Selected Publications using ARCH data

2025

Gazda AJ, Pan D, Erdos K, Abu-Zeinah G, Racanelli A, Horn EM, Scandura JM. High pulmonary hypertension risk by echocardiogram shortens survival in polycythemia vera. Blood Adv. 2025 Mar 25;9(6):1320-1329. doi: 10.1182/bloodadvances.2024013970. PMID: 39693509; PMCID: PMC11950968.

Krichevsky S, Sholle ET, Adekkanattu PM, Abedian S, Ouseph M, Taylor E, Abu-Zeinah G, Jaber D, Sosner C, Cusick MM, Savage N, Silver RT, Scandura JM, Campion TR Jr. Automated Information Extraction from Unstructured Hematopathology Reports to Support Response Assessment in Myeloproliferative Neoplasms. Methods Inf Med. 2025 May 9. doi: 10.1055/a-2590-6456. Epub ahead of print. PMID: 40245940.

Mandel H, Yoo YJ, Allen AJ, Abedian S, Verzani Z, Karlson EW, Kleinman LC, Mudumbi PC, Oliveira CR, Muszynski JA, Gross RS, Carton TW, Kim C, Taylor E, Park H, Divers J, Kelly JD, Arnold J, Geary CR, Zang C, Tantisira KG, Rhee KE, Koropsak M, Mohandas S, Vasey A, Mohammad Mosa AS, Haendel M, Chute CG, Murphy SN, O'Brien L, Szmuszkovicz J, Guthe N, Santana JL, De A, Bogie AL, Halabi KC, Mohanraj L, Kinser PA, Packard SE, Tuttle KR, Hirabayashi K, Kaushal R, Pfaff E, Weiner MG, Thorpe LE, Moffitt RA. Long-COVID incidence proportion in adults and children between 2020 and 2024. Clin Infect Dis. 2025 Feb 5:ciaf046. doi: 10.1093/cid/ciaf046. Epub ahead of print. PMID: 39907495.

Mandel HL, Shah SN, Bailey LC, Carton T, Chen Y, Esquenazi-Karonika S, Haendel M, Hornig M, Kaushal R, Oliveira CR, Perlowski AA, Pfaff E, Rao S, Razzaghi H, Seibert E, Thomas GL, Weiner MG, Thorpe LE, Divers J; RECOVER EHR Cohort. Opportunities and Challenges in Using Electronic Health Record Systems to Study Postacute Sequelae of SARS-CoV-2 Infection: Insights From the NIH RECOVER Initiative. J Med Internet Res. 2025 Mar 5;27:e59217. doi: 10.2196/59217. PMID: 40053748; PMCID: PMC11923460.

Metzger DA, Mesiti A, Johnson J, Li Y, Brouwer J, Manasa M, Lee S, Hsu A, Jafari MD, Pigazzi A. Pouch outcomes after minimally invasive vs. open proctectomy during IPAA reconstruction. Surg Endosc. 2025 Apr;39(4):2436-2442. doi: 10.1007/s00464-025-11574-y. Epub 2025 Feb 20. PMID: 39979620.

Morris JX, Campion TR, Nutheti SL, Peng Y, Raj A, Zabih R, Cole CL. DIRI: Adversarial Patient Reidentification with Large Language Models for Evaluating Clinical Text Anonymization. AMIA Jt Summits Transl Sci Proc. 2025 Jun 10;2025:355-364. PMID: 40502277; PMCID: PMC12150728.

Stringer WS, Labar AS, Geleris JD, Sholle EV, Berlin DA, McGroder CM, Cummings MJ, O'Donnell MR, Yi H, Yang X, Wei Y, Schenck EJ, Baldwin MR. Three hospitalized non-critical COVID-19 subphenotypes and change in intubation or death over time: A latent class analysis with external and longitudinal validation. PLoS One. 2025 Mar 19;20(3):e0316434. doi: 10.1371/journal.pone.0316434. PMID: 40106751; PMCID: PMC11922525.

