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    Lucila Ohno-Machado

    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0728
    CA La Jolla 92093
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      Other Positions
      TitleDirector of BioMedical Informatics for the Clinical and Translational Research Institute
      InstitutionUniversity of California, San Diego

      Collapse Biography 
      Collapse Education and Training
      Stanford University, Palo Alto, CAPh.D.Medical Information Sciences and Computer Science
      University of Sao Paulo, Sao Paulo, BrazilM.D.Medicine
      Fundacao Getulio Vargas, Escola de Administração, Sao Paulo, BrazilM.B.A.Healthcare Administration
      Collapse Awards and Honors
      International Academy of Health Sciences InformaticsElected member
      American College of Medical InformaticsElected fellow
      American Society for Clinical InvestigationElected member
      American Institute for Medical and Biological EngineeringElected fellow

      Collapse Overview 
      Collapse Overview
      Professor of Medicine
      Associate Dean for Informatics and Technology, UCSD School of Medicine
      Chair, UCSD Health Department of Biomedical Informatics
      Editor in Chief, Journal of the American Medical Informatics Association
      Director, San Diego Biomedical Informatics Education and Research

      Collapse Research 
      Collapse Research Activities and Funding
      California Precision Medicine Research Program Consortium
      NIH OT2OD026552Apr 1, 2018 - Mar 31, 2023
      Role: Principal Investigator
      Protecting Privacy and Facilitating Shared Access of Clinical and Genetic Data of Special Populations
      NIH/NHLBI R01HL136835Dec 15, 2017 - Nov 30, 2021
      Role: Principal Investigator
      CALIFORNIA: Cloud-agnostic Architecture to Locate Indexed FAIR Objects and safely Reuse them in New Integrated Analyses
      NIH OT3OD025462Sep 30, 2017 - Jun 30, 2018
      Role: Principal Investigator
      Decentralized differentially-private methods for dynamic data release and analysis
      NIH/NIGMS R01GM118609Jan 1, 2017 - Dec 31, 2020
      Role: Principal Investigator
      California Precision Medicine Consortium
      NIH OT2OD024611Sep 27, 2016 - Aug 31, 2017
      Role: Principal Investigator
      SERGEANT: SEcuRe GEnome Analysis competition
      NIH/NHGRI R13HG009072Sep 12, 2016 - Jun 30, 2018
      Role: Principal Investigator
      iCONCUR: informed CONsent for Clinical data and biosample Use for Research
      NIH/NHGRI R01HG008802Sep 21, 2015 - Jun 30, 2018
      Role: Principal Investigator
      BioCADDIE: Biomedical and healthCAre Data Discovery and Indexing Engine center
      NIH/NIAID U24AI117966Sep 29, 2014 - Aug 31, 2017
      Role: Principal Investigator
      San Diego Biomedical Informatics Education & Research (SABER)
      NIH/NLM T15LM011271Jul 1, 2012 - Jun 30, 2022
      Role: Principal Investigator
      Phenotype Discovery in NHLBI Genomic Studies (PhD)
      NIH/NHLBI UH3HL108785Jul 19, 2011 - Sep 23, 2014
      Role: Principal Investigator
      Phenotype Discovery in NHLBI Genomic Studies (PhD)
      NIH/NHLBI UH2HL108785Jul 19, 2011 - May 31, 2013
      Role: Principal Investigator
      SCANNER: Scalable National Network for Effectiveness Research
      AHRQ R01HS019913Sep 30, 2010 - Sep 29, 2013
      Role: Principal Investigator
      iDASH: Integrating Data for Analysis, Anonymization, and Sharing
      NIH/NHLBI U54HL108460Sep 20, 2010 - Jun 30, 2016
      Role: Principal Investigator
      Global Health Knowledge Collective: A Collaborative Toolkit for Global Health
      NIH/FIC R24TW008805Sep 15, 2010 - Aug 31, 2012
      Role: Principal Investigator
      Assessing quality of individual predictions in medical decision support systems
      NIH/NLM R01LM009520Jun 1, 2007 - Dec 2, 2011
      Role: Principal Investigator
      Biomedical Research Informatics for Global Health Training (BRIGHT) Program
      NIH/FIC D43TW007015Jun 1, 2004 - Jun 30, 2014
      Role: Principal Investigator
      NIH/NLM R13LM006929Jan 3, 2000 - Aug 31, 2000
      Role: Principal Investigator
      NIH/FIC D43TW001279Sep 30, 1999 - May 31, 2004
      Role: Principal Investigator
      NIH/NLM R01LM006538Sep 30, 1998 - Aug 31, 2001
      Role: Principal Investigator
      NIH/NLM R29LM006538Sep 30, 1998 - Aug 31, 2000
      Role: Principal Investigator
      NIH/NLM R55LM006538Sep 15, 1997 - Sep 29, 1998
      Role: Principal Investigator
      AHRQ R03HS008462Sep 1, 1994 - Feb 29, 1996
      Role: Principal Investigator
      Biomedical Informatics and Data Science Research Training Program (BIRT)
      NIH/NLM T15LM007092Jul 1, 1992 - Jun 30, 2022
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. J Am Med Inform Assoc. 2017 Jul 01; 24(4):799-805. PMID: 28339683.
