Current Fellows

UCSF Sandler Fellows:

Mustafa Aydogan, D. Phil. Mustafa is fascinated by how biological time is regulated across different scales, with a particular interest in the regulation of organelle biogenesis. He carried out his doctoral work at the University of Oxford to study how centriole biogenesis is regulated in space and time. In particular, he discovered that an autonomous clock controls the timing of centriole formation – independently of, but in entrainment with, the principal Cdk/Cyclin cell-cycle oscillator. This finding challenges the current model of how cell cycle is regulated and opens a potential new avenue of research to explore whether other such autonomous clocks exist in the cell. The Aydogan Lab currently focuses on timing mechanisms that may be at play in the biogenesis of other organelles. They use state-of-the-art techniques in live super-resolution microscopy, combined with genetics, biochemistry, biophysics and mathematical modelling, to address biological phenomena.

 

Faranak Fattahi, Ph.D. Faranak completed her graduate training in the laboratory of Dr. Lorenz Studer at Memorial Sloan-Kettering Cancer Center. During her PhD, she pioneered strategies to derive highly specific lineages of the peripheral nervous system (PNS) from human pluripotent stem cells and demonstrated their potential in drug discovery and regenerative medicine. As a UCSF Sandler Fellow, she is focused on utilizing this unique framework to study the human PNS development and function in health and disease, with the ultimate goal of developing new therapies for peripheral neuropathies.

 

jain-picIsha Jain, Ph.D. Isha received her PhD from the Harvard-MIT program in Health Sciences and Technology. Her graduate work in Vamsi Mootha's lab led to the foundational discovery that hypoxia could serve as a therapy for mitochondrial disorders. This seemingly contradictory approach extended the lifespan of a mitochondrial disease mouse model by five-fold. A Phase 1 clinical trial is already underway based on this initial discovery. Through this work, Isha has become enthralled by the essential role oxygen plays in dictating cellular metabolism and mammalian physiology. In her independent research program, she plans to use systems-level approaches to identify novel hypoxia adaptations with therapeutic implications for ischemic conditions such as stroke. Additionally, she hopes to identify common conditions which benefit from turning the "oxygen dial" to low or high oxygen, laying the groundwork to understand the role of oxygen in aging and age-associated conditions.

 

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.

 

 Vijay Ramani, Ph.D. Vijay competed his PhD studies in Jay Shendure’s lab at the University of Washington, where he invented high-throughput molecular methods to study biological phenomena at scale. These methods included an assay for studying RNA structure, as well as single-cell genomic assays reliant on in situ DNA barcoding of intact cells and nuclei, to make genome-wide measurements in thousands of single-cells without ever resorting to single-cell isolation. As a Sandler Fellow, Vijay’s lab will continue to develop novel, high-throughput technologies to study biology at the level of single cells and single molecules. His lab will also apply these tools to better understand how genes are regulated at the levels of transcription & translation, specifically in the context of metabolic perturbation.

 

 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.

 

reeves-headshotMelissa Reeves, Ph.D. Melissa did her graduate research in Allan Balmain's lab in the Helen Diller Comprehensive Cancer Center at UCSF, where she studied tumor evolution and heterogeneity. Combining next generation sequencing with multi-color fluorescent lineage tracing, she identified patterns of clonal evolution and timing of clonal sweeps that occur during tumor progression and found that metastases typically spread from the primary tumor in parallel to distant sites, rather than via a regional lymph node. As a UCSF Sandler Fellow, Melissa and her lab will study how tumor heterogeneity impacts the anti-tumor immune response, making use of multi-color lineage tracing tools and next-gen sequencing. Immunotherapy strategies have great potential to treat and even cure cancer patients, but the majority of human tumors exhibit a high level of spatial and genetic heterogeneity, and it is critical for us to understand how that heterogeneity will impact the response of T cells to the tumor.

 

Caroline Vissers, Ph.D. Caroline received her PhD from the Biochemistry, Cellular and Molecular Biology program at Johns Hopkins School of Medicine. Her work in the lab of Hongjun Song was the first to show the regulatory effect of chemical modifications on mRNA, termed “epitranscriptomics,” on mammalian cortical neurogenesis. One methylation in particular, m6A, regulates neural stem cell proliferation and differentiation and allows for pre-patterning of neural stem cell fate prior to differentiation. Additionally, Caroline collaborated with Gregg Semenza to study how m6A regulates breast cancer cell response to hypoxia. She showed that stress-induced dynamics of m6A regulate cancer cell gene expression at both RNA and protein levels, with consequences in cell proliferation and metabolism. As a UCSF Sandler Fellow, Caroline will lead a research program studying how the epitranscriptome is regulated, particularly in response to endogenous (developmental signaling pathways) and exogenous (stress) stimuli. This work will be applied to studies of neural development and disease with the ultimate goal of developing new therapies for developmental and neurodegenerative disorders.

