CZ Biohub Platform and Group Leaders

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Emily Crawford, Ph.D. 

Scientist II, Infectious Disease Initiative
emily.crawford@czbiohub.org

Crawford carried out her Ph.D. thesis research in Jim Wells' lab at UCSF, where she studied the evolution of caspase activity in the programmed cell death of a wide range of metazoans. She developed DegraBase, a database of proteolysis in healthy and apoptotic human cells. As a post-doctoral fellow in Joe DeRisi's lab at UCSF, she devised CRISPR/Cas9-based tools for depleting abundant sequences and enriching rare sequences in next-generation sequencing libraries. As a Project Leader at CZ Biohub, Crawford is developing Cas9-based methods to diagnose infectious diseases and to detect the presence of rare genes that cause resistance to antibiotics and other drugs. She is working closely with physicians at UCSF's hospitals to enable them to track, understand, and control deadly drug-resistant infections.

Spyros Darmanis, Ph.D.

Group Leader, Cell Atlas Initiative
spyros.darmanis@czbiohub.org

Darmanis carried out his Ph.D. thesis research in Ulf Landegren's laboratory at Uppsala University, where he developed high-performance multiplexed protein assays and applied them to identify putative protein biomarkers that could serve as early diagnostic indicators of cancer and other diseases. As a postdoctoral fellow in Stephen Quake's laboratory at Stanford, he carried out single-cell protein and RNA analyses to characterize the diversity of cell types in adult and fetal human brain. At CZ Biohub, he is developing tools to study different molecular entities in single cells in high-throughput and cost-effective ways. He plans to use these tools to study the heterogeneity of human tumors and their interactions with the tumor microenvironment.

Rafael Gómez-Sjöberg, Ph.D.

Director of Bioengineering
rafael.gomez@czbiohub.org

Gómez-Sjöberg obtained a Ph.D. in Electrical and Computer Engineering at Purdue University, where he developed a microfabricated sensor of bacterial metabolism for rapid detection of bacterial contamination in liquid samples. After carrying out postdoctoral work on microfluidics at Caltech and Stanford, he led a microfluidics lab at Lawrence Berkeley National Laboratory. At Quanticel Pharmaceuticals (later Celgene Quanticel Research), he designed and built instruments for isolating single cells from very small cell samples and managed a single cell analysis and sequencing platform. At CZ Biohub, Gómez-Sjöberg and his team are developing cutting-edge optical, electronic, and microfluidic instrumentation to support the work of the Cell Atlas Initiative, the Infectious Disease Initiative, and other research initiatives. A key goal is to proceed swiftly from concept or prototype to robust instruments that enable novel large-scale data acquisition.

Leslie Goo, PH.D., M.P.H.

Group Leader, Infectious Disease Initiative
leslie.goo@czbiohub.org

Goo obtained an MPH in Epidemiology/International Health at the University of Michigan, followed by a Ph.D. at the University of Washington’s Pathobiology Program, where she focused on the development of neutralizing antibodies and their role in preventing HIV transmission. As a postdoctoral fellow at NIH/NIAID, Goo studied the molecular and structural determinants of antibody recognition of flaviviruses and alphaviruses. At CZ Biohub, her research focuses on deconstructing the polyclonal antibody response to antigenically diverse viruses. Goo's overall goal is to inform immunogen design and vaccination strategies by understanding the mechanisms and outcomes of virus-antibody interactions.

Greg Huber, Ph.D.

Senior Biohub Fellow, Theory Group
greg.huber@czbiohub.org

Huber is a biological physicist with a background in statistical mechanics and soft-matter physics.  Prior to joining CZ Biohub, he was a professor in the Physics Department at UC Santa Barbara, and Deputy Director of the Kavli Institute for Theoretical Physics (KITP).  Not only is KITP an international center for theoretical physics, it is a center for forging new ties between Biology and Physics, which was one of Huber’s main objectives during his years there.  Since earning his Ph.D. from Boston University in the group of H.E. Stanley, he has researched and taught at the Niels Bohr Institute (University of Copenhagen), University of Arizona, University of Chicago, University of Connecticut, and University of Massachusetts, and he has worked on a range of problems from phase transitions and turbulence, to how bacteria swim. As one of the organizers of a hub in the New England states (the New England Complex Fluids workshops — www.complexfluids.org), Huber saw ideas from physics, mathematics, engineering and material science regularly and successfully applied to biological and biomimetic systems.  At CZ Biohub, Huber is excited to start a world-class Theory group, with the aim to support the Human Cell Atlas and other Biohub initiatives, as well as to chart completely new directions to understand the complexity of cellular architectures and dynamics through physical and mathematical theory.  Research areas include: physical models of cellular organelles (architecture, activity & interactions); modeling of cytoskeletal and organelle networks in the cell; models of molecular ensembles; protein-protein correlations and localization; general stochastic models of dynamics (synchronization, oscillations, waves, etc.) in biological matter; statistical mechanics of proteomic states.