        View in: PubMed
      2. Ohno-Machado L. Education of informatics professionals and development of electronic information resources for clinicians, patients, health scientists, and study participants. J Am Med Inform Assoc. 2017 Jul 01; 24(4):679. PMID: 28927160.
        View in: PubMed
      3. Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L. DATS, the data tag suite to enable discoverability of datasets. Sci Data. 2017 Jun 06; 4:170059. PMID: 28585923.
        View in: PubMed
      4. Ohno-Machado L, Sansone SA, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj AE, Bell E, Soysal E, Zong N, Kim HE. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet. 2017 May 26; 49(6):816-819. PMID: 28546571.
        View in: PubMed
      5. Ohno-Machado L. Advancing healthcare and biomedical research via new data-driven approaches. J Am Med Inform Assoc. 2017 May 01; 24(3):471. PMID: 28403381.
        View in: PubMed
      6. Malhotra R, Kashani KB, 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. Nephrol Dial Transplant. 2017 Apr 10. PMID: 28402551.
        View in: PubMed
      7. Ohno-Machado L. Electronic health records: usability and utilization by health care providers and patients. J Am Med Inform Assoc. 2017 Apr 01; 24(e1):e1. PMID: 28395061.
        View in: PubMed
      8. Chen F, Wang S, Jiang X, Ding S, Lu Y, Kim J, Sahinalp SC, Shimizu C, Burns JC, Wright VJ, Png E, Hibberd ML, Lloyd DD, Yang H, Telenti A, Bloss CS, Fox D, Lauter K, Ohno-Machado L. PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinformatics. 2017 Mar 15; 33(6):871-878. PMID: 28065902.
        View in: PubMed
      9. Kim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe SF, Ohno-Machado L. iCONCUR: informed consent for clinical data and bio-sample use for research. J Am Med Inform Assoc. 2017 03 01; 24(2):380-387. PMID: 27589942.
        View in: PubMed
      10. Ohno-Machado L. Health information technology and patient safety. J Am Med Inform Assoc. 2017 03 01; 24(2):243. PMID: 28204518.
        View in: PubMed
      11. Sitapati A, Kim H, Berkovich B, Marmor R, Singh S, El-Kareh R, Clay B, Ohno-Machado L. Integrated precision medicine: the role of electronic health records in delivering personalized treatment. Wiley Interdiscip Rev Syst Biol Med. 2017 May; 9(3). PMID: 28207198.
        View in: PubMed
      12. Kuo TT, Rao P, Maehara C, Doan S, Chaparro JD, Day ME, Farcas C, Ohno-Machado L, Hsu CN. Ensembles of NLP Tools for Data Element Extraction from Clinical Notes. AMIA Annu Symp Proc. 2016; 2016:1880-1889. PMID: 28269947.
        View in: PubMed
      13. Kim H, Choi J, Jang I, Quach J, Ohno-Machado L. Feasibility of Representing Data from Published Nursing Research Using the OMOP Common Data Model. AMIA Annu Symp Proc. 2016; 2016:715-723. PMID: 28269868.
        View in: PubMed
      14. Kim J, Shimizu C, Kingsmore SF, Veeraraghavan N, Levy E, Ribeiro Dos Santos AM, Yang H, Flatley J, Hoang LT, Hibberd ML, Tremoulet AH, Harismendy O, Ohno-Machado L, Burns JC. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLoS One. 2017; 12(2):e0170977. PMID: 28151979.
        View in: PubMed
      15. Gabriel RA, Waterman RS, Kim J, Ohno-Machado L. A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries. Anesth Analg. 2017 Jan 11. PMID: 28079580.
        View in: PubMed
      16. Ohno-Machado L. Using health information technology for clinical decision support and predictive analytics. J Am Med Inform Assoc. 2017 Jan; 24(1):1. PMID: 28039394.
        View in: PubMed
      17. Eguchi A, Lazaro RG, Wang J, Kim J, Povero D, Willliams B, Ho SB, Stärkel P, Schnabl B, Ohno-Machado L, Tsukamoto H, Feldstein AE. 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 Feb; 65(2):475-490. PMID: 27639178.
        View in: PubMed
      18. Ohno-Machado L. Data-driven informatics tools targeting patients and providers. J Am Med Inform Assoc. 2016 Nov; 23(6):1039. PMID: 27880716.
        View in: PubMed
      19. Tang H, Jiang X, Wang X, Wang S, Sofia H, Fox D, Lauter K, Malin B, Telenti A, Xiong L, Ohno-Machado L. Protecting genomic data analytics in the cloud: state of the art and opportunities. BMC Med Genomics. 2016 Oct 13; 9(1):63. PMID: 27733153.
        View in: PubMed
      20. Nodora JN, Komenaka IK, Bouton ME, Ohno-Machado L, Schwab R, Kim HE, Farcas C, Perez G, Elena Martinez M. Biospecimen Sharing Among Hispanic Women in a Safety-Net Clinic: Implications for the Precision Medicine Initiative. J Natl Cancer Inst. 2017 02; 109(2). PMID: 27688295.
        View in: PubMed
      21. Wang S, Jiang X, Singh S, Marmor R, Bonomi L, Fox D, Dow M, Ohno-Machado L. Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States. Ann N Y Acad Sci. 2017 Jan; 1387(1):73-83. PMID: 27681358.
