UCSF Sandler Fellows:
Joseph Bondy-Denomy, Ph.D. Joe conducted his Ph.D. training at the University of Toronto where he was a graduate student with Alan Davidson in the Department of Molecular Genetics. The primary goal of his research was understanding the co-evolutionary arms race between bacterial viruses (phages) and their hosts. This work led Joe to study an immune system that bacteria possess to protect them from phages, called CRISPR-Cas. He discovered numerous phage-encoded proteins that inhibit CRISPR-Cas function and characterized their mechanisms of action. As a Fellow at UCSF, Joe will continue to study various aspects of the CRISPR-Cas system, such as characterizing its roles in other pathogenic microbes and searching for proteins that may modulate or redirect CRISPR-Cas function. Joe is also interested in discovering novel bacterial immune systems, using phages to probe for them. His laboratory will use a combination of molecular, microbiological and bioinformatic approaches to identify and characterize novel aspects of bacterial immune systems. Joe’s work will enhance our understanding of bacterial evolution, has potential applications to CRISPR-Cas9 genome editing, and may provide novel therapeutic targets for antibiotic resistant bacteria.
Robert Judson, Ph.D. Robert conducted his dissertation research in Robert Blelloch’s laboratory in the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF. There he pioneered the use of microRNAs for epigenetic reprogramming and discovered two conserved microRNA families that promote the conversion of differentiated cells into induced pluripotent stem cells. Using an siRNA approach to map genetic interactions, he further identified networks of microRNA-regulated genes that cooperate in the stabilization of the fibroblastic cell state. Coordinated inhibition of these networks sensitizes skin cells to epigenetic reprogramming, thereby making them more susceptible to the reacquisition of embryonic programs. As a fellow at the UCSF Helen Diller Family Comprehensive Cancer Center, Robert is now further developing these tools to dissect the similar networks that stabilize the melanocytic cell state. The incidence of melanoma is on the rise and, if given the opportunity to metastasize, the disease is usually lethal. With the goal of developing novel strategies to more accurately determine the metastatic potential of early lesions, Robert is using a combination of primary tumor sequencing, genetic interaction mapping, genome editing, and microRNA manipulation to study the networks of genes that prevent normal melanocytes and primary melanomas from reacquiring embryonic programs.
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.
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.
Georgia Panagiotakos, Ph.D. Georgia has been 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.
Sy Redding, Ph.D. Sy did his graduate work at Columbia University in the laboratories of Eric Greene and David Reichman. Using a single molecule imaging technique called DNA curtains, Sy investigated the physical mechanisms through which proteins locate, recognize, and extract genomic information. His research has explored how bacterial RNA polymerase locates promoter sequences within the genome, the mechanism of sequence alignment during homologous recombination, and how viruses are selectively recognized and destroyed by the CRISPR immune system. At UCSF, Sy will use DNA curtains to explore how protein-DNA interactions change as DNA is organized into chromatin: how nature balances the individual protein’s need to access DNA against the cell’s pressure to organize the genome.
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 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 Thomson, 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.
The California Institute of Quantitative Biosciences (QB3) at UCSF has also recruited Faculty Fellows. These independent research positions are similar to UCSF Sandler Fellows but administered by a different committee.
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.
Physician-Scientist Scholar Program:
The Physician-Scientist Scholar Program (PSSP) attracts the most accomplished and promising young physician/scientists to UCSF and accelerates their transition to independent laboratory-based investigators working on research problems relevant to human health. These are early-career Scholars, like UCSF Sandler Fellows, but are administered by a different committee.
Alexandra Nelson, M.D., Ph.D. Alexandra completed her joint MD and PhD training at University of California, San Diego. Her thesis work under the mentorship of Sascha du Lac at the Salk Institute employed whole-cell electrophysiology in rodents, and identified a novel form of neuronal excitability plasticity involving the regulation of potassium channels. She later found this form of plasticity contributes to motor learning in vivo. After completing her Neurology residency training at UCSF, she began postdoctoral work in the laboratory of Anatol Kreitzer at the Gladstone Institute. There she combined electrophysiology with optogenetics, in order to probe basal ganglia circuitry in mouse models. As a UCSF Physician-Scientist Scholar, Alexandra plans on using in vitro and in vivo electrophysiology, optogenetics, and behavior in mouse models of movement disorders with a goal of identifying the patterns of aberrant neural activity which give rise to involuntary movements. By identifying these patterns and the responsible cellular and synaptic mechanisms, she hopes to identify novel drug or deep brain stimulation targets to restore neural activity patterns and normal movement.