BD-STEP at VA Palo Alto Health Care System
The Big Data-Scientist Training Enhancement Program (BD-STEP) was launched by the Department of Veterans Affairs (VA), in collaboration with the National Cancer Institute (NCI), on September 28, 2015. Junior-level physical scientist trainees from accredited programs in relevant disciplines will be identified by the National Cancer Institute's Center for Strategic Initiatives (CSSI). BD-STEP matches trainees with VA medical centers across the country to leverage VA data systems, supporting clinically-relevant, year-long training and research opportunities in collaboration with VA clinician scientists. Approved sites provide graduate-level training in clinical, health services, and/or bioinformatics research for trainees who have demonstrated experience in bioinformatics, modeling, and management of large data sets. Each site provides an overview of how they understand and apply big data in their clinical research setting, including the ethical and legal implications; how data are generated in the course of providing clinical care and how those data are aggregated at local, regional, and national levels; and how BD-STEP trainees will participate in a research project involving such data. For more information on the national BD-STEP program see https://www.va.gov/oaa/specialfellows/programs/sf_bdstep.asp?p=24.
The BD-STEP program at the VA Palo Alto Health Care System is led by Todd Wagner, PhD and Jennifer Lee, MD, PhD. Fellows at VA Palo Alto will have structured mentoring, in addition to their Stanford (or other academic institution) mentor(s), with VA Palo Alto clinicians and research investigators to gain direct understanding about clinical care and the tremendous capabilities of big healthcare data to impact patient care and the health care system. BD-STEP fellows will participate in a 3-day "data bootcamp" which orients trainees to the VA's electronic health record databases and excellent network of clinicians, researchers, and operational clinical managers who can facilitate important aspects of the fellow's projects. The 2017 VA Data Bootcamp schedule is available here. Potential mentors are listed below. A list of their cancer-related research projects can be found here. The 2017 VA Palo Alto BD-STEP fellows and a brief description of their projects can be found here.
To apply for the BD-STEP fellowship at VA Palo Alto, see the full guidelines at http://med.stanford.edu/rmg/funding/bdstep.html.
VA Palo Alto BD-STEP Fellowship Co-Directors
Todd Wagner, PhD. Co-Director, BD-STEP Fellowship. Director, VA Health Economics Resource Center (HERC). Associate Director, VA Center for Innovation to Implementation COIN (Ci2i). Associate Professor of Research, Department of Surgery, Stanford University. Key contributions to science: how information asymmetries affect consumers, purchasers, and markets so that we can improve the value of care; value and efficiency of health care; and improving access to care and ensuring care is appropriate. (https://profiles.stanford.edu/todd-wagner and https://www.herc.research.va.gov/include/page.asp?id=staff-details&PersonID=14)
Jennifer S. Lee, MD, PhD. Co-Director, BD-STEP Fellowship. Associate Professor of Medicine (Endocrinology, Gerontology, Metabolism) and by courtesy, of Health Research & Policy (Epidemiology). Chief Medical Officer, Palo Alto VA Cooperative Studies Program Coordinating Center. Staff Physician, Medical Services, VA Palo Alto. (https://profiles.stanford.edu/JenniferSLee)
VA Palo Alto BD-STEP Fellowship Potential Mentors
Russ B. Altman, MD, PhD. Professor of Bioengineering, Genetics, Medicine, and (by courtesy) Computer Science. Key contributions to science: Phamacogenomics Knowledgebase, FEATURE suite of programs, how whole human genomes can be annotated, translational bioinformatics, and RNA structure and function modeling. (https://profiles.stanford.edu/russ-altman)
Rebecca Aslakson, MD, PhD, FAAHPM FCCM. Associate Professor, Stanford University School of Medicine. Key contributions to science: ICU-based palliative care, perioperative palliative care, palliative care outcomes research, patient centered outcomes research.