Thorpe LE, Meng Y, Conderino S, Adhikari S, Bendik S, Weiner M, Rabin C, Lee M, Uguru J, Divers J, George A, Dodson JA. COVID-related healthcare disruptions among older adults with multiple chronic conditions in New York City. BMC Health Serv Res. 2025 Mar 5;25(1):340. doi: 10.1186/s12913-024-12114-5. PMID: 40045268; PMCID: PMC11881239.

Zhang D, Stein R, Lu Y, Zhou T, Lei Y, Li L, Chen J, Arnold J, Becich MJ, Chrischilles EA, Chuang CH, Christakis DA, Fort D, Geary CR, Hornig M, Kaushal R, Liebovitz DM, Mosa ASM, Morizono H, Mirhaji P, Dotson JL, Pulgarin C, Sills MR, Suresh S, Williams DA, Baldassano RN, Forrest CB, Chen Y; Researching COVID to Enhance Recovery (RECOVER) Initiative. Pediatric Gastrointestinal Tract Outcomes During the Postacute Phase of COVID-19. JAMA Netw Open. 2025 Feb 3;8(2):e2458366. doi: 10.1001/jamanetworkopen.2024.58366. PMID: 39918822; PMCID: PMC11806396.

2024

Hartman V, Zhang X, Poddar R, McCarty M, Fortenko A, Sholle E, Sharma R, Campion T Jr, Steel PAD. Developing and Evaluating Large Language Model-Generated Emergency Medicine Handoff Notes. JAMA Netw Open. 2024 Dec 2;7(12):e2448723. doi: 10.1001/jamanetworkopen.2024.48723. PMID: 39625719; PMCID: PMC11615705.

Son M, Riley LE, Staniczenko AP, Cron J, Yen S, Thomas C, Sholle E, Osborne LM, Lipkind HS. Nonadjuvanted Bivalent Respiratory Syncytial Virus Vaccination and Perinatal Outcomes. JAMA Netw Open. 2024 Jul 1;7(7):e2419268. doi: 10.1001/jamanetworkopen.2024.19268. PMID: 38976271; PMCID: PMC11231799.

2023

Chen K, Chen J, Smith E, Mathani P, Longman R, Lukin D, Scherl E, Gerber J, Battat R. Serum Ustekinumab Concentrations Are Associated With Improved Outcomes With the Magnetic Resonance Index of Activity for Crohn's Disease. Inflamm Bowel Dis. 2023 Sep 1;29(9):1499-1503. doi: 10.1093/ibd/izac236. PMID: 36421052.

Garagozlo K, Han JY, Worgall S, Thomas C, Wu A, Chang N, Gerber LM, Fiorino EK. Validation of diagnostic coding for children's interstitial lung disease (chILD). Pediatr Pulmonol. 2024 Feb;59(2):521-525. doi: 10.1002/ppul.26773. Epub 2023 Nov 28. PMID: 38014614.

Hartman VC, Bapat SS, Weiner MG, Navi BB, Sholle ET, Campion TR Jr. A method to automate the discharge summary hospital course for neurology patients. J Am Med Inform Assoc. 2023 Nov 17;30(12):1995-2003. doi: 10.1093/jamia/ocad177. PMID: 37639624; PMCID: PMC10654848.

Wong R, Buckholz A, Hajifathalian K, Ng C, Sholle E, Ghosh G, Rosenblatt R, Fortune BE. Liver Severity Score-Based Modeling to Predict Six-Week Mortality Risk Among Hospitalized Cirrhosis Patients With Upper Gastrointestinal Bleeding. J Clin Exp Hepatol. 2024 Jan-Feb;14(1):101255. doi: 10.1016/j.jceh.2023.07.402. Epub 2023 Jul 17. PMID: 38076370; PMCID: PMC10709123.

Ying X, Pan Y, Rosenblatt R, Ng C, Sholle E, Fahoum K, Jesudian A, Fortune BE. Impact of Race and Neighborhood Socioeconomic Characteristics on Liver Cancer Diagnosis in Patients with Viral Hepatitis and Cirrhosis. J Clin Exp Hepatol. 2023 Jul-Aug;13(4):568-575. doi: 10.1016/j.jceh.2023.01.005. Epub 2023 Jan 14. PMID: 37440951; PMCID: PMC10333940.