        View in: PubMed
      22. Ohno-Machado L. Building systems that change clinical practice and advance health sciences research. J Am Med Inform Assoc. 2016 Sep; 23(5):857. PMID: 27562746.
        View in: PubMed
      23. Shi H, Jiang C, Dai W, Jiang X, Tang Y, Ohno-Machado L, Wang S. Secure Multi-pArty Computation Grid LOgistic REgression (SMAC-GLORE). BMC Med Inform Decis Mak. 2016 Jul 25; 16 Suppl 3:89. PMID: 27454168; PMCID: PMC4959358.
      24. Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo TT, Hsu CN, Ohno-Machado L. Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. AMIA Jt Summits Transl Sci Proc. 2016; 2016:225-34. PMID: 27570676; PMCID: PMC5001748.
      25. Doan S, Maehara CK, Chaparro JD, Lu S, Liu R, Graham A, Berry E, Hsu CN, Kanegaye JT, Lloyd DD, Ohno-Machado L, Burns JC, Tremoulet AH. Building a Natural Language Processing Tool to Identify Patients With High Clinical Suspicion for Kawasaki Disease from Emergency Department Notes. Acad Emerg Med. 2016 05; 23(5):628-36. PMID: 26826020.
        View in: PubMed
      26. Ohno-Machado L. Data and the clinical decision support loop. J Am Med Inform Assoc. 2016 Apr; 23(e1):e1. PMID: 27071919; PMCID: PMC4954618 [Available on 04/01/17].
      27. Ohno-Machado L. A message to the next generation of biomedical informatics professionals. J Am Med Inform Assoc. 2016 Mar; 23(2):241. PMID: 26961493.
        View in: PubMed
      28. Ohno-Machado L. Using informatics to engage patients and healthcare providers. J Am Med Inform Assoc. 2016 Jan; 23(1):1. PMID: 26912536.
        View in: PubMed
      29. Kroll JE, Kim J, Ohno-Machado L, de Souza SJ. Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. PeerJ. 2015; 3:e1419. PMID: 26618088; PMCID: PMC4655094.
      30. Li Y, Jiang X, Wang S, Xiong H, Ohno-Machado L. VERTIcal Grid lOgistic regression (VERTIGO). J Am Med Inform Assoc. 2016 May; 23(3):570-9. PMID: 26554428; PMCID: PMC4901373 [Available on 05/01/17].
      31. Han D, Wang S, Jiang C, Jiang X, Kim HE, Sun J, Ohno-Machado L. Trends in biomedical informatics: automated topic analysis of JAMIA articles. J Am Med Inform Assoc. 2015 Nov; 22(6):1153-63. PMID: 26555018; PMCID: PMC5009912 [Available on 11/01/16].
      32. Ohno-Machado L. Mining electronic health record data: finding the gold nuggets. J Am Med Inform Assoc. 2015 Sep; 22(5):937. PMID: 26330468.
        View in: PubMed
      33. Lu CL, Wang S, Ji Z, Wu Y, Xiong L, Jiang X, Ohno-Machado L. WebDISCO: a web service for distributed cox model learning without patient-level data sharing. J Am Med Inform Assoc. 2015 Nov; 22(6):1212-9. PMID: 26159465; PMCID: PMC5009917 [Available on 11/01/16].
      34. Meeker D, Jiang X, Matheny ME, Farcas C, D'Arcy M, Pearlman L, Nookala L, Day ME, Kim KK, Kim H, Boxwala A, El-Kareh R, Kuo GM, Resnic FS, Kesselman C, Ohno-Machado L. A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research. J Am Med Inform Assoc. 2015 Nov; 22(6):1187-95. PMID: 26142423; PMCID: PMC4639714 [Available on 11/01/16].
      35. Ohno-Machado L. Tailoring informatics interventions to patients and healthcare providers. J Am Med Inform Assoc. 2015 Jul; 22(4):747. PMID: 26116707.
        View in: PubMed
      36. Ohno-Machado L. A journal's role in resource sharing and reproducibility. J Am Med Inform Assoc. 2015 May; 22(3):491. PMID: 26048962.
        View in: PubMed
      37. Kim KK, Joseph JG, Ohno-Machado L. Comparison of consumers' views on electronic data sharing for healthcare and research. J Am Med Inform Assoc. 2015 Jul; 22(4):821-30. PMID: 25829461; PMCID: PMC5009901.
      38. Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015; 2015:56-63. PMID: 26306236; PMCID: PMC4525219.
      39. Wu Y, Jiang X, Wang S, Jiang W, Li P, Ohno-Machado L. Grid multi-category response logistic models. BMC Med Inform Decis Mak. 2015 Feb 18; 15:10. PMID: 25886151; PMCID: PMC4342889.
      40. Jiang X, Wu Y, Marsolo K, Ohno-Machado L. Development of a web service for analysis in a distributed network. EGEMS (Wash DC). 2014; 2(1):1053. PMID: 25848586; PMCID: PMC4371401.
      41. Jiang X, Zhao Y, Wang X, Malin B, Wang S, Ohno-Machado L, Tang H. A community assessment of privacy preserving techniques for human genomes. BMC Med Inform Decis Mak. 2014; 14 Suppl 1:S1. PMID: 25521230; PMCID: PMC4290799.
