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dbmi.ucsd.edu 2014-15
Dep
artm
ent
of
Bio
med
ical
Info
rmat
ics
Research
Increased research funding
marks the 5th
anniversary
of our division
Service We will be expanding our
services from research to
clinical decision support
Training
National and international
trainees participate in our
culturally diverse program
New UCSD Health System Department of Biomedical Informatics
The new department will extend informatics outreach
beyond research and training, to clinical decision support
In 2014 we celebrated the 5th
anniversary of the Division of Biomedical Informatics (DBMI) and moved to our new offices. We started with seven people in 2009 and now have more than 70 to fill our mission of delivering the best research, training, and service products to the scientific community and to the public in general.
Initially focused on the research enterprise, our service mission is now significantly extending to the clinical informatics arena, in which many of our novel processes, algorithms and
applications can help improve various aspects of clinical care and health sciences training.
In 2015 the DBMI became a UCSD health system department covering data analysis related to quality of care, research and training. With expanded recruitment of faculty, staff and trainees at several levels, the new DBMI will assist the enterprise in information management by clinicians, patients and other decision makers. This is a unique opportunity for us to make a difference in patient care.
We will continue to pursue a diverse portfolio for our research and facilitate the submission of informatics and information technology research proposals to various funding agencies.
We have much to celebrate. We would not get to this point without a great team. Thank you all for getting us here and let’s together start a new chapter in the history of DBMI.
Lucila Ohno-Machado, MD, MBA, PhD Chair, Department of Biomedical Informatics Associate Dean for Informatics & Technology
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Training Highlights
Shuang Wang, PhD was awarded a NIH/NHGRI K99 grant todevelop algorithms and tools for genome research (Protectingthe Privacy of Genomes in Research Studies)
Juan Chaparro, MD, together with faculty members RobertEl-Kareh, MD, MPH, and Brian Clay, MD continued work aspart of a UC-wide team, led by Dr. Elisa Tong from UC Davis,to create a bi-directional eReferral to the California Smokers’Helpline from all five UC medical centers. This eReferral went live at UCSD in December and creates a reliable connectionbetween our patients and resources to help them quitsmoking. The project is part of UC Quits and is supported bythe UC Center for Healthcare Quality and Innovation.
Edna Shenvi, MD wrote an essay selected as top finalist in the Resident and Associate Society of the American College ofSurgery contest: Five-Year General Surgery Residency:Reform vs. Revolution
Xiaoqian Jiang, PhD, and Amir Schangali are organizing thefirst Pan-Pacific Biomedical Informatics Training Camp atUCSD, to take place in the summer of 2015
Outstanding articles led by Zhanglong Ji, MS and ShuangWang, PhD were referred from the TranslationalBioinformatics Conference to informatics journals
Training Program Leadership
Robert El-Kareh, MD, MPH directs the post-doctoral program
Hyeon-eui Kim, RN, MPH, PhD directs the pre-doctoralprogram and is on the Bioinformatics Program AdmissionsCommittee
Xiaoqian Jiang, PhD directs the internship program
Wei Wei, MS and Jing Zhang are our student representatives
Undergraduate, graduate, and postdoctoral trainees participate in several DBMI programs. Since 2009 we had over 80 trainees with various backgrounds and interests coming for short, medium, and long-term educational experiences.
Open Access Resources and Invited Presentations
Rita Germann-Kurz organized 12 open access iDASH researchand 9 journal club webinars, presented by authors ofoutstanding informatics JAMIA articles. This resource hasreceived more than 33,000 views to date
Cleo Maehara, MD, MSc organized our first monthlybioCADDIE (data indexing) seminar
DBMI members presented their work in four continents
Lucila Ohno-Machado, MD, PhD was an invited lecturer at the Chinese Academy of Sciences
Our Courses at UCSD, 2014
MED264, Principles of Biomedical Informatics, taught byXiaoqian Jiang, PhD, moved to our new facilities in BRF2.Kemal Eren and Stephanie Feudjio-Feupe served as TAs
MED267, Modeling Clinical Data and Knowledge forComputation, taught by Hyeon-eui Kim, RN, MPH, PhD,resulted in several practical projects by student groups. JingZhang served as TA
The Clinical Informatics Journal Club, organized by Robert El-Kareh, MD, MPH, discusses practical applications ofinformatics in clinical settings
The Cancer Genomics Journal Club, organized by OlivierHarismendy, PhD, meets weekly at the Cancer Center
MED262, Trends in Biomedical Informatics, our weeklyseminar organized by Chun-nan Hsu, PhD had 31 sessionswith guest speakers from around the country, and also servedas a venue for trainee presentations
MED263, Bioinformatics Applications in Human Health, wastaught by Sergei Pond, PhD and Jason Young, PhD
Training Programs
Scientific Meetings
National and international collaborators participate in DBMI joint events
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Training News
Gail Moser, training program coordinator, retired in December. She will be missed for her long lasting contributions, which helped shape the DBMI into what it is today.
