New participating faculty members have joined the training program to broaden the scope of the training program and to replace those who either left UCLA or retired. The current 32 participating faculties cover a wide range of biomedical research areas.
Priyanga Amarasekare, PhD, Professor, Ecology and Evolutionary Biology. Dr. Amarasekare is trained as an ecologist and her lab at UCLA uses both observational and theoretical approaches to understand mechanisms that maintain biological diversity in variable environments. By focusing on spatial dynamics and temperature effects of prey-natural enemy interactions, her work spans both basic and applied questions in ecology and evolution. She has previously mentored Kenichi Okamoto and Margaret Simon, both SIBTG trainees.
Dolores Bozovic, PhD, Professor, Physics. Dr. Bozovic studies sensory neuroscience, specifically the physics of auditory hair cells. Her research is interdisciplinary and connects basic sciences to biotechnology. Her lab is part of the California Nanosystems Institute (CNSI) and she teaches a course on the “Physics of sensory Neuroscience.” Dr. Bozovic has been funded by the NSF and the NIH and she will be a member of the Executive Committee.
Dean Buonomano, PhD, Professor, Neurobiology. Dr. Buonomano is a trained experimental neuroscientist who is professor in the department of Neurobiology, with a joint appointment in Psychology. His research seeks to understand how networks of neurons perform computations and how these computations underlie cognition and behavior. One particular question is how neural networks encode and interpret time. Prof. Buonomano’s lab is supported by the NIH.
Arion Chatziioannou, PhD, Professor, Molecular & Medical Pharmacology. Professor Chatziioannou is the Associate Director of the Crump Institute for Biological Imaging in CNSI. He has developed many novel modalities for small animal imaging and for measuring the tracer kinetics in vitro cell lines, and has worked with various biologists and physicians to investigate various biological processes, especially as related to tumors.
Tom Chou, PhD, Professor, Biomathematics/Mathematics. Dr. Chou is trained in statistical and condensed matter physics. His broad research accomplishments include uncovering and quantifying mechanisms of protein aggregation, protein-membrane interactions, cellular aging, hematopoiesis, and neuroendocrine control of the hypothalamus-pituitary-adrenal gland system. Dr. Chou is also developing new mathematical tools for inverse/inference problems and uncertainty quantification. Such new mathematical approaches will potentially be transformative for image analysis and parameter estimation in high-dimensional models in systems biology and immunology. His research has been supported by NSF, NIH, and the Army Research Office. Dr. Chou holds a courtesy appointment in the department of Mathematics and teaches Biomath 201, “Deterministic Modeling in Biology,” a key mathematical modeling course for the SIBTG. His past SIBTG mentees include Robert Rovetti (LMU), Sarah Nowak (RAND), and Joshua Chang (NIH).
Maria R. D'Orsogna, PhD, Professor, Mathematics, CalState-Northridge (CSUN). Dr. D’Orsogna was trained in theoretical physics at UCLA where she studied charge transport along DNA. Her current research interests include swarming of autonomous particles and modeling opinion dynamics and radicalization. She has an adjunct appointment in the department of Biomathematics at UCLA and her research has been consistently funded by the NSF and the Army Research Office. Dr. D’Orsogna has also contributed to outreach of the SIBTG by bringing her undergraduate and masters level students to attend Biomath 200 at UCLA. SIBTG trainees have also visited her class at CSUN to present their research.
Daniel B. Ennis, PhD, Associate Professor, Radiological Sciences. Dr. Ennis is a trained biomedical engineer who develops imaging platforms to study cardiovascular flow and structures. His work uses diffusion tensor MRI and phase contrast MRI techniques to extract 3D vasculature signatures in order to differentiate healthy from diseased tissue. He also collaborates with Professor Van Savage to develop software for the automated extraction of 3D vessel geometry from MRI and CT scans. Besides basic and clinical applications of imaging, Dr. Ennis also uses finite element modeling to characterize myocardial structure, function, and remodeling. He is funded by the NIH.
Eleazar Eskin, PhD, Professor, Computer Science. Dr. Eskin focuses on developing techniques for solving the challenging computational problems that arise in attempting to understand the genetic basis of human disease. Current projects include complex traits in inbred mouse strains, the genetics of gene expression and developing webservers for genetic research. Prof. Eskin is active in the Bioinformatics Interdepartmental Program and received an Alfred P. Sloan Fellowship in 2009.
