Lucila Ohno-Machado

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Recent trends in biomedical informatics: a study based on JAMIA articles
    Xiaoqian Jiang
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California, USA
    J Am Med Inform Assoc 20:e198-205. 2013
  2. doi request reprint To share or not to share: that is not the question
    Lucila Ohno-Machado
    School of Medicine, University of California San Diego, 9500 Gilman Drive, MC 0505, La Jolla, CA 92093, USA
    Sci Transl Med 4:165cm15. 2012
  3. pmc iDASH: integrating data for analysis, anonymization, and sharing
    Lucila Ohno-Machado
    Division of Biomedical Informatics, University of California San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 19:196-201. 2012
  4. pmc A potential role for intragenic miRNAs on their hosts' interactome
    Ludwig Christian G Hinske
    Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
    BMC Genomics 11:533. 2010
  5. pmc AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
    Jihoon Kim
    Division of Biomedical Informatics, University of California, San Diego, CA, USA
    BMC Bioinformatics 12:75. 2011
  6. pmc WebGLORE: a web service for Grid LOgistic REgression
    Wenchao Jiang
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA and Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
    Bioinformatics 29:3238-40. 2013
  7. pmc Preserving Institutional Privacy in Distributed binary Logistic Regression
    Yuan Wu
    Division of Biomedical Informatics, Department of Medicine University of California San Diego, La Jolla 92093, USA
    AMIA Annu Symp Proc 2012:1450-8. 2012
  8. pmc A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support
    Xiaoqian Jiang
    Division of Biomedical Informatics, University of California at San Diego, La Jolla, California 92093 0728, USA
    J Am Med Inform Assoc 19:e137-44. 2012
  9. pmc Grid Binary LOgistic REgression (GLORE): building shared models without sharing data
    Yuan Wu
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 19:758-64. 2012
  10. pmc Selecting cases for whom additional tests can improve prognostication
    Xiaoqian Jiang
    Division of Biomedical Informatics, Department of Medicine University of California at San Diego, La Jolla, CA 92093, USA
    AMIA Annu Symp Proc 2012:1260-8. 2012

