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Deciphering the Exact Breakpoints of Structural Variations Using Long Sequencing Reads with DeBreak. Nature Communications. 2023 Jan 17. Vol 14, Issue 1. Chen Y, Wang A, Barkley C., Zhang Y., Zhao X, Gao M, Edmonds M, Chong, Z

Returning Integrated Genomic Risk and Clinical Recommendations: The eMERGE Study. Genet Med.. 2023 Jan 6. Vol 25, Issue 4.  Linder JE, Allworth A, Bland ST, Cimino JJ, et al. 

A Visual Analytic Tool (VIADS) to Assist the Hypothesis Generation Process in Clinical Research: Mixed Methods Usability Study. JMIR Hum Factors. 2023 Apr 27. PMID: 37011112, DOI: 10.2196/44644. Jing X, Patel V, Cimino JJ, Shubrook J, Zhou Y, Draghi B, Ernst M, Liu C 6, De Lacalle S.

Returning Integrated Genomic Risk and Clinical Recommendations: The eMERGE Study. Genet Med. 2023 Apr. Vol 25, Issue 4. PMCID: PMC10085845, DOI: 10.1016/j.gim.2023.100006. Linder J, Allworth A, Bland S, Caraballo P, Chisholm R, Clayton E, Cimino JJ, et al.

Coumarin-Based Fluorescent Inhibitors for Photocontrollable Bioactivation. Mol Pharm. 2023 Apr 27. PMID: 37104703, DOI: 10.1021/acs.molpharmaceut.3c00279. Gao M, Ren F, Zhu W, Yang S, Zhang C, Hou Y, Li R, Wen J, Zou L, et al.    

Corrigendum to 'Integrating Coronary Atherosclerosis Burden and Progression with Coronary Artery Disease Risk Factors to Guide Therapeutic Decision Making.' The American Journal of Medicine. 2023 Apr 15. pp. 260-269. PMID: 37068988. DOI: 10.1016/j.amjmed.2023.03.021. Freeman A, Raman S, Aggarwal M, Maron D, Bhatt D, Parwani P, Osborne J, et al.

Delirium Mediates Incidence of Hospital-Associated Disability Among Older Adults. J Am Med Dir Assoc. 2023 Apr. Vol 24, Issue 4, pp. 533-540. PMID: 36931323, DOI: 10.1016/j.jamda.2023.02.006. Freeman H, Martin R, Whittington C, Zhang Y, Osborne J, Vickers J, Flood K, et al.

IL-6 prevents Th2 Cell Polarization by Promoting SOCS3-dependent Suppression of IL-2 Signaling. Cell Mol Immunol. 2023 Apr 12. PMID: 37046042, DOI: 10.1038/s41423-023-01012-1. Bachus H, Rosenberg A, Benveniste E, Lewis C, Papillion A, et al.

A Transcriptionally Distinct Subset of Influenza-specific Effector Memory B Cells Predicts Long-lived Antibody Responses to Vaccination in Humans. Immunity. 2023 Apr 11. Vol 56, Issue 4, pp. 847-863. PMID: 36958335. DOI: 10.1016/j.immuni.2023.03.001. Nellore A, Zumaquero E, Scharer C, Fucile C, Tipton C, Rosenberg A, Boss J, et al.

Systematic Review: Zone IV Extensor Tendon Early Active Mobilization Programs. J Hand Ther. 2023 Apr 7. PMID: 37032244, DOI: 10.1016/j.jht.2022.12.001. Collocott S, Wang A, Hirth M

Preclinical Validation of a Novel Therapeutic Strategy for Choroid Plexus Carcinoma. J Control Release. 2023 Apr 22. PMID: 37054779, DOI: 10.1016/j.jconrel.2023.04.016. Martin B, Garman T, Wang A, Zhang X, Beck E, Wilson K, et al.

