Crohn's Patients and Healthy Infants Share Immunodominant B Cell Response to Commensal Flagellin Peptide Epitopes. Gastroenterology. 20 Aug 2024. Zhao Q, Duck L, Killian J, Rosenberg A, Mannon P, King R, Denson L, Kugathasan S, Janoff E, Jenmalm M, Elson C. DOI: 10.1053/j.gastro.2024.08.015

Defining Documentation Burden for All Health Professionals: A Scoping Review. Applied Clinical Informatics. Levy DR, Withall JB, Mishuris RG, Tiase V, Diamond C, Douthit B, Grabowska M, Lee RY, Moy AJ, Sengstack P, Adler-Milstein J, Detmer DE, Johnson KB, Cimino JJ, Corley S, Murphy J, Rosenbloom ST,  Cato K, Rossetti SC. 2024: In press. DOI: 10.1055/a-2385-1654

Single Versus Multi-Ancestry Polygenic Risk Scores for Chronic Kidney Disease in Black Americans. Journal of the American Society of Nephrology. Jones AC, Patki A, Srinivasasainagendra V, Tiwari HK, Armstrong ND, Chaudhary NS, Limdi NA, Hidalgo BA, Davis B, Cimino JJ, Khan A, Kiryluk K, Lange LA, Lange EM, Arnett DK, Young BA, Diamantidis CJ, Franceschini N, Wassertheil-Smoller S, Rich SS, Rotter JI, Mychaleckyj JC, Kramer HJ, Chen Y-DI, Psaty BM, Brody JA, De Boer IH, Bansal N, Bis JC, Irvin MR. 2024: In press.

Smooth Muscle Cells-Expressed Bmal1 Regulates Vascular Calcification Independent of the Canonical Circadian Pathway. bioRxiv. 2024 July 22: Preprint. He M, Sun Y, Huang F, Zhu Z, Velazquez-Miranda E, Chong Z, Chen Y. DOI: 10.1101/2024.07.22.604443

Proteobacteria Impair Anti-tumor Immunity in the Omentum by Consuming Arginine. Cell Host and Microbe. 2024 July 10. Volume 32, Issue 7. Meza-Perez S, Liu M, Silva-Sanchez A, Morrow C, Eipers P, Lefkowitz E, Ptacek T, Scharer C, Rosenberg A, Hill D, Arend R, Gray M, Randall T. DOI: 10.1016/j.chom.2024.06.003

Molecular Differentiation Between Complete and Incomplete Responders to Neoadjuvant Therapy in Rectal Cancer. Chong Z, Huang F, McLeod M, Irwin R, Smithson M, Yue Z, Gao M, Hardiman K. Research Square. 2024 July 1: Preprint. DOI: 10.21203/rs.3.rs-4456000/v1

Proteobacteria Impair Anti-tumor Immunity in the Omentum by Consuming Arginine. Cell Host & Microbe. 27 June 2024. Meza-Perez S, Liu M, Silva-Sanchez A, Morrow CD, Eipers PG, Lefkowitz EJ, Ptacek T, Scharer CD, Rosenberg AF, Hill DD, Arend RC, Gray MJ, Randall TD. DOI: 10.1016/j.chom.2024.06.003

Injection Drug Use Alters Plasma Regulation of the B Cell Response. Cells. 10 June 2024. Sarkar S, Hill D, Rosenberg A, Eaton E, Kutsch O, Kobie J. DOI: 10.3390/cells13121011

Multi-task Transfer Learning for the Prediction of Entity Modifiers in Clinical Text: Application to Opioid Use Disorder Case Detection. Journal of Biomedical Semantics. 7 June 2024. Vol 15, Issue 1. Almudaifer A, Covington W, Hairston J, Deitch Z, Anand A, Carroll C, Crisan E, Bradford W, Walter L, Eaton E, Feldman S, Osborne J. DOI: 10.1186/s13326-024-00311-4

Issues and Challenges of Communicating Interfacility Transfer Patient Information in the United States: A Systematic Review. Research and Theory for Nursing Practice. 7 June 2024. Galatzan B, Johnson E, Judson T. DOI: 10.1891/RTNP-2023-0113

Multi-task Transfer Learning for the Prediction of Entity Modifiers in Clinical Text: Application to Opioid Use Disorder Case Detection. Journal of Biomedical Semantics. 7 June 2024. Vol 15, Issue 1. Almudaifer A, Covington W, Hairston J, Deitch Z, Anand A, Carroll C, Crisan E, Bradford W, Walter L, Eaton E, Feldman S, Osborne J. DOI: 10.1186/s13326-024-00311-4

