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dbmi.ucsd.edu 2014-15 Department of Biomedical Informatics Research Increased research funding marks the 5 th 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 5 th 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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Page 1: Biomedical Informatics Department of · PDF filedbmi.ucsd.edu 2014-15 Department of Biomedical Informatics Research Increased research funding marks the 5th anniversary of our division

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

Page 2: Biomedical Informatics Department of · PDF filedbmi.ucsd.edu 2014-15 Department of Biomedical Informatics Research Increased research funding marks the 5th anniversary of our division

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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