Spencer Bliven Nordstrasse 313 Zürich 8037 Switzerland Mobile (CH): +41 79 172 77 07 Mobile (US): +1 425 503 1042 Email: [email protected] Skype: spencer.bliven

Personal Information • Birthdate: 22 May 1986 • Nationality: United States of America • Residency: Zürich, Permit B • Marital Status: Married, no children Education PhD in , September 2009–Present University of California, San Diego (San Diego, CA) BS in Computer Science and Biochemistry, September 2004–March 2009 University of Washington (Seattle, WA) Study Abroad, September 2007–August 2008 Eidgenössische Technische Hochschule (Zürich, CH) High School Diploma, June 2004 Newport High School (Bellevue, WA)

Employment History Graduate Student Philip Bourne, Skaggs School of and Pharmaceutical Sciences, UCSD September 2009–Present My research with Dr. Bourne focuses on computational methods for analyzing protein structure. I have developed structural comparison methods for detecting circular permutations and internal symmetry. Other research focuses on applying computational analysis globally over the to gain insights on the nature of fold space and the relationship between protein structure and function. Before joining the Bourne lab in 2011, I was involved in several research projects with UCSD faculty: Pavel Pevzner (mass spectrometry), Pat Jennings and Jose Onuchic (molecular dynamics), Mike MacCoss (mass spectrometry & crosslinking), and Virgil Woods (hydrogen-deuterium exchange). Guest Scientist Guido Capitani, Paul Scherrer Institute, Switzerland February 2014–Present I am currently located in the Laboratory of Biomolecular Research at PSI. I collaborate with Dr. Capitani's group on protein complexes and their EPPIC server for interface prediction while continuing my research with Dr. Bourne. Senior Thesis Baker Lab, UW Biochemistry September 2008–August 2009 David Baker's structural biology research centers around the Rosette program for protein structure prediction and design. I improved Rosetta's handling of disulfide bonds and used this capability to design disulfide-stabilized proteins.

Spencer Bliven - Résumé - page 1 Lab Intern Hilvert Group, ETHZ Biochemistry July 2008–August2008 I modified an artificial protein to recover activity in yeast. This involved excising a specific portion of the DNA and doing appropriate controls and analysis to verify that no mutations where introduced. Finally I sequenced the entire gene and transformed yeast with the modified protein. Throughout the project, I carried out standard procedures in E. coli and yeast such as cell culture, PCR, and gel electrophoresis. Undergraduate Researcher Children's Hospital/UW Dept. Biomedical and June 2007–August 2007 Working under Eugene Kolker, I contributed to the development of a standard for high throughput proteomics. Scripts I developed allowed the selection of proteins for the standard. I was also presented with a broad overview of informatics. The summer culminated in a formal presentation of my research. Software Intern Exbiblio July 2006–January 2007 I contributed to this company's Mac software. I worked on both the GUI and underlying USB drivers. I used Cocoa extensively, as well as the IOKit framework. Publications • Douglas Myers-Turnbull, Spencer E Bliven, Peter W Rose, Zaid K Aziz, Philippe Youkharibache, Philip E Bourne, Andreas Prlic. “Systematic detection of internal symmetry in proteins using CE-Symm.” Submitted to J Mol Biol (2013) • Andreas Prlic, Spencer Bliven, Peter Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard Holland, Gediminas Rimša, Michael L. Heuer, H. Brandstätter–Müller, Philip E. Bourne, and Scooter Willis. “BioJava: an open-source framework for bioinformatics in 2012.” Bioinformatics (2012) 28(20), 2693–2695. [PMID 22877863] • Spencer Bliven and Andreas Prlic. “Circular Permutation in Proteins.” PLoS Comput Biol (2012) 8(3): e1002445. [PMID 22496628] • Andreas Prlic, Spencer Bliven, Peter W Rose, Wolfgang F. Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne. “Precalculated Protein Structure Alignments at the RCSB PDB website.” Bioinformatics (2010) vol. 26 (23) pp. 2983-2985. [PMID 20937596] Technical Skills • Programming: Java, C, Python, Objective-C, C++, Matlab • Web Development: HTML, PHP, CSS, JavaScript • Data Structures and Algorithms • Database Architecture • BioJava contributor Areas of Study • Computational Structural Biology • Protein evolution • Molecular Dynamics • Proteomics and Mass Spectrometry • Machine Learning • Statistics • Protein Structure Prediction • Protein Crosslinking • Hydrogen-Deuterium Exchange Additional Qualifications • Proficient in German • Member of the International Society for Computational Biology

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