Sponsored by the Institute for Computational Medicine and the Institute for Clinical and Translational Research Symposium on Computational Medicine September 24, 2012 9 a.m. 5 p.m. Chevy Chase Conference Center Zayed Tower, Johns Hopkins Hospital
Symposium on Computational Medicine Jointly Sponsored by the Institute for Computational Medicine & the Institute for Clinical and Translational Research 9:00 a.m. Words of Welcome Daniel Ford, MD, MPH Director, Institute for Clinical and Translational Research research Overview Raimond Winslow, PhD Director, Institute for Computational Medicine 9:30 a.m. Session 1 Modeling Networks: Learning Molecular Signatures of Cancer 11:00 11:15 a.m. Break Rachel Karchin, PhD... Coordinated Interactions among Gene Mutations, Differentially Expressed Genes, and Drug Response Profiles in Cancer Michael Ochs, PhD... Identifying Target Pathways and Proteins in Cancer Luigi Marchionni, MD, PhD... The Prostate Cancer Transcriptome: Dissection by Gleason Grade 11:15 a.m. Session 2 Modeling Physiology: Perturbed Function in Disease 12:45 2:00 p.m. Lunch Session 2A Models of HIV Pathogenesis and Treatment Feilim Mac Gabhann, PhD Models of HIV therapies targeting host/virus protein interactions Jeffrey J. Gray, PhD Computational Analysis of HIV-Protein Structure, Specificity, and Drug Resistance Robert Siliciano, MD, PhD A Quantitative Basis for Antiretroviral Therapy for HIV Infection
2:00 p.m. Session 2B Models of Neurological Disorders and Deep Brain Stimulation Treatment 3:30 3:45 p.m. Break Sridevi Sarma, PhD Towards Closed-Loop Deep Brain Stimulation for Parkinson s Disease William S. Anderson, MD, PhD Clinical and Therapeutic Implications of Cortical Neural Network Modeling Sarah Ying, MD Modeling Cerebellar Learning, and Clinical Applications to Ataxia 3:45 p.m. Special Session 3 modeling Populations: Spread of Disease Joshua Epstein, PhD Agent-Based Computational Modeling of Infectious Disease: From Playground to Planet 4:30 p.m. Concluding Remarks by Drs. Ford and Winslow
The Symposium Speakers Rachel Karchin, PhD: Dr. Karchin received her PhD in Computer Science from the University of California, Santa Cruz and was a postdoctoral fellow in the laboratory of Dr. Andrej Sali at University of California, San Francisco s Department of Pharmaceutical Sciences and Pharmacogenomics. Since 2006, she has been an Assistant Professor in the Department of Biomedical Engineering at Johns Hopkins, with a joint appointment in Computer Science. She is a member of the core faculty of the Institute for Computational Medicine and is also a preceptor in the Human Genetics Program. Dr. Karchin s primary interests are in the genetic variability underlying human disease. Her work focuses on computational prediction and modeling of disease susceptibilities, heterogeneity in cancer genomes, and the relationship of genomic measurements to drug response, with an emphasis on high-throughput analysis of large amounts of data. Michael Ochs, PhD: Dr. Ochs holds a PhD in Physics from Brandeis University with a focus on radio astronomy and the astrophysics of quasars. He migrated into medical research through in vivo spectroscopic imaging research, and directed the Bioinformatics Group at the Fox Chase Cancer Center until September 2006, when he joined the faculty at Johns Hopkins. Dr. Ochs has served as director of the Bioinformatics Shared Resource since 2009. Dr. Ochs s research focus is in three areas: 1) developing Bayesian matrix factorization methods that integrate epigenetic and functional genomics measurements to infer signaling activity, 2) techniques for data integration that can lead to patient-specific biomarkers of signaling deregulation, and 3) developing hybrid graphical and differential equation models of multicellular systems. Luigi Marchionni, MD, PhD: Dr. Marchionni is an Assistant Professor of Oncology in the program of Cancer Biology at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins. Dr. Marchionni trained in Medicine at the University of Turin, Italy, obtained his PhD degree in Structural and Functional Genomics at the International School for Advanced Studies (ISAS-SISSA), Trieste, Italy, and completed his training in Biostatistics with Luigi Parmigiani, in the Oncology Biostatistics Division at Johns Hopkins. Dr. Marchionni is a skilled computational biologist, and he has extensive experience in the analysis and interpretation of genome-wide data. Dr. Marchionni s current research focuses on knowledge integration across different genomic data types, on the development of novel prediction algorithms for cancer prognostication and prediction, and on the integration of genomic-based predictors into current clinical management of cancer patients.
