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2018 Biomedical Informatics Seminars

December 7, 2018

Dr. Richard Scheuermann, PhD

Explainable Artificial Intelligence (XAI) and Single Cell Genomics of Human Brain

Bio: Richard H. Scheuermann, PhD, is the director of the La Jolla Campus at the J. Craig Venter Institute (JCVI) and an adjunct professor of pathology at U.C. San Diego. He received a BS in Life Sciences from the Massachusetts Institute of Technology, and a PhD in Molecular Biology from the University of California, Berkeley. After completing his doctoral research, he accepted an independent research position at the Basel Institute for Immunology in Basel, Switzerland. In 1992, he joined the faculty in the Department of Pathology at the University of Texas Southwestern Medical Center in Dallas where he rose to the rank of Professor with tenure. In 2001, he made a career shift into the discipline of bioinformatics, initiated with a sabbatical year at the San Diego Supercomputer Center. In 2012, Dr. Scheuermann moved to San Diego to become the Director of Informatics at JCVI, and in 2016 was promoted to Director of the La Jolla Campus. 
Dr. Scheuermann has applied his deep knowledge in molecular immunology and infectious disease toward the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, novel methods for the analysis of gene expression, protein network and flow cytometry data, and novel comparative genomics methods. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database (IRD), the Virus Pathogen Resource (ViPR), and the Immunology Database and Analysis Portal (ImmPort) supported by the U.S. National Institutes of Health.

November 30, 2018

Dr. KJ Yang, PhD

Liberate the Fear of Heart Failure

Abstract: Heart Failure is a global issue that is spiraling out of control with an aging society. As of today, 8 million Americans have heart failure and it accounts for $41B in medical expenditures. Its 5 years mortality rate is 50%, more than most cancers. Its 30-day readmission rate is top among all the other diseases and hence introduces a heavy financial burden to the health care system. There is significant emphasis on treatment, which only covers half of the issue. The other half is recovery: how to help patients regain health. KURA provides a solution to that issue by providing clinically significant daily health information, insightful analytics, to help patients and the care team work together.  

Bio: Dr. Yang graduated from UCSD Electrical Engineering Ph.D program in 2007 with a full scholarship from Qualcomm. Subsequently, he successfully commercialized his Ph.D work, using visual neuron model to achieve perceptual video compression on mobile chip system, with Qualcomm. He has more than 10 years’ experience on product and business development in Qualcomm, where he managed multiple teams across USA, China and India. Despite lots of exiting projects achieved in a big company, he cannot stop thinking about how to make health care more efficient and accessible. After he left Qualcomm, he focuses on bridging health care and IT technology using big data and artificial intelligence. His focus is precision care for heart failure and other chronic diseases. He serves as the founder and CEO of KURA care LLC.

November 16, 2018

Dr. Job Godino, PhD

Advancing methods and interventions in behavioral medicine and chronic disease prevention

Abstract: Dr. Job Godino is an Assistant Professor at the Department of Family Medicine and Public Health. He is a principal investigator in the Center for Wireless and Population Health Systems and the Director of the Exercise and Physical Activity Resource Center. He will discuss his research, much of which focuses on the development, conduct, and evaluation of complex interventions that utilize mobile and wearable technology (e.g., smart phones, accelerometers, and heart rate monitors) to promote healthy changes in physical activity, sedentary behavior, diet, and sleep for the primary and secondary prevention of obesity, diabetes, and cardiovascular disease. He is also actively engaged in the development and evaluation of new methods to conduct biomedical research, including assessing the validity and reliability of on- and off-body sensors that measure various components of human physiology and behavior.   

Bio: The majority of Dr. Godino’s research focuses on the development, conduct, and evaluation of complex interventions that utilize mobile and wearable technology (e.g., smart phones, accelerometers, and heart rate monitors) to promote healthy changes in physical activity, sedentary behavior, and diet for the primary and secondary prevention of obesity, diabetes, and cardiovascular disease. Mobile and wearable technologies that capture data and contextualize health behaviors in real-time provide a mechanism through which theory-based interventions can be personalized and widely disseminated. Furthermore, they empower individuals to collect large amounts of personal health data, which, if appropriately leveraged, has the potential to transform the conduct of epidemiological research and reduce health disparities. Dr. Godino is broadly interested in the prevention of chronic diseases and disorders that disproportionately afflict minority and medically underserved populations and has worked on several NIH-funded projects in this area. In his role as Director of Research and Applied Technology for the Exercise and Physical Activity Resource Center (EPARC), he is actively engaged in the development and evaluation of on- and off-body sensors that measure various components of human physiology and behavior.

November 9, 2018

Dr. Rob Knight, PhD

Spatial Mapping of the Human Microbiome

Abstract: Although we often speak of “the microbiome”, each of us contains a multitude of different microbial communities in different parts of the body. In mapping projects such as the Human Microbiome Project, it first became apparent that different parts of the skin, the mouth, and the GI tract have markedly different microbial communities that interact with host immunity in different ways. Recent advances in spatially resolved mapping of the skin, the gut, the lung, and other environments are allowing us to map these differences at much finer spatial scale and relate them to immune and inflammatory processes. Here I describe the latest advances in mapping across the body, and how improved connections to high-throughput immune profiling could greatly assist in our understanding of health and disease.  
Bio: Rob Knight is the founding Director of the Center for Microbiome Innovation and Professor of Pediatrics and Computer Science & Engineering at UC San Diego. Before that, he was Professor of Chemistry & Biochemistry and Computer Science in the BioFrontiers Institute of the University of Colorado at Boulder, and an HHMI Early Career Scientist. He is a Fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology. He received the 2017 Massry Prize for his microbiome research. In 2015 he received the Vilceck Prize in Creative Promise for the Life Sciences. He is the author of “Follow Your Gut: The Enormous Impact of Tiny Microbes” (Simon & Schuster, 2015), coauthor of “Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System (St. Martin’s Press, 2017) and spoke at TED in 2014. His lab has produced many of the software tools and laboratory techniques that enabled high-throughput microbiome science, including the QIIME pipeline (cited over 10,000 times as of this writing) and UniFrac (cited over 5000 times including its web interface). He is co-founder of the Earth Microbiome Project, the American Gut Project, and the company Biota, Inc., which uses DNA from microbes in the subsurface to guide oilfield decisions. His work has linked microbes to a range of health conditions including obesity and inflammatory bowel disease, has enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world.

