Publications describing ARCH services

2025

Chen C, Bradford LR, Epstein MA, Gossey JT, Mansour MN, O'Connor CM, Tschinkel BJ, Campion TR. A Method for Enabling Digital Health Technologies in Clinical and Translational Research at an Academic Medical Center. AMIA Jt Summits Transl Sci Proc. 2025 Jun 10;2025:134-140. PMID: 40502275; PMCID: PMC12150704.

2024

Davila MA 3rd, Sholle ET, Fuld X, Israel ML, Cole CL, Campion TR Jr. Linking Patient Encounters across Primary and Ancillary Electronic Health Record Systems: A Comparison of Two Approaches. ACI open. 2024 Jan;8(1):e43-e48. doi: 10.1055/s-0044-1782679. Epub 2024 Apr 10. PMID: 38765555; PMCID: PMC11101195.

Goldstein JS, Aggarwal A, Sholle ET, Nino I, Campion TR Jr. A Comparison of Rule-based, Machine Learning, and Large Language Model Methods for Extracting Adverse Events from Clinical Notes. Amia Jt Summits Transl Sci Proc. 2024.

2023

Campion TR Jr, Sholle ET, Abedian S, Fuld X, McGregor R, Lewis AN, Gripp LT, Leonard JP, Cole CL. Implementation of a commercial federated network of electronic health record data to enable sponsor-initiated clinical trials at an academic medical center. Int J Med Inform. 2024 Feb;182:105322. doi: 10.1016/j.ijmedinf.2023.105322. Epub 2023 Dec 18. PMID: 38128198; PMCID: PMC10843646.

2022

Campion TR, Sholle ET, Pathak J, Johnson SB, Leonard JP, Cole, CL. An architecture for research computing in health to support clinical and translational investigators with electronic patient data. J AM Med Inform Assoc. 2022

Pfaff ER, Girvin AT, Gabriel DL, Kostka K, Morris M, Palchuk MB, Lehmann HP, Amor B, Bissell M, Bradwell KR, Gold S, Hong SS, Loomba J, Manna A, McMurry JA, Niehaus E, Qureshi N, Walden A, Zhang XT, Zhu RL, Moffitt RA, Haendel MA, Chute CG; N3C Consortium; Adams WG, Al-Shukri S, Anzalone A, Baghal A, Bennett TD, Bernstam EV, Bernstam EV, Bissell MM, Bush B, Campion TR, Castro V, Chang J, Chaudhari DD, Chen W, Chu S, Cimino JJ, Crandall KA, Crooks M, Davies SJD, DiPalazzo J, Dorr D, Eckrich D, Eltinge SE, Fort DG, Golovko G, Gupta S, Haendel MA, Hajagos JG, Hanauer DA, Harnett BM, Horswell R, Huang N, Johnson SG, Kahn M, Khanipov K, Kieler C, Luzuriaga KR, Maidlow S, Martinez A, Mathew J, McClay JC, McMahan G, Melancon B, Meystre S, Miele L, Morizono H, Pablo R, Patel L, Phuong J, Popham DJ, Pulgarin C, Santos C, Sarkar IN, Sazo N, Setoguchi S, Soby S, Surampalli S, Suver C, Vangala UMR, Visweswaran S, Oehsen JV, Walters KM, Wiley L, Williams DA, Zai A. Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative. J Am Med Inform Assoc. 2022 Mar 15;29(4):609-618. doi: 10.1093/jamia/ocab217. PMID: 34590684; PMCID: PMC8500110.

Wood EA, Campion TR. Design and implementation of an integrated data model to support clinical and translational research administration. 2022

Yin AL, Guo WL, Sholle ET, Rajan M, Alshak MN, Choi JJ, Goyal P, Jabri A, LI HA, Pinheiro LC, Wehmeyer GT, Weiner M, Weill Cornell COVID-19 Data Abstraction Consortium, Safford MM, Campion TR, Cole C. Comparing automated vs. manual data collection for COVID-specific medications from electronic health records. Int J Med Inform. 2022

2021

Abedian S, Sholle ET, Adekkanattu PM, Cusick MM, Weiner SE, Shoag JE, Hu JC, Campion TR Jr. Automated Extraction of Tumor Staging and Diagnosis Information From Surgical Pathology Reports. JCO Clin Cancer Inform. 2021

Cusick M, Adekkanattu P, Campion TR Jr, Sholle ET, Myers A, Banerjee S, Alexopoulos G, Wang Y, Pathak J. Using weak supervision and deep learning to classify clinical notes for identification of current suicidal ideation. J Psychiatr Res. 2021 Apr;136:95-102. doi: 10.1016/j.jpsychires.2021.01.052. Epub 2021 Feb 2. PMID: 33581461; PMCID: PMC8009838.

Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR; N3C Consortium. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. J Am Med Inform Assoc. 2021 Mar 1;28(3):427-443. doi: 10.1093/jamia/ocaa196. PMID: 32805036; PMCID: PMC7454687.

Patra BG, Sharma MM, Vekaria V, Adekkanattu P, Patterson OV, Glicksberg B, et al. Extracting social determinants of health from electronic health records using natural language processing: a systematic review. Journal of the American Medical Informatics Association. 2021

Schenck EJ, Hoffman KL, Cusick M, Kabariti J, Sholle ET, Campion TR Jr. Critical carE Database for Advanced Research (CEDAR): An automated method to support intensive care units with electronic health record data. J Biomed Inform. 2021

Yin AL, Guo WL, Sholle ET, Rajan M, Alshak MN, Choi JJ, Goyal P, Jabri A, Li HA, Pinheiro LC, Wehmeyer GT, Weiner M; Weill Cornell COVID-19 Data Abstraction Consortium; Safford MM, Campion TR, Cole CL. Comparing automated vs. manual data collection for COVID-specific medications from electronic health records. Int J Med Inform. 2022 Jan;157:104622. doi: 10.1016/j.ijmedinf.2021.104622. Epub 2021 Oct 21. PMID: 34741892; PMCID: PMC8529289.

2020

Adekkanattu P, Jiang G, Luo Y, Kingsbury PR, Xu Z, Rasmussen LV, Pacheco JA, Kiefer RC, Stone DJ, Brandt PS, Yao L, Zhong Y, Deng Y, Wang F, Ancker JS, Campion TR, Pathak J. Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. AMIA Annu Symp Proc. 2020 Mar 4;2019:190-199. PMID: 32308812; PMCID: PMC7153064.

Characterizing Basic and Complex Usage of i2b2 at an Academic Medical Center - PubMed

Chen C, Lee Pou-I, Pain KJ, Delgado D, Cole CL, Campion TR. Replacing Paper Informed Consent with Electronic Informed Consent for Research in Academic Medical Centers: A Scoping Review. AMIA Joint Summits on Translational Science proceedings AMIA Joint Summits on Translational Science [Internet]. 2020

Cusick MM, Sholle ET, Davila MA, Kabariti J, Cole CL, Campion TR Jr. A Method to Improve Availability and Quality of Patient Race Data in an Electronic Health Record System. Appl Clin Inform. 2020

Fu JT, Sholle E, Krichevsky S, Scandura J, Campion TR. Extracting and classifying diagnosis dates from clinical notes: A case study. Journal of Biomedical Informatics. 2020

Michael C, Sholle E, Wulff RT, Roboz GJ, Campion TR. Mapping Local Biospecimen Records to the OMOP Common Data Model. 2020

Sholle ET, Cusick M, Davila MA, Kabariti J, Flores S, Campion TR. Characterizing Basic and Complex Usage of i2b2 at an Academic Medical Center. AMIA Jt Summits Transl Sci Proc. 2020

2019

Adekkanattu P, Jiang G, Luo Y, Kingsbury PR, Xu Z, Rasmussen LV, et al. Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study. 2019

Campion TR Jr, Pompea ST, Turner SP, Sholle ET, Cole CL, Kaushal R. A method for integrating healthcare provider organization and research sponsor systems and workflows to support large-scale studies. AMIA Jt Summits Transl Sci Proc. 2019

Chen CC, Turner SP, Sholle ET, Brown SW, Blau VLI, Brouwer J, Lewis AN, Cole CL, Nanus DM, Shah MA, Leonard JP, Campion TR Jr. Evaluation of a REDCap-based workflow for supporting federal guidance for electronic informed consent. AMIA Jt Summits Transl Sci Proc. 2019