Do Electronic Health Record Systems “dumb down” Clinicians? Journal of the American Medical Informatics Association. 2022 Dec 13. Vol 30, Issue 1, pp. 172-177. Melton GB, Cimino JJ, Lehman CU, Sengstack PR, Smith JC, Tierney WM, Miller RA. 

IL-4-Induced Quiescence of Resting Naive B Cells Is Disrupted in Systemic Lupus Erythematosus. Journal of Immunology. 2022 Oct 15. Vol 209, Issue 8. pp. 1513-1522. Gao M, Liu S, Chatham W, Mountz J, Hsu, H 

IL-4 Receptor Blockade is a Global Repressor of Naïve B Cell Development and Responses in a Dupilumab-treated Patient. Clinical Immunology. 2022 Sep 20. pp.1-12. Mountz J, Gao M, Ponder D, Liu S, Sullivan K, et al. 

A Nonredundant Role for T Cell-Derived Interleukin 22 in Antibacterial Defense of Colonic Crypts. Immunity. 2022 Mar 8. Vol 55, Issue 3, pp. 494-511. Zindl C, Witte S, Laufer V, Gao M, et al. 

A Research Agenda to Support the Development and Implementation of Genomics-Based Clinical Informatics Tools and Resources. Journal of the American Medical Informatics Association. 2022 Apr 29. Wiley K, Findley L, Cimino J, Deverka P, et al. 

An In Vivo Model of Glioblastoma Radiation Resistance Identifies Long Noncoding RNAs and Targetable Kinases. JCI Insight. 2022 Aug 22. Vol 7, Issue 16. Anderson J, Nguyen T, Stackhouse C, Chen J, et al.

B-Assembler: A Circular Bacterial Genome Assembler. BMC Genomics. 2022 May 11. Vol 23, Issue 4. Huang F, Xiao L, Gao M,Atkinson T, et al. 

Racial Disparity in Clinial Alert Overrrides. AMIA Annual Symposium Proceedings. 2022 Feb 21. pp. 314-323. Cimino, J. 

Synergies Between Centralized and Federated Approaches to Data Quality: A Report from the National COVID Cohort Collaborative. Journal of the Medical Informatics Association. 2022 Mar 15. Vol 29, Issue 4, pp. 609-618. Pfaff E, Girvin A, Gabriel D, Cimino J, et al. 

The Biomedical Informatics Short Course at Woods Hole/Georgia: Training to Support Institutional Change. Information Services & Use. 2022 May 10. Vol 42, Issue 1, pp. 47-59. Cimino, J. 

A State-Based Approach to Genomics for Rare Disease and Population Screening. Genetics in Medicine. 2021 Apr. Vol 23, Issue 4, pp. 777-781. East K, Kelley W, Cannon A, Cimino, J, et al.

Accurate Long-Read de Novo Assembly Evaluation with Inspector. Genome Biology. 2021 Nov 14. Vol 22, Issue 1, pp. 1-21. Chen Y, Wang A, Zhang Y, Gao M, Chong Z

AllergyMap: An Open Source Corpus of Allergy Mention Normalizations. AMIA Annual Symposium Proceedings.

Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative. American Medical Association. 2021 Jul 1. Vol 4, Issue 7, Page e2116901-e2116901. Bennett T, Moffitt R, Hajagos J, Amor B, Cimino J, et al

Developing Real-World Evidence fro Real-World Data: Tranforming Raw Data into Analytical Datasets. Wiley Online Library. 2021 Oct 14. Bastarache L, Brown J, Cimino J, Dorr D, et al.

Evolving Phenotypes of Non-hospitalized that Indicate Long COVID. BMC Medicine. 2021 Sep 27. Estiri, H., Strasser, Z., Brat, G., Consortium for Characterization of COVID-19 by EHR (4CE), et al. 

Haplotype-resolved Fiverse Human Genomes and Integrated Analysis of Structural Variation. Science. American Association for the Advancement of Science. 2021 Apr 2. Vol 372, Issue 6537: eabf7117. Ebert P, Audano P, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder M, Sulovari A, Ebler J, Chong Z, et al.

Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn's Disease. Gastroenterology. 2021 Aug. Vol 161, Issue 2, pp. 522-535. Rosenberg A, Elson C, Alexander K, Zhao Q

International Analysis of Electronic Health Records of Children and Youth Hospitalized with COVID-19 Infection in 6 Countries. JAMA Network Open. 2021 June 11. Bourgeois F, Keller M, Aronow B, Issitt R, Cimino J, Colicchio T, et al.

International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study. Journal of Medical Internet Research. 2021 Oct 11. Vol 23, Issue 10. Weber G, Zhang H, Hong C, Colicchio T, Cimino J, et al.

Multinational Characterization of Neurological Phenotypes in Patients Hospitalized with COVID-19. Scientific Reports. 2021 Oct 12. Le T, Son J, South A, Omenn G, Cimino J, Colicchio T, et al. 

Opportunity for Genotype-Guided Prescribing Among Adult Patients in 11 U.S. Health Systems. American Society for Clinical Pharmacology and Therapeutics. Vol 110, Issue 1, pp. 179-188. Hicks J, Ong H, Ramsey L, Peterson J, Cimino J, et al. 

PAGER-CoV: A Comprehensive Collection of Pathways, Annotated Gene-lists and Gene Signatures for Coronavirus Disease Studies. Nucleic Acids Research, 2021 Jan 8. Volume 49, Issue D1, pp. D589-D599. Yue Z, Zhang E, Batra N, Chen J, Cimino J, et al. 

Physicians' Perceptions About Narrative Note Sections Format and Content: A Multi-Speciaty Survey. Science Direct. 2021 Jul. Vol 151, Issue 1. Collicchio T, Dissanayake P, Cimino, J

Research Informatics and the COVID-19 Pandemic: Challenges, Innovations, Lessons Learned, and Recommendations. Cambridge University Press. 2021 Mar 16. Vol 5, Issue 1. Bookman R, Cimino J, Harle C, Kost R, Mooney S, et al. 

The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment. Journal of the American Medical Informatics Association. 2021 Mar. Vol 28, Pages 427-443. Haendel M, Chute C, Bennett, T, Cimino J, et al.

Vitamin D and Lumisterol Derivatives Can Act on Liver X Receptors (LXRs). Nature Publishing Group. 2021 Apr 13. Vol 11, Issue 1, Pages 1-23. Slominski A, Kim T, Qayyum S, Song Y, Chen J, et al.

What Every Reader Should Know About Studies Using Electronic Health Record Data, But May Be Afraid to Ask. Journal of Medical Internet Research. 2021 Mar 2. Vol. 23, Issue 3, Page e22219. Kohane, I, Aronow, B, Avillach P, Beaulieu-Jones B, Bellazzi R, Bradford R, Cimino J, et al.

AllergyMap: An Open Source Corpus of Allergy Mention Normalizations. AMIA Annual Symposium Proceedings. 2020. pp. 1249-1257. Danila M, Wang A, Osborne J, Naidech A, Liebovitz, D

Decoding SARS-CoV-2 Hijacking of Host Mitochondria in COVID-19 Pathogenesis. American Journal of Physiology-Cell Physiology. 2020 Aug 1. Vol 319, Issue 2, Pages C258-C267. Singh K, Chaubey G, Chen J, Suravajhala P

Formal Representation of Patients’ Care Context Data: The Path to Improving the Electronic Health Record. Journal of the American Medical Informatics Association. 2020 Nov. Vol 27, Issue 11, Pages 1648-1657. Dissanayake P, Colicchio, T, Cimino J

Health Information Technology as a Learning Health System: Call for a National Monitoring System. Learning Health Systems. 2020 Jan. Vol 4, Issue 1, Page e10207. Colicchio T, Del Fiol G, Cimino J

International Electronic Health Record-Derived COVID-19 Clinical Course Profiles: The 4CE Consortium. NPJ Digital Medicine. 2020 Aug 19. Vol 3, Issue 1, pp. 1-9. Brat, G., Weber G, Gehlenborg N, Avillach P, Palmer N, Chiovato L, Cimino J, et al.  