November 2, 2018

Dr. Eric Poon, MD, MPH, FACMI

The Spectrum of Analytics and Data Science at Duke

Bio: I currently serve as the Chief Health Information Officer for Duke Medicine. I also practice primary care internal medicine at the Durham Medical Center as part of Duke Primary Care. In my capacity as CHIO, I am responsible for the visioning and strategic planning of clinical and analytic information systems that impact patient care, research and education.  I work with the Duke Medicine leadership to ensure technology solutions are well aligned with our overall organizational objectives. I oversee the optimization of the Maestro Care (Epic) electronic health record, and partner with physicians, patients and operational leaders to effectively leverage innovative IT in support of the Duke mission.  I also have a keen interest in IT innovation, and work with investigators across Duke to pursue new and innovative ways to efficiently deliver high quality care to our patients.
My research interests have revolved around the use of health information technology to improve the quality of care and patient safety in both the ambulatory and hospital settings.  My work in the ambulatory setting has focused on the efficient delivery of decision support to clinicians to prevent errors of omission and commission during diagnostic test ordering and review of test results. I have also worked to use information technology, including secure on-line patient portals, to improve the communication between clinicians and patients around health maintenance and the follow-up of abnormal test results.  In the inpatient setting, I have conducted several studies to delineate the barriers to and facilitators of the wide-spread diffusion of computerized physician order entry and have led many studies evaluating the safety, financial and socio-technical impact of barcode technology in the hospital pharmacy and nursing units.

October 24, 2018

Dr. Philip Payne, PhD, FACMI

Precision Health: Faster Research, More Cures, Healthier Communities

Abstract: The healthcare and life science research, education, and practice domains are undergoing tremendous change, driven by a combination of economic, policy, and technology factors.  At the core of these changes are: 1) an increased focus on the use of patient-derived data, contextualized by the best available scientific evidence, in order to deliver highly tailored and individualized wellness and clinical care interventions; and 2) a simultaneous demand to transform healthcare at a population-level through the pursuit of a triple aim concerned with increasing quality and safety while also decreasing costs.  While these two areas of endeavor are often approached as distinct from each other, they in fact share a common set of data, information, and knowledge based needs that can be satisfied using a systems-level approach to biomedical informatics and data science.  This presentation will explore these critical issues, focusing upon the changing landscape of healthcare and life science, the role of computation and data science in both driving and adapting to such change, illustrated by a number of active research and innovation projects currently underway within the Washington University Institute for Informatics (I2).
Bio: Dr. Payne is the Robert J. Terry Professor and founding Director of the Institute for Informatics (I2) at the Washington University in St. Louis School of Medicine.   He also serves as a Professor of General Medical Sciences in the School of Medicine’s Department of Medicine and as a Professor of Computer Science and Engineering in the School of Engineering and Applied Science. Dr. Payne is an internationally recognized leader in the field of clinical research informatics (CRI) and translational bioinformatics (TBI). Dr. Payne received his Ph.D. with distinction in Biomedical Informatics from Columbia University, where his research focused on the use of knowledge engineering and human-computer interaction design principles in order to improve the efficiency of multi-site clinical and translational research programs.  His current research interests include: 1) knowledge-based and integrative approaches to the discovery and analysis of bio-molecular and clinical phenotypes and the ensuing identification of precision diagnostic and therapeutic strategies; 2) interventional approaches to the use of electronic health records and decision support systems to enable patient-centered decision making in information intensive environments; 3) the study of human factors and workflow issues surrounding the optimal use of healthcare information technology; and 4) The design and evaluation of open-science platforms that enable collaborative and cumulative approaches to biomedical data analytics.

October 19, 2018

Dr. Eric Granholm, PhD

Mobile Assessment and Intervention in Serious Mental Illness

Abstract: The functional disability associated with serious mental illness (SMI) places immense burden on individuals, families, and society, and disability often persists even after efficacious treatment of psychiatric symptoms. Traditional methods of measuring functioning in SMI have serious limitations, and numerous obstacles lead to limited availability of effective evidence-based interventions that have been developed to improve functioning in SMI. This talk will describe the potential of technological innovations for overcoming the challenges involved in both functional assessment and intervention in people with SMI. Ecological momentary assessment (EMA), which involves the repeated sampling of naturalistic behaviors and experiences while individuals carry out their daily lives, provides a feasible, reliable and more valid approach to measuring functioning. EMA presents several advantages over traditional assessment methods and has in recent years evolved into mobile-based platforms such as text messages and smartphone apps that can be used for both assessment and treatment of SMI. Promising data regarding the acceptability, adherence, and efficacy of EMA-based mobile technologies will be presented to illustrate how these technologies can extend the reach and impact of evidence-based psychosocial rehabilitative interventions in SMI.  

Bio: Dr. Granholm is Professor of Psychiatry and Director of the Center for Mental Health and Technology (MHTech Center) at UC San Diego and Chief of Psychology and Co-Section Chief of Psychosocial Rehabilitation and Recovery Services at the VA San Diego Healthcare System.  He received his Ph.D. in Clinical Psychology from the University of California, Los Angeles in 1991, and completed a postdoctoral fellowship at the UCLA Semel Institute for Neuroscience and Human Behavior. At UCLA, he conducted research on neuropsychology, pupillometry, social skills training and family therapy for schizophrenia and bipolar disorder. Since joining the faculty at UC San Diego in 1993, Dr. Granholm has been an active basic and clinical researcher in the areas of neuropsychology, pupillometry, ecological momentary assessment, and psychosocial and mobile interventions for schizophrenia and Alzheimer’s disease.

