devkota B, DuVall SL, Follett RW, Ganslandt T, Gradinger T, Griffier R, Hanauer DA, Holmes JH, Horki P, Huling KM, Issitt RW, Jouhet V, Keller MS, Kraska D, Liu M, Luo Y, Lynch KE, Malovini A, Mandl KD, Mao C, Maram A, Matheny ME, Maulhardt T, Mazzitelli M, Milano M, Moore JH, Morris JS, Morris M, Mowery DL, Naughton TP, Ngiam KY, Norman JB, Patel LP, Pedrera Jimenez M, Ramoni RB, Schriver ER, Scudeller L, Sebire NJ, Serrano Balazote P, Spiridou A, Tan AL, Tan BW, Tibollo V, Torti C, Trecarichi EM, Vitacca M, Zambelli A, Zucco C, Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Kohane IS, Cai T, Brat GA, Gutiérrez-Sacristán A, Serret-Larmande A, García Barrio N. International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study. medRxiv. 2021 Feb 05. PMID: 33564777; PMCID: PMC7872369.
      Citations: 1     
    26. Le TT, Son J, Hong C, South AM, Beaulieu-Jones BK, Loh NHW, Luo Y, Morris M, Ngiam KY, Patel LP, Samayamuthu MJ, Schriver E, Tan AL, Moore J, Cai T, Omenn GS, Avillach P, Kohane IS, 4CE Consortium, Visweswaran S, Mowery DL, Xia Z, Gutiérrez-Sacristán A. Multinational Prevalence of Neurological Phenotypes in Patients Hospitalized with COVID-19. medRxiv. 2021 Jan 29. PMID: 33655281; PMCID: PMC7924306.
      Citations:    
    27. Saqib M, Zhu Y, Wang MD, Beaulieu-Jones B. Regularization of Deep Neural Networks for EEG Seizure Detection to Mitigate Overfitting. Proc COMPSAC. 2020 Jul; 2020:664-673. PMID: 33073266; PMCID: PMC7567426.
      Citations: 1     
    28. Norgeot B, Quer G, Beaulieu-Jones BK, Torkamani A, Dias R, Gianfrancesco M, Arnaout R, Kohane IS, Saria S, Topol E, Obermeyer Z, Yu B, Butte AJ. Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist. Nat Med. 2020 09; 26(9):1320-1324. PMID: 32908275; PMCID: PMC7538196.
      Citations: 161     Fields:    Translation:Humans
    29. Brat GA, Weber GM, Gehlenborg N, Avillach P, Palmer NP, Chiovato L, Cimino J, Waitman LR, Omenn GS, Malovini A, Moore JH, Beaulieu-Jones BK, Tibollo V, Murphy SN, Yi SL, Keller MS, Bellazzi R, Hanauer DA, Serret-Larmande A, Gutierrez-Sacristan A, Holmes JJ, Bell DS, Mandl KD, Follett RW, Klann JG, Murad DA, Scudeller L, Bucalo M, Kirchoff K, Craig J, Obeid J, Jouhet V, Griffier R, Cossin S, Moal B, Patel LP, Bellasi A, Kraska D, Sliz P, Tan ALM, Ngiam KY, Zambelli A, Mowery DL, Schiver E, Devkota B, Bradford RL, Daniar M, Daniel C, Benoit V, Bey R, Paris N, Serre P, Orlova N, Dubiel J, Hilka M, Jannot AS, Breant S, Leblanc J, Griffon N, Burgun A, Bernaux M, Sandrin A, Salamanca E, Cormont S, Ganslandt T, Gradinger T, Champ J, Boeker M, Martel P, Esteve L, Leprovost D, Mensch A, Haverkamp C, Bosari S, Krantz ID, South A, Cai T, Kohane IS, Prokosch HU, Gramfort A, Grisel O, Moreau T, Varoquaux G, Vie JJ, Wassermann D, Caucheteux C, Lemaitre G. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium. NPJ Digit Med. 2020; 3:109. PMID: 32864472; PMCID: PMC7438496.
      Citations: 96     
    30. Bush WS, Wheeler N, Beaulieu-Jones B, Darabos C. Packaging Biocomputing Software to Maximize Distribution and Reuse. Pac Symp Biocomput. 2020; 25:739-742. PMID: 31797644.
      Citations:    Fields:    
    31. Beaulieu-Jones BK, Finlayson SG, Yuan W, Altman RB, Kohane IS, Prasad V, Yu KH. Examining the Use of Real-World Evidence in the Regulatory Process. Clin Pharmacol Ther. 2020 04; 107(4):843-852. PMID: 31562770; PMCID: PMC7093234.
      Citations: 54     Fields:    Translation:Humans
    32. Beaulieu-Jones B, Finlayson SG, Chivers C, Chen I, McDermott M, Kandola J, Dalca AV, Beam A, Fiterau M, Naumann T. Trends and Focus of Machine Learning Applications for Health Research. JAMA Netw Open. 2019 10 02; 2(10):e1914051. PMID: 31651969; PMCID: PMC6822089.
      Citations: 23     Fields:    Translation:Humans
    33. Beaulieu-Jones BK, Wu ZS, Williams C, Lee R, Bhavnani SP, Byrd JB, Greene CS. Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing. Circ Cardiovasc Qual Outcomes. 2019 07; 12(7):e005122. PMID: 31284738; PMCID: PMC7041894.
      Citations: 67     Fields:    Translation:Humans
    34. Beaulieu-Jones BK, Kohane IS, Beam AL. Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify Phenotypes. Pac Symp Biocomput. 2019; 24:8-17. PMID: 30864306; PMCID: PMC6417814.
      Citations: 4     Fields:    Translation:Humans
    35. Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS, Segler MHS. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018 04; 15(141). PMID: 29618526; PMCID: PMC5938574.
      Citations: 563     Fields:    Translation:Humans
    36. Beaulieu-Jones BK, Lavage DR, Snyder JW, Moore JH, Pendergrass SA, Bauer CR. Characterizing and Managing Missing Structured Data in Electronic Health Records: Data Analysis. JMIR Med Inform. 2018 Feb 23; 6(1):e11. PMID: 29475824; PMCID: PMC5845101.
      Citations: 62     
    37. Beaulieu-Jones BK, Orzechowski P, Moore JH. Mapping Patient Trajectories using Longitudinal Extraction and Deep Learning in the MIMIC-III Critical Care Database. Pac Symp Biocomput. 2018; 23:123-132. PMID: 29218875.
      Citations: 20     Fields:    Translation:Humans
    38. Beaulieu-Jones BK, Greene CS. Reproducibility of computational workflows is automated using continuous analysis. Nat Biotechnol. 2017 04; 35(4):342-346. PMID: 28288103; PMCID: PMC6103790.
      Citations: 57     Fields:    
    39. Beaulieu-Jones BK, Moore JH. MISSING DATA IMPUTATION IN THE ELECTRONIC HEALTH RECORD USING DEEPLY LEARNED AUTOENCODERS. Pac Symp Biocomput. 2017; 22:207-218. PMID: 27896976; PMCID: PMC5144587.
      Citations: 43     Fields:    Translation:Humans
    40. Beaulieu-Jones BK, Greene CS, Pooled Resource Open-Access ALS Clinical Trials Consortium. Semi-supervised learning of the electronic health record for phenotype stratification. J Biomed Inform. 2016 12; 64:168-178. PMID: 27744022.
      Citations: 66     Fields:    Translation:Humans
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