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2016 Department Retreat Maumee Bay Lodge and Conference Center, Ohio September 30 – October 2 2016

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2016 Department Retreat Maumee Bay Lodge and Conference Center, Ohio September 30 – October 2 2016 2016 Department Retreat Maumee Bay Lodge and Conference Center, Ohio September 30 – October 2 2016 Keynote Speakers: Sharon C. Glotzer, Ph.D. John W. Cahn Distinguished University Professor of Engineering, and Stuart W. Churchill Collegiate Professor of Chemical Engineering Scott E. Page, Ph.D. Leonid Hurwicz Collegiate Professor of Complex Systems, Political Science, and Economics Featured Events: Introduction of new students & post-doctoral fellows Scientific talks by faculty, posters and students State-of-the-Department address by Dr. Brian Athey, Department Chair Sharon Glotzer Sharon C. Glotzer is the John Werner Cahn Distinguished University Professor of Engineering and the Stuart W. Churchill Collegiate Professor of Chemical Engineering, and Professor of Materials Science and Engineering, Physics, Applied Physics, and Macromolecular Science and Engineering at the University of Michigan in Ann Arbor. She is a member of the National Academy of Sciences and the American Academy of Arts and Sciences, and a fellow of the American Physical Society, the American Association for the Advancement of Science, the American Institute of Chemical Engineers, and the Royal Society of Chemistry. She received her B.S. degree from the University of California, Los Angeles, and her Ph.D. degree from Boston University, both in physics. Prior to joining the University of Michigan in 2001, she worked for eight years at the National Institute of Standards and Technology where she was co-founder and Director of the NIST Center for Theoretical and Computational Materials Science. Professor Glotzer’s research on computational assembly science and engineering aims toward predictive materials design of colloidal and soft matter, and is sponsored by the NSF, DOE, DOD and Simons Foundation. Among other notable findings, Glotzer invented the idea of “patchy particles,” a conceptual approach to nanoparticle design. She showed that entropy can assemble shapes into many structures, which has implications for materials science, thermodynamics, mathematics, and nanotechnology. Her group’s “shape space diagram” shows how matter self-organizes based on the shapes of the constituent elements, making it possible to predict what kind of material—glass, crystal, liquid crystal, plastic crystal, or quasicrystal—will emerge. Glotzer runs a large computational research group of 35 students, postdocs, and research staff, and has published over 200 refereed papers and presented over 300 plenary, keynote and invited talks around the world. She has provided leadership and input on roadmapping for federal granting agencies on many research topics, including simulation-based engineering and science, and three of her reports are among the first six references cited by the Materials Genome Initiative. She serves on several boards and advisory committees of the National Science Foundation, the Department of Energy, and the National Research Council. She is a Simons Investigator, a former National Security Science and Engineering Faculty Fellow, and the recipient of numerous other awards and honors, including the 2016 Alpha Sigma Chi Award from the American Institute of Chemical Engineers, 2014 MRS Medal from the Materials Research Society and the 2008 Charles M.A. Stine Award from the American Institute of Chemical Engineers. Department of Computational Medicine and Bioinformatics Scott Page Scott E Page serves as Leonid Hurwicz Collegiate Professor of Complex Systems, Political Science, and Economics at the University of Michigan and as an external faculty member of the Santa Fe Institute. His research focuses on complex systems and diversity in social systems. He is the author of three books and more than seventy-five research papers in economics, political science, sociology, psychology, philosophy, physics, public health, geography, computer science, and management. He has filmed two video series for The Great Courses, and his online course Model Thinking has attracted over three quarters of a million participants. A frequent public speaker to corporations and government agencies including NASA, Bloomberg, Google, Boeing, the IMF, Genentech, Gilead, the United States Federal Reserve, and Pimco, Scott has also been a featured speaker at The World Economic Forum – Davos and The Aspen Ideas Festival. In addition to his teaching, Scott has consulted with Yahoo! Ford, DARPA, Procter and Gamble, and AB InBev. He has been the recipient of a Guggenheim Fellowship as well as fellowship at the Center for Advanced Studies in the Behavioral Sciences at Stanford. In 2011, he was elected a fellow of the American Academy of Arts and Sciences. Department