Feilim Mac Gabhann, PhD: Dr. Mac Gabhann joined Johns Hopkins University s Institute for Computational Medicine as an Assistant Professor in 2009, having completed his PhD in Biomedical Engineering in 2007 at Johns Hopkins University, working with Aleksander S. Popel to create mathematical models of growth factor networks in peripheral artery disease and cancer. During postdoctoral work with Shayn M. Peirce and Thomas C. Skalak at the University of Virginia, he conducted experimental research on microvascular remodeling in mouse skeletal muscle. The Mac Gabhann lab studies mathematical models of disease and therapeutics, including peripheral artery disease, cancer, ALS, preeclampsia and HIV. Dr. Mac Gabhann is a Sloan Research Fellow and recipient of a K99/ R00 NIH Pathway to Independence Award, the 2010 August Krogh Young Investigator Award from the Microcirculatory Society, and the 2012 Arthur C. Guyton Award for Excellence in Integrative Physiology from the American Physiology Society. He is the author of 37 peer-reviewed papers, and is an Associate Editor for PLoS Computational Biology and BMC Physiology. Jeffrey J. Gray, PhD: Dr. Gray received his BSE in Chemical Engineering at the University of Michigan and his PhD in Chemical Engineering at the University of Texas at Austin. He completed postdoctoral training working on protein-protein docking at the University of Washington. In 2002 he joined the Department of Chemical and Biomolecular Engineering at the Johns Hopkins University as an Assistant Professor and in 2009 he was promoted to Associate Professor. Dr. Gray s research focuses on computational protein structure prediction and design, particularly protein-protein docking, therapeutic antibodies, and protein-surface interactions. He has been funded by the NIH, the NSF, DARPA, ACS, the Beckman Foundation, and the UCB pharmaceutical company. Dr. Gray has received the Beckman Young Investigator Award, the Johns Hopkins Alumni Association Excellence in Teaching Award, and the National Science Foundation s CAREER Award, and he has been named the F. Stuart Hodgson Faculty Scholar. He serves on the editorial board of Proteins, on the scientific advisory board of the Rosetta Design Group, and on the board of directors of the Ingenuity Project. Dr. Gray s lab leads the development of RosettaDock, RosettaAntibody, the associated web servers, and the PyRosetta interactive platform for protein structure prediction and design; these tools are used widely by the research community. Dr. Gray s lab has produced the most accurate complex structure for several targets in The CAPTRI blind protein-protein docking challenge.