 

Kevin Yackle, M.D., Ph.D. Kevin completed his training at Stanford University where his dissertation in Mark Krasnow’s lab made a foundational contribution towards understanding the cellular and molecular bases of breathing rhythm generation. Breathing is a simple, essential behavior triggered roughly fifteen times per minute by the breathing pacemaker, the preBötzinger Complex (preBötC), a brainstem nucleus of several thousand neurons. Kevin defined more than 50 molecularly distinct preBötC neural subtypes and in initial studies characterizing the first five subtypes, he discovered that molecular defined preBötC cell types that have exquisitely specific, distinct and interesting functions in the breathing behavior. For example, he identified ~200 preBötC neurons that are sufficient to induce and selectively required for the control of sighing, a specific breath type, and ~175 different neurons that are expendable for breathing rhythm generation and instead project to, synapse with, and activate a higher order brain center that promotes arousal, perhaps explaining the connection between breathing and calmness or anxiety. The discovery of dozens of molecularly distinct preBötC neural cell types, each with an important and distinct role in breathing, suggests that a subset will be critical for generating a breath and controlling the pace of breathing. At UCSF, Kevin will continue his dissection of preBötC cell types in order to identify the key neural types and the molecules they use to generate and pace breathing.

 

Affiliated Fellows:

 

QBI Fellows: The QBI (Quantitative Biosciences Institute) Fellowship attracts early-career scientists who are on the cutting edge of new technologies and discovery.  The fellowship hastens their growth towards independent basic research problems relating to human health and advancement.

 

Kliment Verba, Ph.D. Klim completed his Ph.D in David Agard’s laboratory at UCSF, training in a variety of biophysical methods with focus in cryo electron microscopy. Recent breakthroughs in the field and novel methods he helped develop in house allowed him to obtain astructure of a chaperone-kinase complex with the kinase being in a previously unseen, partially folded state. Not only this provided the first high resolution structural insight of how Hsp90 chaperone machinery recognizes substrates but also how kinases may use unfolded states for regulation. Key signalling kinases act as parts of larger signalling complexes and it is likely that binding partners other than chaperones utilize the fluidity of the native state to gain fine allosteric regulation of the kinase activity. This is an exciting hypothesis which until recently has been completely out of the realm of structural biology. As a QBI fellow Klim plans to interrogate large, transient and heterogeneous kinase signalling complexes combining methods like cryoEM and mass spectrometry, and where required developing novel methods, to see just how this fluidity may be utilized in signalling.

 

 

Chan Zuckerberg Biohub Fellows: The Biohub Fellows program attracts early-career scientists who are on the cutting edge of new technologies and discovery with a focus on applied or fundamental aspects of Infectious Disease or Mapping of Cellular Functions and States.  The Biohub Fellows Program offers a dynamic environment with the opportunity to develop an independent research program while also interacting closely with colleagues working in the above focus areas.

 

Lillian Cohn, Ph.D. Lillian received her Ph.D. from Rockefeller University in 2018. As a student in Michel Nussenzweig’s laboratory, she used single cell strategies to investigate latent viral infection in HIV-1 infected individuals. This research revealed insights into the mechanisms of viral persistence and maintenance of the HIV-1 latent reservoir. As a Biohub Fellow appointed between the Cell Atlas and Infectious Disease initiatives, Lillian is using novel strategies to investigate latent viral infection and characterize human immune cells. In particular, she is interested in understanding the contribution of tissue-resident cells to viral persistence, developing new isolation techniques to study rare latently infected cells, and elucidating how the virus and host cellular environment work together to maintain latency.

 

Daniel Itzhak, Ph.D. Daniel obtained his Ph.D. in the multidisciplinary Wellcome Trust Program for mechanism-based drug discovery, at the Institute of Cancer Research in London. As a postdoctoral fellow at the Max Planck Institute of Biochemistry with Dr Georg Borner, he developed a mass spectrometry-based approach to map protein translocation events at a subcellular level. At CZ Biohub in the Cell Atlas Initiative, he will work closely with the Leonetti group to complement high-throughput genome engineering with cutting-egde mass spectrometry.

