The GenomeSample Text Scientist Volume 4 Number 1 Autumn 2008 Genome Sciences Welcomes Three New Faculty Members www.gs.washington.edu UW Genome Sciences Dr. Maitreya Dunham Dr. Christine Queitsch Dr. Jay Shendure IN THIS ISSUE: Notes from the Chair 2 Faculty News & Honors 3-4 News & Notes 4-5 New Faculty Members 6-7 Research Highlights 8-9 Student News 10-15 The Genome Scientist is published by the Department of Genome Sciences at the University of Washington. For more information, please visit our website: www.gs.washington.edu the genome scientist 1 Not es From the Chair Genome Sciences is an excit- to identify a person’s individual (rare) mutations. Suc- ing place these days. Three cess here will drop costs to a few thousand dollars per new faculty members have person, opening the way to broad resequencing of cases joined us in the past year, and and controls. Josh Akey, working with Jay, Mike Mac- a fourth will arrive in Decem- Coss and Stan Fields, is analyzing 35 or more diff erent ber. Advances in technology yeast isolates to examine the impact of DNA sequence are opening new avenues to variation comprehensively on mRNAs, proteins and attack problems with a scope metabolites, a tour de force simply unfathomable a few and precision unimaginable years ago. John Stamatoyannopoulos is applying this even just a few years ago. Our next-generation sequencing technology to identify DNa- Bob Waterston new digs in the Foege Build- seI hypersensitive sites (regions of open chromatin) in ing are a delight. These factors genomes from yeast to human. The data are so rich that, combine to attract top notch graduate students and in a collaboration with Stan Fields and Bill Noble, the post-docs, who suff use the place with energy and enthu- individual binding sites of specifi c transcription factors siasm. Let me expand on each of these. are being identifi ed across the yeast genome in a single experiment. Evan Eichler is at the forefront of eff orts As you can read elsewhere in the newsletter, Jay Shen- to develop methods to explore segmental duplications dure and Christine Queitsch joined the department just in the genome and their role in disease. In proteomics, over a year ago, with Jay bringing fi rst-hand knowledge Mike MacCoss and Bill Noble have devised methods that of the latest sequencing technologies, and Christine increase the effi cacy of protein identifi cation by 50% and creating a local green revolution by bringing Arabidop- are pursuing other strategies for still further improve- sis to study fundamentals of phenotypic robustness in ments. Almost half the proteins in yeast grown under the face of genetic variation. Maitreya Dunham arrived one condition can now be identifi ed in a single experi- this past summer, continuing the illustrious line of yeast ment. All this is simply amazing! scientists in the department. She is studying the role of structural rearrangements and other changes in adap- The Foege Building now feels like home. We know who tive evolution as yeast is shifted to new growth condi- resides in what labs and can wander the building on tions. Jim Bruce will move soon from WSU to anchor our autopilot and still end up in the right place. It is a lovely Proteomics Resource at the South Lake Union campus. place to work, with bright, well-laid out labs, spacious Jim is devising methods to use mass-spectrometry to common areas and wonderful views over the water and detail protein-protein interactions. With these additions, - on clear days - of the mountains. But even better, the more than half our faculty will have joined since the layout of the building promotes interactions between formation of the Department, mixing their fresh per- labs, catalyzing new science. The collegiality of the spective with our strong traditions and making the place Department has always been a strong point, but the amazingly vibrant and exciting. Foege Building is raising it to another plane. Apparently the strong sense of community was a major factor in New technologies are transforming how we do science. attracting our fantastic new faculty, and they have only The new generation of DNA sequencing technologies, enhanced it. which Jay helped to bring about, are dropping the costs of DNA sequencing faster than the stock market, and the Of course the newer faculty, the building and the new amount of data obtained in a single run is almost over- technologies are only a part of the story. The Depart- whelming. Jay, along with Debbie Nickerson, is devel- ment thrives because of the talent and hard work of our oping methods to capture the functional regions of the students, post-doctoral fellows and staff . A couple proj- human genome (or indeed any particular regions from ects are highlighted elsewhere in the Newsletter along any genome), thereby vastly decreasing the amount with some selected publications from our students. (and cost) of sequence that needs to be determined