Enhancing Skin Cancer Diagnosis Using Swin Transformer with Hybrid Shifted Window-Based Multi-head Self-attention and SwiGLU-Based MLP. Journal of Imaging Informatics in Medicine. 5 June 2024. Pacal I, Alaftekin M, Zengul F. DOI: 10.1007/s10278-024-01140-8

Molecular Characterization of Juxtaglomerular Cell Tumors: Evidence of Alterations in MAPK-RAS Pathway. Modern Pathology. 1 June 2024. Vol 37, Issue 6. Lobo J, Canete-Portillo S, Pena M, McKenney J, Aron M, Worthey E, et al. DOI: 10.1016/j.modpat.2024.100492

Exome and Genome Sequencing in a Heterogeneous Population of Patients with Rare Disease: Identifying Predictors of a Diagnosis. 1 June 2024. Vol 26, Issue 6. Pucel J, Briere L, Reuter C, Gochyyev P, Acosta M, Adams D, Might M, et al. DOI: 10.1016/j.gim.2024.101115

Pharmacogenomics of Coronary Artery Response to Intravenous Gamma Globulin in Kawasaki Disease. NPJ Genomic Medicine. 30 May 2024. Vol 9, Issue 1. Shrestha S, Wiener H, Chowdhury S, Kajimoto H, Srinivasasainagendra V, Mamaeva O, Brahmbhatt U, Ledee D, Lau Y, Padilla L, Chen J, Dahdah N, Tiwari H, Portman M. DOI 10.1101/2024.01.30.24301800

PAGER-scFGA: Unveiling Cell Functions and Molecular Mechanisms in Cell Trajectories Through Single-cell Functional Genomics Analysis. Frontiers in Bioinformatics. 16 April 2024. Volume 4. Huang F, Weiner R, Chen J, Yue Z. DOI: 10.3389/fbinf.2024.1336135

Photo-neuro-immuno-endocrinology: How the ultraviolet radiation regulates the body, brain, and immune system. Proceedings of the National Academy of Sciences. 2 April 2024. Vol 121, Issue 14. Slominski R, Chen J, Raman C, Slominski A. DOI: 10.1073/pnas.2308374121

Spatiotemporal Immune Atlas of a Clinical-Grade Gene-Edited Pig-to-Human Kidney Xenotransplant. Nature Communications. 11 April 2024. Cheung M, Asiimwe R, Erman E, Fucile C, Liu S, Sun C, Hanumanthu V, Pal H, Wright E, Ghajar-Rahimi G, Epstein D, Orandi B, Kumar V, Anderson D, Greene M, Bell M, Yates S, Moore K, LaFontaine J, Killian J, Baker G, Perry J, Khan Z, Reed R, Little S, Rosenberg A, George J, Locke J, Porrett P. DOI: 10.21203/rs.3.rs-2382345/v1

Integrative Genomics Identifies Evolutionary, Temporal, and Cell-lineage Origin of Hydrocephalus Risk Gene. Neurosurgery. 1 April 2024. Hale A, Song Y, Chong Z. DOI: 10.1227/neu.0000000000002809_268

Wearable Fiber-free Optical Sensor for Continuous Monitoring of Neonatal Cerebral Blood Flow and Oxygenation. Pediatric Research. 19 March 2024. Liu X, Mohtasebi M, Safavi P, Fathi F, Haratbar S, Chen L, Chen J, Bada H, Chen L, Jawdeh E, Yu G. DOI: 10.1038/s41390-024-03137-z

Chronic TNF Exposure Induces Glucocorticoid-like Immunosuppression in the Alveolar Macrophages of Aged Mice that Enhances Their Susceptibility to Pneumonia. Aging Cell. 8 March 2024. Kruckow K, Murray E, Shayhidin E, Rosenberg A, Bowdish D, Orihuela C. DOI: 10.1111/acel.14133.