Career advancements
Tyler Bath, undergraduate internworking with Jihoon Kim, MS joined theDBMI programming team led by ClaudiuFarcas, PhD
Michael Conway, PhD started asAssistant Professor of BiomedicalInformatics, University of Utah
Alex Hsieh started at the BMI PhDprogram at Columbia University, afteremployment at DBMI and Illumina
Wenchao Jiang, MS, formerinternational trainee, was accepted tothe PhD program in Bioinformatics atthe University of Minnesota
Mindy Ross, MD, MBA, MAS joinedRady Children’s Hospital clinical andinformatics teams
Krystal Tse, undergraduate intern,started at the PhD program ininternational relations at UCSD
Rebecca Walker, former staff member,was accepted to the doctoral programin bioinformatics at UCLA
Christopher Woelk, PhD joined thefaculty at the University ofSouthampton, UK
International Training
We continued our fifteen years ofcollaboration with Heimar Marin, RN,PhD, from the Universidade Federal de São Paulo, for informatics training inBrazil and Mozambique
Sandro de Souza, PhD, BeatrizStransky Ferreira, PhD, Jorge deSouza, PhD from UFRN and i2bio,Brazil, Valter Nuaila, UniversidadeEduardo Mondlane, Maputo and theDBMI organized the 1
st Short Course in
Bioinformatics in Maputo,Mozambique with help from FranciscoMabila and David Bila, PhD
We established new partnerships withHong Kong Baptist University andSoochow University in China
Shanghai JiaoTong University studentsYong Li and Yuchen Zhang, advised byHongkai Xiong, PhD and SoochowUniversity student Yujie (Jenny)Zhu, advised by Bairong Cheng, PhDstarted their internships at DBMI
Morgan von Ebke is now supervisingthe processing of all new trainee andscholar appointments and visas
We pride ourselves for collectivelyspeaking more than 20 worldlanguages: Cantonese, English, Farsi,French, German, Greek, Gujarati,Hindi, Italian, Japanese, Korean,Mandarin, Norwegian, Portuguese,Romenian, Russian, Sanskrit, Spanish,Taiwanese, and Vietnamese. This is inaddition to several programminglanguages…
Pre- and Post-Doctoral Trainees
Adam Rule, Skylar Kerzner, YingxiangHuang, joined pre-doctoral BMIprogram students Eric Levy, JingZhang, Kemal Eren, StephanieFeudjio-Feupe, Wei Wei, MS, ZacharyLipton, and Zhanglong Ji, MS
Graduate students Arya Iranmehr,Brian Sudjiati, Gordon Lin, PriyankaGanapathi, Samuel Ko, Shima SalimiTari, Shitij Bhargava, and Suvir Jainjoined our research projects
Juan Chaparro, MD, Rady Children’sHospital, Gilbert Ramirez, MD, UCSF-Fresno, Augustine Obirieze, MD, MPH, Howard-Hopkins Surgical OutcomesResearch Center, and Meng Wang,PhD, UCSD, joined postdoc fellowsDivya Chhabra, MD, KatherineHomann, MD, Edna Shenvi, MD, andShuang Wang, PhD
Wenrui Dai, PhD, former exchangestudent, accepted a position aspostdoctoral fellow in the DBMI
Interns
Dexter Friedman and Briana Herrerajoined Hyeon-eui Kim, RN, PhD in theiCONCUR project
We hosted summer interns Feng Chen, U Oklahoma, Steve Cook, UCRiverside, Haoran Li, Emory, Sisi Lu,Pittsburgh, Ruiling Liu, UT Houston,Lichang Wang, Northwest A&F, XuefuWang, Indiana, Emily Fireman,Quentin Gautier, Arya Iranmehr, Mark Myslin, Alex Richardson, and AmandaRitchart, UCSD
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2014 ended on a high note with an award from the National Institutes of Health for the biomedical & healthCAre Data Discovery Index Ecosystem (bioCADDIE), a project led by Lucila Ohno-Machado, MD, PhD, and coordinated by Cleo Maheara, MD, MSc, in collaboration with
Hua Xu, PhD, UT Houston, chair of the Data Shop taskforce,and investigators Elmer Bernstam, MD, Trevor Cohen, MBBS,PhD, Todd Johnson, PhD, Cui Tao, PhD, and Jim Zheng, PhD
UCSD professor Maryann Martone, PhD and StephanieHagstrom who are organizing a large community ofresearchers and publishers, and Peter Rose, PhD from the PDB
Susanna Assunta-Sansone, PhD, Oxford University, who leadsour collaborative effort with the CEDAR BD2K Center ofExcellence
George Alter, PhD, University of Michigan, who leads ourinteractions with data repositories
Ian Fore, PhD, National Cancer Institute, NIH science officer
DBMI members Chun-nan Hsu, PhD, Xiaoqian Jiang, PhD,Hyeon-eui Kim, RN, PhD, Claudiu Farcas, PhD and RitaGermann-Kurz and several trainees
Investigators from eight NIH-funded research projects and NIHrepresentatives from several institutes
The DBMI team continues to expand as we take on new projects and collaborations. In its fourth year, our internship program attracted young talent from several institutions around the world.