2022

Brandt PS, Pacheco JA, Adekkanattu P, Sholle ET, Abedian S, Stone DJ, Knaack DM, Xu J, Xu Z, Peng Y, Benda NC, Wang F, Luo Y, Jiang G, Pathak J, Rasmussen LV. Design and validation of a FHIR-based EHR-driven phenotyping toolbox. J Am Med Inform Assoc. 2022 Aug 16;29(9):1449-1460. doi: 10.1093/jamia/ocac063. PMID: 35799370; PMCID: PMC9382394.

Cusick M, Velupillai S, Downs J, Campion TR, Sholle ET, Dutta R, et al. Portability of natural language processing methods to detect suicidality from clinical text in US and UK electronic health records. Journal of affective disorders reports 2022 Dec 1;10:100430–0.

Hartman V, Campion TR. A Day-to-Day Approach for Automating the Hospital Course Section of the Discharge Summary. AMIA Jt Summits Transl Sci Proc. 2022 May 23;2022:216-225.

Lee HG, Sholle E, Beecy A, Al'Aref S, Peng Y. Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. In Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, pages 4533–4538, Online. Association for Computational Linguistics.

Waldrop G, Safavynia SA, Barra ME, Agarwal S, Berlin DA, Boehme AK, et al. Prolonged Unconsciousness is Common in COVID-19 and Associated with Hypoxemia. Annals of neurology. 2022 Mar 7;91(6):740–55.

2021

Abu-Zeinah G, Krichevsky S, Cruz T, Hoberman G, Jaber D, Savage N, et al. Interferon-alpha for treating polycythemia vera yields improved myelofibrosis-free and overall survival. Leukemia [Internet]. 2021 Sep 1;35(9):2592–601.

Bhambhvani HP, Rodrigues AJ, Yu JS, Carr JB, Hayden Gephart M. Hospital volumes of 5 medical emergencies in the COVID-19 pandemic in 2 US Medical Centers. JAMA Internal Medicine. 2021;181(2):272.

Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, et al. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature communications [Internet]. 2021 Mar 12 [cited 2021 Jun 5];12(1):1660.

Cusick M, Adekkanattu P, Campion TR, Sholle ET, Myers A, Banerjee S, et al. Using weak supervision and deep learning to classify clinical notes for identification of current suicidal ideation. Journal of psychiatric research. 2021 Apr;136:95-102.

Lee HG, Sholle E, Beecy A, Al'Aref S, Peng Y. Leveraging Deep Representations of Radiology Reports in Survival Analysis for Predicting Heart Failure Patient Mortality. Proc Conf. 2021 Jun;2021:4533-4538. doi: 10.18653/v1/2021.naacl-main.358. PMID: 35463193; PMCID: PMC9034454.

Khan U, Ho K, Eun Kyeong Hwang, Cristian Peña, Brouwer J, Hoffman KL, et al. Impact of Use of Antibiotics on Response to Immune Checkpoint Inhibitors and Tumor Microenvironment. American Journal of Clinical Oncology. 2021 Apr 5;44(6):247–53.

Manohar J, Abedian S, Martini R, Kulm S, Salvatore M, Ho K, et al. Social and Clinical Determinants of COVID-19 Outcomes: Modeling Real-World Data from a Pandemic Epicenter. 2021Apr 7 [cited 2023 Feb 13]

Patra BG, Sharma MM, Vekaria V, Adekkanattu P, Patterson OV, Glicksberg B, Lepow LA, Ryu E, Biernacka JM, Furmanchuk A, George TJ, Hogan W, Wu Y, Yang X, Bian J, Weissman M, Wickramaratne P, Mann JJ, Olfson M, Campion TR, Weiner M, Pathak J. Extracting social determinants of health from electronic health records using natural language processing: a systematic review. J Am Med Inform Assoc. 2021 Nov 25;28(12):2716-2727. doi: 10.1093/jamia/ocab170. PMID: 34613399; PMCID: PMC8633615.

