Big Data Sharing for Better Health

Researchers at University of California, San Diego School of Medicine have been awarded a $9.2 million grant to help modernize and transform how researchers share, use, find and cite biomedical datasets.

The 3-year project, in collaboration with The University of Texas Health Science Center at Houston, is part of a federal initiative to increase the utility of biomedical research data, launched this week by the National Institutes of Health (NIH) through its Big Data to Knowledge (BD2K) program. … Read the full story from the UC San Diego Newsroom


Dr. Lucila Ohno-MachadoLucila Ohno-Machado, MD, PhD, is lead investigator on the Biomedical and healthCAre Data Discovery and Indexing Ecosystem (BioCADDIE) project.

Dr. Ohno-Machado, professor of medicine, is founding chief of the Division of Biomedical Informatics.

Read the BioCADDIE project description on the NIH RePORTER

University of California Launches its First Tool for Data Sharing Among Medical Centers with UC Research eXchange

Announcement for UC Investigators

Gary S. Firestein, MD
Chair, University of California Biomedical Research
Acceleration, Integration and Development (UCBRAID)
Professor of Medicine
Dean and Associate Vice Chancellor, Translational Medicine
Director, Clinical and Translational Research Institute
UC San Diego

Dr. Gary Firestein

Dr. Gary Firestein, UC BRAID Chair

The University of California Biomedical Research Acceleration, Integration and Development (UC BRAID; ucbraid.org) is pleased to announce the launch of the UC Research eXchange (UC ReX) and the UC ReX Data Explorer tool. This system enables exploration of a combined population of over 12 million patients from medical center databases at UC Los Angeles, UC Irvine, UC Davis, UC San Diego, and UC San Francisco.

UC ReX Data Explorer gives researchers and quality specialists access to cohort counts derived from de-identified clinical data collected at the point of care to improve medical care and advance research.

UC ReX was initiated by UC BRAID in 2011 with a 5-year grant of $5 million from the UC Office of the President (UCOP) and developed through a collaboration of the medical campuses and their Chief Information Officers and CTSAs.

An important part of UC BRAID’s mission is to improve UC collaborative research opportunities. UC ReX is a great example of how UC BRAID facilitates integration of research programs, clinical informatics, technology, and resources across University of California campuses.

To start exploring UC ReX with Data Explorer, please go to ucrex.org for more information.  |  See UC ReX Flier

Access UC-ReX via UC San Diego Clinical and Translational Research Institute

 

IDASH Projects: Protecting Privacy and Patient Rights in the Name of Scientific Progress

In the years since the best-selling book “The Immortal Life of Henrietta Lacks” made the issue of informed consent and patient privacy a national topic of conversation, scientists and clinicians have continued to struggle to develop a comprehensive methodology for collecting and sharing data from patients and research subjects without jeopardizing their rights.

The University of California, San Diego’s iDASH project aims to address some of these fundamental challenges to research progress with its most recent series of “Driving Biological Projects” (DBPs) … Read the full story from the UCSD Newsroom


Dr. Lucila Ohno-MachadoLead investigator in the iDASH project is Lucila Ohno-Machado, MD, MBA, PhD, professor of medicine, founding chief of the Division of Biomedical Informatics and associate dean for informatics and technology at UC San Diego.

Among other research and education projects directed by Dr. Ohno-Machado are the Biomedical Research Informatics for Global Health training program and the biomedical informatics component of the UC San Diego – Universidade Eduardo Mondlane Medical Education Partnership Initiative.  |  See all DBMI research projects

Dr. Ohno-Machado joined the UC San Diego faculty from Harvard Medical School in 2009. She was elected to the American Society for Clinical Investigation in 2010.

More Information:

Next Generation: Thomas Ohno-Machado Lobbies for Federal Research Funding

One in a Series of Occasional Stories About Faculty Members’ Children

Dr. Lucila Ohno-Machado and Thomas Ohno-Machado with Senator Barbara Boxer Lucila Ohno-Machado, MD, PhD; her son Thomas and California Senator Barbara Boxer.

Recently, to his mother’s wonderment, 17-year-old Thomas Ohno-Machado revealed that he is interested and quite active in politics.

It seemed to happen overnight, his mother said, and without any particular encouragement from his parents. “It doesn’t run in the family,” she mused.

Thomas, a senior at Torrey Pines High School, is the oldest of Dr. Lucila Ohno-Machado’s three sons. Lucila Ohno-Machado, MD, PhD, is associate dean for informatics for the UCSD School of Medicine and professor and chief of the Division of Biomedical Informatics in the Department of Medicine.

Thomas is now the founder and president of the Torrey Pines High School Autism Awareness Club and an advocate for children with disabilities. He and his friends have successfully organized a funding drive and raised money to benefit a local school for children with special needs.