      42. Kim H, Ohno-Machado L, Oh J, Jiang X. Trends in publication of nursing informatics research. AMIA Annu Symp Proc. 2014; 2014:805-14. PMID: 25954387; PMCID: PMC4419947.
      43. Bell EA, Ohno-Machado L, Grando MA. Sharing my health data: a survey of data sharing preferences of healthy individuals. AMIA Annu Symp Proc. 2014; 2014:1699-708. PMID: 25954442; PMCID: PMC4419941.
      44. Ohno-Machado L. Focusing on the patient: mHealth, social media, electronic health records, and decision support systems. J Am Med Inform Assoc. 2014 Nov-Dec; 21(6):953. PMID: 25301806; PMCID: PMC4215063.
      45. Ohno-Machado L. Disseminating informatics knowledge and training the next generation of leaders. J Am Med Inform Assoc. 2014 Nov-Dec; 21(6):954-6. PMID: 25301807; PMCID: PMC4215064.
      46. Zhao Y, Wang X, Jiang X, Ohno-Machado L, Tang H. Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. J Am Med Inform Assoc. 2015 Jan; 22(1):100-8. PMID: 25352565; PMCID: PMC4433380.
      47. Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. Cancer Inform. 2014; 13(Suppl 1):95-102. PMID: 25392687; PMCID: PMC4216048.
      48. Ohno-Machado L. Structuring text and standardizing data for clinical and population health applications. J Am Med Inform Assoc. 2014 Sep-Oct; 21(5):763. PMID: 25117592; PMCID: PMC4147604.
      49. Ross MK, Wei W, Ohno-Machado L. "Big data" and the electronic health record. Yearb Med Inform. 2014 Aug 15; 9:97-104. PMID: 25123728; PMCID: PMC4287068.
      50. Bates DW, Saria S, Ohno-Machado L, Shah A, Escobar G. Big data in health care: using analytics to identify and manage high-risk and high-cost patients. Health Aff (Millwood). 2014 Jul; 33(7):1123-31. PMID: 25006137.
        View in: PubMed
      51. Ohno-Machado L. Networking the country to promote health and scientific discovery. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):575. PMID: 24908676; PMCID: PMC4078300.
      52. Li H, Xiong L, Ohno-Machado L, Jiang X. Privacy preserving RBF kernel support vector machine. Biomed Res Int. 2014; 2014:827371. PMID: 25013805; PMCID: PMC4071990.
      53. Kim 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 Oct; 30(19):2826-7. PMID: 24907367; PMCID: PMC4173015.
      54. Ji Z, Jiang X, Wang S, Xiong L, Ohno-Machado L. Differentially private distributed logistic regression using private and public data. BMC Med Genomics. 2014; 7 Suppl 1:S14. PMID: 25079786; PMCID: PMC4101668.
      55. Wang S, Kim J, Jiang X, Brunner SF, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Med Genomics. 2014; 7 Suppl 1:S9. PMID: 25077821; PMCID: PMC4101446.
      56. Ohno-Machado L, Agha Z, Bell DS, Dahm L, Day ME, Doctor JN, Gabriel D, Kahlon MK, Kim KK, Hogarth M, Matheny ME, Meeker D, Nebeker JR. pSCANNER: patient-centered Scalable National Network for Effectiveness Research. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):621-6. PMID: 24780722; PMCID: PMC4078293.
      57. Menon AK, Jiang X, Kim J, Vaidya J, Ohno-Machado L. Detecting Inappropriate Access to Electronic Health Records Using Collaborative Filtering. Mach Learn. 2014 Apr 01; 95(1):87-101. PMID: 24683293.
        View in: PubMed
      58. Ohno-Machado L. NIH's Big Data to Knowledge initiative and the advancement of biomedical informatics. J Am Med Inform Assoc. 2014 Mar-Apr; 21(2):193. PMID: 24509598; PMCID: PMC3932475.
      59. Ohno-Machado L. Electronic health record systems: risks and benefits. J Am Med Inform Assoc. 2014 Feb; 21(e1):e1. PMID: 24453123; PMCID: PMC3957407.
      60. Doan S, Conway M, Phuong TM, Ohno-Machado L. Natural language processing in biomedicine: a unified system architecture overview. Methods Mol Biol. 2014; 1168:275-94. PMID: 24870142.
        View in: PubMed
      61. Ohno-Machado L. The role of scientific publication in times of change. J Am Med Inform Assoc. 2014 Jan-Feb; 21(1):1. PMID: 24335250; PMCID: PMC3912704.
      62. Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. J Am Med Inform Assoc. 2014 Mar-Apr; 21(2):363-73. PMID: 24368726; PMCID: PMC3932469.
      63. Kim KK, Browe DK, Logan HC, Holm R, Hack L, Ohno-Machado L. Data governance requirements for distributed clinical research networks: triangulating perspectives of diverse stakeholders. J Am Med Inform Assoc. 2014 Jul-Aug; 21(4):714-9. PMID: 24302285; PMCID: PMC4078279.
      64. Ohno-Machado L. Game changer: how informatics moved from a supporting role to a central position in healthcare. J Am Med Inform Assoc. 2013 Dec; 20(e2):e197. PMID: 24302668; PMCID: PMC3861937.