A Survey of Clinicians’ Views of the Utility of Large Language Models. Applied Clinical Informatics. 5 March 2024. Vol 15, Issue 2. Spotnitz M, Idnay B, Gordon E, Rebecca Shyu, Zhang G, Liu C, Cimino J, Weng C. DOI: 10.1055/a-2281-7092

The Genetic Basis of Hydrocephalus: Genes, Pathways, Mechanisms, and Global Impact. Fluids and Barriers of the CNS. 4 March 2024. Hale A, Boudreau H, Rishi Devulapalli R, Duy P, Atchley T, Dewan M, Goolam M, Fieggen G, Spader H, Smith A, Blount J, Johnston J, Rocque B, Rozzelle C, Chong Z, et al. DOI: 10.1186/s12987-024-00513-z

Delirium Due to Potentially Avoidable Hospitalizations Among Older Adults. The Journals of Gerontology Series A. 3 Mar 2024. Vol 79, Issue 3. Whittington C, Skains R, Zhang Y, Osborne J, O'Leary T, Hyun B. Freeman R, Martin J, Vickers K, Flood A, Markland T, Brown C, Kennedy R. DOI: 10.1093/gerona/glad256

Selection, Optimization and Validation of Ten Chronic Disease Polygenic Risk Scores for Clinical Implementation in Diverse US Populations. Nature Medicine. Vol 30. 19 Feb 2024. Lennen N, Kottyan L, Kachulis C, Abull-Husn N, Arias J, Belbin G, Below J, Berndt S, Chung W, Cimino J, Kenny E, et al. DOI: 10.1101/2023.05.25.23290535 

An NLP-based Technique to Extract Meaningful Features from Drug SMILES. iScience. 8 Feb 2024. Vol 27, Issue 3. Sharma R, Saghapour E, Chen J. DOI: 10.1016/j.isci.2024.109127

Annotation of Opioid Use Disorder Entity Modifiers in Clinical Text. Studies in Health Technology and Informatics. 25 January 2024. Osborne J, Hairston J, Deitch Z, Crisan E, Riggs K, et al. DOI: 10.3233/SHTI231243

Body Weight Correlates with Molecular Variances in Cancer Patients. Cancer Research. 8 January 2024. Huang F, Xu P, Yue Z, Song Y, Chong Z, Hu K, Zhao X, Gao M. DOI: 10.1158/0008-5472.CAN-23-1463.

Data-driven Hypothesis Generation Among Inexperienced Clinical Researchers: A Comparison of Secondary Data Analyses with Visualization (VIADS) and Other Tools. medRxiv. 4 January 2024. Jing X, Cimino J. Patel V, Zhou Y, Shubrook J, et al. DOI: 10.1101/2023.05.30.23290719.

High-throughput Target Trial Emulation for Alzheimer's Disease Drug Repurposing with Real-world Data. Nature Communications. 2023 Dec 11. Vol 14, Issue 1. Zang C, Zhang H, Chen J, Xu J, Zhang H, et al. doi: 10.1038/s41467-023-43929-1.

An Open Natural Language Processing (NLP) Framework for EHR-based Clinical Research: A Case Demonstration Using the National COVID Cohort Collaborative (N3C). Journal of the Medical Informatics Association (JAMIA). 2023 Nov 17. Vol 30, Issue 12: pp. 2036-2040. Osborne J, Liu S, Wen A, Wang L, He H, Fu S, Miller R, et al. doi: 10.1093/jamia/ocad134.

Beyond the Override: Using Evidence of Previous Drug Tolerance to Suppress Drug Allergy Alerts, a Retrospective Study of Opioid Alerts. Journal of Biomedical Informatics. 2023 Nov: 147:104508. Colicchio, T, Cimino J. doi: 10.1016/j.jbi.2023.104508.

Interferon-γ Production by Tfh Cells is Required for CXCR3(+) Pre-memory B Cell Differentiation and Subsequent Lung-resident Memory B Cell Responses. Immunity. 2023 Oct 10. Vol 56, Issue 10: pp.2358-2372.e5. Arroyo-Díaz NM, Rosenberg A, Bachus H, Papillion A, et al. doi: 10.1016/j.immuni.2023.08.015. 

Sugar Accumulation Enhancement in Sorghum Stem is Associated with Reduced Reproductive Sink Strength and Increased Phloem Unloading Activity. Frontiers in Plant Science. 2023 Sep 11: 14:133813. Xue X, Beuchat G, Chen J, Wang J, Yu Y, Moose S, Chen LQ. doi: 10.3389/fpls.2023.1233813.

Highly Cross-Reactive and Protective Influenza A Virus H3N2 Hemagglutinin- and Neuraminidase-Specific Human Monoclonal Antibodies. Microbiol Spectr. 2023 Aug 17. Vol 11, Issue 4. Piepenbrink M, Oladunni F, Rosenberg A, Nogales A, et al. doi: 10.1128/spectrum.04728-22.