One day out of the blue Thomas asked Dr. Ohno-Machado, “Mom, can we go to Washington, DC?”

It turned out he had written to Senator Barbara Boxer’s office and arranged to visit and express his concerns about federal support for biomedical and behavioral research, particularly for the National Institutes of Health, and for the increasing numbers of children who have special needs.

Dr. Ohno-Machado agreed to go. She arranged for him to add a one-day visit to Washington DC to a trip she had already scheduled. He purchased his first suit, from Macy’s, and carried it on the plane so that it would not wrinkle in flight.

She suggested he prepare for his audience with the senator, and he assured her, “Don’t worry.”

They arrived at Senator Boxer’s office and, with the Archbishop of California and a California judge who had come in with them, waited their turn to speak with one of the senator’s staff members.

The time came. Prepared with statistics to back him up, Thomas Ohno-Machado expressed his concern and asked to know what the senator was going to do about federal medical research funding and the rising numbers of special needs children in the United States.

The senator’s staffer responded by showing Thomas documents detailing how Senator Boxer and another senator are addressing these issues.

Said Dr. Ohno-Machado of the meeting, “I didn’t speak a single word.”

She and Thomas had tried but weren’t able to set up a visit to California Senator Diane Feinstein’s office on the same trip. In a separate solo trip, Thomas visited the governor of Massachusetts and a school for special needs children in the Boston area. Recently, he pressed his causes at the San Diego mayor’s office.

He is headed to UC Santa Cruz this fall. He plans on a political career.

Dr. Ohno-Machado is still marveling at how a strong interest can reveal itself so suddenly in one’s offspring.

“He’s very excited about it,” she said. “He has a bright future.”

DELPHI Project Foretells Future of Personalized Population Health

NSF awards $2 million over four years to UC San Diego computer scientists and physicians

Imagine a new type of healthcare app that does it all – it helps you understand your current health status, assists you in making changes in your life to improve your health, and takes into account the perspective of your entire life history, others in your age group–and perhaps even your neighborhood– who share similar characteristics.

That’s the vision put forward by a team of physicians and computer scientists at the University of California, San Diego who are collaborating on a new digital resource that would take advantage of advances in databases, cyberinfrastructure and machine learning to usher in a new era of health and health care…. Read the full story from the UCSD Newsroom


Dr. Lucila Ohno-MachadoLucila Ohno-Machado, MD, PhD, FACMI, is an investigator on the project, whose title is “Data E-platform Leveraged for Patient Empowerment and Population Health Improvement (DELPHI).”

Dr. Ohno-Machado is professor of medicine and founding chief of the Division of Biomedical Informatics. She directs, among other projects, another UCSD biomedical cyberinfrastructure, the Integrating Data for Analysis, Anonymizing and Sharing (iDASH) project. IDASH is a National Center for Biomedical Computing under the auspices of the NIH Roadmap for Bioinformatics and Computational Biology. Under AHRQ funding, she directs the related project Scalable National Network for Effectiveness Research (SCANNER).

Dr. Ohno-Machado’s research specialty is predictive modeling with an emphasis on calibration methods that combine phenotype and genotype/gene expression data for personalized medicine.

More Information:

SDSC’s “Big Data” Expertise Aiding Genomics Research

Focus on Genomics Medicine is Growing, says SDSC’s Norman

The San Diego Supercomputer Center (SDSC) at the University of California, San Diego, has in the last three years undergone a major reboot, remaking itself into a center of expertise on all aspects of “big data” research including genomics, one of the fastest growing areas of scientific study. …. Read the full story from the UCSD Newsroom

Dr. Lucila Ohno-Machado
Among the current “big data” genomics projects at the San Diego Supercomputer Center is the Integrating Data for Analysis, Anonymization, and Sharing (iDASH) center, led by Lucila Ohno-Machado, MD, PhD, pictured above.

Ohno-Machado is professor of medicine, founding chief of the Division of Biomedical Informatics and associate dean for informatics and technology at UC San Diego.

iDASH is supported by the National Institutes of Health through the NIH Roadmap for Medical Research.  |  Read iDASH project abstract  |  Visit iDASH website  |   Visit San Diego Supercomputer Center website
Photo of Dr. Ohno-Machado: John Hanacek, Calit2 UC San Diego.

Tumor Metastasis with a Twist

Protein is key to early embryonic development, but later promotes spread of cancer

In the early stages of human embryogenesis, a transcription factor called Twist1 plays a key regulatory role in how the embryo assumes form and function. Much later in life, however, researchers at the University of California, San Diego School of Medicine, say Twist1 can re-emerge, taking a darker and more deadly turn…. Read the full story from the UCSD Newsroom

Dr. Lucila Ohno-Machado (pictured) and Jihoon Kim of the Division of Biomedical Informatics are among the authors of the study report. Lucila Ohno-Machado, M.D., Ph.D., is professor and chief of the division; Jihoon Kim, M.S., is senior statistician. Read the published article (full text).