      65. Li 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(11):e80377. PMID: 24282536; PMCID: PMC3840021.
      66. Jiang X, Tse K, Wang S, Doan S, Kim H, Ohno-Machado L. Recent trends in biomedical informatics: a study based on JAMIA articles. J Am Med Inform Assoc. 2013 Dec; 20(e2):e198-205. PMID: 24214018; PMCID: PMC3861936.
      67. Ohno-Machado L. Data science and informatics: when it comes to biomedical data, is there a real distinction? J Am Med Inform Assoc. 2013 Nov-Dec; 20(6):1009. PMID: 24114329; PMCID: PMC3822125.
      68. Jiang W, Li P, Wang S, Wu Y, Xue M, Ohno-Machado L, Jiang X. WebGLORE: a web service for Grid LOgistic REgression. Bioinformatics. 2013 Dec 15; 29(24):3238-40. PMID: 24072732; PMCID: PMC3842761.
      69. Ohno-Machado L, Nadkarni P, Johnson K. Natural language processing: algorithms and tools to extract computable information from EHRs and from the biomedical literature. J Am Med Inform Assoc. 2013 Sep-Oct; 20(5):805. PMID: 23935077; PMCID: PMC3756279.
      70. Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J Am Med Inform Assoc. 2014 Jan-Feb; 21(1):31-6. PMID: 23989082; PMCID: PMC3912702.
      71. Jiang X, Sarwate AD, Ohno-Machado L. Privacy technology to support data sharing for comparative effectiveness research: a systematic review. Med Care. 2013 Aug; 51(8 Suppl 3):S58-65. PMID: 23774511; PMCID: PMC3728160.
      72. Butte AJ, Ohno-Machado L. Making it personal: translational bioinformatics. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):595-6. PMID: 23757438; PMCID: PMC3721179.
      73. Ohno-Machado L. Electronic health records: monitoring the return on large investments. J Am Med Inform Assoc. 2013 Jun; 20(e1):e1. PMID: 23687172; PMCID: PMC3715341.
      74. Wang S, Jiang X, Wu Y, Cui L, Cheng S, Ohno-Machado L. EXpectation Propagation LOgistic REgRession (EXPLORER): distributed privacy-preserving online model learning. J Biomed Inform. 2013 Jun; 46(3):480-96. PMID: 23562651; PMCID: PMC3676314.
      75. Jiang X, Ji Z, Wang S, Mohammed N, Cheng S, Ohno-Machado L. Differential-Private Data Publishing Through Component Analysis. Trans Data Priv. 2013 Apr; 6(1):19-34. PMID: 24409205.
        View in: PubMed
      76. Dai W, Xiong H, Jiang X, Ohno-Machado L. An Adaptive Difference Distribution-based Coding with Hierarchical Tree Structure for DNA Sequence Compression. Proc Data Compress Conf. 2013; 2013:371-380. PMID: 26501129.
        View in: PubMed
      77. Vaidya J, Shafiq B, Jiang X, Ohno-Machado L. Identifying inference attacks against healthcare data repositories. AMIA Jt Summits Transl Sci Proc. 2013; 2013:262-6. PMID: 24303279; PMCID: PMC3845790.
      78. Ohno-Machado L, Farcas C, Kim J, Wang S, Jiang X. Genomes in the cloud: balancing privacy rights and the public good. AMIA Jt Summits Transl Sci Proc. 2013; 2013:128. PMID: 24303320.
        View in: PubMed
      79. Shimizu C, Kim J, Stepanowsky P, Trinh C, Lau HD, Akers JC, Chen C, Kanegaye JT, Tremoulet A, Ohno-Machado L, Burns JC. Differential expression of miR-145 in children with Kawasaki disease. PLoS One. 2013; 8(3):e58159. PMID: 23483985; PMCID: PMC3590129.
      80. Ohno-Machado L. Informatics that works for you. J Am Med Inform Assoc. 2013 Mar-Apr; 20(2):211. PMID: 23400397; PMCID: PMC3638197.
      81. Thawait SK, Kim J, Klufas RA, Morrison WB, Flanders AE, Carrino JA, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. AJR Am J Roentgenol. 2013 Mar; 200(3):493-502. PMID: 23436836.
        View in: PubMed
      82. Ohno-Machado L. Sharing data for the public good and protecting individual privacy: informatics solutions to combine different goals. J Am Med Inform Assoc. 2013 Jan 01; 20(1):1. PMID: 23243087; PMCID: PMC3555342.
      83. Roozgard A, Barzigar N, Wang S, Jiang X, Ohno-Machado L, Cheng S. Nucleotide sequence alignment using sparse coding and belief propagation. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:588-91. PMID: 24109755; PMCID: PMC3909563.
      84. Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 Jan; 56(1):83-93. PMID: 25284821.
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      85. Ohno-Machado L. To share or not to share: that is not the question. Sci Transl Med. 2012 Dec 19; 4(165):165cm15. PMID: 23253606.
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      86. Mohammed N, Jiang X, Chen R, Fung BC, Ohno-Machado L. Privacy-preserving heterogeneous health data sharing. J Am Med Inform Assoc. 2013 May 01; 20(3):462-9. PMID: 23242630; PMCID: PMC3628047.
