DownloadHi-Res Photo

Jihoon Kim

Instructor of Biomedical Informatics and Data Science

Research & Publications
Biography
News

Coauthors

Selected Publications

Endothelial Cell Response in Kawasaki Disease and Multisystem Inflammatory Syndrome in ChildrenKim J, Shimizu C, He M, Wang H, Hoffman H, Tremoulet A, Shyy J, Burns J. Endothelial Cell Response in Kawasaki Disease and Multisystem Inflammatory Syndrome in Children. International Journal Of Molecular Sciences 2023, 24: 12318. PMID: 37569694, PMCID: PMC10418493, DOI: 10.3390/ijms241512318.
Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research programWang X, Ryu J, Kim J, Ramirez A, Mayo K, Condon H, Vaitinadin N, Ohno-Machado L, Talavera G, Ellinor P, Lubitz S, Choi S. Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program. Journal Of Human Genetics 2023, 68: 565-570. PMID: 37072623, PMCID: PMC10524735, DOI: 10.1038/s10038-023-01147-z.
Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutionsKuo T, Pham A, Edelson M, Kim J, Chan J, Gupta Y, Ohno-Machado L, Anderson D, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bell D, Bernstam E, Ngan C, Day M, Doctor J, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hinske L, Hu Z, Ir D, Jiang X, Kim K, Kim J, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Matheny M, Meeker D, Mou Z, Neumann L, Nguyen N, Nick A, Ohno-Machado L, Park E, Paul P, Pletcher M, Post K, Rieder C, Scherer C, Schilling L, Soares A, SooHoo S, Soysal E, Steven C, Tep B, Toy B, Wang B, Wu Z, Xu H, Yong C, Zheng K, Zhou Y, Zucker R. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. Journal Of The American Medical Informatics Association 2023, 30: 1167-1178. PMID: 36916740, PMCID: PMC10198529, DOI: 10.1093/jamia/ocad049.
WICOX: Weight-Based Integrated Cox Model for Time-to-Event Data in Distributed Databases Without Data-SharingPark J, Kim T, Kim J, Park Y. WICOX: Weight-Based Integrated Cox Model for Time-to-Event Data in Distributed Databases Without Data-Sharing. IEEE Journal Of Biomedical And Health Informatics 2023, 27: 526-537. PMID: 36318551, DOI: 10.1109/jbhi.2022.3218585.
Comparative Safety and Effectiveness of Biologic Therapy for Crohn’s Disease: A CA-IBD Cohort StudySingh S, Kim J, Luo J, Paul P, Rudrapatna V, Park S, Zheng K, Syal G, Ha C, Fleshner P, McGovern D, Sauk J, Limketkai B, Dulai P, Boland B, Eisenstein S, Ramamoorthy S, Melmed G, Mahadevan U, Sandborn W, Ohno-Machado L. Comparative Safety and Effectiveness of Biologic Therapy for Crohn’s Disease: A CA-IBD Cohort Study. Clinical Gastroenterology And Hepatology 2022, 21: 2359-2369.e5. PMID: 36343846, DOI: 10.1016/j.cgh.2022.10.029.
The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competitionKuo T, Jiang X, Tang H, Wang X, Harmanci A, Kim M, Post K, Bu D, Bath T, Kim J, Liu W, Chen H, Ohno-Machado L. The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. Journal Of The American Medical Informatics Association 2022, 29: 2182-2190. PMID: 36164820, PMCID: PMC9667175, DOI: 10.1093/jamia/ocac165.
Ethnic and Racial Inequities in Cancer Screening During the COVID-19 Pandemic: a multi-site observational study in the United StatesIdossa D, Borno H, Wang K, Pletcher M, Gresham G, Canchola A, Bell D, Matheny M, Schilling L, Perkins A, Zheng K, Ohno-Machado L, Kim J, Soohoo S, Meeker D, Gomez S. Ethnic and Racial Inequities in Cancer Screening During the COVID-19 Pandemic: a multi-site observational study in the United States. International Journal Of Cancer Care And Delivery 2022, 2 DOI: 10.53876/001c.37412.