October 12, 2018

Dr. Michael Hogarth, MD, FACMI, FACP

Informatics and the Merging of Research and Quality Measures with Bedside Care

Abstract: The pressures of rising medical expenses, value-based care, and drug discovery costs are necessitating a revolution in healthcare. Big data and informatics are being increasingly relied upon to support and revolutionize the healthcare system. Three areas ripe for investigation are: 1) clinical trial design—reducing cost and latency; 2) observational cohort data—leveraging widespread EHR adoption; and 3) meeting quality improvement goals. Dr. Hogarth will discuss the forces in the biomedical ecosystem that are leading to a convergence of care, quality, and research at the point of care. Finally, he will discuss how informatics can be leveraged to achieve these goals, current successes, and what barriers still remain.

Bio: Dr. Michael Hogarth is board certified Internal Medicine physician and a faculty in biomedical informatics. He currently also serves as Chief Clinical Research Information Officer for UC San Diego Health. He is also engaged in a number of grant and contract funded activities. These include the California Electronic Death Registration System (California EDRS), the Maryland Death Registration System, the Athena Breast Health Network project (, the novel I-SPY2 adaptive breast cancer clinical trial, the pSCANNER clinical data research network (CDRN), and the California Precision Medicine Consortium (CaPMC). In 2015 he was elected to the American College of Medical Informatics (ACMI).  Dr. Hogarth's research interests include the development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.

October 5, 2018

Dr. Christian Dameff, MD, MS

Hacking Humanity: Patient Safety in the Era of Hyperconnected Healthcare

Bio: Dr. Christian Dameff is an Emergency Medicine physician and researcher. He is currently a Clinical Informatics fellow at the University of California San Diego. Published clinical works include post cardiac arrest care including hypothermia, novel drug targets for acute myocardial infarction patients, ventricular fibrillation waveform analysis , cardiopulmonary resuscitation (CPR) quality and optimization, dispatch assisted CPR, tele-toxicology and medical education topics using Google Glass. Dr. Dameff is also a hacker and security researcher interested in the intersection of healthcare, patient safety, and cyber security. He has spoken at some of the world’s most prominent hacker forums including Defcon, BSides: Las Vegas, and is one of the co-founders of the CyberMed Summit, a novel multidisciplinary conference with emphasis on medical device and infrastructure cyber security. Published cyber security topics include hacking 911 systems, HL7 messaging vulnerabilities, and malware.

September 28, 2018

Taylor Davis, MS STAT

Unlocking the EHR Revolution

Abstract: Almost ten years ago, US healthcare digitization began in earnest, based on an assumption that caregivers and computers together can deliver highest quality and more efficient care than caregivers and paper.  Today, over half of physicians nationally feel that the EHR does not improve their ability to deliver care, and even more feel that it slows them down. What happened?  To understand why computerization of healthcare appears to not be working, we need to talk to the users. Join Taylor Davis of the Arch Collaborative as he explores over 50,000 clinician EHR surveys and the solutions that are starting to emerge from this research.

Bio: Taylor Davis has been with KLAS for 11 years and has played a leadership role in KLAS research and efforts studying HIE, CPOE, pharmacy, population health, ERP, business intelligence and value based care services.  Recently Taylor has help found the KLAS Arch Collaborative, a network of provider organizations working together to ensure that EHR technology brings the patient care and efficiency gains that it has the potential to drive.  Taylor is KLAS’s lead statistician.

June 8, 2018

Professor Brenda Simon, JD

Legal and Policy Issues Regarding Data Aggregation

Bio: Professor Simon joined the TJSL faculty in 2010.  Prior to that, she was the teaching fellow for the Law, Science and Technology LL.M. Program at Stanford Law School, and a fellow in the Center for Law and the Biosciences. Before joining Stanford, Professor Simon was an associate at Fenwick & West, where she represented technology clients in intellectual property litigation, counseling and patent prosecution. Her pro bono representation of clients included successful appeals before the Ninth and Federal Circuits. In 2000-2001, she served as a law clerk to Judge Mariana R. Pfaelzer of the U.S. District Court for the Central District of California. Her research focuses on intellectual property and bioethics. Professor Simon’s recent articles have been published in the Houston Law Review, the Michigan Telecommunications and Technology Law Review, Nature Biotechnology, and the Stanford Journal of Law, Science & Policy. Her article, Rules, Standards, and the Reality of Obviousness, 65 CASE W. RES. L. REV. 25 (2014), was selected as one of the year’s best law review articles related to intellectual property and republished in Intellectual Property Law Review (West 2015).  

June 1, 2018

Dr. Laurel Riek

Healthcare Robotics: Supporting Patients, Caregivers, and the Clinical Workforce

Abstract: Robots are now entering our daily lives - in the home, on the road, in offices, and in hospitals. To operate proximately with people, robots need the ability to dynamically and quickly interpret human activities, understand context, and take appropriate (and safe) actions. They also need to learn from and adapt to people long term. My research focuses on building robots that autonomously solve problems in human environments, particularly those that are safety critical (e.g., hospitals, homes, and factories). Recent contributions include new methods to model stochastic environments and circumvent sensor noise and occlusion, new techniques to enable robots to robustly solve problems under limited computational resources, and methods for robots to perceive and learn from people long term. Our primary application focus is healthcare, and recent projects include supporting older adults in home environments, including people with cognitive impairments, as well as new ways to use robots to support the clinical workforce. This talk will describe several recent projects in this space.

