Lucila Ohno-Machado

University of California, San Diego, San Diego, California, United States

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Publications (256)475.93 Total impact

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    ABSTRACT: Multi-category response models are very important complements to binary logistic models in medical decision-making. Decomposing model construction by aggregating computation developed at different sites is necessary when data cannot be moved outside institutions due to privacy or other concerns. Such decomposition makes it possible to conduct grid computing to protect the privacy of individual observations. This paper proposes two grid multi-category response models for ordinal and multinomial logistic regressions. Grid computation to test model assumptions is also developed for these two types of models. In addition, we present grid methods for goodness-of-fit assessment and for classification performance evaluation. Simulation results show that the grid models produce the same results as those obtained from corresponding centralized models, demonstrating that it is possible to build models using multi-center data without losing accuracy or transmitting observation-level data. Two real data sets are used to evaluate the performance of our proposed grid models. The grid fitting method offers a practical solution for resolving privacy and other issues caused by pooling all data in a central site. The proposed method is applicable for various likelihood estimation problems, including other generalized linear models.
    BMC Medical Informatics and Decision Making 12/2015; 15(1). DOI:10.1186/s12911-015-0133-y · 1.50 Impact Factor
  • Katherine K Kim, Jill G Joseph, Lucila Ohno-Machado
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    ABSTRACT: New models of healthcare delivery such as accountable care organizations and patient-centered medical homes seek to improve quality, access, and cost. They rely on a robust, secure technology infrastructure provided by health information exchanges (HIEs) and distributed research networks and the willingness of patients to share their data. There are few large, in-depth studies of US consumers' views on privacy, security, and consent in electronic data sharing for healthcare and research together. This paper addresses this gap, reporting on a survey which asks about California consumers' views of data sharing for healthcare and research together. The survey conducted was a representative, random-digit dial telephone survey of 800 Californians, performed in Spanish and English. There is a great deal of concern that HIEs will worsen privacy (40.3%) and security (42.5%). Consumers are in favor of electronic data sharing but elements of transparency are important: individual control, who has access, and the purpose for use of data. Respondents were more likely to agree to share deidentified information for research than to share identified information for healthcare (76.2% vs 57.3%, p < .001). While consumers show willingness to share health information electronically, they value individual control and privacy. Responsiveness to these needs, rather than mere reliance on Health Insurance Portability and Accountability Act (HIPAA), may improve support of data networks. Responsiveness to the public's concerns regarding their health information is a pre-requisite for patient-centeredness. This is one of the first in-depth studies of attitudes about electronic data sharing that compares attitudes of the same individual towards healthcare and research. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com For numbered affiliations see end of article.
    Journal of the American Medical Informatics Association 03/2015; DOI:10.1093/jamia/ocv014 · 3.93 Impact Factor
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    ABSTRACT: To answer the need for the rigorous protection of biomedical data, we organized the Critical Assessment of Data Privacy and Protection initiative as a community effort to evaluate privacy-preserving dissemination techniques for biomedical data. We focused on the challenge of sharing aggregate human genomic data (e.g., allele frequencies) in a way that preserves the privacy of the data donors, without undermining the utility of genome-wide association studies (GWAS) or impeding their dissemination. Specifically, we designed two problems for disseminating the raw data and the analysis outcome, respectively, based on publicly available data from HapMap and from the Personal Genome Project. A total of six teams participated in the challenges. The final results were presented at a workshop of the iDASH (integrating Data for Analysis, 'anonymization,' and SHaring) National Center for Biomedical Computing. We report the results of the challenge and our findings about the current genome privacy protection techniques.
    BMC Medical Informatics and Decision Making 12/2014; 14(Suppl 1):S1. DOI:10.1186/1472-6947-14-S1-S1 · 1.50 Impact Factor
  • Lucila Ohno-Machado
    Journal of the American Medical Informatics Association 11/2014; 21(6):954-6. DOI:10.1136/amiajnl-2014-NovEditorial · 3.93 Impact Factor
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    ABSTRACT: To propose a new approach to privacy preserving data selection, which helps the data users access human genomic datasets efficiently without undermining patients' privacy.