Publisher Correction: An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki diseaseGhosh P, Katkar G, Shimizu C, Kim J, Khandelwal S, Tremoulet A, Kanegaye J, Bocchini J, Das S, Burns J, Sahoo D. Publisher Correction: An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. Nature Communications 2022, 13: 4729. PMID: 35953486, PMCID: PMC9372045, DOI: 10.1038/s41467-022-32479-7.
RNA Sequencing Reveals Beneficial Effects of Atorvastatin on Endothelial Cells in Acute Kawasaki DiseaseShimizu C, Kim J, He M, Tremoulet A, Hoffman H, Shyy J, Burns J. RNA Sequencing Reveals Beneficial Effects of Atorvastatin on Endothelial Cells in Acute Kawasaki Disease. Journal Of The American Heart Association 2022, 11: e025408. PMID: 35861833, PMCID: PMC9707837, DOI: 10.1161/jaha.122.025408.
Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort StudyGu P, Luo J, Kim J, Paul P, Limketkai B, Sauk J, Park S, Parekh N, Zheng K, Rudrapatna V, Syal G, Ha C, McGovern D, Melmed G, Fleshner P, Eisenstein S, Ramamoorthy S, Dulai P, Boland B, Grunvald E, Mahadevan U, Ohno-Machado L, Sandborn W, Singh S. Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. The American Journal Of Gastroenterology 2022, 117: 1639-1647. PMID: 35973139, DOI: 10.14309/ajg.0000000000001855.
Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort StudyNguyen N, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai P, Boland B, Mahadevan U, Sandborn W, Ohno-Machado L, McGovern D, Singh S. Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Clinical Gastroenterology And Hepatology 2022, 21: 173-181.e5. PMID: 35644340, PMCID: PMC9701245, DOI: 10.1016/j.cgh.2022.05.008.
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki diseaseGhosh P, Katkar G, Shimizu C, Kim J, Khandelwal S, Tremoulet A, Kanegaye J, Bocchini J, Das S, Burns J, Sahoo D. An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. Nature Communications 2022, 13: 2687. PMID: 35577777, PMCID: PMC9110726, DOI: 10.1038/s41467-022-30357-w.
Su1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBDNguyen N, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Boland B, Mahadevan U, Sandborn W, Ohno-Machado L, Mcgovern D, Singh S. Su1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBD. Gastroenterology 2022, 162: s-482-s-483. DOI: 10.1016/s0016-5085(22)61145-4.
Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitisPovero D, Tameda M, Eguchi A, Ren W, Kim J, Myers R, Goodman Z, Harrison S, Sanyal A, Bosch J, Ohno-Machado L, Feldstein A. Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. Scientific Reports 2022, 12: 3027. PMID: 35194091, PMCID: PMC8863778, DOI: 10.1038/s41598-022-06809-0.
No Benefit of Continuing 5-Aminosalicylates in Patients with Crohn’s Disease Treated with Anti-metabolite TherapyPicetti D, Kim J, Zhu W, Sandborn W, Jairath V, Singh S. No Benefit of Continuing 5-Aminosalicylates in Patients with Crohn’s Disease Treated with Anti-metabolite Therapy. Digestive Diseases And Sciences 2021, 67: 3115-3123. PMID: 34797442, PMCID: PMC9117569, DOI: 10.1007/s10620-021-07301-x.
Abstract 13032: Endothelial Cell Response to Intravenous Immunoglobulin, Infliximab and Atorvastatin Treatment During the Acute Phase of Kawasaki DiseaseShimizu C, Kim J, He M, Hoffman H, Shyy J, Burns J, Tremoulet A. Abstract 13032: Endothelial Cell Response to Intravenous Immunoglobulin, Infliximab and Atorvastatin Treatment During the Acute Phase of Kawasaki Disease. Circulation 2021, 144: a13032-a13032. DOI: 10.1161/circ.144.suppl_1.13032.
Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain trackKuo T, Bath T, Ma S, Pattengale N, Yang M, Cao Y, Hudson C, Kim J, Post K, Xiong L, Ohno-Machado L. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. International Journal Of Medical Informatics 2021, 154: 104559. PMID: 34474309, PMCID: PMC9933142, DOI: 10.1016/j.ijmedinf.2021.104559.
Privacy-protecting, reliable response data discovery using COVID-19 patient observationsKim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.
Kawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic ProfilesJackson H, Menikou S, Hamilton S, McArdle A, Shimizu C, Galassini R, Huang H, Kim J, Tremoulet A, Thorne A, Fischer R, de Jonge M, Kuijpers T, Wright V, Burns J, Casals-Pascual C, Herberg J, Levin M, Kaforou M, On Behalf Of The Perform Consortium. Kawasaki Disease Patient Stratification and Pathway Analysis Based on Host Transcriptomic and Proteomic Profiles. International Journal Of Molecular Sciences 2021, 22: 5655. PMID: 34073389, PMCID: PMC8198135, DOI: 10.3390/ijms22115655.
VERTIcal Grid lOgistic regression with Confidence Intervals (VERTIGO-CI).Kim J, Li W, Bath T, Jiang X, Ohno-Machado L. VERTIcal Grid lOgistic regression with Confidence Intervals (VERTIGO-CI). AMIA Joint Summits On Translational Science Proceedings 2021, 2021: 355-364. PMID: 34457150, PMCID: PMC8378611.
Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki diseaseHoggart C, Shimizu C, Galassini R, Wright V, Shailes H, Bellos E, Herberg J, Pollard A, O’Connor D, Choi S, Seaby E, Menikou S, Hibberd M, Sallah N, Burgner D, Brogan P, Patel H, Kim J, Tremoulet A, Salo E, van Stijn D, Kuijpers T, Burns J, Levin M. Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease. European Journal Of Human Genetics 2021, 29: 1734-1744. PMID: 33772158, PMCID: PMC7994355, DOI: 10.1038/s41431-021-00838-5.
Predictive Analytics for Glaucoma Using Data From the All of Us Research ProgramBaxter S, Saseendrakumar B, Paul P, Kim J, Bonomi L, Kuo T, Loperena R, Ratsimbazafy F, Boerwinkle E, Cicek M, Clark C, Cohn E, Gebo K, Mayo K, Mockrin S, Schully S, Ramirez A, Ohno-Machado L, Investigators A. Predictive Analytics for Glaucoma Using Data From the All of Us Research Program. American Journal Of Ophthalmology 2021, 227: 74-86. PMID: 33497675, PMCID: PMC8184631, DOI: 10.1016/j.ajo.2021.01.008.
Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1.Rawat P, Brummel S, Singh K, Kim J, Frazer K, Nichols S, Seage G, Williams P, Van Dyke R, Harismendy O, Trout R, Spector S. Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1. The Journal Of Infectious Diseases 2020, 224: 870-880. PMID: 33373444, PMCID: PMC8408770, DOI: 10.1093/infdis/jiaa792.
No benefit of continuing vs stopping 5‐aminosalicylates in patients with ulcerative colitis escalated to anti‐metabolite therapySingh S, Kim J, Zhu W, Dulai P, Sandborn W, Jairath V. No benefit of continuing vs stopping 5‐aminosalicylates in patients with ulcerative colitis escalated to anti‐metabolite therapy. Alimentary Pharmacology & Therapeutics 2020, 52: 481-491. PMID: 32573825, PMCID: PMC8015755, DOI: 10.1111/apt.15876.
Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis miceEguchi A, Yan R, Pan S, Wu R, Kim J, Chen Y, Ansong C, Smith R, Tempaku M, Ohno-Machado L, Takei Y, Feldstein A, Tsukamoto H. Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice. Journal Of Molecular Medicine 2020, 98: 1021-1034. PMID: 32556367, PMCID: PMC7810220, DOI: 10.1007/s00109-020-01926-7.
Privacy-preserving model learning on a blockchain network-of-networksKuo T, Kim J, Gabriel R. Privacy-preserving model learning on a blockchain network-of-networks. Journal Of The American Medical Informatics Association 2020, 27: 343-354. PMID: 31943009, PMCID: PMC7025358, DOI: 10.1093/jamia/ocz214.
Patient Perspectives About Decisions to Share Medical Data and Biospecimens for ResearchKim J, Kim H, Bell E, Bath T, Paul P, Pham A, Jiang X, Zheng K, Ohno-Machado L. Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research. JAMA Network Open 2019, 2: e199550. PMID: 31433479, PMCID: PMC6707015, DOI: 10.1001/jamanetworkopen.2019.9550.