Bio: Dr. Laurel Riek is an Associate Professor in Computer Science and Engineering at the University of California, San Diego, with joint appointments in the Department of Emergency Medicine and Contextual Robotics Institute. Dr. Riek directs the Healthcare Robotics Lab, and leads research in human-robot teaming, computer vision, and healthcare engineering, and builds autonomous systems which work proximately with people. Riek's current research projects have applications in critical care, neurorehabilitation, and home health. Dr. Riek received a Ph.D. in Computer Science from the University of Cambridge, and B.S. in Logic and Computation from Carnegie Mellon. Riek served as a Senior Artificial Intelligence Engineer and Roboticist at The MITRE Corporation from 2000-2008, working on learning and vision systems for robots, and held the Clare Boothe Luce chair in Computer Science and Engineering at the University of Notre Dame from 2011-2016. Dr. Riek has received the NSF CAREER Award, AFOSR Young Investigator Award, Qualcomm Research Award, and multiple best paper awards.

May 25, 2018

Dr. Charles Jaffe

HL7 FHIR for the Information Scientist

Abstract: The unambiguous sharing of healthcare data is insufficient to meet the needs of our delivery system. Moreover, the means for exchanging data has not facilitated data reuse for a broad range of purposes, including quality evaluation, decision support, clinical research, primary medical science, and public health. Standards must rapidly evolve despite an environment constrained by the limited resources, by government regulation and by a rapidly evolving knowledge base. The Department of Health & Human Resources has replaced the requirements of Meaningful Use with Interoperability. The standards development community has applied innovative approaches to realizing these goals. HL7 FHIR (Fast Healthcare Interoperability Resources) has brought us closer to true interoperability. Today, FHIR has become even easier to implement, and the world has embraced the opportunity.  

Bio: Charles Jaffe is the Chief Executive Officer of Health Level 7 International (HL7). He completed his medical training at Johns Hopkins and Duke Universities and post-doctoral training at the National Institutes of Health and the Lombardi Cancer Center. He has served in various academic positions in the Departments of Medicine and Pathology, as well as in the School of Engineering. Prior to joining HL7, he was the Senior Global Strategist at Intel. In addition, he led a national research consortium, found a consultancy for research informatics, served as the VP of Medical Informatics at AstraZeneca, and the VP of Life Sciences at SAIC. Dr. Jaffe has been the contributing editor for several journals and has published on clinical management, informatics deployment, and healthcare policy.

May 18, 2018

Dr. Hannah Carter, PhD

Are Tumors Predictable? Inherited Immune Variation Constrains Tumor Evolution

Abstract: Recent studies have characterized the extensive somatic alterations that arise during cancer and various studies have probed rare inherited mutations that lead to early onset cancer syndromes. However, little is understood about the role of genetic background in ‘sporadic’ adulthood cancers. The somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. The region encoding the Major Histocompatibility Complex Class (MHC) is one of the most variable regions in the human population. MHC molecules expose peptide fragments on the cell surface, allowing T cell recognition of cells contaminated by foreign peptide. Although this system has evolved specifically as a defense against microbial and viral agents, MHC can also trigger elimination of cells with mutant peptides as are common in cancer. Each individual carries multiple MHC alleles that define the set of peptides that can be effectively presented for immune surveillance. We hypothesized that individual variation in MHC could create personal gaps in immune surveillance, generating individual-specific susceptibility for cells to acquire specific oncogenic mutations. We tested this hypothesis through the development and application of residue-centric MHC patient presentation scores to 1,018 recurrent oncogenic mutations in 9,176 cancer patients. This analysis found that cancer causing mutations were more likely to be observed when a patient’s genotype-based scores suggested poor MHC-based presentation of those mutations. Mutations there were poorly presented by most patients were also more likely to reach high frequency among tumors. Individual coverage of driver mutations by MHC-based presentation was also found to be a determinant of age at diagnosis. Thus the landscape of oncogenic mutations observed in clinically diagnosed tumors is shaped by MHC genotype-restricted immunoediting during tumor formation, and individual MHC genotype provides information about the mutations likely to emerge in tumors that develop later in life. 

Bio: Dr. Carter is an Assistant Professor in the Department of Medicine. She received her PhD in Biomedical Engineering at Johns Hopkins University. Her research focuses on computational modeling and analysis of tumor genomes in order to identify determinants of cancer risk and response to therapy. Dr. Carter is a recipient of a 2013 NIH Director’s Early Independence Award, a Siebel Scholar and a CIFAR Azrieli Global Scholar.

May 11, 2018

Dr. Gary Fogel

Applications of Computational Intelligence in Bioinformatics

Abstract: At its core, the field of biomedicine focuses on an understanding of molecular processes, their possible physiological pathologies, and resulting medical treatment. This includes diagnostics that can classify individuals and their risk of disease based on molecular and other information. Given an overwhelming abundance of information at the molecular level, there exists a growing opportunity to use computational intelligence to improve our basic understanding of disease. In this lecture I will provide examples of how these bioinformatics approaches can be used to help inform discovery towards new diagnostics, and review some of the hurdles that remain for clinical settings. 

Bio: Dr. Gary Fogel is Chief Executive Officer of Natural Selection, Inc. (NSI) in San Diego, California, a company with a 25-year history of applied computational intelligence. Dr. Fogel received his Ph.D. in biology from U.C. Los Angeles focusing on the evolution of histone proteins. His more recent efforts include many applications of computational intelligence to biology, chemistry, and medicine from genomics to clinical drug development. Dr. Fogel has over 140 publications in technical journals, conferences, and other venues and holds 3 patents. He also helped establish the IEEE Computational Intelligence Society (CIS) Bioinformatics and Bioengineering Technical Committee, and IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. He has also served on the editorial boards for 10 journals, including as a founding associate editor for IEEE Transactions on Computational Biology and Bioinformatics and IEEE Transactions on Emerging Topics in Computational Intelligence. He currently serves as Editor-in-Chief for the journal BioSystems. Dr. Fogel is an IEEE Fellow and member of the IEEE CIS Administrative Committee.

April 27, 2018

Dr. CT Lin

Four Tools to Address Physician Burnout with Practice Efficiency

Abstract: Physician Burnout is at epidemic levels in the United States, and electronic health records (EHRs) are cited as a major cause. UCHealth has initiated several projects to improve practice efficiency, a major component of burnout. This includes APSO note format to improve EHR readability, Sprints to improve physician adoption and use of EHR, Innovation partnerships to create better tools and Practice Transformation to change staffing and extend team-based care. 