Steven M. Asch, MD. Professor of Medicine, Stanford University. Director, Center for Innovation to Implementaton, VA Palo Alto Health Care System. Associate Chief of Staff of Clinical Effectiveness, VA Palo Alto Health Care System. Vice-Chief, Stanford Division of Primary Care and Population Health. Key contributions to science: measurement of quality and access, implementation science, value of care, vulnerable populations, and cancer and palliative care. (https://profiles.stanford.edu/steven-asch)
James D. Brooks, MD. Keith and Jan Hurlbut Professor of Urology, Stanford University. Chief of Urologic Oncology. Associate Dean, Academic Affairs, Stanford University School of Medicine. Vice Chair, Department of Urology. Key contributions to science: identification of clinical biomarkers of urologic cancer, DNA methylation in prostate and kidney cancer, prostate cancer preventive interventions, defining the targets of androgen signaling, and management of screen-detected prostate cancers. (https://profiles.stanford.edu/james-brooks)
Carlos Bustamante, PhD, MS. Professor, Department of Genetics, Stanford University. Director of Informatics, Stanford Center for Genomics and Personalized Medicine. Chair and Professor, Biomedical Data Science Department, Stanford University. Key contributions to science: methods for population genomics analysis, genomics in understudied populations and indigenous communities, Whole genome In-Solution Capture (WISC), and improving computational methods for the Clinical Genomics Consortium (ClinGen) and the Population Architecture using Genomics and Epidemiology Consortium (PAGE). (https://profiles.stanford.edu/carlos-bustamante)
Mark R. Cullen, MD. Professor of Medicine, Stanford University. Director, Stanfor Center for Population Health Sciences. Professor of Biomedical Data Science, Stanford University. Senior Associate Dean for Research, Stanford University School of Medicine. Key contributions to science: rediscovery of occupational medicine and the interface between occupational health and clinical medicine; exploration of administrative "big data" sets for use in observational, etiologic research; workplace benefits and health care in the evolution of health disparities; health disparities, integrative advances in environmental and social epidemiologic approaches with administrative outcome data; and demographic studies exploring novel appraches to explain disparities by race, geography, and sex. (https://profiles.stanford.edu/mark-cullen)
Catherine Curtin, MD. Staff Physician, Department of Surgery (Hand/Plastic Surgery Division), VA Palo Alto Health Care System. Associate Professor, Division of Plastic Surgery, Stanford University. Key contributions to science: improving postoperative pain, big data used to improve quality and efficacy of surgical care, improving surgical care of spinal cord injured patients, and improving care of palmar fibrosis. (https://profiles.stanford.edu/catherine-curtin)
Millie Das, MD. Clinical Assistant Professor, Department of Medicine, Stanford University. Chair, VA Thoracic Tumor Board, VA Palo Alto Health Care System. Associate Program Director, Stanford Oncology Program. Chair, VA Cancer Care Committee, VA Palo Alto Health Care System. Chief, Oncology, VA Palo Alto Health Care System. Key contributions to science: conducting and analyzing results from clinical trials in patients with lung cancer; work with other medical oncologists, as well as basic scientists, thoracic surgeons, and radiation oncologists. (https://profiles.stanford.edu/millie-das)
Elisabeth Diver, MD. Clinical Assistant Professor, Department of Obstetrics and Gynecology, Division of Oncology, Stanford University. Key contributions to science: gestational trophoblastic disease and its malignant subset gestational trophoblastic neoplasia, endometrial cancer, reducing morbidity and improving outcomes for gynecologic malignancy surgical patients, gynecologic oncology and rare histologies, and end-of-life care and treatment of patients with ovarian cancer. (https://profiles.stanford.edu/elisabeth-diver)
Oliver Dorigo, MD, PhD. Director and Associate Professor, Division Gynecologic Oncology. Director, Gynecologic Oncology Clinical Care Program, Stanford Women's Cancer Center. Director Mary Lake Polan Gynecologic Oncology Research Laboratory Department of Obstetrics and Gynecology, Stanford University. Key contributions to science: immunotherapy for cancer, gene therapy, and PI3 kinase/Akt pathway. (https://profiles.stanford.edu/oliver-dorigo)
Mary Hawn, MD, MPH, FACS. Professor and Chair of Surgery, Stanford University. Staff Surgeon, VA Palo Alto Health Care System. Key contributions to science: understanding the effectiveness of surgical care improvement, risk prediction for readmission following major surgical procedures, risk prediction for major complications and mortality following elective surgery, and understanding the risk of perioperative adverse cardiac events in patients with coronary stents. (https://profiles.stanford.edu/mary-hawn)
Tina Hernandez-Boussard, PhD, MS, MPH. Associate Professor, Department of Medicine, Surgery and Biomedical Data Sciences, Stanford University. Key contributions to science: bioinformatics tools that address a need to manipulate and synthesize large scale, high throughput genomic data; cancer epidemiology and health policy research through the investigatoin of national and sate-wide datasets; and utilization of the electronic health record to accurately and efficiently monitor, measure, and predict healthcare care outcomes. (https://profiles.stanford.edu/tina-hernandez-boussard)