of Computational Medicine and Bioinformatics Artur Veloso Scott E Page serves as Leonid Hurwicz Collegiate Professor of Complex Systems, Political Science, and Economics at the University of Michigan and as an external faculty member of the Santa Fe Institute. His research focuses on complex systems and diversity in social systems. He is the author of three books and more than seventy-five research papers in economics, political science, sociology, psychology, philosophy, physics, public health, geography, computer science, and management. He has filmed two video series for The Great Courses, and his online course Model Thinking has attracted over three quarters of a million participants. A frequent public speaker to corporations and government agencies including NASA, Bloomberg, Google, Boeing, the IMF, Genentech, Gilead, the United States Federal Reserve, and Pimco, Scott has also been a featured speaker at The World Economic Forum – Davos and The Aspen Ideas Festival. In addition to his teaching, Scott has consulted with Yahoo! Ford, DARPA, Procter and Gamble, and AB InBev. He has been the recipient of a Guggenheim Fellowship as well as fellowship at the Center for Advanced Studies in the Behavioral Sciences at Stanford. In 2011, he was elected a fellow of the American Academy of Arts and Sciences. Department of Computational Medicine and Bioinformatics Jayson Falkner Jayson earned his PhD in 2008 from the University of Michigan. His graduate work was in Phil Andrews lab and the National Resource for Proteomics and Pathways. He focused on tools that enabled working with, sharing and analyzing high-throughput tandem MS/MS proteomics data sets. This work was continued in a start-up funded in part by SBIR grants. Jayson's undergraduate degree was in EEN and CS from the University of Miami, FL. He worked for several years as the CTO of a start-up Java web development company, including helping to design the Java web tier specifications (JavaServer Pages and Servlets) and building the reference API and publishing four books. Post- graduation, he was the CTO of a biotech startup and worked to sell cluster-based MS/MS analysis and targeted MRM quantitation software. He went on to work for Dow AgroSciences with a focus on NGS-based genomics analyses, water and nitrogen use efficiency and building high-throughput plant phenotyping pipelines using greenhouse and field-based automation. He then joined as an early engineer at a Bay Area start-up, Counsyl, leading the wetlab software engineering team, interfacing with the automated lab and supporting NGS-based clinical screens for inherited diseases and prenatal cell-free DNA. Jayson currently works remotely from Ann Arbor, MI, for Pacific Biosciences of California (aka PacBio). A company that designs and sells a high-throughput single-molecule, long- read DNA sequencer. He is a staff engineer with a focus on secondary analyses and improving the tools used by internal groups." Department of Computational Medicine and Bioinformatics RETREAT POSTERS # Author Lab Title 1 Fan Zhang Abecasis FASTQuick: Real-time comprehensive quality assessment of ultra-high-throughput sequence data”. 2 Sai Chen Abecasis New Raremetal: a more efficient and flexible tool for meta-analysis 3 Hye Kyong Kweon Andrews Regulatory Protein Phosphorylation in Dynamic Golgi Biogenesis by Quantitative Phosphoproteomic Analysis 4 Alexandr Kalinin Athey Machine learning based pipeline workflow for 3D cell, nuclear and nucleolar modeling and classification 5 Ari Allyn-Feuer Athey The Pharmacogenomics Informatics Pipeline: An integrative multi-omics platform for variant discovery 6 Christopher Castro Boyle Identifying De Novo Functional Variants in Noncoding Regions of Autism Patients 7 Shengcheng Dong Boyle lab Predicting regulatory SNPs using functional genomic data 8 Sierra Nishizaki Boyle Predicting effects of SNPs and methylation on transcription factor binding affinity 9 Xinqiang Ding Brooks Accelerating Protein-Ligand Docking Using FFTs on GPUs 10 Rucheng Diao Freddolino Searching for anticipatory regulation in E. coli under stress conditions in high-throughput data sets 11 Bryan Moyers G. Zhang De novo gene birth accounts for a large portion of orphan genes 12 Hongyang Li Grant Comparative Structural Dynamic Analysis of G Proteins 13 Shashank Jariwala Grant The Bio3D Project: Interactive Tools for Structural Bioinformatics 14 Hongjiu Zhang Guan A ultra-fast density-assisted estimation- maximisation method to infer tumour subclones from bulk-sequencing data 15 Yaya Zhai Hero 'A multivariate approach to biochronicity pathway analysis’ 16 Zhengting Zou J. Zhang Codon usage affects non-synonymous transition - transversion bias 17 Jedidiah Carlson Li A high-resolution atlas of human germline mutation rates 18 Akima George Mills Gene expression in the developing mouse pituitary gland: long non-coding RNAs and transcription
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