continued on page 5 2 the genome scientist Faculty News & Honors Olson Awarded Gruber Genetics Prize Jarvik Selected as Head of UW Medical Genetics Dr. Maynard Olson, Professor of Genome Sciences and of Medicine, Dr. Gail Jarvik, Professor of Medi- has been awarded the 2007 Genet- cine and of Genome Sciences, ics Prize of the Gruber Founda- was selected in 2007 to lead the tion, becoming the third Genome Department of Medicine’s Division Sciences faculty winner in the last of Medical Genetics as the Arno 4 years to be awarded the Gruber G. Motulsky Endowed Professor of prize. Dr. Olson’s original concepts Medicine. Dr. Jarvik is a and technological and experimental innovations played distinguished investigator of the a central role in laying the foundations for the Human genetics of complex disease. Genome Project. Byers Receives March of Dimes Award Horwitz Receives NIH Pioneer Award Dr. Peter Byers, Professor of Medi- Dr. Marshall Horwitz, Professor cine and of Pathology, Adjunct of Pathology and of Medicine, Professor of Genome Sciences, Adjunct Professor of Genome has received the March of Dimes Sciences, has received a 2007 NIH / Colonel Harland Sanders Award, Director’s Pioneer Award, one of given annually to an individual only 12 awards given that year. Dr. whose lifetime body of research, Horwitz will use his Pioneer Award education, or clinical service has funding to chart cell lineages by made a signifi cant contribution to the genetic sciences. tracking mutations in order to better understand how Dr. Byers’ primary clinical and research specialty is inher- stem cells contribute to development and cancer. ited connective tissue disorders. Felsenstein Awarded Green Selected as Darwin-Wallace Medal UW Inventor of the Year Dr. Joseph Felsenstein, Professor of Dr. Philip Green, Professor of Ge- Genome Sciences and of Biology, nome Sciences, has received the has been awarded a 2008 Darwin- Fourth Annual Inventor of the Year Wallace Medal for major advances Award. The award honors a UW in evolutionary biology since 1958. faculty researcher who exempli- The award is presented every 50 fi es the philosophy of technology years and commemorates the transfer by taking their inventions 150th anniversary of the reading from the lab to industrial applica- of the joint Darwin-Wallace paper “On the Tendency of tions. Dr. Green was also recently awarded an honorary Species to form Varieties; and on the Perpetuation of doctorate from the University of North Carolina. Varieties and Species by Natural Means of Selection” at the Linnean Society of London in 1858. Dr. Felsenstein’s Dr. Green’s software has made the sequencing of the research interests include evolution and population three billion pairs in the human genome possible and genetics. represents the most important technical advance in DNA sequencing of the 1990s. The Genome Scientist layout: Brian Giebel questions / comments: [email protected] the genome scientist 3 Faculty News & Honors Thompson Elected to National Academy of Sciences Dr. Elizabeth Thompson, Professor of Statistics and Adjunct Professor of Genome Sciences, has been elected to the National Academy of Sciences. Election to the Academy is considered one of the highest honors that can be accorded a U.S. scientist. Dr. Thompson’s research interest is in the development of methods for inference from genetic data, and particularly from data observed on large and complex pedigree structures. News & Notes 2008 Symposium UW Launches Northwest Institute The Personal Genome: of Genetic Medicine Implications for Medicine The University of Washington has received a $5.3 million This year’s symposium included a community panel grant from the state of Washington’s Life Sciences Discov- discussion, “The Personal Genome: Consequences for ery Fund to support the translation of human genetic re- Society”. The panel discussion was moderated by Dr. search into clinical medicine. The Northwest Institute of Maynard Olson, Professor of Genome Sciences and of Genetic Medicine will be a collaborative eff ort between Medicine, and a pioneer in human genome discoveries. researchers at the UW, Seattle Children’s Hospital Re- Speakers included George Church, Professor of Genet- search Institute, Group Health, and local biotech compa- ics at Harvard Medical School and Director of the Center nies. It will facilitate the design, development and execu- for Computational Genetics; Bill Gates III, Microsoft; Eric tion of translational genetic studies that bridge the gap Lander, founder of The Broad Institute; and Leona Pel- between basic science research and clinical studies. tonen of The Wellcome Trust Sanger Institute. The institute will be led by Dr. Gail Jarvik, Professor of Symposium speakers included : Medicine and Genome Sciences. The leadership team also includes Genome Sciences faculty members Dr. Deb- Dr. George Church, Harvard University orah Nickerson, Dr. Michael Bamshad, and Dr.