John Leppert, MD, MS. Associate Professor, Department of Urology, Stanford University. Associate Professor, by courtesy, Department of Medicine/Nephrology, Stanford University. Associate Faculty, Stanford Cancer Institute. Core Investigator, Center for Innovation to Implementation, VA Palo Alto. Investigator, Parker Institute of Cancer Immunotherapy. Key contributions to science: the role of p75, a nerve growth factor receptor, in basal forebrain signaling in mice; prostate cancer outcomes in VHA; application of advanced epidemiologic and econometric methods in the study of diabetes, diabetic severity, and metabolism syndrome in urinary stone disease and other urologic conditions; and comparative effectiveness research in renal cell carcinoma. (https://profiles.stanford.edu/john-leppert)
Lawrence Leung, MD. Maureen Lyles D'Ambrogio Professor of Medicine and Senior Associate Dean, Stanford University School of Medicine. Chief of Staff, VA Palo Alto Health Care System. Key contributions to science: characterization of plately membrane GPIIb-IIIa as a fibrinogen receptor, thrombospondin as a multifunctional protein in vascular biology, thrombin aptamer as a new class of anticoagulant, structure-function mapping of thrombin, and carboxypeptidase B2 in the crosswalk between hemostasis, thrombosis, inflammation and innate immunity. (https://profiles.stanford.edu/lawrence-leung)
Jan Liphardt, PhD. Director, Stanford Distributed Trust Initiative. Founder, CancerBase.org. Associate Professor, Bioengineering, Stanford University. Key contributions to science: mechanical manipulation of single biopolymers; use of super-localization imaging to characterize dynamics of molecules in the nucleus, on membranes, and in the cytoplasm; advanced optical labels and tools for multimodal and/or super-resolution optical imaging; and cancer microbiology. (https://profiles.stanford.edu/jan-liphardt)
Karl Lorenz, MD, MSHS. Section Chief, VA Palo Alto-Stanford Palliative Care Program. General Internal Medicine and Palliative Care Consultant, VA Palo Alto. Professor, Stanford University School of Medicine. Key contributions to science: development of quality measures for palliative and end of life care, development and evaluation of routine pain and other symptom screening measures, and characterizing policy relevant aspects of the quality of palliative and end of life care in the United States, including hospice services. (https://profiles.stanford.edu/karl-lorenz)
Parag Mallick, PhD. Assistant/Associate Professor, Department of Radiology, Stanford University. Key contributions to science: developing novel approaches for proteome-scale prediction of protein structure and function, biomarkers and factors governing biomarker presence in the circulation, development of tools that help manage divers data or improve experimental workflows through the use of sophisticated data analytics, experimental and computational systems approaches to study biological systems from a multi-level perspective, and developing diverse multi-omic and multi-scale models to understand cancer cellular properties and progression. (https://profiles.stanford.edu/parag-mallick)
Arash Momeni, MD. Assistant Professor of Surgery, Division of Plastic & Reconstructive Surgery, Stanford University. Director, Clinical Outcomes Resesarch, Division of Plastic & Reconstructive Surgery, Stanford University. Ryan-Upson Scholar in Plastic and Reconstructive Surgery, Division of Plastic & Reconstructive Surgery, Stanford University. Key contributions to science: evidence-based medicine and quality of clinical research in plastic surgery, breast reconstruction and clinical outcomes, venous thromboembolism and plastic surgery, and health services research. (https://profiles.stanford.edu/arash-momeni)
Arden M. Morris, MD, MPH. Professor and Vice Chair for Clinical Research, Stanford School of Medicine Department of Surgery. Director, Stanford-Surgery Policy Improvement Research and Education Center, Stanford School of Medicine Department of Surgery. Attending Surgeon, Division of General Surgery, VA Palo Alto Health Care System. Adjunct Professor, Departments of Surgery and Family Medicine, University of Michigan. Key contributions to science: values, preferences, and quality of life; use of mixed methods to understand decision making for cancer care among American Indians/Alaska Natives; examining the quality of care in the face of changing evidence; and patient centered costs of care and financial toxicity. (https://profiles.stanford.edu/arden-morris)
Mark Musen, MD, PhD. Professor of Medicine (Medical Informatics), Stanford University School of Medicine. Director, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine. Key contributions to science: building intelligent systems from large scale, reusable building blocks -- namely domain ontologies and abstract problem-solving methods -- yielding the Protege system; development of computer systems that store knowledge of clinical protocols or practice guidelines, and that use knowledge of a patient's situation gleaned from the electronic medical record to offer situation-specific advice; ways to contruct and merge ontologies; experiments related to practical application of ontologies; and the National Center for Biomedical Ontology's Center for Expanded Data Annotation and Retrieval (CEDAR), one of the 11 centers of excellence supported by the NIH Big Data to Knowledge Program (BD2K). (https://profiles.stanford.edu/mark-musen)