    Journal of the American Medical Informatics Association 10/2014; DOI:10.1136/amiajnl-2014-003043 · 3.93 Impact Factor
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    ABSTRACT: MicroRNAs (miRNAs) are a class of small (∼22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their host genes for five species (human, rhesus monkey, mouse, chicken and opossum). miRIAD contains the genomic classification of all miRNAs (inter- and intragenic), as well as classification of all protein-coding genes into host or non-host genes (depending on whether they contain an intragenic miRNA or not). We collected and processed public data from several sources to provide a clear visualization of relevant knowledge related to intragenic miRNAs, such as host gene function, genomic context, names of and references to intragenic miRNAs, miRNA binding sites, clusters of intragenic miRNAs, miRNA and host gene expression across different tissues and expression correlation for intragenic miRNAs and their host genes. Protein–protein interaction data are also presented for functional network analysis of host genes. In summary, miRIAD was designed to help the research community to explore, in a user-friendly environment, intragenic miRNAs, their host genes and functional annotations with minimal effort, facilitating hypothesis generation and in-silico validations. Database URL: http://www.miriad-database.org
    Database The Journal of Biological Databases and Curation 10/2014; 2014. DOI:10.1093/database/bau099 · 4.46 Impact Factor
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    ABSTRACT: The US health care system is rapidly adopting electronic health records, which will dramatically increase the quantity of clinical data that are available electronically. Simultaneously, rapid progress has been made in clinical analytics-techniques for analyzing large quantities of data and gleaning new insights from that analysis-which is part of what is known as big data. As a result, there are unprecedented opportunities to use big data to reduce the costs of health care in the United States. We present six use cases-that is, key examples-where some of the clearest opportunities exist to reduce costs through the use of big data: high-cost patients, readmissions, triage, decompensation (when a patient's condition worsens), adverse events, and treatment optimization for diseases affecting multiple organ systems. We discuss the types of insights that are likely to emerge from clinical analytics, the types of data needed to obtain such insights, and the infrastructure-analytics, algorithms, registries, assessment scores, monitoring devices, and so forth-that organizations will need to perform the necessary analyses and to implement changes that will improve care while reducing costs. Our findings have policy implications for regulatory oversight, ways to address privacy concerns, and the support of research on analytics.
    Health Affairs 07/2014; 33(7):1123-31. DOI:10.1377/hlthaff.2014.0041 · 4.32 Impact Factor
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    Haoran Li, Li Xiong, Lucila Ohno-Machado, Xiaoqian Jiang
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    ABSTRACT: Data sharing is challenging but important for healthcare research. Methods for privacy-preserving data dissemination based on the rigorous differential privacy standard have been developed but they did not consider the characteristics of biomedical data and make full use of the available information. This often results in too much noise in the final outputs. We hypothesized that this situation can be alleviated by leveraging a small portion of open-consented data to improve utility without sacrificing privacy. We developed a hybrid privacy-preserving differentially private support vector machine (SVM) model that uses public data and private data together. Our model leverages the RBF kernel and can handle nonlinearly separable cases. Experiments showed that this approach outperforms two baselines: (1) SVMs that only use public data, and (2) differentially private SVMs that are built from private data. Our method demonstrated very close performance metrics compared to nonprivate SVMs trained on the private data.
    06/2014; 2014:1-10. DOI:10.1155/2014/827371
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    ABSTRACT: Summary: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. MAGI’s salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication.Availability and implementation: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu.Contact: j5kim@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.
    Bioinformatics 06/2014; 30(19). DOI:10.1093/bioinformatics/btu377 · 4.62 Impact Factor
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    ABSTRACT: Background Privacy protecting is an important issue in medical informatics and differential privacy is a state-of-the-art framework for data privacy research. Differential privacy offers provable privacy against attackers who have auxiliary information, and can be applied to data mining models (for example, logistic regression). However, differentially private methods sometimes introduce too much noise and make outputs less useful. Given available public data in medical research (e.g. from patients who sign open-consent agreements), we can design algorithms that use both public and private data sets to decrease the amount of noise that is introduced. Methodology In this paper, we modify the update step in Newton-Raphson method to propose a differentially private distributed logistic regression model based on both public and private data. Experiments and results We try our algorithm on three different data sets, and show its advantage over: (1) a logistic regression model based solely on public data, and (2) a differentially private distributed logistic regression model based on private data under various scenarios. Conclusion Logistic regression models built with our new algorithm based on both private and public datasets demonstrate better utility than models that trained on private or public datasets alone without sacrificing the rigorous privacy guarantee.