Reiterer M, Rajan M, GÃ³mez-Banoy NÃ¡, Lau JD, Gomez-Escobar LG, Ma L, et al. Hyperglycemia in acute COVID-19 is characterized by insulin resistance and adipose tissue infectivity by SARS-CoV-2. Cell metabolism 2021

Schenck EJ, Hoffman KL, Oromendia C, Sanchez E, Finkelsztein EJ, Hong KS, et al. A Comparative Analysis of the Respiratory Subscore of the Sequential Organ Failure Assessment Scoring System. 2021 Nov 1;18(11):1849–60.

Su C, Xu Z, Hoffman K, Goyal P, Safford MM, Lee J, et al. Identifying organ dysfunction trajectory-based subphenotypes in critically ill patients with COVID-19. Scientific Reports. 2021 Aug 5;11(1).

Winston GM, Guadix S, Lavieri MT, Uribe-Cardenas R, Kocharian G, Williams N, et al. Closed-loop vagal nerve stimulation for intractable epilepsy: A single-center experience. Seizure. 2021 May;88:95–101.

Zhang Y, Wang S, Hermann A, Joly R, Pathak J. Development and validation of a machine learning algorithm for predicting the risk of postpartum depression among pregnant women. Journal of Affective Disorders. 2021;279:1–8.

2020

Beecy AN, Gummalla M, Sholle E, Xu Z, Zhang Y, Michalak K, et al. Utilizing electronic health data and machine learning for the prediction of 30-day unplanned readmission or all-cause mortality in heart failure. Cardiovascular digital health journal. 2020 Sep 1;1(2):71–9.

Brar G, Pinheiro LC, Shusterman M, Swed B, Reshetnyak E, Soroka O, et al. Covid-19 severity and outcomes in patients with cancer: A matched cohort study. Journal of Clinical Oncology. 2020;38(33):3914–24.

Brandt PS, Kiefer RC, Pacheco JA, Adekkanattu P, Sholle ET, Ahmad FS, Xu J, Xu Z, Ancker JS, Wang F, Luo Y, Jiang G, Pathak J, Rasmussen LV. Toward cross-platform electronic health record-driven phenotyping using Clinical Quality Language. Learn Health Syst. 2020 Jun 25;4(4):e10233. doi: 10.1002/lrh2.10233. PMID: 33083538; PMCID: PMC7556419.

Choi JJ, Wehmeyer GT, Li HA, Alshak MN, Nahid M, Rajan M, et al. D-dimer cut-off points and risk of venous thromboembolism in adult hospitalized patients with COVID-19. Thrombosis Research. 2020;196:318–21. Goyal P, Choi JJ, Pinheiro LC, Schenck EJ, Chen R, Jabri A, et al. Clinical Characteristics of Covid-19 in New York City. New England Journal of Medicine. 2020 Apr 17

Fu JT, Sholle E, Krichevsky S, Scandura J, Campion TR. Extracting and classifying diagnosis dates from clinical notes: A case study. J Biomed Inform. 2020 Oct;110:103569. doi: 10.1016/j.jbi.2020.103569. Epub 2020 Sep 16. PMID: 32949781.

Goyal P, Ringel JB, Rajan M, Choi JJ, Pinheiro LC, Li HA, et al. Obesity and COVID-19 in New York City: A Retrospective Cohort Study. Annals of Internal Medicine. 2020 Nov 17;173(10):855–8.

Hajifathalian K, Sharaiha RZ, Kumar S, Krisko T, Skaf D, Ang B, et al. Development and external validation of a prediction risk model for short-term mortality among hospitalized U.S. COVID-19 patients: A proposal for the COVID-AID risk tool. Kou YR, editor. PLOS ONE. 2020 Sep 30;15(9):e0239536.

Lee JR, Silberzweig J, Akchurin O, Choi ME, Srivatana V, Lin J, et al. Characteristics of acute kidney injury in hospitalized COVID-19 patients in an urban academic medical center. Clinical Journal of the American Society of Nephrology. 2020;16(2):284–6.