Bio: CT Lin MD is CMIO at UCHealth, an 9-hospital, 400-clinic system in the Rocky Mountain region. In 2016, UCHealth achieved HIMSS Stage 7, indicating highest achievement in EHR effectiveness. In 2017, UCHealth achieved Most Wired status from Hospitals and Health Networks.  He is Professor of Medicine at University of Colorado School of Medicine, and board-certified in Internal Medicine and Clinical Informatics. He sees internal medicine patients and also facilitates workshops on "Physician-patient communication to improve health outcomes" for students, residents and practicing physicians. His national publications and talks include: Physician Adoption of IT, EHR Usability, Online patient communication and patient accessible records with Open Test Results and Open Notes. His national awards include "Healthcare IT innovator" and "Electronic Physician of the Year." He leads a team of 32 physician informaticians, whose main work is now reducing physician burnout and the EHR burden. Our vision: "We improve physician and team resilience and effectiveness by building world-class relationships and innovative tools."

April 20, 2018

Dr. Jeffrey S. Grethe

Data and Resource Discovery in Biomedical Science

Abstract: Data and information on research resources are everywhere, in numerous repositories and download sites, and more floods in every day. What’s a researcher to do? In order to be able to use shared data, the first fundamental rule is that you have to be able to find it.  We have search engines like Google for web documents, PubMed and Google Scholar for articles, NCBI for selected genomics resources. This talk will examine data and resource discovery through experiences gained from a number of sponsored projects being conducted at UCSD. 

Bio: Dr. Jeffrey Grethe has more than 2 decades of experience in providing collaborative data environments to biomedical researchers in order to advance scientific inquiry leading to new discoveries and treatments of human disorders. Within the Center for Research in Biological Systems (CRBS; at the University of California, San Diego he is the Principal Investigator for the NIDDK Information Network (dkNET;, which serves the needs of basic and clinical investigators by providing seamless access to large pools of data, information, and resources relevant to the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The infrastructure underlying NIF and dkNET, SciCrunch (, now supports a number of research communities. SciCrunch was designed to allow communities of researchers to create focused portals that provide access to resources, databases, information and tools of relevance to their research areas. Most recently, he is the UCSD Principal Investigator for a newly funded NIH P41 Biomedical Technology Research Center – the Center for Reproducible Neuroimaging Computation (CRNC) – dedicated to establishing and promoting reproducible neuroimaging research.

April 13, 2018

Dr. Xiaoqian Jiang

Differential Privacy Models in Biomedical Informatics

Abstract: Differential privacy is state-of-the-art criteria for privacy. It is a rigorous framework and can provide provable guarantees to the outcome of query/analysis. Different from syntactic models that protect data, it is a semantic framework that protects the procedure to access data.  In this talk, I will give basic concepts and discuss about some interesting applications related to differential privacy. We will cover data release, model release and distributed model publishing schemes. 

Bio: Xiaoqian Jiang is an associate professor in Biomedical Informatics. He received his PhD in Computer Science from Carnegie Mellon University and joined UCSD in 2011. He is an associate editor of BMC Medical Informatics and Decision Making and serves as the editorial board member of Journal of American Medical Informatics Association and Harvard Papers on Technology Science (H-POTS). He has received several awards for best and distinguished paper awards at American Medical Informatics Association (AMIA) Joint Summits on Translational Science (2012, 2013, 2016).

April 6, 2018

Dr. Tsung-Ting Kuo

The Blockchain: How Crypto-currency can Transform Healthcare

Abstract: In this talk, Dr. Tsung-Ting Kuo will introduce blockchain technologies including their benefits, challenges, and the latest applications in the biomedical and healthcare domains. Also, He will discuss a study of technology systematic review for a set of blockchain platforms to identify their technical features. Finally, Dr. Kuo will present a use case of adapting blockchain for privacy-preserving machine learning to avoid security risks such as single-point-of-failure. To summarize, he will give an overview of blockchain for biomedical/healthcare field, to reveal the impact of this emerging technology and its potential applications. 

Bio: Dr. Tsung-Ting Kuo is a Postdoctoral Fellow in UCSD DBMI. He earned his Ph.D. in CS from National Taiwan University in Computer Science. He was major contributor of UCSD DBMI team to win the ONC healthcare blockchain challenge, and NTU team to win four times of ACM KDDCup. He published a recent, highly-read biomedical/healthcare blockchain review paper in JAMIA, and was awarded a K99 award for blockchain-based biomedical and healthcare study. His research focuses on blockchain technologies.

March 28, 2018 

Dr. Blanca Himes

Biomedical Informatics Approaches to Study Asthma

Abstract: Various efforts are underway to gather a wide range of patient-specific data, including symptoms, medication utilization, environmental exposures, and genomics, with the expectation that collection and integration of this data will enable personalized medicine. This talk will illustrate different approaches taken specifically to study asthma, ranging from the use of electronic-health record (EHR)-derived data to the analysis of transcriptomic data. 

Bio: Dr. Himes’ research focuses on gaining insights into asthma pathogenesis and treatment using biomedical informatics approaches. She has performed genome-wide association studies of asthma and related traits as a lead investigator and as part of large collaborations. She has used probabilistic graphical models to find genetic association networks and designed a computational algorithm to search through large datasets for optimal predictors of a phenotype. She has identified and characterized subjects for asthma genomics studies using patient-derived data from electronic medical records. Most recently, she has used RNA-Seq to study human airway smooth muscle cell response to asthma medications, vitamin D, and to identify differences in response between fatal asthma patients vs. individuals without asthma. 