      87. Jiang 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(11):e48823. PMID: 23139819; PMCID: PMC3490990.
      88. Jiang X, Kim J, Wu Y, Wang S, Ohno-Machado L. Selecting cases for whom additional tests can improve prognostication. AMIA Annu Symp Proc. 2012; 2012:1260-8. PMID: 23304404; PMCID: PMC3540468.
      89. Que J, Jiang X, Ohno-Machado L. A collaborative framework for Distributed Privacy-Preserving Support Vector Machine learning. AMIA Annu Symp Proc. 2012; 2012:1350-9. PMID: 23304414; PMCID: PMC3540462.
      90. Wu Y, Jiang X, Ohno-Machado L. Preserving Institutional Privacy in Distributed binary Logistic Regression. AMIA Annu Symp Proc. 2012; 2012:1450-8. PMID: 23304425; PMCID: PMC3540539.
      91. Ohno-Machado L. Careers in informatics: a diversity of options with an abundance of jobs. J Am Med Inform Assoc. 2012 Nov-Dec; 19(6):919. PMID: 23077280; PMCID: PMC3534476.
      92. Gardner J, Xiong L, Xiao Y, Gao J, Post AR, Jiang X, Ohno-Machado L. SHARE: system design and case studies for statistical health information release. J Am Med Inform Assoc. 2013 Jan 01; 20(1):109-16. PMID: 23059729; PMCID: PMC3555328.
      93. Ohno-Machado L. Informatics 2.0: implications of social media, mobile health, and patient-reported outcomes for healthcare and individual privacy. J Am Med Inform Assoc. 2012 Sep-Oct; 19(5):683. PMID: 22879365; PMCID: PMC3422848.
      94. von Muhlen M, Ohno-Machado L. Reviewing social media use by clinicians. J Am Med Inform Assoc. 2012 Sep-Oct; 19(5):777-81. PMID: 22759618; PMCID: PMC3422846.
      95. Kim H, Tamayo D, Muhkin M, Kim J, Lam J, Ohno-Machado L, Aronoff-Spencer E. Pictogram evaluation and authoring collaboration environment. NI 2012 (2012). 2012; 2012:214. PMID: 24199088; PMCID: PMC3799134.
      96. Ohno-Machado L. Big science, big data, and a big role for biomedical informatics. J Am Med Inform Assoc. 2012 Jun; 19(e1):e1. PMID: 22718034; PMCID: PMC3392845.
      97. Sarin P, Urman RD, Ohno-Machado L. An improved model for predicting postoperative nausea and vomiting in ambulatory surgery patients using physician-modifiable risk factors. J Am Med Inform Assoc. 2012 Nov-Dec; 19(6):995-1002. PMID: 22582204; PMCID: PMC3534465.
      98. Wu Y, Jiang X, Kim J, Ohno-Machado L. Grid Binary LOgistic REgression (GLORE): building shared models without sharing data. J Am Med Inform Assoc. 2012 Sep-Oct; 19(5):758-64. PMID: 22511014; PMCID: PMC3422844.
      99. Jiang X, Boxwala AA, El-Kareh R, Kim J, Ohno-Machado L. A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support. J Am Med Inform Assoc. 2012 Jun; 19(e1):e137-44. PMID: 22493049; PMCID: PMC3392846.
      100. Wu Y, Jiang X, Kim J, Ohno-Machado L. I-spline Smoothing for Calibrating Predictive Models. AMIA Jt Summits Transl Sci Proc. 2012; 2012:39-46. PMID: 22779048; PMCID: PMC3392066.
      101. Ohno-Machado L. Informatics research to enable clinically relevant, personalized genomic medicine. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):149-50. PMID: 22319175; PMCID: PMC3277638.
      102. Ohno-Machado L. Computer-based safety surveillance and patient-centered health records. J Am Med Inform Assoc. 2012 Jan-Feb; 19(1):1. PMID: 22155973; PMCID: PMC3240770.
      103. Menon AK, Jiang XJ, Vembu S, Elkan C, Ohno-Machado L. Predicting accurate probabilities with a ranking loss. Proc Int Conf Mach Learn. 2012; 2012:703-710. PMID: 25285328.
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      104. Ohno-Machado L. Innovative approaches to support patient decision making, improve safety, and enable large-scale clinical research. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i1. PMID: 22180872; PMCID: PMC3241183.
      105. Kim HE, Jiang X, Kim J, Ohno-Machado L. Trends in biomedical informatics: most cited topics from recent years. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i166-70. PMID: 22180873; PMCID: PMC3241182.
      106. Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, Kim H, Kim J, Matheny ME, Resnic FS, Vinterbo SA. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):196-201. PMID: 22081224; PMCID: PMC3277627.
      107. Jiang X, El-Kareh R, Ohno-Machado L. Improving predictions in imbalanced data using Pairwise Expanded Logistic Regression. AMIA Annu Symp Proc. 2011; 2011:625-34. PMID: 22195118; PMCID: PMC3243279.
      108. Kim J, Grillo JM, Boxwala AA, Jiang X, Mandelbaum RB, Patel BA, Mikels D, Vinterbo SA, Ohno-Machado L. Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs. AMIA Annu Symp Proc. 2011; 2011:723-31. PMID: 22195129; PMCID: PMC3243249.