Detail Information

Publications26

  1. pmc Recent trends in biomedical informatics: a study based on JAMIA articles
    Xiaoqian Jiang
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California, USA
    J Am Med Inform Assoc 20:e198-205. 2013
    ..This trend will need to be verified as more data accumulate in coming years. ..
  2. doi request reprint To share or not to share: that is not the question
    Lucila Ohno-Machado
    School of Medicine, University of California San Diego, 9500 Gilman Drive, MC 0505, La Jolla, CA 92093, USA
    Sci Transl Med 4:165cm15. 2012
    ..However, the challenges involved in sharing clinical and biomedical data are seldom discussed. I briefly review some of these challenges and provide an overview of how they are being addressed by the scientific community...
  3. pmc iDASH: integrating data for analysis, anonymization, and sharing
    Lucila Ohno-Machado
    Division of Biomedical Informatics, University of California San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 19:196-201. 2012
    ....
  4. pmc A potential role for intragenic miRNAs on their hosts' interactome
    Ludwig Christian G Hinske
    Department of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
    BMC Genomics 11:533. 2010
    ....
  5. pmc AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
    Jihoon Kim
    Division of Biomedical Informatics, University of California, San Diego, CA, USA
    BMC Bioinformatics 12:75. 2011
    ..Current tools are so tightly coupled with reference information, such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the output results are incorrect and misleading...
  6. pmc WebGLORE: a web service for Grid LOgistic REgression
    Wenchao Jiang
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA and Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
    Bioinformatics 29:3238-40. 2013
    ..WebGLORE seamlessly integrates AJAX, JAVA Applet/Servlet and PHP technologies to provide an easy-to-use web service for biomedical researchers to break down policy barriers during information exchange...
  7. pmc Preserving Institutional Privacy in Distributed binary Logistic Regression
    Yuan Wu
    Division of Biomedical Informatics, Department of Medicine University of California San Diego, La Jolla 92093, USA
    AMIA Annu Symp Proc 2012:1450-8. 2012
    ..We tested our method using both simulated and clinical data, showing how it is possible to protect the privacy of individuals and of institutions using a distributed strategy...
  8. pmc A patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support
    Xiaoqian Jiang
    Division of Biomedical Informatics, University of California at San Diego, La Jolla, California 92093 0728, USA
    J Am Med Inform Assoc 19:e137-44. 2012
    ..The goal was to develop a patient-driven adaptive prediction technique to improve personalized risk estimation for clinical decision support...
  9. pmc Grid Binary LOgistic REgression (GLORE): building shared models without sharing data
    Yuan Wu
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 19:758-64. 2012
    ....
  10. pmc Selecting cases for whom additional tests can improve prognostication
    Xiaoqian Jiang
    Division of Biomedical Informatics, Department of Medicine University of California at San Diego, La Jolla, CA 92093, USA
    AMIA Annu Symp Proc 2012:1260-8. 2012
    ..The same is not true for some other groups...
  11. pmc Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): an algorithm for joint optimization of discrimination and calibration
    Xiaoqian Jiang
    Division of Biomedical Informatics, University California San Diego UCSD, La Jolla, California, USA
    PLoS ONE 7:e48823. 2012
    ..38, p=0.29, and p=0.047) and Logistic Regression (p=0.38, p=0.04, and p<0.0001). DOC-SVM produced a model that was better calibrated without sacrificing discrimination, and hence may be helpful in clinical decision making...
  12. pmc EXpectation Propagation LOgistic REgRession (EXPLORER): distributed privacy-preserving online model learning
    Shuang Wang
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, San Diego, CA 92093 0728, USA
    J Biomed Inform 46:480-96. 2013
    ..The proposed EXPLORER supports asynchronized communication, which relieves the participants from coordinating with one another, and prevents service breakdown from the absence of participants or interrupted communications...
  13. pmc A collaborative framework for Distributed Privacy-Preserving Support Vector Machine learning
    Jialan Que
    University of California, La Jolla, CA, USA
    AMIA Annu Symp Proc 2012:1350-9. 2012
    ..We also provide a free web-service (http://privacy.ucsd.edu:8080/ppsvm/) for multiple participants to collaborate and complete the SVM-learning task in an efficient and privacy-preserving manner...
  14. pmc PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
    Son Doan
    Division of Biomedical Informatics, University of California San Diego, La Jolla, California, USA
    J Am Med Inform Assoc 21:31-6. 2014
    ..In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net. ..
  15. pmc Anomaly and signature filtering improve classifier performance for detection of suspicious access to EHRs
    Jihoon Kim
    Division of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
    AMIA Annu Symp Proc 2011:723-31. 2011
    ..The difference in false negative rates on the independent test set was significant, P=1.6×10(-6). Our study suggests that utilization of integrated filtering strategies to facilitate the construction of classifiers can be helpful...
  16. doi request reprint Automating pressure ulcer risk assessment using documented patient data
    Hyeoneui Kim
    Division of Biomedical Informatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093 0671, USA
    Int J Med Inform 79:840-8. 2010