Mark Frye, PhD, Professor, Integrative Biology and Physiology/Neurobiology. The Frye lab investigates how neural circuitry translates to behavior. Specific areas of research include 2-photon imaging of neurons, neural circuitry in fruit fly and its flight behavior, olfactory tracking, visual and walking behavior, and sensory integration. His research makes heavy use of mathematical and computational approaches for image analysis, motion tracking, and signal processing. Dr. Frye was an Alfred P. Sloan Foundation Fellow in 2006 and a Howard Hughes Medical Institute Early Career Scientists from 2009-2015. He is funded by the NIH, NSF, and Army Research Office.
Tom Graeber, PhD, Professor, Molecular and Medical Pharmacology. Dr. Graeber received his PhD in physics at Stanford University and after postdoctoral research in computational biology, joined UCLA as an assistant professor in 2005. His general goal of his research is to understand the signaling and systems biology underlying disease. Specific interests include cancer, metabolism, immune function, and drug resistance. Prof. Graeber’s was an Alfred P. Sloan Fellow from 2006-2008 and his research has been funded by the NIH and the American Cancer Society.
Elissa Hallem, PhD, Associate Professor, MIMG. Prof. Hallem is trained as a neuroscientist and after a postdoctoral position at Caltech, joined UCLA as an assistant professor in 2011. Dr. Hallem focuses on understanding the function and evolution of sensory microcircuits. She studies the C. elegans and other animal models and how neuronal dynamics translate to parasitic behavior. Dr. Hallem teaches and mentors all levels of trainees and teaches dynamics of neural microcircuits and parasitology. She is funded by the NIH, the NSF, the Burroughs Wellcome Fund, and the Howard Hughes Medical Institute (HHMI). Her research has been recognized by an NIH Director’s New Innovator Award, a McKnight Scholar Award, the Searle Scholar Award, and a MacArthur Fellowship (2012).
Alexander Hoffmann, PhD, Professor, MIMG. Dr. Hoffmann was recently recruited from UC-San Diego to lead the new UCLA Institute of Quantitative and Computational Biology (QCB) in 2013. He runs the Signaling Systems Laboratory in which his group employs both experimental and computational approaches to investigate regulatory signaling networks, B-cell activation, and immune response to explain physiological processes. Director Hoffmann has organized weekly seminars and a yearly QCB retreat that is frequently attended by SIBTG trainees.
Steve Horvath, PhD, Professor, Human Genetics. Dr. Horvath is trained both in theoretical physics and statistics, having received PhDs in both. He develops approaches for the computational analysis of DNA and tissue microarray data. His research interests include family-based allelic association tests for finding complex disease genes, tissue microarray data, weighed gene co-expression networks, and systems biology. A particular problem his group currently focuses on is how epigenetic mechanisms mediate the effect of chronological age on chronic diseases. Prof. Horvath’s research has been funded by the NIH.
Tzung K. Hsiai, MD/PhD, Professor, Medicine and Bioengineering. Professor Hsiai is a Bioengineer and MD who uses computational and modeling approaches in his research on sensor and microtransducer design for measuring intravascular shear stress in vivo. He has developed a 4-D cardiac light sheet fluorescent microscope to study cardiac development and also used computational fluid dynamics to study zebrafish cardiac morphogenesis. His research is funded by the NIH and the American Heart Association.
Sotiris Masmanidis, PhD, Assistant Professor, Neurobiology. Dr. Masmanidis is an experimental neuroscientist trained in applied physics at Caltech and joined UCLA as an assistant professor in 2012. Sotiris’ research strives to understand how networks of neurons encode information during rewarded-guided behavior, and how experience affects neural dynamics. He also develops silicon-based probes to enable large-scale recordings and has been funded by the NIH, the McKnight Foundation, the Alfred P. Sloan Foundation and the NSF.
Kenneth Lange, PhD, Professor, Biomathematics. Dr. Lange is a renowned expert in probability, stochastic processes, and optimization. His research interests include human genetics, population biology, and computational statistics. He has worked on problems of linkage and radiation hybrid mapping, risk prediction in genetic counseling, genetic epidemiology, and forensic uses of DNA profiling. These areas tie in well with his activities in computational statistics and highlight his contributions to the computation of complex probabilities on human pedigrees. Dr. Lange has also made important contributions to medical image reconstruction. He is a pioneer in the use of the EM algorithm for statistical reconstruction of tomographic images. Dr. Lange has published four applied mathematics textbook which he uses in key SIBTG courses, including Stochastic Processes, Statistical Genetics, and Optimization. His former SIBTG trainees have included, Neil Risch, Michael Boehnke, Daniel Weeks, Laura Lazzeroni, and Eric Sobel, all leading figures in statistical genetics.