Jim Karkanias

Vice President, Data Science and Information Technology
jim.karkanias@czbiohub.org

Karkanias' background spans science (neuroscience), engineering (bioengineering, code development), technology (neural nets, machine learning, robotics) and business (founder of a software startup in the 90s and then head of clinical operations for the human health division at Merck). He held the role of Partner at Microsoft for the past decade, leading Program Management for Information Management and Machine Learning in the Cloud + Enterprise Division. At CZ Biohub, and in collaboration with partners at Berkeley, Stanford, UCSF, and the Chan Zuckerberg Initiative, Karkanias aims to build a world-class Data Science team to help drive and support advances in bioinformatics, computational biology, image processing, and next generation analytics.

Amy Kistler, Ph.D., M.P.H.

Group Leader, Infectious Disease Initiative
amy.kistler@czbiohub.org

Kistler received her Ph.D. degree in Christine Guthrie's lab at UCSF, where she focused on pre-mRNA splicing in yeast. She then pursued an MPH in Epidemiology at Berkeley to explore her broader interests in infectious disease and global health. As an Investigator in Virology at Novartis, Kistler led a viral pathogen discovery group and an Ebola virus antiviral drug development effort. At CZ Biohub, she is developing reagents and pipelines to enable rapid comparative analyses across viral families and orders to elucidate their basic biology, replication mechanisms, and potential drug targets. In parallel, Kistler will participate in pathogen detection and rapid response efforts.

Manuel Leonetti, Ph.D.

Group Leader, Cell Atlas Initiative
manuel.leonetti@czbiohub.org

Leonetti received his Ph.D. from Rockefeller University. A student in Rod MacKinnon’s lab, he used X-ray crystallography and electrophysiology to study how ion channels are regulated by calcium, voltage, and pH. As a postdoctoral fellow with Jonathan Weissman at UCSF, he developed high-throughput CRISPR methods to precisely insert fluorescent and affinity tags into human genes. At CZ Biohub, Leonetti and his team are developing tools that make it possible to observe proteins in unperturbed living cells and to easily isolate cellular components for biochemical analysis.  Their main effort is to use CRISPR genome engineering technologies to insert GFP directly into human genes to study the corresponding proteins in their native cellular context.

Andrew May, D.PHIL.

Senior Director of Genome Engineering
andy.may@czbiohub.org

After receiving a D.Phil. in Molecular Biophysics from the University of Oxford, May was a Wellcome Trust International Postdoctoral Fellow at Stanford University. He led development teams in single-cell genomics, sequencing, and structural proteomics at Fluidigm before becoming Chief Scientific Officer at Caribou Biosciences, where he built and led the scientific team focused on developing CRISPR-Cas technologies. At CZ Biohub, May is combining single-cell resolution analytical methods with genome-editing in primary cells and tissues to understand complex multicellular populations. He is also developing technologies to enable genome engineering of specific tissues for the treatment of genetic disorders and is building an engineering framework for the design of cellular devices that sense, monitor, record and treat disease states.

Krista McCutcheon

Scientist II, Antibody Discovery, Infectious Disease Initiative
krista.mccutcheon@czbiohub.org

McCutcheon studied Biochemistry and Genetic Engineering at McMaster University in Ontario and obtained an MSc in Neuroscience at the University of British Columbia, where she researched the cytoskeleton of regenerating skeletal muscle. She then joined the Huntington’s disease research group in the lab of Michael R. Hayden at the Center for Molecular Medicine and Therapeutics. Her next move was to the Bay Area, to focus on inventing and developing antibody therapeutics. Her contributions to fibrosis, infectious disease, autoimmunity and cancer therapeutics are in the clinical pipelines at FibroGen, Genentech, ContraFect and Gilead. At the CZ Biohub, she is profiling B cell repertoires circulating in human blood in order to understand the history, evolution, memory, and molecular determinants of successful and failed immune responses to pathogens. She intends to advance immune screening and diagnostic technologies to allow for the rapid identification of safe and effective antibody therapeutics and to inform the design of recombinant protein vaccines. Overall her work aims to identify and elicit defined specificities of memory B cells to protect diverse human populations around the globe.

Shalin Mehta, Ph.D.

