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Current Fellows

 

 

UCSF Sandler Fellows:

 

Richard Daneman, Ph.D. Richard was a graduate student in Ben Barres' laboratory at Stanford University where he studied the cellular and molecular regulation of the blood-brain barrier (BBB). The BBB is a specialized structure formed by the vasculature of the central nervous system that tightly regulates the movement of molecules and ions between the blood and the brain. This is critical for neural function as well as protecting the CNS from injury and disease, as breakdown of the BBB contributes to the severe pathology of many neurological diseases including stroke, multiple sclerosis and brain trauma. In his graduate work Richard developed methods to generate a transcriptional profile of the BBB and elucidated cellular and molecular mechanisms that control BBB development. As a UCSF fellow, Richard will continue this work utilizing cellular, molecular and genetic tools to dissect the mechanisms of BBB formation during development, and how the BBB is dynamically regulated in adulthood during health and disease. The ultimate goal of this work is to develop methods to modulate the BBB to treat neurological diseases.

 

 

Alex Marson, M.D., Ph.D. Alex completed M.D. and Ph.D. training at Harvard Medical School and the MIT Biology Department, and his medical residency at The Brigham and Women's Hospital. His graduate work with Rick Young and Rudolf Jaenisch focused on transcriptional regulatory circuitry in T cells and embryonic stem cells. Alex has come to UCSF as a clinical fellow in Infectious Diseases and is continuing his scientific research program as a UCSF Fellow. He is investigating the gene expression programs that enable CD4+ T cell populations to enact highly specialized cellular functions and of the ways in which disruptions of these mechanisms contribute to human disease. Alex's laboratory uses genomic studies, hi-throughput functional screens and human genetics to enhance our understanding of the functions of regulatory and pro-inflammatory T cells in immunity and autoimmunity.

 

 

Ross Metzger, Ph.D. Ross was a graduate student in Mark Krasnow's lab at Stanford, where he began work on mouse lung development. Ross is interested in the genetic and molecular mechanisms that control the three-dimensional architecture of the lung during development and evolution, and how this patterning information is translated into the cell behaviors of morphogenesis. As a UCSF Fellow, Ross is using comprehensive mutant analysis to identify and assign functions to genes in the airway branching program and to understand how pulmonary vascular and other tissue patterns are coordinated with the airways. He is also using genetic approaches to understand how key genes in the branching program are regulated, and how differences in gene regulation contribute to species-specific differences in pattern.

 

 

Michael Oldham, Ph.D. Michael was a graduate student in Dan Geschwind's laboratory at UCLA, where he studied the organization of the human brain transcriptome using computational methods. By analyzing transcriptome organization in microarray data generated from specific human brain regions, he was able to identify recurrent patterns of gene activity associated with specific cell types and functional processes. As a UCSF Fellow, Michael intends to employ computational and experimental approaches to construct, characterize, and compare gene co-expression networks in discrete regions from the developing and adult human brain. These molecular "maps" of gene activity will facilitate the major goals of Michael's research, which are to: (1) refine the cellular taxonomy of the human brain on the basis of gene expression, (2) annotate gene function in the human brain through the principle of "guilt-by-association", and (3) provide a holistic framework for studying the molecular and cellular evolution of the human brain, as well as perturbations in gene expression that are associated with specific neurological and neuropsychiatric diseases.

 

PangiatakosGeorgia Panagiotakos.  Georgia is currently a graduate student working with Ricardo Dolmetsch and Theo Palmer at the Stanford University School of Medicine and will be joining UCSF late in 2014. She is primarily interested in how immature, undifferentiated neural stem cells integrate a variety of intrinsic and extrinsic signals to generate the diverse array of cell types in the developing brain. Georgia first became passionate about neural development during her time working with Viviane Tabar and Lorenz Studer at Memorial Sloan Kettering Cancer Center, where she focused on the transplantation of pluripotent stem cells that had been directed to differentiate into specific neural cell types. This work shed light on the integration of stem cell-derived neural cells into the brain, in the context of developing strategies to replace cells lost during disease. For her graduate work at Stanford, Georgia continued to explore mechanisms by which neural stem cells decide to become a specific type of neuron, by investigating the role of a calcium channel implicated in neuropsychiatric disease on the differentiation of mouse and human neurons. To do this, she employed a number of different techniques, including in utero electroporation, genetic tools, single cell multiplex qPCR, ratiometric calcium imaging, and human induced pluripotent stem cell culture. As a UCSF Sandler Fellow, Georgia will integrate these complementary approaches to examine the function of early electrical activity and ion channel diversity in sculpting the development and evolution of the brain, with an eye towards understanding how these mechanisms go awry in neurodevelopmental disorders.

 

 

Saul Villeda, Ph.D. Saul was a graduate student with Tony Wyss-Coray at Stanford University, where he investigated how systemic changes in aging blood contribute to age-related impairments in neural stem cell function and cognitive processes. Aging alters both the regenerative capacity and functional integrity of the adult brain, and as a result steadily drives cognitive impairments and susceptibility to neurodegenerative disorders in healthy individuals. In fact, aging remains the single most predominant risk factor for dementia-related neurodegenerative diseases in the elderly, such as Alzheimer's disease. Now considering the rate at which the human population is currently aging, it becomes critical to identify ways by which to maintain cognitive integrity by protecting against, or even counteracting, the effects of aging. As a UCSF fellow, Saul is investigating cellular and molecular mechanisms that promote the rejuvenation of the old brain. Saul employs in vitro and in vivo approaches to elucidate these mechanisms including heterochronic parabiosis surgical procedures, whole genome wide microarray analysis, as well as learning and memory behavioral paradigms. The ultimate goal of this work is to better understand how to ameliorate age-related cognitive dysfunction by harnessing the latent plasticity remaining within the old brain.