Research and Applications
bioCADDIE’s goal is to do for data what PubMed did for the literature: transform the way data are discovered and make them easier to be accessed
Other New Grants
Xiaoqian Jiang, PhD, NIH/NLM R21, to develop homomorphicencryption tools for cloud computing
PCORI awarded a patient-centered privacy protectiontechnology grant to Emory collaborator Li Xiong, PhD, with site investigators Xiaoqian Jiang, PhD and Shuang Wang, PhD
We thank Cher Hehr for grant management support
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The bioCADDIE consortium is part of the NIH’s Big Data to Knowledge (BD2K) initiative. Five initial pilot projects were planned for year 1
Linking publications and underlying data sets using natural language processing
Hua Xu, UT Houston
Rating relationships in imaging reports: Machine learning vs. crowdsourcing approaches
Ricky Taira, UCLA
Data recommendation using machined learning and crowdsourcing
Xiaoqian Jiang, UC San Diego
Intelligent search expansion and visualization of data sets
Todd Johnson, UT Houston
Hyeon-eui Kim, UCSD
Development of citation and data access metrics applied to RCSB protein data bank and related resources Peter Rose and Chun-nan Hsu, UCSD
We also issued a call for collaborators for these projects. An open call for new targeted pilot projects will be issued for year 2 and beyond.
Additionally, we are planning to form working groups to provide recommendations for the data discovery index.
bioCADDIE’s is planning a few workshops. The first one, on Data Citation, was organized by Drs. Martone and Sansone and co-located with the FORCE 2015 meeting in Oxford, UK
1st Data Sharing Meeting
Leveraging the pSCANNER, iDASH, and bioCADDIE projects, we organized a joint conference on Data Sharing in September
This San Diego event, organized by RitaGermann-Kurz, brought collaboratorsfrom academic and healthcareinstitutions, government agencies,patient representatives, ethicists,clinicians and researchers
Our goal is to promote human subjects data sharing in a way that facilitates research while also preserving the privacy of individuals and institutions
iDASH’s 44 data e-communities nowserve more than 150 users in 28institutions in the USA and abroad. Over439,000 files have been downloaded sofar, and 26 tools that impact over 3,000researchers were developed
Patient Engagement
We are developing new collaborations with patient-powered and clinical data networks part of pSCANNER
Howard Taras, MD, leader for patientengagement at UCSD works closely withKathy Kim, PhD, Hugo Campos, andother patient representatives in thepSCANNER stakeholder board
Collaborator News
Daniella Meeker, PhD, pSCANNERtechnical leader, is now assistantprofessor, preventive medicine, and CTSAinformatics core director, USC
Michael Matheny, MD, MS, iDASH andpSCANNER collaborator, is now director,Center for Population Health, BiomedicalInformatics, Vanderbilt
Zia Agha, MD, collaborator on pSCANNERand VA projects, is now Executive Vice-President, Clinical Research and MedicalInformatics at the West Institute. DenaRifkin, MD, PhD is site principalinvestigator for the San Diego VA
Jonathan Nebeker, MD, director for theVA’s clinical warehouse VINCI, and ScottDuvall, PhD lead pSCANNER at the SLC VA
Katherine Kim, MBA, PhD, pSCANNERpatient engagement leader, is nowassistant professor, nursing, UC Davis
Mini Kahlon, PhD, former pSCANNER andUC ReX collaborator, is now Vice Dean forPartnerships & Strategy at UT Dell MedicalSchool, Austin. Mary Whooley, MD is nowpSCANNER site principal investigator, UCSF
Amy Sitapati, MD, biomedical informaticsboard-certified physician and collaboratorfor the iCONCUR project, is now medicaldirector of the UCSD Internal MedicineClinic in La Jolla
Yunan Chen, PhD, collaborator in human-computer interaction, is co-advisor for JingZhang and associate professor at UC Irvine
Linked grant Kevin Patrick, MD, MPH received an NCI
R01 for the iDASH-linked CYCORE project(cyberinfrastructure for cancer research)
Librarians are key collaborators in our
data sharing initiatives
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1. 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;33(7):1123-31. PMID: 25006137
2. Bell E, Ohno-Machado L, Grando MA*. Sharing My Health Data: A Survey of Data Sharing Preferences of Healthy Individuals. AMIA Ann Symp 2014.