Alexander Levine, PhD, Professor, Chemistry. Professor Levine is trained in statistical physics and theoretical condensed matter physics and investigates a broad range of problems in biophysics. Recent research projects include modeling microtubule dynamics, membrane protein interactions, inference of cellular focal adhesions, and cellular and biomaterial microrheology. With Professor James Weiss, he has initiated a new area of research into respiratory rhythms and its control by the pre-Botzinger complex. Professor Levine often teaches a graduate-level statistical physics course in the Physics department (Physics 215A,B) that is highly popular with SIBTG trainees.
James Lloyd-Smith, PhD, Professor, Ecology and Evolutionary Biology. Professor Lloyd-Smith is the De Logi Chair in Biological Sciences and received his PhD in Biophysics from UC Berkeley and joined UCLA as an assistant professor after a postdoc in which he studied infectious disease dynamics. Currently, he studies the ecological and evolutionary dynamics of infectious disease in animal and human populations. By combining theoretical models with data, he aims to discover fundamental principles of disease transmission and adaptation, identify driving mechanisms, and design effective control policies. His work includes California sea lions, monkeypox in humans and wildlife in central Africa, and SARS and other emerging diseases in humans. He is supported by the NSF and the DoD and has recently mentored two SIBTG trainees, Monique Ambrose, Katie Gostic and Christian Mason.
Michael McNitt-Gray, PhD, Professor, Radiological Sciences. Prof. McNitt-Gray is the Director of the Physics and Biology in Medicine Graduate Program (PBM) within the UCLA school of medicine. He works on the quantitative evaluation and characterization of x-ray CT imaging and their various medical/clinical applications. He has trained numerous PhD students in PBM and his research is funded by the NIH.
Matteo Pellegrini, PhD, Professor, Molecular, Cell and Developmental Biology. Prof. Pellegrini is an active member off the Bioinformatics IDP. He was trained in Physics, has industrial experience, and is interested in developing computational tools to analyzed large-scale genomic data. He has developed novel approaches for measuring methylation states of the epigenome. His current efforts center on developing tools for analyzing RNA and DNA methylation data from an immunological perspective. Dr. Pellegrini has mentored numerous predocs and postdocs who have entered the academic and industrial workforce.
Zhilin Qu, PhD, Professor, Medicine. Dr. Qu is a professor in the Cardiology division in the department of Medicine and the co-director of the Cardiac Computation Laboratory. His research interests in computational biology center on using mathematical modeling and computer simulation to study the mechanisms of cardiac arrhythmias, cell cycle control, and the dynamics of biological signal transduction. He applies dynamical theory at the systems level to address clinical problems in the multi-scale modeling of excitation-contraction coupling and arrhythmias (such as ventricular fibrillation) and in understanding the complex network involved in cardiac metabolism. He has taught mathematical modeling courses relevant to SIBTG trainees and is currently mentoring MSTP student and SIBTG trainee Julian Landaw.
Marcus Roper, PhD, Associate Professor, Mathematics. Dr. Roper has a courtesy appointment in the Department of Biomathematics and studies the fluid mechanical aspects of biological processes, particularly collective behavior of particles such as red blood cells and fungi. He teaches classical applied mathematical modeling in fluid and solid mechanics. He teaches a number of key mathematics courses that are critical to the SIB training program and that are frequently taken by the trainees. These key courses include: partial differential equations (Math 266A), Asymptotic Methods (Math 274), Mathematical Aspects of Fluid Mechanics (Math 272B), and Foundations of Continuum Mechanics (Math 272A). Dr. Roper is also currently mentoring Mr. Shea-Shyr Chang, a SIBTG trainee. Dr. Roper’s teaching and mentoring are highly valuable to the SIBTG and he is on the executive committee.
Amy Rowat, PhD, Assistant Professor, Integrative Biology and Physiology. Dr. Rowat obtained her PhD in physics from the University of Southern Denmark. After postdoctoral research at Harvard and Brigham and Women’s Hospital, she started as an assistant professor at UCLA in 2011. Her research links the mechanics of biological materials to their physiology, with a current emphasis on the cell nucleus, which is central to genome integrity, gene expression, and mechanobiology. She explores the structure and organization of the nucleus at multiple levels, from the origins of nuclear shape to subnuclear structure and dynamics, and the resulting consequences for cellular physiology. Her approach is multidisciplinary and includes the development and application of new technologies to connect molecular-scale composition and genotype with biophysical phenotype.