      109. Jiang X, Osl M, Kim J, Ohno-Machado L. Calibrating predictive model estimates to support personalized medicine. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):263-74. PMID: 21984587; PMCID: PMC3277613.
      110. Ohno-Machado L. Realizing the full potential of electronic health records: the role of natural language processing. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):539. PMID: 21846784; PMCID: PMC3168331.
      111. Nadkarni PM, Ohno-Machado L, Chapman WW. Natural language processing: an introduction. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):544-51. PMID: 21846786; PMCID: PMC3168328.
      112. Ohno-Machado L. Biomedical informatics: how we got here and where we are headed. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):351. PMID: 21672903; PMCID: PMC3128422.
      113. Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):498-505. PMID: 21672912; PMCID: PMC3128412.
      114. Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):354-7. PMID: 21561873; PMCID: PMC3128415.
      115. Ohno-Machado L. Informatics is about algorithms, systems, people, and social networks. J Am Med Inform Assoc. 2011 May 01; 18(3):209. PMID: 21486878; PMCID: PMC3078672.
      116. Ohno-Machado L. A hybrid open-access model to bridge the publishing divide and reach out to a broader community. J Am Med Inform Assoc. 2011 May 01; 18(3):210-1. PMID: 21486879; PMCID: PMC3078671.
      117. Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L. AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. BMC Bioinformatics. 2011 Mar 17; 12:75. PMID: 21410990; PMCID: PMC3076267.
      118. Eckert MA, Lwin TM, Chang AT, Kim J, Danis E, Ohno-Machado L, Yang J. Twist1-induced invadopodia formation promotes tumor metastasis. Cancer Cell. 2011 Mar 08; 19(3):372-86. PMID: 21397860; PMCID: PMC3072410.
      119. Jiang X, Osl M, Kim J, Ohno-Machado L. Smooth isotonic regression: a new method to calibrate predictive models. AMIA Jt Summits Transl Sci Proc. 2011; 2011:16-20. PMID: 22211175; PMCID: PMC3248752.
      120. Lehmannm H, Ohno-Machado L. Evaluation of informatics systems: beyond RCTs and beyond the hospital. J Am Med Inform Assoc. 2011 Mar-Apr; 18(2):110-1. PMID: 21385823; PMCID: PMC3116252.
      121. Ohno-Machado L. What's new in informatics. J Am Med Inform Assoc. 2011 Jan-Feb; 18(1):1. PMID: 21169616; PMCID: PMC3005884.
      122. Ohno-Machado L. A new JAMIA. J Am Med Inform Assoc. 2011 Jan-Feb; 18(1):2. PMID: 21169617; PMCID: PMC3005883.
      123. Casas E, Kim J, Bendesky A, Ohno-Machado L, Wolfe CJ, Yang J. Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis. Cancer Res. 2011 Jan 01; 71(1):245-54. PMID: 21199805; PMCID: PMC3025803.
      124. Kim H, Choi J, Thompson S, Meeker L, Dykes P, Goldsmith D, Ohno-Machado L. Automating pressure ulcer risk assessment using documented patient data. Int J Med Inform. 2010 Dec; 79(12):840-8. PMID: 20869303.
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      125. Kim H, Choi J, Secalag L, Dibsie L, Boxwala A, Ohno-Machado L. Building an ontology for pressure ulcer risk assessment to allow data sharing and comparisons across hospitals. AMIA Annu Symp Proc. 2010 Nov 13; 2010:382-6. PMID: 21347005; PMCID: PMC3041354.
      126. 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 Annu Symp Proc. 2010 Nov 13; 2010:567-71. PMID: 21347042; PMCID: PMC3041313.
      127. Sadow CA, Wheeler SC, Kim J, Ohno-Machado L, Silverman SG. Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer. AJR Am J Roentgenol. 2010 Nov; 195(5):W337-43. PMID: 20966298.
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      128. Lacson 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. J Biomed Inform. 2010 Oct; 43(5):709-15. PMID: 20435161; PMCID: PMC2934864.
      129. Pitzer E, Kim J, Patel K, Galante PA, Ohno-Machado L. PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. AMIA Jt Summits Transl Sci Proc. 2010 Mar 01; 2010:25-9. PMID: 21347141; PMCID: PMC3041550.
      130. Pitzer E, Lacson R, Hinske C, Kim J, Galante PA, Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S9. PMID: 19761579; PMCID: PMC2745696.
      131. Racowsky C, Ohno-Machado L, Kim J, Biggers JD. Is there an advantage in scoring early embryos on more than one day? Hum Reprod. 2009 Sep; 24(9):2104-13. PMID: 19493872; PMCID: PMC2727402.
      132. Ohno-Machado L, Ellison D, Shortliffe EH. Presentation of the 2008 Morris F. Collen Award to Robert A. Greenes. J Am Med Inform Assoc. 2009 May-Jun; 16(3):413-8. PMID: 19606540; PMCID: PMC2732226.
      133. Matheny ME, Morrow DA, Ohno-Machado L, Cannon CP, Sabatine MS, Resnic FS. Validation of an automated safety surveillance system with prospective, randomized trial data. Med Decis Making. 2009 Mar-Apr; 29(2):247-56. PMID: 19015285; PMCID: PMC2743924.