3. Carty CL, Bhattacharjee S, Haessler J, Cheng I,Hindorff LA, Aroda V, Carlson CS, Hsu CN, et al. Analysis of metabolic syndrome components in >15 000 African-Americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study. Circ Cardiovasc Genet. 2014 Aug;7(4):505-13.
4. Doan S, Conway M, Phuong TM, Ohno-Machado L. Natural language processing in biomedicine: a unified system architecture overview. Meth Mol Biol. 2014;1168:275-94. doi: 10.1007/978-1-4939-0847-9_16. PMID: 24870142
5. Farcas C, Farcas E, Krueger I. In: Economics Driven Software Architecture. Economics Driven Software Architecture. Elsevier, 2014.
6. Hinske LC, Franca GS, Torres HAM, Ohara DT,Lopes-Ramos CM, Heyn J, Reis LFL, Ohno-Machado L, Kreth S, Galante PAF. miRIAD--integratingmicroRNA inter- and intragenic data. Database. 2014;Oct 6; PMID: 25288656
7. Ji Z*, Jiang X, Wang S*, Xiong L, Ohno-Machado L. Differentially private distributed logistic regression using private and public data. BMC Med Genom. 2014;7 Suppl 1:S14. PMID: 25079786
8. Han H, Jiang X. Disease Biomarker Query from RNA-Seq Data. Cancer Inform. 2014;13(Suppl 1):81-94. PMID: 25392686
9. Hepler LN*, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. PLoS Comput Biol.2014;10(9):e1003842. PMID: 25254639
10. Huang YH, Kao MT, Hsu CN. IdentifyingTransformative Research in Biomedical Sciences. Proc 19th Int Conf Tech AI. 2014.
11. Ji Z*, Jiang X, Wang S*, Xiong L, Ohno-Machado L. Differentially Private Distributed Logistic Regression using Private and Public Data. BMC Med Genom. 2014;7 Suppl 1:S14. PMID: 25079786
12. Ji Z*, Jiang X, Li H*. Select and Label (S & L): a Task-Driven Privacy-Preserving Data Synthesization Framework. Transl Bioinform Conf. 2014.
13. Jiang X, Chen R, Cheng S, Shen B, Xu R, Yi S.Computational Advances in Cancer Informatics, Cancer Inform.2014:13(S1),45-8. PMID: 25484572
14. Jiang X, Wu Y, Marsolo K, Ohno-Machado L. Development of a Web Service for Analysis in a Distributed Network. eGEMs (Gen Evidence & Methods to improve patient outcomes). 2014:2(1).