Platform Leader,  Advanced Optical Microscopy
shalin.mehta@czbiohub.org

Mehta received his Ph.D. at the National University of Singapore, where he worked on optics and biological microscopy. His thesis research led to better mathematical models and novel approaches for imaging cellular morphology. As a postdoctoral fellow and staff scientist at the Marine Biological Laboratory in Woods Hole, Mehta developed novel imaging and computational methods for detecting molecular order across a range of scales in living systems. He built an instantaneous fluorescence polarization microscope that revealed the dynamics of molecular assemblies by tracking the orientation and position of single molecules in live cells. As Director of Advanced Optical Microscopy at CZ Biohub, Mehta is developing integrated imaging and computational platforms and participating in the Cell Atlas Initiative, Infectious Disease Initiative, and other collaborative initiatives.

Norma Neff, Ph.D.

Senior Biohub Fellow, Genomics
norma.neff@czbiohub.org

Neff obtained her Ph.D. at the University of California, Berkeley, where she focused on the mechanism of termination of transcription by bacterial RNA polymerase. As a Damon Runyon Postdoctoral Fellow at MIT with David Botstein, she acquired expertise in yeast molecular genetics and subsequently demonstrated that homologous recombination could knockout genes and introduce new sequences.  She then joined the faculty of Memorial Sloan-Kettering where her lab isolated the first yeast protein to have two distinct enzymatic activities associated with the extein and intein created by a protein self-splicing event.  At Stanford, she established a sequencing program for the Stem Cell Institute and played a central role in the development of novel whole genome sequencing techniques, single cell RNA-seq and genome sequencing, and the application of sequencing to liquid biopsy-based diagnostics. As Director of the Genomics Platform at CZ Biohub, Neff manages sequencing services, continues work on single molecule sequencing, and participates in the development of novel diagnostics.

Andreas Puschnik, Ph.D.

Biohub Fellow, Infectious Disease Initiative
andreas.puschnik@czbiohub.org

Puschnik carried out his thesis research in Jan Carette’s lab at Stanford, where he devised haploid and CRISPR genetic screens to identify host factors that are critical for viral infection. He applied these techniques to dengue, Zika, and hepatitis C, which revealed novel antiviral targets. As a Biohub Fellow, Puschnik plans to continue using CRISPR and other powerful genetic screens to study both persistent and emerging viruses as well as cellular pathways important for their virulence.

Loïc Royer, Dr. rer. nat.

Group Leader, Cell Atlas Initiative
loic.royer@czbiohub.org

Royer first studied engineering in his native France and then obtained a master's degree in Artificial Intelligence, specializing in Cognitive Robotics, followed by a Ph.D. in Bioinformatics from the Dresden University of Technology in Germany. He then joined Gene Myers’ lab, first at HHMI's Janelia Farms and then at the Max Planck Institute of Molecular Cell Biology and Genetics, where he developed novel technology at the intersection of computer science and microscopy, including the first adaptive multi-view light-sheet microscope, which he developed in collaboration with Philipp Keller. As a group leader at CZ Biohub, Royer and his team are building ‘discovery machines’ that not only acquire image data, but also perform online processing, instant 3D visualization, adaptive imaging, and automated photo-manipulation. These integrated instruments bring together state of the art optics, robotics, machine learning, and image analysis with the aim of advancing beyond the automation of repetitive tasks and into the realm of actual automated scientific reasoning.

Cristina M. Tato, PH.D., M.P.H.

Associate Director, Rapid Response Team, Infectious Disease Initiative
cristina.tato@czbiohub.org

Tato received a Ph.D. in Immunology from the University of Pennsylvania, where she studied transcription factor families and their downstream signaling pathways. As a post-doctoral fellow (NIH and Schering-Plough Biopharma) she continued using in vivo models of infection and autoimmune inflammation to gain insight into how these transcription factors mediate host resistance to infection, regulate the production of inflammatory cytokines, and affect the development of innate and adaptive immunity. At Stanford's Institute for Immunity, Transplantation and Infection, Tato focused on the tactical application of systems immunology methods for studying human health and disease and for evaluating vaccine efficacy. She joined the Infectious Disease Initiative’s Rapid Response Team at CZ Biohub to plan and implement activities to strengthen global emergency response efforts to epidemics.

Visitors

Emma Lundberg

Emma Lundberg, PhD.

Associate Professor, KTH Royal Institute of Technology, Sweden
Biohub sabbatical visitor, 2017-2018
emma.lundberg@scilifelab.se

At the interface between bioimaging and proteomics, Lundberg's research aims to define the spatiotemporal organization of the human proteome at a single cell and subcellular level, with the goal of understanding how variations and deviations in protein expression patterns can contribute to cellular function, cell type specificity and disease. In particular, she plans to understand how proteins localizing to multiple subcellular compartments or showing single cell variations contribute to increased cellular diversity.
She is also interested in citizen science through integration with massively multiplayer online games. Lundberg's work includes the creation of the Cell Atlas component of the Human Protein Atlas program (http://www.proteinatlas.org/).