Human induced pluripotent stem cell-derived extracellular vesicles reduce hepatic stellate cell activation and liver fibrosisPovero D, Pinatel E, Leszczynska A, Goyal N, Nishio T, Kim J, Kneiber D, de Araujo Horcel L, Eguchi A, Ordonez P, Kisseleva T, Feldstein A. Human induced pluripotent stem cell-derived extracellular vesicles reduce hepatic stellate cell activation and liver fibrosis. JCI Insight 2019, 5 PMID: 31184999, PMCID: PMC6675559, DOI: 10.1172/jci.insight.125652.
HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki diseaseShimizu C, Kim J, Eleftherohorinou H, Wright V, Hoang L, Tremoulet A, Franco A, Hibberd M, Takahashi A, Kubo M, Ito K, Tanaka T, Onouchi Y, Coin L, Levin M, Burns J, Shike H, Consortium O. HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease. Human Immunology 2019, 80: 731-738. PMID: 31122742, PMCID: PMC10793643, DOI: 10.1016/j.humimm.2019.04.020.
Author Correction: Clustering and climate associations of Kawasaki Disease in San Diego County suggest environmental triggersRypdal M, Rypdal V, Burney J, Cayan D, Bainto E, Skochko S, Tremoulet A, Creamean J, Shimizu C, Kim J, Burns J. Author Correction: Clustering and climate associations of Kawasaki Disease in San Diego County suggest environmental triggers. Scientific Reports 2019, 9: 7401. PMID: 31068599, PMCID: PMC6506480, DOI: 10.1038/s41598-019-42137-6.
Evaluating and sharing global genetic ancestry in biomedical datasetsHarismendy O, Kim J, Xu X, Ohno-Machado L. Evaluating and sharing global genetic ancestry in biomedical datasets. Journal Of The American Medical Informatics Association 2019, 26: 457-461. PMID: 30869786, PMCID: PMC6433181, DOI: 10.1093/jamia/ocy194.
Clustering and climate associations of Kawasaki Disease in San Diego County suggest environmental triggersRypdal M, Rypdal V, Burney J, Cayan D, Bainto E, Skochko S, Tremoulet A, Creamean J, Shimizu C, Kim J, Burns J. Clustering and climate associations of Kawasaki Disease in San Diego County suggest environmental triggers. Scientific Reports 2018, 8: 16140. PMID: 30420674, PMCID: PMC6232126, DOI: 10.1038/s41598-018-33124-4.
Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki diseaseOyamada J, Shimizu C, Kim J, Williams M, Png E, Hibberd M, Tremoulet A, Perry J, Burns J. Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki disease. Congenital Heart Disease 2018, 14: 213-220. PMID: 30395415, DOI: 10.1111/chd.12696.
Genomics and electronic health record systems.Ohno-Machado L, Kim J, Gabriel R, Kuo G, Hogarth M. Genomics and electronic health record systems. Human Molecular Genetics 2018, 27: r48-r55. PMID: 29741693, PMCID: PMC5946823, DOI: 10.1093/hmg/ddy104.
PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screensSpahn P, Bath T, Weiss R, Kim J, Esko J, Lewis N, Harismendy O. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Scientific Reports 2017, 7: 15854. PMID: 29158538, PMCID: PMC5696473, DOI: 10.1038/s41598-017-16193-9.
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies.Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 2017, 33: 3716-3725. PMID: 29036461, PMCID: PMC5860319, DOI: 10.1093/bioinformatics/btx470.
SHINE-LEscobedo L, Ahuja R, Barrera E, Guan C, Zavala E, El-Kareh R, Kim J, Rhee K, Peng W, Xing G, Bi C, Huh J. SHINE-L. 2017, 2560-2568. DOI: 10.1145/3027063.3053231.
A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient SurgeriesGabriel R, Waterman R, Kim J, Ohno-Machado L. A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries. Anesthesia & Analgesia 2017, 124: 1529-1536. PMID: 28079580, DOI: 10.1213/ane.0000000000001827.
A risk prediction score for acute kidney injury in the intensive care unitMalhotra R, Kashani K, Macedo E, Kim J, Bouchard J, Wynn S, Li G, Ohno-Machado L, Mehta R. A risk prediction score for acute kidney injury in the intensive care unit. Nephrology Dialysis Transplantation 2017, 32: 814-822. PMID: 28402551, DOI: 10.1093/ndt/gfx026.
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibilityKim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.