    BMC Medical Genomics 05/2014; 7(Suppl 1):S14. DOI:10.1186/1755-8794-7-S1-S14 · 3.91 Impact Factor
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    ABSTRACT: Background Non-coding sequences such as microRNAs have important roles in disease processes. Computational microRNA target identification (CMTI) is becoming increasingly important since traditional experimental methods for target identification pose many difficulties. These methods are time-consuming, costly, and often need guidance from computational methods to narrow down candidate genes anyway. However, most CMTI methods are computationally demanding, since they need to handle not only several million query microRNA and reference RNA pairs, but also several million nucleotide comparisons within each given pair. Thus, the need to perform microRNA identification at such large scale has increased the demand for parallel computing. Methods Although most CMTI programs (e.g., the miRanda algorithm) are based on a modified Smith-Waterman (SW) algorithm, the existing parallel SW implementations (e.g., CUDASW++ 2.0/3.0, SWIPE) are unable to meet this demand in CMTI tasks. We present CUDA-miRanda, a fast microRNA target identification algorithm that takes advantage of massively parallel computing on Graphics Processing Units (GPU) using NVIDIA's Compute Unified Device Architecture (CUDA). CUDA-miRanda specifically focuses on the local alignment of short (i.e., ≤ 32 nucleotides) sequences against longer reference sequences (e.g., 20K nucleotides). Moreover, the proposed algorithm is able to report multiple alignments (up to 191 top scores) and the corresponding traceback sequences for any given (query sequence, reference sequence) pair. Results Speeds over 5.36 Giga Cell Updates Per Second (GCUPs) are achieved on a server with 4 NVIDIA Tesla M2090 GPUs. Compared to the original miRanda algorithm, which is evaluated on an Intel Xeon E5620@2.4 GHz CPU, the experimental results show up to 166 times performance gains in terms of execution time. In addition, we have verified that the exact same targets were predicted in both CUDA-miRanda and the original miRanda implementations through multiple test datasets. Conclusions We offer a GPU-based alternative to high performance compute (HPC) that can be developed locally at a relatively small cost. The community of GPU developers in the biomedical research community, particularly for genome analysis, is still growing. With increasing shared resources, this community will be able to advance CMTI in a very significant manner. Our source code is available at https://sourceforge.net/projects/cudamiranda/.
    BMC Medical Genomics 05/2014; 7(Suppl 1):S9. DOI:10.1186/1755-8794-7-S1-S9 · 3.91 Impact Factor
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    ABSTRACT: This article describes the patient-centered Scalable National Network for Effectiveness Research (pSCANNER), which is part of the recently formed PCORnet, a national network composed of learning healthcare systems and patient-powered research networks funded by the Patient Centered Outcomes Research Institute (PCORI). It is designed to be a stakeholder-governed federated network that uses a distributed architecture to integrate data from three existing networks covering over 21 million patients in all 50 states: (1) VA Informatics and Computing Infrastructure (VINCI), with data from Veteran Health Administration's 151 inpatient and 909 ambulatory care and community-based outpatient clinics; (2) the University of California Research exchange (UC-ReX) network, with data from UC Davis, Irvine, Los Angeles, San Francisco, and San Diego; and (3) SCANNER, a consortium of UCSD, Tennessee VA, and three federally qualified health systems in the Los Angeles area supplemented with claims and health information exchange data, led by the University of Southern California. Initial use cases will focus on three conditions: (1) congestive heart failure; (2) Kawasaki disease; (3) obesity. Stakeholders, such as patients, clinicians, and health service researchers, will be engaged to prioritize research questions to be answered through the network. We will use a privacy-preserving distributed computation model with synchronous and asynchronous modes. 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.
    Journal of the American Medical Informatics Association 04/2014; 21(4). DOI:10.1136/amiajnl-2014-002751 · 3.93 Impact Factor
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    ABSTRACT: Many healthcare facilities enforce security on their electronic health records (EHRs) through a corrective mechanism: some staff nominally have almost unrestricted access to the records, but there is a strict ex post facto audit process for inappropriate accesses, i.e., accesses that violate the facility’s security and privacy policies. This process is inefficient, as each suspicious access has to be reviewed by a security expert, and is purely retrospective, as it occurs after damage may have been incurred. This motivates automated approaches based on machine learning using historical data. Previous attempts at such a system have successfully applied supervised learning models to this end, such as SVMs and logistic regression. While providing benefits over manual auditing, these approaches ignore the identity of the users and patients involved in a record access. Therefore, they cannot exploit the fact that a patient whose record was previously involved in a violation has an increased risk of being involved in a future violation. Motivated by this, in this paper, we propose a collaborative filtering inspired approach to predicting inappropriate accesses. Our solution integrates both explicit and latent features for staff and patients, the latter acting as a personalized “fingerprint” based on historical access patterns. The proposed method, when applied to real EHR access data from two tertiary hospitals and a file-access dataset from Amazon, shows not only significantly improved performance compared to existing methods, but also provides insights as to what indicates an inappropriate access.