March 16, 2018

Dr. Xiaoqian Jiang

Calibration of Predictive Models for Clinical Decision Making

Abstract: A large number of clinical decision support applications rely on predictive models for binary outcomes. These models usually estimate the probability for an outcome of interest (e.g., probability of readmission to the hospital within a time window). Given that clinical decisions rely on these probability estimates, it is critical that they be well calibrated (i.e., the estimates are sufficiently close to the true underlying probability that the event will occur). Surprisingly, the evaluation of predictive models rarely includes an assessment of calibration, while essentially all include an assessment of discrimination (e.g., AUC: areas under the ROC curve). I will describe the perils of using non-calibrated models for making clinical and administrative decisions, describe various methods to recalibrate existing models or to include calibration in model development algorithms.  

Bio: Xiaoqian Jiang is an associate professor in Biomedical Informatics. He received his PhD in Computer Science from Carnegie Mellon University and joined UCSD in 2011. He is an associate editor of BMC Medical Informatics and Decision Making and serves as the editorial board member of Journal of American Medical Informatics Association and Harvard Papers on Technology Science (H-POTS). He has received several awards for best and distinguished paper awards at American Medical Informatics Association (AMIA) Joint Summits on Translational Science (2012, 2013, 2016).

March 9, 2018

Dr. Alex Cloninger

Precision Treatment Rules with Machine Learning

Abstract: This talk will cover several topics on causal inference, and the ways in which machine learning can play a role in moving to personalized treatment decisions.  We will discuss how deep learning can be structured to address this problem in a randomized setting, and also address various problems with generalizing to observational data, including improvements to propensity matching and methods for determining distances between treated and control groups.

Bio: Alex Cloninger is an Assistant Professor of Mathematics at UCSD. He received his PhD in Applied Mathematics and Scientific Computation from the University of Maryland in 2014, and was then a Gibbs Assistant Professor of Mathematics at Yale University until 2017, when he joined UCSD. His research interests are in applied harmonic analysis, machine learning and neural networks, diffusion geometry, analysis of graphs and data sets sampled from continuous geometric structures embedded in high-dimensional spaces, and applications in treatment effectiveness, medical imaging, and other various scientific domains.

March 2, 2018

Dr. Ming Tai-Seale

Improving Patient-Centered Communication in Primary Care

Abstract: Ming Tai-Seale, PhD, MPH will discuss the design and plan of a $5.8 million, multi-site study funded by the Patient-Centered Outcomes Research Institute (PCORI): “Improving Patient-Centered Communication in Primary Care: A Cluster Randomized Controlled Trial of the Comparative Effectiveness of Three Interventions.” To rigorously answer the question of which approach is more effective and more scalable in promoting patient-centered communication, it does a head-to-head comparison of three different interventions: Open Communication High Touch, Open Communication High Tech, and ASK (a preexisting simple intervention). The study will have three arms, with twenty one clinics in three health care delivery systems, including UCSD Health.  

Bio: Ming Tai-Seale, PhD, MPH, Professor of Family Medicine and Public Health, UCSD School of Medicine, and Director of Outcomes Analysis at UCSD Health IS Department, is a health economist and health services researcher. Tai-Seale examines the impact of financial and organizational incentives on health services delivery and patient outcomes. She collaborates with physicians, patients, clinic leaders, and researchers from multiple disciplinary backgrounds to study patient-physician communication, primary care transformation, and how physicians allocate time and effort in office visits by taking a detailed look at patient-physician communication captured by video- or audio-recordings and the access log of EpicCare. A paper resulting from analyses of EpicCare Logs was the second most read paper in Health Affairs in 2017.

February 23, 2018 

Dr. Eric Hekler

Using Mobile Health Technologies to Affect Behavior Change

Abstract: Three emerging trends are disrupting current models for promoting health and treating illness: 1) unsustainable growth in the complexity and cost of healthcare & health promotion; 2) a movement towards more human-centered and personalized strategies for fostering health and treating disease; and 3) an explosion in information, communication, and computing technologies and the “big data” these systems produce. There is great excitement about the possibility of leveraging the second and third trends to realize the vision of a human-centered, preventive, cost-effective health system and corresponding “Culture of Health” but myriad technical and, perhaps more importantly, cultural challenges need to be overcome. PURPOSE: The purpose of this presentation is to present conceptual work on an “agile” scientific process for creating, optimizing, and repurposing useful and usable behavior change interventions, coupled with empirical research related to more personalized and precise digital health interventions focused on behavior change that can help to enable this broader vision. OUTLINE: The talk will begin with a brief summary on how the “agile science” process is an alternative way of conceptualizing evidence-based practice for behavior change that acknowledges the above three trends. Following this, key empirical work will be presented that with regard to the use of control systems engineering for behavior change, just-in-time adaptive interventions, and supporting individuals in conducting their own “self-experiments” for behavior change.  I will conclude with examples of ongoing projects that I’m involved in with partners in academia, industry, clinical practice, and patient-lead scientists, as illustrations of the many plausible use-cases of agile science.  

Bio: Eric Hekler, PhD, is an Associate Professor in the Department of Family Medicine and Public Health at UCSD. He is also Director of the Center for Wireless & Population Health Systems and faculty member of the Design Lab at UCSD. His research focuses on facilitating individualized behavior change for fostering long-term health and well-being via digital health tools. Prior to UCSD, Dr. Hekler was a faculty member at Arizona State University.  He completed his postdoctoral training at Stanford University and received his Ph.D. in Clinical Health Psychology from Rutgers University.

February 16, 2018 

Dr. Michael Hogarth

Keeping us Safe: An overview of US public health informatics systems and architectures

Abstract: Modern society is highly dependent on the provisioning of clean water, healthy and plentiful food, breathable air, and prompt intervention to curtail disease outbreaks. The public health system is critical in supporting these activities. Today’s information technology provides public health practitioners key capabilities in maintaining the health of the population. This lecture will provide a basic foundation of knowledge about public health practice for clinical informaticians, and highlight specialized information systems and data standards used in public health today.  We will explore the existing public health informatics infrastructure including surveillance systems, the process of electronic laboratory reporting (ELR) of notifiable diseases, vital statistics systems, and the critical importance of  GIS systems in the public health.  