Extracellular vesicles released by hepatocytes from gastric infusion model of alcoholic liver disease contain a MicroRNA barcode that can be detected in bloodEguchi A, Lazaro R, Wang J, Kim J, Povero D, Willliams B, Ho S, Stärkel P, Schnabl B, Ohno‐Machado L, Tsukamoto H, Feldstein A. Extracellular vesicles released by hepatocytes from gastric infusion model of alcoholic liver disease contain a MicroRNA barcode that can be detected in blood. Hepatology 2017, 65: 475-490. PMID: 27639178, PMCID: PMC5407075, DOI: 10.1002/hep.28838.
ADAM12 induction by Twist1 promotes tumor invasion and metastasis via regulation of invadopodia and focal adhesionsEckert M, Santiago-Medina M, Lwin T, Kim J, Courtneidge S, Yang J. ADAM12 induction by Twist1 promotes tumor invasion and metastasis via regulation of invadopodia and focal adhesions. Journal Of Cell Science 2017, 130: 2036-2048. PMID: 28468988, PMCID: PMC5482979, DOI: 10.1242/jcs.198200.
SAT-438 Induced pluripotent stem cells-derived extracellular vesicles shuttle bioactive molecules with anti-fibrotic potential in vitro and in vivoPovero D, Pinatel E, Kim J, Goyal N, Johnson C, Kneiber D, Feldstein A. SAT-438 Induced pluripotent stem cells-derived extracellular vesicles shuttle bioactive molecules with anti-fibrotic potential in vitro and in vivo. Journal Of Hepatology 2017, 66: s649-s650. DOI: 10.1016/s0168-8278(17)31760-9.
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionSChen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp S, Shimizu C, Burns J, Wright V, Png E, Hibberd M, Lloyd D, Yang H, Telenti A, Bloss C, Fox D, Lauter K, Ohno-Machado L. PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinformatics 2016, 33: 871-878. PMID: 28065902, PMCID: PMC5860394, DOI: 10.1093/bioinformatics/btw758.
iCONCUR: informed consent for clinical data and bio-sample use for researchKim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe S, Ohno-Machado L. iCONCUR: informed consent for clinical data and bio-sample use for research. Journal Of The American Medical Informatics Association 2016, 24: 380-387. PMID: 27589942, PMCID: PMC5391727, DOI: 10.1093/jamia/ocw115.
Personas in online health communitiesHuh J, Kwon B, Kim S, Lee S, Choo J, Kim J, Choi M, Yi J. Personas in online health communities. Journal Of Biomedical Informatics 2016, 63: 212-225. PMID: 27568913, PMCID: PMC5268468, DOI: 10.1016/j.jbi.2016.08.019.
Developing a Semantic Model to Describe Physical Activity Data.Kim H, Kim J, Shenvi E, Quach J, Sutjiadi B, Richardson A, Lin K. Developing a Semantic Model to Describe Physical Activity Data. 2016, 225: 447-51. PMID: 27332240.
Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing dataKroll J, Kim J, Ohno-Machado L, de Souza S. Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. PeerJ 2015, 3: e1419. PMID: 26618088, PMCID: PMC4655094, DOI: 10.7717/peerj.1419.
Safety and efficacy of pharmacological thromboprophylaxis for hospitalized patients with cirrhosis: a single‐center retrospective cohort studyShatzel J, Dulai P, Harbin D, Cheung H, Reid T, Kim J, James S, Khine H, Batman S, Whyman J, Dickson R, Ornstein D. Safety and efficacy of pharmacological thromboprophylaxis for hospitalized patients with cirrhosis: a single‐center retrospective cohort study. Journal Of Thrombosis And Haemostasis 2015, 13: 1245-1253. PMID: 25955079, PMCID: PMC6658183, DOI: 10.1111/jth.13000.
Abstract O.17: Whole Genome Sequencing of a six-member African American family with two Kawasaki disease-affected siblings identifies novel susceptibility variantsKim J, Shimizu C, Yang H, Harismendy O, Truong Hoang L, Levy E, Cimaz R, Burgner D, Yeung R, Khor C, Davila S, Levin M, Kuijpers T, Hibberd M, Ohno-Machado L, Burns J. Abstract O.17: Whole Genome Sequencing of a six-member African American family with two Kawasaki disease-affected siblings identifies novel susceptibility variants. Circulation 2015, 131 DOI: 10.1161/circ.131.suppl_2.o17.