Mixed Origins: HIV gp120-Specific Memory Develops from Pre-Existing Memory and Naive B Cells Following Vaccination in Humans. AIDS Res Hum Retroviruses. 2023 July. Vol 39, Issue 7:pp. 350-366. Basu M, Rosenberg A, Fucile C, Piepenbrink MS, Bunce CA, Man LX, Liesveld J, Keefer MC, Kobie. doi: 10.1089/AID.2022.0104.

A Comparative Effectiveness Study on Opioid Use Disorder Prediction Using Artificial Intelligence and Existing Risk Models. IEEE Journal of Biomedical and Health Informatics. 2023 July. Vol 27, Issue 7: pp. 3589-3598. Fouladvand S, Talbert J, Chen J, Dwoskin L, Bush H, et al. doi: 10.1109/JBHI.2023.3265920.

B cell and Antibody Targeting of Transplant Alloantigen Epitopes is Supported by Both Self and Allo-recognition. bioRxiv. 2023 Jun 24; Killian JT, King RG, Rosenberg A, Kizziah JL, Fucile CF, et al. doi: 10.1101/2023.03.31.534734. 

Activation of Regulatory Dendritic Cells by Mertk Coincides with a Temporal Wave of Apoptosis in Neonatal Lungs. Science Immunology. 2023 Jun 23. Vol 8, Issue 84. Silva-Sanchez A, Meza-Perez S, Rosenberg A, Liu M, et al. doi: 10.1126/sciimmunol.adc9081. 

Single-cell Analysis of Human Nasal Mucosal IgE Antibody Secreting Cells Reveals a Newly Minted Phenotype. Mucosal Immunol. 2023 June. Vol 16, Issue 3: pp. 287-301. Ramonell RP, Brown M, Rosenberg A, Woodruff MC, Levy JM, et al. doi: 10.1016/j.mucimm.2023.02.008. 

A Metadata Framework for Computational Purposes. JAMIA Open. 2023 May 9. Vol 6, Issue 2. Spotnitz M, Acharya N, Cimino J, Murphy S, Namjou B, et al. 

Hospital‐associated Disability Due to Avoidable Hospitalizations Among Older Adults. Journal of the American Geriatrics Society. 2023 May. Vol 71, Issue 5. Skains R, Osborne J, Zhang Y, O’Leary T, Fowler M, 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.

Analysis of Cardiac Single-cell RNA-sequencing Data Can be Improved by the Use of Artificial Intelligence-based Tools. Scientific Reports. 2023 Apr 26. Vol 13, Issue 1. Nguyen T, Wei Y, Nakada Y, Chen J, ZHou Y, Walcott G, Zhang J. 

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. 

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.

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.

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

Delirium Mediates Incidence of Hospital-Associated Disability Among Older Adults. Journal of the American Medical Directors Association. 2023 Apr 4. Vol 24, Issue 4. Freeman H, Martin R, Whittington C, Zhang Y, Osborne J, et al.

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.

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.

A Transcriptionally Distinct Subset of Influenza-specific Effector Memory B Cells Predicts Long-lived Antibody Responses to Vaccination in Humans. Immunity. 2023 Mar 22. Issue 56, pp. 1-17. Nellore A, Rosenberg A, Scharer C, Fucile C, Tipton C, et al. 

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

Spatiotemporal Immune Atlas of the First Clinical-grade, Gene-edited Pig-to-Human Kidney Xenotransplant. Res Sq. 2023 Jan 9. Cheung M, Asiimwe R, Rosenberg A, Erman E, Fucile C, et al. doi: 10.21203/rs.3.rs-2382345/v1

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. 

Gene Fusion Detection and Characterization in Long-read Cancer Transcriptome Sequencing Data with FusionSeeker. Cancer Research. 2023 Jan 4. Vol 83, Issue 1. Chen Y, Wang Y, Chen W, Tan Z, Chong Z, et al.

Do Electronic Health Record Systems “Dumb Down” Clinicians? Journal of the American Medical Informatics Association. 2023 Jan 1. Vol 30, Issue 1. pp. 172-177. Melton G, Cimino JJ, Lehmann C, Sengstack P, Smith J, Tierney W, Miller R.

Long-term Kidney Function Recovery and Mortality After COVID-19-associated Acute Kidney Injury: An International Multi-centre Observational Cohort Study. 2023 Jan 1. EClinicalMedicine. Vol 55. Tan B, Schriver E, Das P, Cimino JJ, 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.