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 factors 19 Tony Chun Mills Plans to prensent a poster/sent an email to send me the title of poster 20 Xuefang Zhao Mills VaLoR: a high-speed validation approach for structural variation using long-read sequencing 21 Craig Biwer Najarian Persistent Homology for Signal Processing: Application in Diet Efficacy 22 Negar Farzaneh Najarian Automated Abdominoprlvic Traumatic Injury/Decision Support and Severity Assessment 23 Andy Kong Nesvizhskii MSFragger: Fast and comprehensive peptide identifications through index-based database search 24 Gilbert Omenn Omenn Proteomics, Bioinformatics & Splice Isoforms 25 Arushi Varshney Parker Stretchy, super, HOT, broad enhancers and the genetics of gene expression regulation 26 Peter Orchard Parker "Integration of genetic and epigenetic signals in a rat model for running capacity" 27 Ricardo D'Oliveira Albanus Parker Information Theory Analyses of Chromatin Accessibility Predict Transcription Factor Binding and Residence Time 28 Yasuhiro Kyono Parker Characterizing Enhancer Activity of Genetic Variants Associated with Type 2 Diabetes Using Massively Parallel Reporter Assay 29 Marlena Duda PIBS Prioritizing autism candidate genes through functional relationship networks 30 Zhengda Li Qian Incoherent Input Increases the Robustness of Biological Oscillators 31 Laura Seaman Rajapakse High-resolution mapping of chromosomal aberrations in the cancer nucleome by chromosome conformation capture 32 Brooke Wolford Willer Using related family members to improve power of Type 2 diabetes GWAS in HUNT data 33 Wei Zhou Willer Improving power of association tests using genotypes imputed from different reference panels 34 Ming Lin Ye Lab Selecting Candidate Clinical Variables to Identify MCI Converters: Application of Big Data Analytical Approaches to NACC Data 35 Wallace Chan Y. Zhang (BC) Development of Ligand Profile for Virtual Screening of G Protein Coupled Receptors 36 Chengxin Zhang Zhang/Freddolino Structure-based Gene Ontology Prediction of Microbe Proteins DEPARTMENT OF COMPUTATIONAL MEDICINE & BIOINFORMATICS RETREAT 2016

FRIDAY, September 30

2:45pm – 3:45 pm Research Presentation Session #1 – Egret/Tern Moderator: Gil Omenn

2:45pm Peter Freddolino

3:05pm Philip Andrews

3:25 pm Alan Boyle

3:45pm – 4:15 pm Welcome and Departmental Overview – Eagle/Heron Presentation of Student Awards and Faculty Teaching Award Brian Athey SNACK: The Big Dipper

4:15pm – 4:45 pm New Student Introduction – Egret/Tern Margit Burmeister

4:45pm – 5:30 pm BREAK and CHECK-IN

5:30pm – 6:30 pm Keynote Address – Egret/Tern “Shape, Entropy and Emergence” Sharon Glotzer: John W. Cahn Distinguished University Professor of Engineering, and Stuart W. Churchill Collegiate Professor of Chemical Engineering

6:30pm – 8:00 pm DINNER: The Lakeside Buffet – Eagle/Heron

8:00pm – 9:30 pm Poster Session I (even numbered posters only) – Eagle/Heron

9:30pm – 11:30 pm Bonfire: Smore’s, Sodas, Beer and Wine – Firepit East (Wetlands)

Department of Computational Medicine and Bioinformatics SATURDAY, October 1

7:00am – 8:00 am 5K run/walk with Dr. Indika Rajapakse Please meet at the 3 flags in the front of the building

8:00am – 9:00 am BREAKFAST: The Mohican Buffett – Eagle/Heron

9:00am – 10:00 am Research Presentation Session #2 - Egret/Tern Moderator: Indika Rajapakse

9:00 am Gil Omenn

9:20 am Gerry Higgins

9:40 am Yang Zhang

10:00am – 12:00pm RECREATION: golfing, swimming (indoor pool), fitness center, hot tubs, saunas, outdoor playground, horseshoes, shuffleboard, game room, tennis courts, sand volleyball courts, basketball courts, indoor racquetball/wallyball courts, hiking/biking trails, nature center, bike rentals, pickle ball courts and massage therapy (by advance appointment only)

12:00pm-1:30 pm LUNCH: Executive Box Lunch – Eagle/Heron

1:30pm – 3:00 pm RECREATION: see above

2:30pm – 3:00 pm SNACK: The Sweet and Salty – Eagle/Heron

3:00pm – 5:00 pm (Students) Alumni Career Panel – Egret/Tern

Jayson Falkner Staff Engineer, Pacific Biosciences

Artur Veloso Investigator, Novartis Institutes for BioMedical Research

3:00pm – 5:00 pm Predictive Index Workshop for Faculty and Staff - Eagle/Heron Jennifer Bryant: Management Consultant & Client Service Coordinator ADVISA

5:00pm – 6:00 pm Research Presentation Session #3 - Eagle/Heron Moderator: Gerry Higgins

5:00 pm Jeff Kidd

5:20 pm Maureen Sartor

5:40 pm Oliver He

6:15pm – 7:30 pm DINNER: Maumee Bay Grill Buffet – Eagle/Heron

7:30pm – 9:30 pm Poster Session II (odd numbered posters only) - Eagle/Heron

9:30pm – 11:00 pm Student-led Social activities – Egret/Tern SNACK: Quick Time Out

Department of Computational Medicine and Bioinformatics

SUNDAY, October 2

7:30am – 9:00 am BREAKFAST and CHECKOUT: Sunrise Continental - Egret/Tern

9:00am – 10:30 am Diversity Workshop “The Bonus Logics: How Diversity Improves Performance” – Egret/Tern Scott Page: Leonid Hurwicz Collegiate Professor of Complex Systems, Political Science, and Economics

10:30am – 11:50 am Research Presentation Session #4 – Egret/Tern Moderator: Alan Boyle

10:30 am Ming Lin

10:50 am Qiong Yang

11:10 am Yuanfang Guan

11:50am – 12:10 pm Closing Remarks/Award Presentations – Egret/Tern Poster Awards and 5K Winners Presentation Brian Athey

Department of Computational Medicine and Bioinformatics