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructureKim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics 2014, 30: 2826-2827. PMID: 24907367, PMCID: PMC4173015, DOI: 10.1093/bioinformatics/btu377.
GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRandaWang S, Kim J, Jiang X, Brunner S, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Medical Genomics 2014, 7: s9. PMID: 25077821, PMCID: PMC4101446, DOI: 10.1186/1755-8794-7-s1-s9.
Reducing Communication Delays and Improving Quality of Care with a Tuberculosis Laboratory Information System in Resource Poor Environments: A Cluster Randomized Controlled TrialBlaya J, Shin S, Yagui M, Contreras C, Cegielski P, Yale G, Suarez C, Asencios L, Bayona J, Kim J, Fraser H. Reducing Communication Delays and Improving Quality of Care with a Tuberculosis Laboratory Information System in Resource Poor Environments: A Cluster Randomized Controlled Trial. PLOS ONE 2014, 9: e90110. PMID: 24721980, PMCID: PMC3982951, DOI: 10.1371/journal.pone.0090110.
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned readsLi P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. Journal Of The American Medical Informatics Association 2014, 21: 363-373. PMID: 24368726, PMCID: PMC3932469, DOI: 10.1136/amiajnl-2013-002147.
Prediction of MicroRNA Precursors Using Parsimonious Feature SetsStepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. Cancer Informatics 2014, 13s1: cin.s13877. PMID: 25392687, PMCID: PMC4216048, DOI: 10.4137/cin.s13877.
DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling TechniqueLi P, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X. DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique. PLOS ONE 2013, 8: e80377. PMID: 24282536, PMCID: PMC3840021, DOI: 10.1371/journal.pone.0080377.
Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)Lin K, Tharp M, Conway M, Hsieh A, Ross M, Kim J, Kim H. Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP). PLOS ONE 2013, 8: e76384. PMID: 24058713, PMCID: PMC3776754, DOI: 10.1371/journal.pone.0076384.
Detecting inappropriate access to electronic health records using collaborative filteringMenon A, Jiang X, Kim J, Vaidya J, Ohno-Machado L. Detecting inappropriate access to electronic health records using collaborative filtering. Machine Learning 2013, 95: 87-101. PMID: 24683293, PMCID: PMC3967851, DOI: 10.1007/s10994-013-5376-1.
Genomes in the cloud: balancing privacy rights and the public good.Ohno-Machado L, Farcas C, Kim J, Wang S, Jiang X. Genomes in the cloud: balancing privacy rights and the public good. AMIA Joint Summits On Translational Science Proceedings 2013, 2013: 128. PMID: 24303320.
Differential Expression of miR-145 in Children with Kawasaki DiseaseShimizu C, Kim J, Stepanowsky P, Trinh C, Lau H, Akers J, Chen C, Kanegaye J, Tremoulet A, Ohno-Machado L, Burns J. Differential Expression of miR-145 in Children with Kawasaki Disease. PLOS ONE 2013, 8: e58159. PMID: 23483985, PMCID: PMC3590129, DOI: 10.1371/journal.pone.0058159.
Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis.Thawait S, Kim J, Klufas R, Morrison W, Flanders A, Carrino J, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. American Journal Of Roentgenology 2013, 200: 493-502. PMID: 23436836, DOI: 10.2214/ajr.11.7192.
Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and CalibrationJiang X, Menon A, Wang S, Kim J, Ohno-Machado L. Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration. PLOS ONE 2012, 7: e48823. PMID: 23139819, PMCID: PMC3490990, DOI: 10.1371/journal.pone.0048823.
Selecting cases for whom additional tests can improve prognostication.Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L. Selecting cases for whom additional tests can improve prognostication. AMIA Annual Symposium Proceedings 2012, 2012: 1260-8. PMID: 23304404, PMCID: PMC3540468.
A robust feature selection method for novel pre-microRNA identification using a combination of nucleotide-structure tripletsStepanowsky P, Kim J, Ohno-Machado L. A robust feature selection method for novel pre-microRNA identification using a combination of nucleotide-structure triplets. 2012, 1: 61-61. DOI: 10.1109/hisb.2012.20.