    Machine Learning 04/2014; DOI:10.1007/s10994-013-5376-1 · 1.69 Impact Factor
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    Son Doan, Mike Conway, Tu Minh Phuong, Lucila Ohno-Machado
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    ABSTRACT: In modern electronic medical records (EMR) much of the clinically important data - signs and symptoms, symptom severity, disease status, etc. - are not provided in structured data fields, but rather are encoded in clinician generated narrative text. Natural language processing (NLP) provides a means of "unlocking" this important data source for applications in clinical decision support, quality assurance, and public health. This chapter provides an overview of representative NLP systems in biomedicine based on a unified architectural view. A general architecture in an NLP system consists of two main components: background knowledge that includes biomedical knowledge resources and a framework that integrates NLP tools to process text. Systems differ in both components, which we will review briefly. Additionally, challenges facing current research efforts in biomedical NLP include the paucity of large, publicly available annotated corpora, although initiatives that facilitate data sharing, system evaluation, and collaborative work between researchers in clinical NLP are starting to emerge.
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    ABSTRACT: MicroRNAs (miRNAs) are a class of short noncoding RNAs that regulate gene expression through base pairing with messenger RNAs. Due to the interest in studying miRNA dysregulation in disease and limits of validated miRNA references, identification of novel miRNAs is a critical task. The performance of different models to predict novel miRNAs varies with the features chosen as predictors. However, no study has systematically compared published feature sets. We constructed a comprehensive feature set using the minimum free energy of the secondary structure of precursor miRNAs, a set of nucleotide-structure triplets, and additional extracted sequence and structure characteristics. We then compared the predictive value of our comprehensive feature set to those from three previously published studies, using logistic regression and random forest classifiers. We found that classifiers containing as few as seven highly predictive features are able to predict novel precursor miRNAs as well as classifiers that use larger feature sets. In a real data set, our method correctly identified the holdout miRNAs relevant to renal cancer.
    Cancer informatics 01/2014; 13(Suppl 1):95-102. DOI:10.4137/CIN.S13877
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    Xiaoqian Jiang, Yuan Wu, Keith Marsolo, Lucila Ohno-Machado
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    ABSTRACT: We describe functional specifications and practicalities in the software development process for a web service that allows the construction of the multivariate logistic regression model, Grid Logistic Regression (GLORE), by aggregating partial estimates from distributed sites, with no exchange of patient-level data. We recently developed and published a web service for model construction and data analysis in a distributed environment. This recent paper provided an overview of the system that is useful for users, but included very few details that are relevant for biomedical informatics developers or network security personnel who may be interested in implementing this or similar systems. We focus here on how the system was conceived and implemented. We followed a two-stage development approach by first implementing the backbone system and incrementally improving the user experience through interactions with potential users during the development. Our system went through various stages such as concept proof, algorithm validation, user interface development, and system testing. We used the Zoho Project management system to track tasks and milestones. We leveraged Google Code and Apache Subversion to share code among team members, and developed an applet-servlet architecture to support the cross platform deployment. During the development process, we encountered challenges such as Information Technology (IT) infrastructure gaps and limited team experience in user-interface design. We figured out solutions as well as enabling factors to support the translation of an innovative privacy-preserving, distributed modeling technology into a working prototype. Using GLORE (a distributed model that we developed earlier) as a pilot example, we demonstrated the feasibility of building and integrating distributed modeling technology into a usable framework that can support privacy-preserving, distributed data analysis among researchers at geographically dispersed institutes.
    01/2014; 2(1):1053. DOI:10.13063/2327-9214.1053
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    ABSTRACT: Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. The proposed method produced a compression ratio in the range 0.5-0.65, which corresponds to 35-50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. Our method requires having different reference genomes and prolongs the execution time for additional alignments. The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms.
    Journal of the American Medical Informatics Association 12/2013; 21(2). DOI:10.1136/amiajnl-2013-002147 · 3.93 Impact Factor
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    ABSTRACT: There is currently limited information on best practices for the development of governance requirements for distributed research networks (DRNs), an emerging model that promotes clinical data reuse and improves timeliness of comparative effectiveness research. Much of the existing information is based on a single type of stakeholder such as researchers or administrators. This paper reports on a triangulated approach to developing DRN data governance requirements based on a combination of policy analysis with experts, interviews with institutional leaders, and patient focus groups. This approach is illustrated with an example from the Scalable National Network for Effectiveness Research, which resulted in 91 requirements. These requirements were analyzed against the Fair Information Practice Principles (FIPPs) and Health Insurance Portability and Accountability Act (HIPAA) protected versus non-protected health information. The requirements addressed all FIPPs, showing how a DRN's technical infrastructure is able to fulfill HIPAA regulations, protect privacy, and provide a trustworthy platform for research.