Sholle ET, Davila MA, Lee K, Pathak J, Campion TR Jr. Extension of the ACHILLES heel data quality assessment framework from OMOP to i2b2. AMIA Jt Summits Transl Sci Proc. 2019

Sholle ET, Pinheiro LC, Adekkanattu P, Davila MA, Johnson SB, Pathak J, Sinha S, Li C, Lubansky SA, Safford MM, Campion TR. Underserved populations with missing race ethnicity data differ significantly from those with structured race/ethnicity documentation. J Am Med Inform Assoc. 2019 Aug 1;26(8-9):722-729. doi: 10.1093/jamia/ocz040. PMID: 31329882; PMCID: PMC6696506.

Turner SP, Pompea ST, Williams KL, Kraemer DA Jr, Sholle ET, Chen C, Cole CL, Kaushal R, Campion TR Jr. Implementation of informatics to support the NIH All of Us research program in a healthcare provider organization. AMIA Jt Summits Transl Sci Proc. 2019

2018

Adekkanattu P, Sholle ET, DeFerio J, Pathak J, Johnson SB, Campion TR Jr. Ascertaining Depression Severity by Extracting Patient Health Questionnaire-9 (PHQ-9) Scores from Clinical Notes. AMIA Annu Symp Proc. 2018

Chen C, Wulff RT, Sholle ET, Roboz GJ, Kraemer DA Jr, Campion TR Jr. Evaluating Generalizability of a Biospecimen Informatics Approach: Support for Local Requirements and Best Practices. AMIA Jt Summits Transl Sci Proc. 2018

Johnson SB, Adekkanattu P, Campion TR Jr, Flory J, Pathak J, Patterson OV, DuVall SL, Major V, Aphiyanaphongs Y. From Sour Grapes to Low-Hanging Fruit: A Case Study Demonstrating a Practical Strategy for Natural Language Processing Portability. AMIA Jt Summits Transl Sci Proc. 2018

Sholle ET, Davila MA, Kabariti J, Schwartz JZ, Varughese VI, Cole CL, Campion TR Jr. A scalable method for supporting multiple patient cohort discovery projects using i2b2. J Biomed Inform. 2018

Sholle ET, Kabariti J, Johnson SB, Leonard JP, Pathak J, Varughese VI, Cole CL, Campion TR Jr. Secondary Use of Patients' Electronic Records (SUPER): An Approach for Meeting Specific Data Needs of Clinical and Translational Researchers. AMIA Annu Symp Proc. 2018 Apr 16;2017:1581-1588. PMID: 29854228; PMCID: PMC5977622.

Oxley PR, Ruffing J, Campion TR Jr, Wheeler TR, Cole Cl. Design and Implementation of a Secure Computing Environment for Analysis of Sensitive Data at an Academic Medical Center. AMIA Annu Symp Proc. 2018

2017

Campion TR Jr, Sholle ET, Davila MA. Generalizable middleware to support use of REDCap Dynamic Data Pull for integrating clinical and research data. AMIA Jt Summits Transl Sci Proc. 2017:76-81. eCollection 2017

Sholle ET, Bollapragada R, Campion TR Jr. Research data repositories: a tailored approach to secondary use of electronic health record data. AMIA Jt Summits Transl Sci Proc. 2017

Sholle ET, Kabariti J, Johnson SB, Leonard JP, Pathak J, Varughese V, Cole CL, Campion TR Jr. Secondary Use of Patients’ Electronic Records (SUPER): An Approach for Meeting Specific Data Needs of Clinical and Translational Researcher. AMIA Annu Symp Proc. 2017

2014

Kaushal R, Hripcsak G, Ascheim DD, Bloom T, Campion TR Jr, Caplan AL, Currie BP, Check T, Deland EL, Gourevitch MN, Hart R, Horowitz CR, Kastenbaum I, Levin AA, Low AF, Meissner P, Mirhaji P, Pincus HA, Scaglione C, Shelley D, Tobin JN; NYC-CDRN. Changing the research landscape: the New York City Clinical Data Research Network. J Am Med Inform Assoc. 2014 Jul-Aug;21(4):587-90. doi: 10.1136/amiajnl-2014-002764. Epub 2014 May 12. PMID: 24821739; PMCID: PMC4078297.