      134. Curtis DW, Pino EJ, Bailey JM, Shih EI, Waterman J, Vinterbo SA, Stair TO, Guttag JV, Greenes RA, Ohno-Machado L. SMART--an integrated wireless system for monitoring unattended patients. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):44-53. PMID: 17947629; PMCID: PMC2274866.
      135. Matheny ME, Ohno-Machado L, Resnic FS. Risk-adjusted sequential probability ratio test control chart methods for monitoring operator and institutional mortality rates in interventional cardiology. Am Heart J. 2008 Jan; 155(1):114-20. PMID: 18082501.
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      136. Matheny ME, Arora N, Ohno-Machado L, Resnic FS. Rare adverse event monitoring of medical devices with the use of an automated surveillance tool. AMIA Annu Symp Proc. 2007 Oct 11; 518-22. PMID: 18693890; PMCID: PMC2655807.
      137. Matheny ME, Morrow DA, Ohno-Machado L, Cannon CP, Resnic FS. Validating an automated outcomes surveillance application using data from a terminated randomized, controlled trial (OPUS [TIMI-16]). AMIA Annu Symp Proc. 2007 Oct 11; 1043. PMID: 18694141.
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      138. Matheny ME, Resnic FS, Arora N, Ohno-Machado L. Effects of SVM parameter optimization on discrimination and calibration for post-procedural PCI mortality. J Biomed Inform. 2007 Dec; 40(6):688-97. PMID: 17600771; PMCID: PMC2170520.
      139. Vinterbo SA, Dreiseitl S, Ohno-Machado L. Approximation properties of haplotype tagging. BMC Bioinformatics. 2006 Jan 09; 7:8. PMID: 16401341; PMCID: PMC1395335.
      140. Ohno-Machado L, Resnic FS, Matheny ME. Prognosis in critical care. Annu Rev Biomed Eng. 2006; 8:567-99. PMID: 16834567.
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      141. Matheny ME, Ohno-Machado L, Resnic FS. Monitoring device safety in interventional cardiology. J Am Med Inform Assoc. 2006 Mar-Apr; 13(2):180-7. PMID: 16357356; PMCID: PMC1447549.
      142. Zou KH, Resnic FS, Talos IF, Goldberg-Zimring D, Bhagwat JG, Haker SJ, Kikinis R, Jolesz FA, Ohno-Machado L. A global goodness-of-fit test for receiver operating characteristic curve analysis via the bootstrap method. J Biomed Inform. 2005 Oct; 38(5):395-403. PMID: 16198998.
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      143. Vinterbo SA, Kim EY, Ohno-Machado L. Small, fuzzy and interpretable gene expression based classifiers. Bioinformatics. 2005 May 01; 21(9):1964-70. PMID: 15661797.
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      144. Matheny ME, Ohno-Machado L, Resnic FS. Exploration of a Bayesian updating tool to provide real-time safety monitoring for new medical devices. AMIA Annu Symp Proc. 2005; 1045. PMID: 16779332; PMCID: PMC1560574.
      145. Ohno-Machado L, Silveira PS, Vinterbo S. Protecting patient privacy by quantifiable control of disclosures in disseminated databases. Int J Med Inform. 2004 Aug; 73(7-8):599-606. PMID: 15246040.
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      146. Kuo WP, Kim EY, Trimarchi J, Jenssen TK, Vinterbo SA, Ohno-Machado L. A primer on gene expression and microarrays for machine learning researchers. J Biomed Inform. 2004 Aug; 37(4):293-303. PMID: 15465482.
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      147. Resnic FS, Zou KH, Do DV, Apostolakis G, Ohno-Machado L. Exploration of a bayesian updating methodology to monitor the safety of interventional cardiovascular procedures. Med Decis Making. 2004 Jul-Aug; 24(4):399-407. PMID: 15271278.
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      148. Weber G, Vinterbo S, Ohno-Machado L. Multivariate selection of genetic markers in diagnostic classification. Artif Intell Med. 2004 Jun; 31(2):155-67. PMID: 15219292.
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      149. Albrecht A, Vinterbo SA, Ohno-Machado L. An Epicurean learning approach to gene-expression data classification. Artif Intell Med. 2003 May; 28(1):75-87. PMID: 12850314.
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      150. Resnic FS, Wainstein M, Lee MK, Behrendt D, Wainstein RV, Ohno-Machado L, Kirshenbaum JM, Rogers CD, Popma JJ, Piana R. No-reflow is an independent predictor of death and myocardial infarction after percutaneous coronary intervention. Am Heart J. 2003 Jan; 145(1):42-6. PMID: 12514653.
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      151. Ohno-Machado L, Vinterbo S, Dreiseitl S, Jenssen TK, Kuo W. Comparing imperfect measurements with the Bland-Altman technique: application in gene expression analysis. Proc AMIA Symp. 2002; 572-6. PMID: 12463888; PMCID: PMC2244491.
      152. Ray HN, Boxwala AA, Anantraman V, Ohno-Machado L. Providing context-sensitive decision-support based on WHO guidelines. Proc AMIA Symp. 2002; 637-41. PMID: 12463901; PMCID: PMC2244156.
      153. Weber G, Vinterbo S, Ohno-Machado L. Building an asynchronous web-based tool for machine learning classification. Proc AMIA Symp. 2002; 869-73. PMID: 12463949; PMCID: PMC2244467.