Lin E, Lantos JE, Strauss SB, Phillips CD, Campion TR, Navi BB, et al. Brain Imaging of Patients with COVID-19: Findings at an Academic Institution during the Height of the Outbreak in New York City. American Journal of Neuroradiology [Internet]. 2020 Aug 20 [cited 2022 May 14];41(11):2001–8.

Merkler AE, Parikh NS, Mir S, Gupta A, Kamel H, Lin E, et al. Risk of Ischemic Stroke in Patients With Coronavirus Disease 2019 (COVID-19) vs Patients With Influenza. JAMA Neurology. 2020 Jul 2;77(11).

Pandey M, Xu Z, Sholle E, Maliakal G, Singh G, Fatima Z, et al. Extraction of radiographic findings from unstructured thoracoabdominal computed tomography reports using convolutional neural network based natural language processing. PloS one. 2020 Jul 30;15(7):e0236827–7

Racine-Brzostek SE, Yang HS, Chadburn A, Orlander D, An A, Campion TR, et al. COVID-19 Viral and Serology Testing in New York City Health Care Workers. American Journal of Clinical Pathology. 2020 Sep 11;154(5):592–5.

Shah MA, Mayer S, Emlen F, Sholle E, Christos P, Cushing M, et al. Clinical screening for COVID-19 in asymptomatic patients with cancer. JAMA Network Open. 2020;3(9).

Singh G, Hussain Y, Xu Z, Sholle E, Michalak K, Dolan K, et al. Comparing a novel machine learning method to the Friedewald formula and Martin-Hopkins equation for low-density lipoprotein estimation. PLOS ONE. 2020;15(9).

Zhang Y, Tayarani M, Al’Aref SJ, Beecy AN, Liu Y, Sholle E, et al. Using electronic health records for Population Health Sciences: A case study to evaluate the associations between changes in left ventricular ejection fraction and the built environment. JAMIA Open. 2020;3(3):386–94.

Zhang Y, Zhang Y, Sholle E, Abedian S, Sharko M, Turchioe MR, et al. Assessing the impact of social determinants of health on predictive models for potentially avoidable 30-day readmission or death. PLoS ONE [Internet]. 2020 Jun 25;15(6).

2019

Kamel H, Okin PM, Merkler AE, Navi BB, Campion TR, Devereux RB, et al. Relationship between left atrial volume and ischemic stroke subtype. Annals of clinical and translational neurology. 2019 Jul 26;6(8):1480–6.

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 May 6;2019:602-609

2018

Khan R, Sholle E, Razavi A, Gelber SE. Predictive cutoffs of 1-hour GCT prior to 16 weeks in diagnosing carbohydrate intolerance in early gestation [36l]. Obstetrics & Gynecology. 2018;131(1).

Morash M, Mitchell H, Yu A, Campion T, Beltran H, Elemento O, Pathak J. CATCH-KB: Establishing a Pharmacogenomics Variant Repository for Chemotherapy-Induced Cardiotoxicity. AMIA Joint Summits on Translational Science proceedings AMIA Joint Summits on Translational Science [Internet]. 2018 [cited 2023 Jul 28];2017:168–77

Pacheco JA, Rasmussen LV, Kiefer RC, Campion TR, Speltz P, Carroll RJ, et al. A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record. Journal of the American Medical Informatics Association. 2018 Aug 16 [cited 2023 Jul 28];25(11):1540–6.

Sholle E, Krichevsky S, Scandura J, Sosner C, Campion T. Lessons learned in the development of a computable phenotype for response in myeloproliferative neoplasms. 2018 IEEE International Conference on Healthcare Informatics (ICHI). 2018;

Sholle E, Krichevsky S, Scandura J, Sosner C, Savage N, Campion TR. Development of an automated tool for assessing response in patients with Polycythemia Vera. Blood. 2018;132(Supplement 1):5462–.

2025

2024

2023

2022

2021

2020

2019

2018

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