 

 

Andreas Puschnik, Ph.D. Andreas did his graduate work in the laboratory of Jan Carette in the Microbiology and Immunology Department at Stanford University. There, he applied large-scale genetic perturbation screens based on haploid insertional mutagenesis and CRISPR gene editing to study the cellular pathways and components required for viral infections. His work focused on the family of the Flaviviridae, which include mosquito-borne viruses such as dengue, Zika and West Nile, as well as the blood-borne hepatitis C virus. Andreas identified endoplasmic reticulum localized protein complexes that are critical for flaviviral replication. He demonstrated that a small molecule targeting the uncovered host cell complex led to reduction of infection with mosquito-borne flaviviruses. Host-targeted therapy may therefore provide an alternative, more broad-spectrum antiviral strategy.  At CZ Biohub, Andreas will utilize this approach to study other viral families as well as look for novel immune regulators to control viral infection and pathogenesis.

 

 

Cell Design Fellows:  The Cell Design Fellowship attracts interdisciplinary early-career scientists at the intersection of synthetic and systems biology, cell therapy, and immunology. The Fellows have the opportunity to launch their own independent research program while working together in close collaboration with the other Fellows and labs in the Cell Design Initiative to develop new technology for engineering therapeutic immune cells.

 

Joseph Choe, Ph.D. Joe completed his graduate training in the laboratory of Dr. Wendell Lim at the University of California, San Francisco. During his PhD, he developed strategies to engineer therapeutic T cells that harness combinatorial antigen recognition in order to overcome tumor heterogeneity in glioblastoma. As a UCSF Cell Design Fellow, he is focused on developing tools and platforms to enable advancement in immune cell engineering, with the ultimate goal of generating cells that is more reliable, effective, and safe at combating cancer.

 

 

Andrew Ng, Ph.D. Andrew received his PhD from the Joint Graduate Program in Bioengineering at UC Berkeley and UCSF in the laboratories of Hana El-Samad and John Dueber. There, he pioneered the use of de novo designer proteins as powerful tools for synthetic biology in collaboration with David Baker at University of Washington. Andrew helped develop the first bioactive designer protein switch (LOCKR) for controlling signal peptides, and used this tool to program feedback behavior in synthetic and endogenous signaling circuits. As a Cell Design Fellow, Andrew will lead a research team to build new tools and circuits to enable cell autonomous regulation of T cell signaling. He hopes that these feedback circuits will increase the safety and efficacy of existing CAR T therapies and unlock new therapeutic behaviors for engineered immune cells.

 

Jasper Williams, Ph.D. Jasper completed his PhD research in Wendell Lim’s lab at UCSF as a member of the Pharmaceutical Sciences and Pharmacogenomics graduate program.  There, he caught the synthetic biology bug and became obsessed with developing new ways to control the behavior of engineered therapeutic T cells.  Jasper's work largely focused on designing and engineering a suite of new T cell multi-antigen pattern recognition circuits that provide an array of ways to specifically recognize cancers. Additionally, he established a collaboration with Tejal Desai’s lab to develop approaches that wed biomatierals engineering and cell engineering to precisely modulate therapeutic T cell activity.  As a UCSF Cell Design Fellow, Jasper’s lab will continue to develop synthetic biology and cell engineering tools to overcome hurdles facing the establishment of cell-based therapies as a new pillar of medicine.

 

 

California Academy of Sciences Fellow:

 

Alison Gould, Ph.D. Alison earned her Ph.D. from the University of Michigan in Ecology and Evolutionary Biology where she studied theevolutionary ecology of a bioluminescent symbiosis between a coral reef fish and a luminous bacterium in the Vibrio family. Having established the foundational context with which to study this association at a more mechanistic level, she is currently developing this highly specific, binary association as a new model with which to disentangle the complex mechanisms regulating our gut microbiome. In partnership with the California Academy of Sciences, Alison will study this bioluminescent symbiosis to determine how host-microbe specificity is established and maintained from the broad evolutionary scale down to the molecular level, identifying critical pathways involved in symbiont recognition, integration, and persistence within a host.

 

Physician-Scientist Scholar Program: The PSSP was established by the UCSF School of Medicine in partnership with the clinical departments to identify and support young physician/scientists who engage in medical practice and have shown exceptional promise to launch an independent laboratory research program, like UCSF Sandler Fellows. Information on these Fellows can be found here.