15. Jiang, X, Zhao Y, Wang X, Malin B, Wang S*, Ohno-Machado L, Tang H. A Community Assessment of Privacy Preserving Techniques on Human Genome Data, BMC Med Inform Dec Making, 14(S1): 2014. PMID: 25521230
16. Karimi S, Jiang X, Cosman P, Flexible Methods for Segmentation Evaluation: Results from CT-based Luggage Screening. J X-Ray Sci Tech, 22(2): 175-95,2014. PMID: 24699346
30. Ohno-Machado L. Health IT and clinical decision support systems: human factors and successful
adoption. J Am Med Inform Assoc. 2014; 21(e2):e180. PMID: 25200586
31. Ohno-Machado L. Networking the country to promote health and scientific discovery. J AmMed Inform Assoc. 2014;21(4):575. PMID: 24908676
32. Ohno-Machado L. Structuring text and standardizing data for clinical and population health applications. J Am Med Inform Assoc. 2014;21(5):763. PMID: 25117592
33. Ohno-Machado L. Focusing on the patient: mHealth, social media, electronic health records, and decision support systems. J Am Med Inform Assoc. 2014;21(6):953. PMID: 25301806
34. Ohno-Machado L. Disseminating informatics knowledge and training the next generation of leaders. J Am Med Inform Assoc. 2014;21(6):953. PMID: 25301806
35. Ross MK*, Wei W*, Ohno-Machado L. “Big Data” and the Electronic Health Record. Yearb Med Inform, 2014;9:96-104. PMID: 25123728
36. Roozgard A*, Barzigar N, Wang S*, Jiang X, ChengS. Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment. Cancer Inform, accepted
37. Shenvi EC*, Meeker D, Boxwala AA. Understanding data requirements of retrospective studies. Int J Med Inform. 2014 Oct 12. PMID:25453276
38. Shenvi E*, El-Kareh R. Clinical criteria to screen for inpatient diagnostic errors: a scoping review. Diagnosis. doi: 10.1515/dx-2014-0047. Epub Oct 2014.
39. 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
40. Wang B, Jiang X, Xiong H, Chen CW. Data-driven Hierarchical Structure Kernel for Multiscale Part Based Object Recognition, IEEE Trans Imag Proc, 23(2), 1765-1778, 2014. PMID: 24808345
41. 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
42. Wang S*, Jiang X, Cui L, Cheng S. Streamlined Genome Sequence Compression using Distributed Source Coding. Cancer Inform. 2014;S1:123-131. PMID: 25520552
43. Wang S*, Jiang X, Mohammed N, Chen R, Wang S. Differentially Private Genome Data Dissemination Through Top-Down Specialization. BMC Med Inform Dec Making. 2014. PMID: 25521306
44. Wu Y, Jiang X, Wang S, Jiang W, Li P, Ohno-Machado L. Grid Multi-Category Response Logistic Models. BMC Med Inform Dec Making, accepted.
45. Yu F, Ji Z*. Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies: An Application to iDASH Healthcare Privacy Protection Challenge. BMC Med Inform Dec Making. 2014. PMID:
17. Kim H, Chung H, Wang S*, Jiang X, Choi J. SAPPIRE: a prototype mobile tool for pressure ulcer risk assessment. Stud Health Technol Inform. 2014;201:433-40. PMID: 24943578
18. Kim H, Ohno-Machado L, Oh J, Jiang X. Trends in Publication of Nursing Informatics Research. AMIA Ann Symp 2014.
19. 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 Jun 6. PMID:24907367
20. Li H*, Xiong L, Ohno-Machado L, Jiang X. Privacy Preserving RBF Kernel Support Vector Machine. Biomed Res Int. 2014;2014:827371. Epub 2014 Jun 12. PMID: 25013805
21. Li H*, Xiong L, Zhang L, Jiang X. DBSynthesizer: Differentially Private Data Synthesizer for Privacy Preserving Data Sharing. Very Large Data Bases. 2014.
22. Li H*, Jiang X, Ji Z*, Xiong L. Differentially Private SNP selection in Genome-Wide Association Studies. Translational Bioinformatics Conference. 2014.
23. Lyumkis D, Oliveira Dos Passos D, Tahara EB,Webb K, Bennett EJ, Vinterbo S, Potter CS,Carragher B, Joazeiro CA. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. Proc Natl Acad Sci USA. 2014;111(45): 15981-6. PMID: 25349383
24. Matheny ME, Ohno-Machado L. Generation of Knowledge for Clinical Decision Support: Statistical and Machine Learning Techniques. Clinical Decision Support (Greenes R, editor), 2nd Edition. Burlington (MA): Academic Press;2014.