Bio: Dr. Michael Hogarth is board certified Internal Medicine physician and a faculty in biomedical informatics. He currently also serves as Chief Clinical Research Information Officer for UC San Diego Health. He is also engaged in a number of grant and contract funded activities. These include the California Electronic Death Registration System (California EDRS), the Maryland Death Registration System, the Athena Breast Health Network project (, the novel I-SPY2 adaptive breast cancer clinical trial, the pSCANNER clinical data research network (CDRN), and the California Precision Medicine Consortium (CaPMC). In 2015 he was elected to the American College of Medical Informatics (ACMI).  Dr. Hogarth's research interests include the development of next generation public health information systems, terminology/ontology infrastructure in biomedical informatics, and developing systems that support clinical research at the point of care.

February 9, 2018 

Dr. Erik Viirre

The Qualcomm Tricorder XPRIZE: Experience and Inspiration

Abstract: The Qualcomm Tricorder XPRIZE had the biggest prize purse for Medicine in history: $10 Million. Conceived in 2011 and completed in 2017, competitors from around the world designed, tested and delivered mobile health systems to the UCSD CTRI where the QTXP Test Program was hosted. Consumers with a wide variety of health conditions were solicited from the UCSD Health System and brought for extended interactions with the systems… with no medical or technical experts allowed. Consumers successfully used the systems and described high levels of acceptance. In this presentation, the conception, plans, successes and failures of the competition will be described. Most exciting, some prize funds have been dedicated back to UCSD for a follow-on program to further develop the systems and bring them to commercial reality.  

Bio: Dr. Viirre was the Medical and Technical Director of the Qualcomm Tricorder XPRIZE and the Nokia Sensing XCHALLENGE, since the opening of the competitions in 2012. These competitions are the most valuable prizes in Medical history and are dedicated to development of mobile health platforms. Dr. Viirre’s primary appointment is Adjunct Professor in the UCSD Departments of Neurosciences, Surgery and Cognitive Science. His clinical specialties are vertigo, balance problems and tinnitus. In the UCSD Health System, he treats people with disorders such as Migraine, Meniere’s Disease, inner ear infections and Benign Positional Vertigo (BPV). At UCSD, under Dr. Viirre’s supervision, the human Test Program for the Tricorder XPRIZE took place. Dr. Viirre’s scientific interests include vision, hearing and the vestibular system and higher cognitive function where he is extensively published in the scientific literature. At the Arthur C Clarke Center for Human Imagination, he is the Associate Director, dedicatd to the neuroscience of Imagination. Dr. Viirre has done research for the National Institutes of Health, the United States Navy, DARPA and NASA. He is an experienced technology developer with numerous patents and completed engineering projects. He is has been a consultant for groups such as medical research foundations, the National Academy of Science and a variety of medical and computer technology companies. Dr. Viirre has participated in a variety of start-up companies, including Zero G Corporation, and Otosound LLC, which is bringing to market technology for treatment of tinnitus that he developed and patented at UCSD.
Dr. Viirre received his Ph.D. in Neurophysiology in 1987 at the University of Western Ontario in London, Canada and his M.D. in 1988. Also in 1988, he was in the inaugural class of International Space University. He completed a Rotating Internship at St. Josephs's Medical Center in London, Canada in 1989. After his internship in London, he was a fellow at the Robarts Research Institute in functional imaging and had an eye care practice. In 1994, Dr. Viirre was a Visiting Professor in Neurology and Ophthalmology at UCLA where he did a fellowship in Medical Neurotology, the management of inner ear disorders. In 1995-99 he was a Scientist at the Human Interface Technology Lab at the University of Washington. He was a Senior Scientist in the Human Performance Department of the US Navy’s Naval Health Research Center from 2001 to 2012.

February 2, 2018

Dr. Ali Torkamani

High Definition Medicine

Abstract: The foundation for a new era of data-driven medicine has been set by recent technological advances that enable the assessment and management of human health at an unprecedented level of resolution – what we refer to as high definition medicine. Dr. Torkamani will discuss our progress towards high-definition medicine through examples of research conducted at The Scripps Translational Science Institute using a combination of genomic and digital health approaches to characterize and return useful health insights to individuals.  

Bio: Dr. Torkamani obtained his undergraduate degree in chemistry at Stanford University, where he received a Bing Foundation Chemistry Research Fellowship, and his doctorate in biomedical sciences at the University of California, San Diego, (in record time) under the mentorship of Dr. Nicholas Schork as an NIH Genetics Predoctoral Training awardee. In 2008, he joined the Scripps Translational Science Institute as a Research Scientist and Donald C. and Elizabeth M. Dickinson Fellow, and shortly thereafter as an Assistant Professor of Molecular and Experimental Medicine and Mario R. Alvarez Fellow. In 2012, Dr. Torkamani advanced to Director of Genome Informatics at STSI where he leads various human genome sequencing and other genomics initiatives. Dr. Torkamani was also co-founder and Chief Scientific Officer of Cypher Genomics Inc – acquired by Human Longevity Inc in 2015.

January 26, 2018 

Dr. Lucila Ohno-Machado

Biomedical Informatics at UCSD: From Data to Precision Medicine

Bio: Lucila Ohno-Machado, MD, MBA, PhD received her medical degree from the University of São Paulo and her doctoral degree in medical information sciences and computer science from Stanford. She is Associate Dean for Informatics and Technology, and the founding chair of the Health System Department of Biomedical Informatics at UCSD, where she leads a group of faculty with diverse backgrounds in medicine, nursing, informatics, and computer science. Prior to her current position, she was faculty at Brigham and Women’s Hospital, Harvard Medical School and at the MIT Division of Health Sciences and Technology. Dr. Ohno-Machado is an elected fellow of the American College of Medical Informatics, the American Institute for Medical and Biological Engineering, and the American Society for Clinical Investigation. She serves as editor-in-chief for the Journal of the American Medical Informatics Association since 2011. She directs the patient-centered Scalable National Network for Effectiveness Research funded by PCORI (and previously AHRQ), a clinical data research network with over 24 million patients and 14 health systems, as well as the NIH/BD2K-funded Data Discovery Index Consortium. She was one of the founders of UC-Research eXchange, a clinical data research network that connected the data warehouses of the five University of California medical centers. She was the director of the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, ‘anonymization,’ and Sharing) based at UCSD with collaborators in multiple institutions. iDASH funded collaborations involving study of consent for data and biospecimen sharing in underserved and under-represented populations.