Robert Siliciano, MD, PhD: Dr. Siliciano is a member of the Howard Hughes Medical Institute and a Professor of Medicine and Molecular Biology and Genetics at the Johns Hopkins University School of Medicine. Dr. Siliciano did his undergraduate work at Princeton University and then received his MD and PhD degrees from Johns Hopkins. After a postdoctoral fellowship at Harvard Medical School, he joined the faculty at Johns Hopkins. He is the recipient of a Distinguished Clinical Scientist Award from the Doris Duke Charitable Foundation and two NIH Merit Awards. In 2002, he became an Investigator in the Howard Hughes Medical Institute. He is a past Chairman of the NIH AIDS and Related Research Study Section. He currently directs the MD-PhD Program at Johns Hopkins. In 2008, he received a major award in AIDS research, the Bernard N. Fields Memorial Lecture at the Conference for Retroviruses and Opportunistic Infections. In 1995, Dr. Siliciano s lab provided the first demonstration that latently infected memory CD4+ T cells were present in patients with HIV-1 infection. He went on to characterize this latent reservoir and to show that latently infected cells persist even in patients on prolonged highly active antiretroviral therapy (HAART). These studies indicated that eradication of HIV-1 infection with HAART alone would never be possible, a finding which led to a fundamental change in the treatment strategy for HIV-1 infection. This latent reservoir is now widely recognized as the major barrier to curing HIV-1 infection and is the subject of an intense international research effort. Sridevi Sarma, PhD: Dr. Sarma received her BS degree in Electrical Engineering from Cornell University in 1994, and MS and PhD degrees in Electrical Engineering and Computer Science from the Massachusetts Institute of Technology in 1997 and 2006, respectively. She was a Postdoctoral Fellow in the Brain and Cognitive Sciences Department at MIT from 2006 to 2009. She is now an Assistant Professor in the Institute for Computational Medicine in the Department of Biomedical Engineering at the Johns Hopkins University. Her research interests include modeling, estimation, and control of neural systems. Dr. Sarma is a recipient of the GE Faculty for the Future scholarship, the National Science Foundation graduate research fellow, the L Oreal for Women in Science fellow, the Burroughs Wellcome Fund Careers at the Scientific Interface Award, the NSF CAREER award, and the Presidential Early Career Award for Scientists and Engineers (PECASE).
William S. Anderson, MD, PhD: Dr. Anderson is a functional neurosurgeon at the Johns Hopkins Hospital, performing procedures to treat epilepsy and movement disorders. Dr. Anderson holds a PhD in Physics from Princeton University, and an MD from Johns Hopkins. After finishing residency in Neurosurgery at Johns Hopkins, he was an attending neurosurgeon at the Brigham and Women s Hospital, Harvard Medical School. The Anderson laboratory focuses on the computational modeling of epilepsy as a method to understand the time and spatial evolutionary properties of seizures. Modeling methods include large array single compartment models and multicompartment simulations for the extraction of local field potentials. The laboratory also explores the effects on memory encoding of theta phase specific stimulation during working memory tasks. Recordings derived from deep brain stimulation procedures are also used to learn more about motor imagery and motor planning. Sarah Ying, MD: Dr. Ying received her MD from Johns Hopkins University in 1995 and has completed fellowships in Internal Medicine, Neurology, Neuroimaging of Neurotology, and Neuropthalmology at Johns Hopkins Hospital, Barnes-Jewish Hospital, and the University of California at Los Angeles. She served as a clinical instructor of Neurology at UCLA before joining Johns Hopkins University as an Assistant Professor of Neurology in 2004. She holds joint appointments in Radiology and Ophthalmology. Dr. Ying has been the recipient of the Young Investigator Award from the National Alliance for Research on Schizophrenia and Depression and the Johns Hopkins University Clinician Scientist Award. Her research interests include the use of neuroimaging technology to understand systems-level cerebellar control in health and disease. Joshua Epstein, PhD: Dr. Epstein is Professor of Emergency Medicine at Johns Hopkins University, with joint appointments in the Departments of Applied Mathematics, Economics, Biostatistics, International Health, and Environmental Health Sciences. He is also the Director of the JHU Center for Advanced Modeling in the Social, Behavioral, and Health Sciences. He is an External Professor at the Santa Fe Institute, a member of the New York Academy of Sciences, and he recently served on the Institute of Medicine s Committee on Identifying and Prioritizing New Preventive Vaccines. Earlier, Dr. Epstein was Senior Fellow in Economic Studies and Director of the Center on Social and Economic Dynamics at the Brookings Institution. He is a pioneer in agent-based computational modeling of biomedical and social dynamics. He has authored or coauthored several books including Growing Artificial Societies: Social Science from the Bottom Up, with Robert Axtell (MIT Press/Brookings Institution); Nonlinear Dynamics, Mathematical Biology, and Social Science (Addison-Wesley); and Generative Social Science: Studies in Agent-Based Computational Modeling (Princeton University Press). Dr. Epstein holds a Bachelor of Arts degree from Amherst, a PhD from MIT, and has taught at Princeton and lectured worldwide. In 2008, he received an NIH Director s Pioneer Award, and in 2010 an Honorary Doctorate of Science from Amherst College.