25. Mehta SR, Vinterbo SA, Little SJ. Ensuring privacy in the study of pathogen genetics. Lancet Infect Dis. 2014;14(8):773-7. PMID: 24721230
26. Ohno-Machado L. The role of scientific publication in times of change. J Am Med InformAssoc. 2014; 21(1):1. PMID: 24335250
27. Ohno-Machado L. NIH's Big Data to Knowledge initiative and the advancement of biomedical informatics. J Am Med Inform Assoc 2014;21(2): 193. PMID: 24509598
28. Ohno-Machado L. Electronic health recordsystems: risks and benefits. J Am Med InformAssoc. 2014;21(e1):e1. PMID: 24453123
29. Ohno-Machado L, et al. pSCANNER: Patient-Centered Scalable National Network for Effectiveness Research. J Am Med Inform Assoc 2014;21(4): 621-6 PMID: 24780722
2014 DBMI Publications (* trainee)
Located at the new research building on the UCSD campus, DBMI is in close proximity to our other offices at Building 2
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Service roles allow us to stay connected to real world
issues that need to be solved in practice and allow
our trainees to have a broad training experience.
Our division started its service mission by
implementing and managing information systems for
the clinical and translational research enterprise.
As our division evolved into a department, our
mission is expanding to service and collaboration for
clinical decision support and education.
Starting in 2015 we will recruit information
technology executives, managers, and technologists
in addition to several faculty.
Service and collaboration to help researchers, clinicians, and educators
Innovations need to be designed to address problems in real settings where biomedical research and clinical decisions are made. Our team has
expanded significantly with the implementation of an enterprise-wide clinical trial management system and several research database systems.
The Clinical and Translational ResearchInstitute informatics technical team isled by Antonios Koures, PhD
Andrea Barker, Daniel Clark Jr, ErikaPaul, James Graczyk, Jocelyn Saria,Karen Welborne, Melissa Generoso,Narimene Lekmine, Perry Shipman,and Zhaohong (Tony) Chen were joinedthis year by Carol Johnson, HelenaShevchuk, Natalya Abramovich, andKyla Kelly
The CTRI team now manages over 400studies, 800 investigators, and datafrom more than 120,000 biosamples
We are integrating research systemswith the electronic health record tofacilitate research and administration
Paulina Paul directs our Clinical DataWarehouse for Research and, assistedby Wendy Zhu, PhD, continues toprovide data to our CTSA researchcommunity and lead UC ReX at UCSD
Statisticians Jihoon Kim, MS and HaiYang, MS ensure that our researchmeets the highest technical standards
Five years ago we helped launch the UC Research eXchange (UC ReX) consortium for informatics, linking the clinical data warehouses of five UC medical centers for research. The project helped our participation in other tranformative nationwide
initiatives
pSCANNER, patient-centeredSCAlable National Network forEffectiveness Research, funded byPCORI, is a network that includesrecords for more than 21 millionpatients in all USA states andterritories. Michele Day, PhD ispSCANNER’s program manager
ACT, Accrual for Clinical Trials,funded by NIH/NCATS, is a networkof 13 institutions funded by NIHClinical Translational ScienceAwards. Gary Firestein, MD, UCSD, is ACT’s co-PI with CTSA colleaguesfrom Pittsburgh, Harvard, and UTSouthwestern
The scope and the size of the informatics service team continue to grow
The iDASH private HIPAA-CLOUD, architectedby Antonios Koures, PhD and our secureHIPAA resource designed by Claudiu Farcas,PhD are becoming FISMA-certified
Jihoon Kim, MS and Olivier Harismendy, PhDdesigned the first “recipes” for the cloud
Over 400 data sets from several institutionsworldwide are hosted in iDASH and privacy-protecting analytic software developed by ourteam is now frequently downloaded
Elizabeth Bell, MPH supports UC ReX users
Claudiu Farcas, PhD developed an “honestbroker” system to host clinical research datafor UC ReX, pSCANNER, and other projects
We thank Hai Yang, MS for DBMI photos in this newsletter and in our web site http://dbmi.ucsd.edu
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The Division of Biomedical Informatics was established in the summer of 2009 with support from the School of Medicine and the Medical Center. In early 2015 it
expanded into the Health System Department of Biomedical Informatics. It has now over 70 members among faculty, trainees, and staff in addition to regional,
national and international collaborators. Located at UCSD in La Jolla, the DBMI develops and implements technology for privacy-protecting data sharing and cloud
computing, patient-centered outcomes research, clinical decision support, and distributed predictive analytics.
Department of Biomedical Informatics @ UCSD
9500 Gilman Dr. MC0728
La Jolla, CA 92093-0728
Biomedical informatics: advancing healthcare and research in San Diego
Biomedical informatics: advancing healthcare, research, and education