Neonatal Exposure to Commensal-Bacteria-Derived Antigens Directs Polysaccharide-Specific B-1 B Cell Repertoire Development. Immunity. Vol 53, Issue 1, pp.172-186. Rosenberg A, Kearney J, New J, King R

Pan-cancer Analysis of Whole Genomes Identifies Driver Rearrangements Promoted by LINE-1 Retrotransposition. Nature Genetics. 2020 Mar. Vol 52, Issue 3, pp. 306-319. Rodriguez-Martin B, Alvarez, E, Baez-Ortega, Zamora A, Supek F, Demeulemeester J, Santamarina M, Temes J, Detering H, Chong, Z., et al

Using Clinical Reasoning Ontologies to Make Smarter Clinical Decision Support Systems: A Systematic Review and Data Synthesis. Journal of the American Medical Informatics Association. 2020 Jan. Vol 27, Issue 1, Pages 159-174. Dissanayake P, Colicchio T, Cimino J

Broad and Protective Influenza B Virus Neuraminidase Antibodies in Humans After Vaccination and Their Clonal Persistence as Plasma Cells. mBio Journal. 2019 Mar 12. Vol 10, Issue 2, pp. 1-17. Nogales A, Fucile C, Liesveld J, Rosenberg A, et al. 

Differential Transcriptome and Development of Human Peripheral Plasma Cell Subsets. JCI Insights. 2019 May 2. Vol 4, Issue 9. Saney C, Gibson G, Sanz I, Rosenberg A, et al.

Human-specific Tandem Repeat Expansion and Differential Gene Expression during Primate Evolution. Proceedings of the National Academy of Sciences. Vol 116, Issue 46, pp. 23243-23253. Sulovari A, Li R, Audano P, Porubsky D, Chong Z, et al. 

IFNγ Induces Epigenetic Programming of Human T-bethi B Cells and Promotes TLR7/8 and IL-21 Induced Differentiation. eLife. 2019 May 15. Volume 8. Kimberly R, Jenks, S, Botta D, Ptacek T, Edberg J, Rosenberg A, et al.

Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes. Nature Communications. Vol 10, Issue 1, pp. 1-16. Chaisson M, Sanders A, Zhao X, Malhotra A, Rausch T, Chong Z, et al. 

Putting the "why" in "HER": Capturing and Coding Clinical Cognition. Journal of the American Medical Informatics Association. Vol 26, Issue 11, pp. 1379-1384. Cimino J

T-bet Transcription Factor Promotes Antibody-Secreting Cell Differentiation by Limiting the Inflammatory Effects of IFN-γ on B Cells. Immunity. 2019 May 21. Vol 50, Issue 5, pp. 1172-1187. Stone S, Peel J, Scharer C, Chisolm D, Rosenberg A, et al.

The "All of Us" Research Program. New England Journal of Medicine. 2019 Aug 15. Vol 381, Issue 7, pp. 668-676. All of Us Research Program Investigators. 

Unintended Consequences of Nationwide Electronic Health Record Adoption: Challenges and Opportunities in the Post-Meaningful Use Era. Journal of Medical Internet Research. 2019 Jun 3. Vol 21, Issue 6, page e13313. Colicchio T, Cimino J, Del Fiol G

Regenerative Potential of Neonatal Porcine Hearts. Circulation. Vol 138, Issue 24, pp. 2809-2816. Zhu W, Zhang E, Zhao M, Fan C, Tang Y, Chen J, et al.

Integrated Genomic and Molecular Characterization of Cervical Cancer. Nature. 2017 Mar. Vol 543, page 16. NFE2L2 HLA-B.

Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness. Scientific Reports. 2017 Jul 26. Vol 7, Issue 1. Corbett A, Topham D, Walsh E, Baran A, Rosenberg A, et al.