    ..A rule-based prototype decision support tool; Braden-scale based Automated Risk-assessment Tool (BART) was developed to test whether pressure ulcer risk scores can be determined automatically based on the documented patient data...
  17. pmc DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique
    Pinghao Li
    Division of Biomedical Informatics, University of California San Diego, La Jolla, California, United States of America Department of Electronic Engineering, Shanghai Jiao Tong University, Shanghai, China
    PLoS ONE 8:e80377. 2013
    ..8 MB to 15.8 MB at a comparable decompression cost with existing algorithms. DNAcompact is freely available at https://sourceforge.net/projects/dnacompact/for research purpose. ..
  18. pmc Privacy technology to support data sharing for comparative effectiveness research: a systematic review
    Xiaoqian Jiang
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA
    Med Care 51:S58-65. 2013
    ..These concerns have spurred the development of new technologies for privacy-preserving data sharing and data mining. Our goal is to review existing and emerging techniques that may be appropriate for data sharing related to CER...
  19. pmc Calibrating predictive model estimates to support personalized medicine
    Xiaoqian Jiang
    Division of Biomedical Informatics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 19:263-74. 2012
    ..Our goal is to develop a new calibration method to conserve as much information as possible, and would compare favorably to existing methods in terms of important performance measures: discrimination and calibration...
  20. ncbi request reprint Natural language processing in biomedicine: a unified system architecture overview
    Son Doan
    Division of Biomedical Informatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
    Methods Mol Biol 1168:275-94. 2014
    ....
  21. pmc Trends in biomedical informatics: most cited topics from recent years
    Hyeon eui Kim
    Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
    J Am Med Inform Assoc 18:i166-70. 2011
    ..Results suggest that there is a positive association between free access and citation rate for JAMIA articles...
  22. pmc Reviewing social media use by clinicians
    Marcio von Muhlen
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, California 92093 0728, USA
    J Am Med Inform Assoc 19:777-81. 2012
    ..Posting of unprofessional content and breaches of patient confidentiality, especially by students, are not uncommon and have prompted calls for social media guidelines...
  23. pmc I-spline Smoothing for Calibrating Predictive Models
    Yuan Wu
    Division of Biomedical Informatics, University of California at San Diego, La Jolla, California 92093
    AMIA Summits Transl Sci Proc 2012:39-46. 2012
    ..e.,1.6x, 1.4x, and 1.4x on the three datasets compared to the average of competitors-Binning, Platt Scaling, Isotonic Regression, Monotone Spline Smoothing, Smooth Isotonic Regression) without deterioration of discrimination...
  24. pmc pSCANNER: patient-centered Scalable National Network for Effectiveness Research
    Lucila Ohno-Machado
    Division of Biomedical Informatics, Department of Medicine and Clinical Translational Research Institute, University of California San Diego, La Jolla, California, USA Division of Health Services Research and Development, Veterans Affairs, San Diego Healthcare System, La Jolla, California, USA
    J Am Med Inform Assoc 21:621-6. 2014
    ..The distributed system will be based on a common data model that allows the construction and evaluation of distributed multivariate models for a variety of statistical analyses. ..
  25. pmc Differential expression of miR-145 in children with Kawasaki disease
    Chisato Shimizu
    Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    PLoS ONE 8:e58159. 2013
    ..To understand the role that microRNAs play in modifying gene expression in Kawasaki disease, we studied microRNAs from whole blood during the acute and convalescent stages of the illness...
  26. pmc Improving predictions in imbalanced data using Pairwise Expanded Logistic Regression
    Xiaoqian Jiang
    Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
    AMIA Annu Symp Proc 2011:625-34. 2011
    ..The method we propose, Pairwise Expanded Logistic Regression, improved discrimination and had higher accuracy when compared to existing methods in two imbalanced datasets, thus showing promise as a potential remedy for this problem...

Research Grants6

  1. Assessing quality of individual predictions in medical decision support systems
    Lucila Ohno Machado; Fiscal Year: 2007
    ..We will compare the performance of the new methods with existing ones in different predictive models derived from real clinical data related to different medical domains. ..
  2. Assessing quality of individual predictions in medical decision support systems
    Lucila Ohno Machado; Fiscal Year: 2009
    ..We will compare the performance of the new methods with existing ones in different predictive models derived from real clinical data related to different medical domains. ..
  3. Assessing quality of individual predictions in medical decision support systems
    Lucila Ohno Machado; Fiscal Year: 2009
    ..We will compare the performance of the new methods with existing ones in different predictive models derived from real clinical data related to different medical domains. ..
  4. SCANNER: Scalable National Network for Effectiveness Research
    Lucila Ohno Machado; Fiscal Year: 2010
    ..It also implements tools for data analyses and feedback to the clinicians. Such a network will enable conduct of certain types of research studies to be conducted more efficiently and at a larger scale. ..
  5. Assessing quality of individual predictions in medical decision support systems
    Lucila Ohno Machado; Fiscal Year: 2010
    ..We will compare the performance of the new methods with existing ones in different predictive models derived from real clinical data related to different medical domains. ..