Photo of Dr. Ohno-Machado: John Hanacek, Calit2 UC San Diego.

Dr. Lucila Ohno-Machado Elected to the American Society for Clinical Investigation

Dr. Lucila Ohno-Machado

Dr. Lucila Ohno-Machado

Dr. Lucila Ohno-Machado, Professor of Medicine and founding chief of the Division of Biomedical Informatics, has been elected to the American Society for Clinical Investigation (ASCI).

Membership in the ASCI is a distinction that recognizes the nation’s most outstanding physician-scientists.

The honorees for 2010 were introduced April 24 at a joint meeting of the ASCI and the Association of American Physicians in Chicago.

Lucila Ohno-Machado, M.D., Ph.D., is a groundbreaking researcher and a respected director of advanced training programs in biomedical informatics. She joined the Department of Medicine faculty from Harvard Medical School in 2009.

“Lucila has always been a leader, and she will continue to lead UCSD in new directions in biomedical informatics, developing critical new tools that will help both basic researchers and clinicians in moving their programs forward,” said Kenneth Kaushansky, M.D., M.A.C.P., Helen M. Ranney Distinguished Professor and Chair of the Department of Medicine.

“Her election to ASCI highlights both her accomplishments and the increasing recognition of her field as a critical component of the academic medical center,” he said.

Dr. Ohno-Machado’s primary research interest is prognostic modeling, the development of statistical models to predict clinical outcomes. She is principal investigator of an NIH-funded grant to develop methods for improving the calibration of prognostic models and of another research project funded by the Komen Foundation to validate breast cancer biomarkers using computational techniques.

Dr. Ohno-Machado received her M.D. degree from the University of São Paulo and her Ph.D. in Medical Information Sciences and Computer Science from Stanford University.

She is an elected fellow of the American College of Medical Informatics and the American Institute for Medical and Biological Engineering. She serves as associate editor for both the Journal of the American Medical Informatics Association and the Journal of Biomedical Informatics.

Since 2004, during her tenure at the Brigham and Women’s Hospital of Harvard Medical School, Dr. Ohno-Machado has directed the Biomedical Research Informatics for Global Health Training (BRIGHT) Program, an educational consortium funded by the Fogarty International Center of the NIH.

The aim of the program is to unite U.S. researchers and institutions in a collaborative effort to conduct research and to develop informatics research training programs in low- and middle-income countries.

In its first five years, the program concentrated its efforts in Brazil, where it developed a certificate program in clinical informatics and supported a new doctoral program in bioinformatics at the University of São Paulo.

With a new 5-year, $1.23-million grant awarded last fall, the BRIGHT program is expanding its efforts to include Maputo, Mozambique, as well as additional areas of Brazil.

$1.23M Grant Will Fund Biomedical Research Informatics for Global Health Training

Lucila Ohno-Machado, MD, PhDThe National Institutes of Health has awarded $1.23 million to a team of UC San Diego researchers led by Lucila Ohno-Machado, MD, PhD, Professor of Medicine and founding Chief of the new Division of Biomedical Informatics.

The award, which comes from the Fogarty International Center, will support multi-departmental efforts under the Biomedical Research Informatics for Global Health Training (BRIGHT) Program.


Read the full story
from UC San Diego News


 

Dr. Lucila Ohno-Machado Is Chief of New Division of Biomedical Informatics

Dr. Lucila Ohno-Machado

Dr. Lucila Ohno-Machado

The Department of Medicine has appointed Dr. Lucila Ohno-Machado, a leading medical information scientist and educator from Harvard Medical School, to head the new Division of Biomedical Informatics.

Lucila Ohno-Machado, MD, PhD, started in her new position at UC San Diego on July 1.

Dr. Ohno-Machado has performed groundbreaking research and directed advanced training programs in the field of biomedical informatics. Her primary research interest is prognostic modeling, the development of statistical models to predict clinical outcomes.

Read more about Dr. Ohno-Machado and the new Biomedical Informatics division in the UC San Diego News release.

Recent Publications from Dr. Ohno-Machado

  • 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 (in press).   Abstract
  • 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. Medical Decision Making. 2009; Mar-Apr;29(2):247-56.   Abstract
  • 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.   Abstract
  • Robles V, Bielza C, Larranaga P, Gonzales S, Ohno-Machado L: Optimizing logistic regression coefficients for discrimination and calibration using estimation of distribution algorithms. TOP. 2008;16(2):345-66.   Full Text PDF (UCSD only)
  • 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.   Abstract
  • 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.   Abstract