Van Savage, PhD, Professor, Ecology & Evolutionary Biology. Prof. Savage is trained as a theoretical physics and has a half-time appointment in the Department of Biomathematics. Dr. Savage’s research is aimed at developing new models for tumor growth that can connects properties of vascular architecture, the process of angiogenesis, host capillary density, blood supply, and cellular metabolic rate. Savage also works closely with Dan Ennis, an SIBTG faculty member from the Department of Radiology, to develop software for the automated extraction of 3D vessel geometry from MRI and CT scans across length scales in the vascular system. Moreover, Savage has helped develop models and novel tests using empirical data for the function and duration of sleep as well as cell size and the rate of evolution for species, including collaborations with multiple members of the Ecology and Evolutionary Biology department.
Janet Sinsheimer, PhD, Professor, Human Genetics. Dr. Sinsheimer's research is focused on statistical method development in order to answer genetic, genomic and phylogenetic questions. Most recently, her group has been working on (1) methods that allow for both maternal and offspring genetic effects and that disentangle maternal genetic effects from environment, (2) optimization approaches applied to genomic data and (3) methods for realistic inference of evolutionary relationships. She also collaborates on multidisciplinary research projects in these areas. Prof. Sinsheimer has courtesy appointments in the Departments of Biomathematics and Biostatistics and teaches a core statistical genetics course (M207A). Her past SIBTG trainees include Jennifer Tom (Scientist, Genentech) Karin Dorman (Professor Iowa State, holder of the Dale D. Grosvenor Endowed Chair) and Marc Suchard (Professor UCLA).
Marc Suchard, MD/PhD, Professor, Human Genetics. Dr. Suchard uses mathematical and computational approaches to analyze stochastic processes in molecular sequence data, phylogeny, and clinical health records. He is helping develop the nascent field of evolutionary medicine which harnesses the power of methods and theory from evolutionary biology and phylogenetics to advance our understanding of human disease processes, particularly in the study of rapidly evolving pathogens. He received a 2008 Guggenheim Fellowship, was elected to Fellow of the American Statistical Association in 2012, and received the COPSS President’s Award in 2012. He was a past SIBTG trainee and currently mentors SIBTG trainee Yuxi Tian, who is developing computational methods for analyzing patient data.
Ren Sun, PhD, Professor, Molecular and Medical Pharmacology. Ren Sun is a member of the Molecular Biology Institute, the AIDS Institute, the Jonsson Comprehensive Cancer Center, the Dental Research Institute, and the California NanoSystems Institute, where he is the chair of the education committee. He has also established the “Cross-disciplinary Scholars in Science and Technology” (CSST) program, a campus-wide program that promotes training across all fields in science and engineering. Prof. Sun uses computational methods and models of evolution in his research on tumor-associated herpesviruses, HIV and HCV. He is the director of the Interdisciplinary in Virology and Gene Therapy T32 training grant and his research is supported by the NIH.
James Weiss, PhD, Professor, Medicine. Professor Weiss is the chief of the Division of Cardiology, and Director of the Cardiovascular Research Laboratory. His research focuses on ion channel biophysics, cardiac electrophysiology, arrhythmias, and ischemia and mitochondrial biology. His research group spans the range from basic sciences to clinical applications and uses systems approaches integrating experimental biology at the molecular to organ level with mathematical modeling to investigate arrhythmias, ischemia biology and cardioprotection.
Shenshen Wang, PhD, Assistant Professor, Physics. Dr. Wang is trained in theoretical Biophysics and received her PhD from UC San Diego modeling the cytoskeleton and actomyosin networks. After a postdoctoral position at MIT during which she studied immunology and viral infections, she started at UCLA in 2015. Her research interests lie in understanding the adaptive immune system, particularly how cross-reactive antibodies are produced. She is an active member in the Center for Biological Physics.
Roy Wollman, PhD, Associate Professor, Integrative Biology and Physiology. Dr. Wollman is trained in biology and mathematics and runs an experimental laboratory that investigates information processing in cell signaling and wound healing. His research relies heavily on mathematical modeling and statistical analysis. He is joint-appointed in the Department of Chemistry and Biochemistry and is currently funded by two NIH R01 grants.
Gerard Wong, PhD, Professor, Bioengineering. Professor Wong is trained in physics and materials science and has a courtesy appointment in the department of Chemistry and Biochemistry. Dr. Wong leads an experimental laboratory that heavily relies on supporting mathematical and computational approaches. He is a leading expert on biomacromolecular self-assembly, bacterial communities, and the mechanisms of antibiotic resistance and was elected to Fellow of the American Physical Society in 2012. His research has direct clinical applications and has been supported by NSF, NIH, the Alfred P. Sloan Foundation, and the Human Frontiers Science Program. Dr. Wong mentored Ernest Lee, an MSTP student trainee on the SIBTG in 2015-2016.