Lorene Nelson, PhD, MS. Associate Professor, Department of Health Research and Policy, Division of Epidemiology, Stanford University. Associate Director, Stanford Center for Population Health Sciences. Key contributions to science: environmental and lifestyle determinants of neurodegenerative diseases (PD, ALS), genetic determinants of neurodegenerative disease risk, etiologic and prognostic factors for multiple sclerosis, and methodology and biostatistics. (https://profiles.stanford.edu/lorene-nelson)
Lesley S. Park, PhD, MPH. Associate Director, Research and Data Strategy, Stanford Center for Population Health Services. Co-Director, Cancer Core, Veterans Aging Cohort Study. Course Instructor, Department of Health Research and Policy, Stanford University. Key contributions to science: assessment of a national HIV prevention program, liver cancer predictions in persons living with HIV/AIDS, and cancer outcomes and trends in persons living with HIV/AIDS. (https://profiles.stanford.edu/lesley-park)
Suzann Pershing, MD, MS. Chief, Opthamology and Eye Care Services, VA Palo Alto Health Care System. Assistant Professor of Opthamology, Byers Eye Institute at Stanford University School of Medicine. Key contributions to science: cataract surgery, health services research in opthamology, opthamology clinical data registry development and data analysis, and telemedicine in opthamology. (https://profiles.stanford.edu/suzann-pershing)
Nigam H. Shah, MBBS, PhD. Associate Professor of Medicine (Biomedical Informatics Research), Stanford University. Key contributions to science: pharmacovigilance using electronic medical records; combining machine learning, text mining, and prior knowledge in medical ontologies to enable the learning health care system; learning from the collective practice of clinicians spanning the care of multiple patients; and the development of the Annotator Web service, the most widely used Web service at teh National Center for Biomedical Ontology, which enables users to annotate datasets with ontology terms from ontologies in BioPortal. (https://profiles.stanford.edu/nigam-shah)
Michael Snyder, PhD. Chair of Genetics and Director of Center of Genomics and Personalized Medicine, Stanford University School of Medicine. Key contributions to science: personal omics profiling, big data, and systems medicine; invention of high throughput gene/protein characterization/systems biology; genome characterization technologies; and regulatory networks and human variation. (https://profiles.stanford.edu/michael-snyder)
Leslee L. Subak, MD. Professor and Chair, Department of Obstetrics & Gynecology and Urology (secondary), Stanford University School of Medicine. Key contributions to science: association of weight and urinary incontinence in women and clinical trials evaluating strategies to improve outcomes in women's genitourinary health; reduce barriers to the diagnosis and treatment of women with lower urinary tract symptoms using novel interventions; epidemiology of female lower urinary tract and pelvic floor disorders to identify risk factors, particularly those that are modifiable; and economics, cost-effectiveness, and health utility assessments of illness and of women's personal management of urinary inconvintence, pelvic organ prolapse surgery, urinary incontinence, LUTS, and weight loss. (https://profiles.stanford.edu/leslee-subak)
Alex Sox-Harris, PhD, MS. Core Investigator, VA HSR&D Center for Innovation to Implementation. Associate Professor (research), Department of Surgery, Stanford University School of Medicine. Key contributions to science: surgical health services research, treatment quality measurement and management, and addiction health services and implementation research. (https://profiles.stanford.edu/alexander-sox-harris)
Suzanne Tamang, PhD, MS. Instructor, Department of Biomedical Data Science, Stanford Univeristy School of Medicine. Research Associate, Veterans Health Administration, VA Palo Alto. Research Economist, National Bureau of Economic Review. Intramural Investigator, National Institute of Health. Assistant Faculty Director of Data Science, Stanford Center for Population Health Sciences. Key contributions to science: social HMO evaluation, information exchange from open domain text, prediction of high-cost patients, and information extraction tools for performance and quality measures. (https://profiles.stanford.edu/suzanne-tamang)
Philip S. Tsao, PhD. Professor of Medicine, Stanford University School of Medicine. Associate Chief of Staff - R&D, VA Palo Alto Health Care System. Key contributions to science: role of nitric oxide (NO) and reactive oxygen species (ROS) as signaling molecules to induce both acute and chronic changes in vascular cells; underlying mechanisms of vascular inflammation and AAA disease; and trasncriptional profiling and pathway analysis to identify gene networks that influence disease initiation and progression. (https://profiles.stanford.edu/philip-tsao)
Wing Hung Wong, PhD, MS. Professor of Statistics and Biostatistics, Stanford University. Key contributions to science: data augmentation algorithm, sequential importance sampling, collapsed Gibbs sampler, population-based Markov Chain Monte Carlo, and equi-energy sampling for Bayesian inference; nonparametric and semi-parametric statistical models; and the development of methods and software for the analysis of high throughput genomics data. (https://profiles.stanford.edu/wing%20wong).