Grid Binary LOgistic REgression (GLORE): building shared models without sharing dataWu Y, Jiang X, Kim J, Ohno-Machado L. Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. Journal Of The American Medical Informatics Association 2012, 19: 758-764. PMID: 22511014, PMCID: PMC3422844, DOI: 10.1136/amiajnl-2012-000862.
A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision supportJiang X, Boxwala A, El-Kareh R, Kim J, Ohno-Machado L. A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support. Journal Of The American Medical Informatics Association 2012, 19: e137-e144. PMID: 22493049, PMCID: PMC3392846, DOI: 10.1136/amiajnl-2011-000751.
I-spline Smoothing for Calibrating Predictive Models.Wu Y, Jiang X, Kim J, Ohno-Machado L. I-spline Smoothing for Calibrating Predictive Models. AMIA Joint Summits On Translational Science Proceedings 2012, 2012: 39-46. PMID: 22779048, PMCID: PMC3392066.
Calibrating predictive model estimates to support personalized medicineJiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. Journal Of The American Medical Informatics Association 2012, 19: 263-274. PMID: 21984587, PMCID: PMC3277613, DOI: 10.1136/amiajnl-2011-000291.
iDASH: integrating data for analysis, anonymization, and sharingOhno-Machado L, Bafna V, Boxwala A, Chapman B, Chapman W, Chaudhuri K, Day M, Farcas C, Heintzman N, Jiang X, Kim H, Kim J, Matheny M, Resnic F, Vinterbo S, team A. iDASH: integrating data for analysis, anonymization, and sharing. Journal Of The American Medical Informatics Association 2012, 19: 196-201. PMID: 22081224, PMCID: PMC3277627, DOI: 10.1136/amiajnl-2011-000538.
Trends in biomedical informatics: most cited topics from recent yearsKim H, Jiang X, Kim J, Ohno-Machado L. Trends in biomedical informatics: most cited topics from recent years. Journal Of The American Medical Informatics Association 2011, 18: i166-i170. PMID: 22180873, PMCID: PMC3241182, DOI: 10.1136/amiajnl-2011-000706.
A multi-layered framework for disseminating knowledge for computer-based decision supportBoxwala A, Rocha B, Maviglia S, Kashyap V, Meltzer S, Kim J, Tsurikova R, Wright A, Paterno M, Fairbanks A, Middleton B. A multi-layered framework for disseminating knowledge for computer-based decision support. Journal Of The American Medical Informatics Association 2011, 18: i132-i139. PMID: 22052898, PMCID: PMC3241169, DOI: 10.1136/amiajnl-2011-000334.
Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs.Kim J, Grillo J, Boxwala A, Jiang X, Mandelbaum R, Patel B, Mikels D, Vinterbo S, Ohno-Machado L. Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs. AMIA Annual Symposium Proceedings 2011, 2011: 723-31. PMID: 22195129, PMCID: PMC3243249.
Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cellsKamberov Y, Kim J, Mazitschek R, Kuo W, Whitman M. Microarray profiling reveals the integrated stress response is activated by halofuginone in mammary epithelial cells. BMC Research Notes 2011, 4: 381. PMID: 21974968, PMCID: PMC3197508, DOI: 10.1186/1756-0500-4-381.
Using statistical and machine learning to help institutions detect suspicious access to electronic health recordsBoxwala A, Kim J, Grillo J, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. Journal Of The American Medical Informatics Association 2011, 18: 498-505. PMID: 21672912, PMCID: PMC3128412, DOI: 10.1136/amiajnl-2011-000217.
Abstract 4747: Twist1-induced invadopodia formation promotes tumor metastasisEckert M, Lwin T, Chang A, Kim J, Danis E, Ohno-Machado L, Yang J. Abstract 4747: Twist1-induced invadopodia formation promotes tumor metastasis. Cancer Research 2011, 71: 4747-4747. DOI: 10.1158/1538-7445.am2011-4747.
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithmKim J, Patel K, Jung H, Kuo W, Ohno-Machado L. AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics 2011, 12: 75. PMID: 21410990, PMCID: PMC3076267, DOI: 10.1186/1471-2105-12-75.
Smooth isotonic regression: a new method to calibrate predictive models.Jiang X, Osl M, Kim J, Ohno-Machado L. Smooth isotonic regression: a new method to calibrate predictive models. AMIA Joint Summits On Translational Science Proceedings 2011, 2011: 16-20. PMID: 22211175, PMCID: PMC3248752.
