Discovery Centers

UW Medicine

Allen Discovery Center at UW Medicine, Caltech and University of Basel

Cell Lineage Tracing

Scientists have been asking questions about the ancestry and lineage of cells for over a century, but tracing the relationships between generations of cells has faced significant technical challenges. In the past several years, teams led by Jay Shendure, M.D., Ph.D., at the University of Washington, Michael Elowitz, Ph.D., and Long Cai, Ph.D., at Caltech and Alex Schier, Ph.D., at Harvard have created new technologies that take advantage of modern gene editing methods to effectively trace cells as they divide, move and differentiate throughout an organism’s development.

The Allen Discovery Center for Cell Lineage Tracing will use these new technologies and paradigms to develop lineage maps for the zebrafish and mouse – the first global maps of development in any vertebrate. They will also develop genomic systems to record the molecular events that regulate development. The Center’s other investigators are Carlos Lois, Ph.D., research professor of Biology at Caltech, Marshall Horwitz, M.D., Ph.D., UW professor of Pathology, and Cole Trapnell, Ph.D., UW assistant professor of Genome Sciences, Magda Zernicka-Goetz, Ph.D., professor of Biology and Biological Engineering at Caltech, and Kelley Harris, Ph.D., assistant professor of Genome Sciences at UW.

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Jay Shendure, M.D., Ph.D.

Jay Shendure is an Investigator of the Howard Hughes Medical Institute and Professor of Genome Sciences at the University of Washington. His 2005 PhD included one of the first successful demonstrations of massively parallel or next generation DNA sequencing. Dr. Shendure's research group in Seattle pioneered exome sequencing and its earliest applications to gene discovery for Mendelian disorders (e.g. Miller and Kabuki syndrome) and autism; cell-free DNA diagnostics for cancer and reproductive medicine; molecular profiling of single cells; massively parallel reporter assays and saturation genome editing; and whole organism lineage tracing. He is the recipient of the 2012 Curt Stern Award from the American Society of Human Genetics, the 2013 FEDERAprijs, a 2013 NIH Director's Pioneer Award, and the 2014 HudsonAlpha Life Sciences Prize. He serves or has served on the Advisory Committee to the NIH Director, its Working Group on the US Precision Medicine Initiative, and the National Human Genome Research Advisory Council.

Michael Elowitz, Ph.D.

California Institute of Technology

Michael Elowitz is an HHMI Investigator and Professor of Biology, Bioengineering, and Applied Physics at Caltech. He received his Ph.D. in Physics at Princeton in 1999, and did postdoctoral research at the Rockefeller University, before moving to Caltech in 2003. Dr. Elowitz's research has focused on understanding the design principles that allow circuits of interacting genes and proteins to perform their many critical and amazing functions in living cells. In 2000 he showed how a simple circuit of three repressor genes could produce clock-like protein oscillations in individual bacterial cells. This circuit, dubbed the Repressilator, helped start the new field of synthetic biology. He has also focused on the role of randomness, or 'noise', in the operation of genetic circuits, showing how noise originates in cells, how it impacts gene circuit dynamics, and how it can enable cells to control behaviors like differentiation in a probabilistic fashion. His laboratory has discovered new design principles of the Notch signaling pathways, revealed pulsatile operating modes in gene regulation systems, and analyzed the role of noise in the evolution of bacterial development. His laboratory is now bringing synthetic biology approaches to fundamental developmental problems underlying multicellular signaling, memory, and pattern formation. His work has been recognized by several awards, including fellowships from the Packard and Searle foundations, his selection as a Macarthur Fellow, and the HFSP Nakasone Award.

Alex Schier, Ph.D.

Alex Schier obtained his Ph.D. from the Biocenter in Basel, Switzerland, where he studied the transcriptional regulation of homeobox genes in Walter Gehring's lab. He spent his postdoc in Wolfgang Driever's lab in Boston, where he screened for and characterized mutants affecting zebrafish development. He started his lab in 1996 at the Skirball Institute of the New York University School of Medicine and joined Harvard University in 2005, where is the Leo Erikson Life Sciences Professor of Molecular and Cellular Biology and Chair of the Department of Molecular and Cellular Biology. Dr. Schier’s lab has contributed to the understanding of the molecular basis of embryogenesis and behavior and to the development of zebrafish as a model system. Dr. Schier was a McKnight Scholar for Neuroscience, an Irma T. Hirschl Scholar, and an Established Investigator of the American Heart Association and received the Harland Winfield Mossman Developmental Biologists Award of the American Association of Anatomists and the Everett Mendelsohn Award for Excellence in Graduate Student Mentoring. He received a NIH MERIT award in 2016. Members of his lab have gone on to PI positions at leading institutions, including Princeton, Caltech, UCLA, University of Toronto, Yale, NYU School of Medicine, University College London, MPI Dresden, UCSD, IMP Vienna, and MPI Tuebingen.

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