 

 

David Weinberg, Ph.D. David was a graduate student with Dave Bartel at the Whitehead Institute at MIT and joined UCSF in 2013. While a student, he uncovered key RNAi pathway components and target genes in budding yeast. David also discovered how the Dicer processing enzyme uses an unusual mechanism and structure to act a molecular ruler, and how Argonaute utilizes guide RNAs in RISC complexes.  While still at MIT, he initiated an independent program to study eukaryotic translation regulation, including the roles of cellular context, RNA sequence, and mRNA looping on translational efficiency, and the proteins involved, and is now investigating these aspects as a UCSF Sandler Fellow.

 


Systems Biology Fellows:

The UCSF Center for Systems and Synthetic Biology has recruited additional Faculty Fellows. These independent research positions are similar to UCSF Sandler Fellows but are administered by a different committee.

 

Lei (Stanley) Qi, Ph.D. Stanley was a graduate student in Adam’s Arkin’s lab at UC Berkeley, where he studied the design principles of large-scale genetic circuitry programming with noncoding RNAs. He developed methods to synthetically generate large libraries of RNA regulatory elements based on in vitro, in vivo and in silico designs that can detect cellular or environmental signals and form complex regulatory networks for biocomputation and cellular information processing. As a Systems Biology Fellow, Stanley is developing novel synthetic RNA-targeted technologies as a potentially superior alternative to RNA interference to interrogate the kinetic coordination of collections of multiple genes during development and pathogenicity. He is also applying synthetic biology principles to develop customizable remediable strategies by building therapeutically useful yet non-invasive genetic circuits to reliably detect and reverse disease states.

 

 

David Sivak, Ph.D. David was a Biophysics graduate student with Phillip Geissler at University of California, Berkeley where he developed coarse-grained mechanical models of DNA.  As a Physics post-doc with Gavin Crooks at Lawrence Berkeley National Laboratory he studied the nonequilibrium statistical mechanics of nanoscale systems.  In particular, he developed basic theory describing the nonequilibrium behaviour, optimal control and optimal response of driven microscopic systems. Now as a Systems Biology Fellow, David is exploring the generalisation of these nonequilibrium results (that primarily addressed single molecule systems), to the more biologically meaningful context of networks. For example, how do we re-conceptualize optimal response, extending the framework of a single molecule responding to a single source of perturbations, to a regulatory network integrating many fluctuating external signals?

 

 

David Soloveichik, Ph.D. David did his graduate work with Erik Winfree at Caltech, focusing on algorithmic self-assembly and on synthetic networks of nucleic-acid interactions based on strand displacement cascades. He is interested in "molecular programming": the systematic design of complex molecular systems based on the principles of computer science and distributed computing. More generally, he is trying to create a theoretical foundation of chemical computation applicable to both synthetic and natural systems.

 

 

 

Matt Thompson, Ph.D. Matt's graduate research at Harvard University focused on understanding how molecular circuits enable individual cells to make cell fate decisions in response to developmental signals. Currently, Matt is exploring cellular decisions that occur in cell populations, for example, within the tissues of a developing organism or within our immune system. How do large numbers of progenitor cells within a developing organism exchange information and coordinate their state to construct a complex tissue? What are the rules that organize multi-cellular phenomena and how are these rules implemented in molecular circuits that operate in single cells? He is using a combination of approaches including mathematical models, statistical analysis of high-throughput gene expression data, and single cell imaging experiments. His current work is reconstituting a set of developmental processes in the lab using embryonic stem cell differentiation and developing imaging methods for tracking and perturbing the activity of signaling pathways and transcriptional regulators in many single cells at once. Matt will use this data with computational models to classify mechanisms used by tissues to develop and repair themselves without centralized control.

 

 

QB3 and Cancer Center Fellows:

The California Institute of Quantitative Biosciences (QB3) and the UCSF Helen Diller Family Comprehensive Cancer Center have also recruited Faculty Fellows. These independent research positions are similar to UCSF Fellows but administered by a different committee.

 

 Sourav Bandyopadhyay, Ph.D. Sourav was a graduate student with Trey Ideker at the University of California, San Diego. His work was on the generation and analysis of high-throughput protein-protein and genetic interaction networks. In yeast, he revealed that synthetic lethal relationships between genes are largely condition-dependent and could be used to reveal condition-specific signaling events. As a QB3/Cancer Center Fellow, Sourav intends to employ the lessons learned mapping genetic interactions in yeast to explore the relationships among proteins that collaborate in various aspects of cancer progression using a combination of RNAi and small molecules. One major goal of this work is to systematically identify molecules that could be used in combination to inhibit various cancers.

 

 

Graham Johnson, Ph.D. Graham was a graduate student in the Molecular Graphic Lab at Scripps.  He focuses primarily on developing algorithms to enable scientists to generate, simulate, and visualize molecular models of cells, namely a software called autoFill/autoCell and continues to work with Ludovic Autin to develop ePMV in continued collaboration with Arthur Olson's lab at Scripps. His lab also develops outreach software that enables scientists and illustrators to interoperate the computational tools of science and art and works closely on these fronts with Tom Ferrin's Computer Graphics Lab (CGL) at UCSF as a Resource for Biocomputing, and Visualization, and Informatics (RBVI) collaborator, and with the Molecular Graphics Lab (MGL) at The Scripps Research Institute as a former National Biomedical Computational Resource (NBCR) member and current collaborator.