Twist1-Induced Invadopodia Formation Promotes Tumor MetastasisEckert M, Lwin T, Chang A, Kim J, Danis E, Ohno-Machado L, Yang J. Twist1-Induced Invadopodia Formation Promotes Tumor Metastasis. Cancer Cell 2011, 19: 372-386. PMID: 21397860, PMCID: PMC3072410, DOI: 10.1016/j.ccr.2011.01.036.
Snail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and MetastasisCasas E, Kim J, Bendesky A, Ohno-Machado L, Wolfe C, Yang J. Snail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis. Cancer Research 2011, 71: 245-254. PMID: 21199805, PMCID: PMC3025803, DOI: 10.1158/0008-5472.can-10-2330.
Full impact of laboratory information system requires direct use by clinical staff: cluster randomized controlled trialBlaya J, Shin S, Contreras C, Yale G, Suarez C, Asencios L, Kim J, Rodriguez P, Cegielski P, Fraser H. Full impact of laboratory information system requires direct use by clinical staff: cluster randomized controlled trial. Journal Of The American Medical Informatics Association 2011, 18: 11-16. PMID: 21113076, PMCID: PMC3005868, DOI: 10.1136/jamia.2010.005280.
Effect of data combination on predictive modeling: a study using gene expression data.Osl M, Dreiseitl S, Kim J, Patel K, Baumgartner C, Ohno-Machado L. Effect of data combination on predictive modeling: a study using gene expression data. AMIA Annual Symposium Proceedings 2010, 2010: 567-71. PMID: 21347042, PMCID: PMC3041313.
Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer.Sadow C, Wheeler S, Kim J, Ohno-Machado L, Silverman S. Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer. American Journal Of Roentgenology 2010, 195: w337-43. PMID: 20966298, DOI: 10.2214/ajr.09.4147.
Electronic laboratory system reduces errors in National Tuberculosis Program: a cluster randomized controlled trial.Blaya J, Shin S, Yale G, Suarez C, Asencios L, Contreras C, Rodriguez P, Kim J, Cegielski P, Fraser H. Electronic laboratory system reduces errors in National Tuberculosis Program: a cluster randomized controlled trial. The International Journal Of Tuberculosis And Lung Disease 2010, 14: 1009-15. PMID: 20626946, PMCID: PMC8324019.
DSGeo: Software tools for cross-platform analysis of gene expression data in GEOLacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: Software tools for cross-platform analysis of gene expression data in GEO. Journal Of Biomedical Informatics 2010, 43: 709-715. PMID: 20435161, PMCID: PMC2934864, DOI: 10.1016/j.jbi.2010.04.007.
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.Pitzer E, Kim J, Patel K, Galante P, Ohno-Machado L. PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. AMIA Joint Summits On Translational Science Proceedings 2010, 2010: 25-9. PMID: 21347141, PMCID: PMC3041550.
Towards large-scale sample annotation in gene expression repositoriesPitzer E, Lacson R, Hinske C, Kim J, Galante P, Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics 2009, 10: s9. PMID: 19761579, PMCID: PMC2745696, DOI: 10.1186/1471-2105-10-s9-s9.
Is there an advantage in scoring early embryos on more than one day?Racowsky C, Ohno-Machado L, Kim J, Biggers J. Is there an advantage in scoring early embryos on more than one day? Human Reproduction 2009, 24: 2104-2113. PMID: 19493872, PMCID: PMC2727402, DOI: 10.1093/humrep/dep198.
Personal digital assistants to collect tuberculosis bacteriology data in Peru reduce delays, errors, and workload, and are acceptable to users: cluster randomized controlled trialBlaya JA, Cohen T, Rodríguez P, Kim J, Fraser HS. Personal digital assistants to collect tuberculosis bacteriology data in Peru reduce delays, errors, and workload, and are acceptable to users: cluster randomized controlled trial. International Journal Of Infectious Diseases 2008, 13: 410-418. PMID: 19097925, PMCID: PMC2673336, DOI: 10.1016/j.ijid.2008.09.015.

Edit Profile

Contact Information

Research & Publications

Biography

News

Coauthors

Selected Publications