January 19, 2018

Dr. Vitaly Herasevich

Implementation and evaluation of clinical informatics applications: journey of “AWARE” and “Sepsis Sniffer”

Abstract: Development and implementation of sepsis alert systems is challenging, particularly outside the monitored intensive care unit (ICU) setting. Barriers to wider use of sepsis alerts include evolving clinical definitions of sepsis, information overload, and alert fatigue, due to suboptimal alert performance. Outside the ICU, barriers include differences in health care delivery models, charting behaviors, and availability of electronic data. Current evidence does not support routine use of sepsis alert systems in clinical practice. Continuous improvement in the afferent and efferent aspects will help translate theoretic advantages into measurable patient benefit.  

Bio: Vitaly Herasevich, MD, PhD is an Associate Professor of Anesthesiology and Medicine in the Department of Anesthesiology and Perioperative Medicine, Division of Critical Care, Mayo Clinic, Rochester, Minnesota. He has been involved in medical informatics for over 20 years, with a specific concentration on applied clinical informatics in critical care and the science of health care delivery.
He was born in Belarus, where he earned his M.D. and Ph.D. degrees, and joined the Mayo Clinic in 2006. Later he finished MSc in clinical research at Mayo Clinic and became Certified Professional in Healthcare Management Systems (CPHIMS).
He codirects the Clinical Informatics in Intensive Care program as part of a research group that works to decrease complications and improve outcomes for critically ill patients through systematic research and quality improvement. He is interested in studying and developing clinical syndromic surveillance alerting systems ("sniffers"), clinical data visualization (novel patient-centered EMR), and complex large data warehousing for health care predictive and prescriptive analytics as well as outcome reporting. He is co-inventor of number of technologies including AWARE platform, resulting in technologies commercialization. He has coauthored 80 articles and authored book Health Information Evaluation. As part of an education effort, Dr. Herasevich developed curriculums and teaches clinical informatics to medical students, residents, fellows at the Mayo Medical School and Mayo Graduate School. He is Fellow of Society of Critical Care Medicine and active within informatics and professional societies serving on a number of committees.

January 12, 2018 

Dr. Matt Eisenberg 

Health Information Exchange: What’s taking so long, what are the real barriers and why won’t the fax machine just die?

Abstract: Easy access to clinical information that travels with the patient wherever she seeks care was supposed to revolutionize medicine and provide dramatic cost savings to the US Health System.  Even as most health systems and provider offices have successfully adopted EHR technology and report sharing data with outside organizations (see graph), interoperability and open health information exchange for the purpose of treatment and care coordination (forget about research) still seems like a pipe dream to many providers and patients.  Let’s find out why… 

Bio: Dr. Matthew Eisenberg joined Stanford Health Care as a Medical Informatics Director for Analytics and Innovation in February 2013.  His work at Stanford Health Care focuses on interoperability – specifically health information exchange, quality and regulatory reporting, population health and analytics for improvement.  Stanford Health Care is a HIMSS Stage 7 certified hospital and outpatient organization.  Prior to joining Stanford Health Care, he was the Medical Vice President for Clinical Informatics at MultiCare Health System in Tacoma, Washington.
Dr. Eisenberg is board certified in Pediatrics and Clinical Informatics.  He is Clinical Assistant Professor (Affiliated) in the Stanford Center for Biomedical Informatics Research within Stanford University’s School of Medicine.  He is currently a member of the eHealth Exchange Coordinating Committee, the Sequoia Project Board of Directors, the Carequality Advisory Council and the Chair of the Epic Care Everywhere Governing Council.  He serves as the Associate Program Director for the Stanford Clinical Informatics Fellowship Program.  He is a member of the American Academy of Pediatrics Council on Clinical Information Technology, the AMIA Clinical Decision Support Workgroup, the American Association for Physician Leadership, the Association of Medical Directors of Information Services and HIMSS.
After completing medical school at the University of California, San Francisco and pediatric residency at Boston Children’s, Dr. Eisenberg began his private practice career in general pediatrics at The Palo Alto Medical Clinic back in 1990 when medical records were still on papyrus.  After moving to the Pacific Northwest he joined the Virginia Mason Medical Center in 1996.  He completed a fellowship training program in Evidence Based Pediatrics at the University of Washington in 1998.  In 2003 Dr. Eisenberg joined Seattle Children’s as an informatics physician and began work on their acute care CPOE implementation using a Cerner Millennium EMR platform.  His work focused initially on order set development and physician training and he expanded his informatics role as Seattle Children’s implemented their ambulatory EMR with CPOE. During his tenure at Seattle Children’s, Dr. Eisenberg was an active member of the Cerner Physician Reference Group.  He completed the Oregon Health and Science University AMIA 10 x 10 training course in 2006.  In 2007 Dr. Eisenberg joined MultiCare Health System, an integrated delivery system in Tacoma, WA as their new Medical Director of Information Services.  MultiCare was an early adopter of Epic systems software dating back to 1998.  After Dr. Eisenberg’s arrival, MultiCare extended their electronic health record across the enterprise to include four of five hospitals, implemented bedside bar coding, installed an integrated enterprise content management system and pushed the envelope of health information exchange as an early participant in the nationwide health information network (NwHIN) via the Virtual Lifetime Electronic Record (VLER) project.  In 2009, MultiCare was awarded the HIMSS Davies Organizational Award.