    Journal of the American Medical Informatics Association 12/2013; 21(4). DOI:10.1136/amiajnl-2013-002308 · 3.93 Impact Factor
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    ABSTRACT: Genome data are becoming increasingly important for modern medicine. As the rate of increase in DNA sequencing outstrips the rate of increase in disk storage capacity, the storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We propose a two-pass lossless genome compression algorithm, which highlights the synthesis of complementary contextual models, to improve the compression performance. The proposed framework could handle genome compression with and without reference sequences, and demonstrated performance advantages over best existing algorithms. The method for reference-free compression led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which were approximately 3.7% and 2.6% better than the state-of-the-art algorithms. Regarding performance with reference, we tested on the first Korean personal genome sequence data set, and our proposed method demonstrated a 189-fold compression rate, reducing the raw file size from 2986.8 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.
    PLoS ONE 11/2013; 8(11):e80377. DOI:10.1371/journal.pone.0080377 · 3.53 Impact Factor
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    ABSTRACT: In a growing interdisciplinary field like biomedical informatics, information dissemination and citation trends are changing rapidly due to many factors. To understand these factors better, we analyzed the evolution of the number of articles per major biomedical informatics topic, download/online view frequencies, and citation patterns (using Web of Science) for articles published from 2009 to 2012 in JAMIA. The number of articles published in JAMIA increased significantly from 2009 to 2012, and there were some topic differences in the last 4 years. Medical Record Systems, Algorithms, and Methods are topic categories that are growing fast in several publications. We observed a significant correlation between download frequencies and the number of citations per month since publication for a given article. Earlier free availability of articles to non-subscribers was associated with a higher number of downloads and showed a trend towards a higher number of citations. This trend will need to be verified as more data accumulate in coming years.
    Journal of the American Medical Informatics Association 11/2013; 20(E2). DOI:10.1136/amiajnl-2013-002429 · 3.93 Impact Factor

Publication Stats

4k Citations
475.93 Total Impact Points

Institutions

  • 2010–2015
    • University of California, San Diego
      • Department of Medicine
      San Diego, California, United States
  • 2014
    • Duke University
      Durham, North Carolina, United States
  • 2013
    • Toyota Technological Institute at Chicago
      Chicago, Illinois, United States
  • 1993–2013
    • Stanford Medicine
      • Department of Pediatrics
      Stanford, CA, United States
  • 2012
    • University of Pittsburgh
      Pittsburgh, Pennsylvania, United States
  • 1996–2012
    • Harvard Medical School
      • • Department of Radiology
      • • Division of Emergency Medicine
      • • Department of Genetics
      Boston, Massachusetts, United States
  • 1996–2010
    • Brigham and Women's Hospital
      • • Decision Systems Group
      • • Department of Radiology
      Boston, Massachusetts, United States
  • 2001–2009
    • Harvard University
      Cambridge, Massachusetts, United States
  • 1999–2007
    • Massachusetts Institute of Technology
      • • Computer Science and Artificial Intelligence Laboratory
      • • Division of Health Sciences and Technology
      Cambridge, MA, United States
  • 2005–2006
    • Universidade Federal de São Paulo
      San Paulo, São Paulo, Brazil
  • 2003–2005
    • Teikyo University Hospital
      Edo, Tōkyō, Japan
  • 2004
    • Partners HealthCare
      Boston, Massachusetts, United States
    • University of Massachusetts Boston
      Boston, Massachusetts, United States
  • 2002
    • Federal University of Rio de Janeiro
      Rio de Janeiro, Rio de Janeiro, Brazil
    • University of Hertfordshire
      • School of Computer Science
      Hatfield, ENG, United Kingdom
  • 1999–2002
    • Stanford University
      Palo Alto, California, United States
  • 2000
    • Consorcio Hospital General Universitario de Valencia
      • Departamento de Cardiología
      Valencia, Valencia, Spain
  • 1997
    • University of Southern California
      • Department of Chemical Engineering and Materials Science
      Los Angeles, CA, United States