One Miramar St 929801 Boyko Kakaradov (650) 387-7631 San Diego, CA 92092-9801 [email protected] EDUCATION 2008 – University of California, San Diego Ph.D. Bioinformatics and Systems Biology (completed first-year lab rotations) 2003 – 2008 Stanford University B.S. Mathematics (3.8 GPA in major) M.S. Computer Science (Artificial Intelligence and Computational Biology, 4.0 GPA) with Distinction in Research (M.S. thesis advisors: Daphne Koller, Russ Altman) PEER REVIEWED JOURNAL PUBLICATIONS 2009 A Complex-Based Reconstruction of the S. cerevisiae Interactome Haidong Wang, Boyko Kakaradov, Sean R. Collins, Lena Karotki, Dorothea Fiedler, Michael Shales, Kevan M. Shokat, Tobias Walther, Nevan J. Krogan, Daphne Koller; Molecular & Cellular Proteomics. 2005 Chemoselective Covalent Coupling of Oligonucleotide Probes to Self-Assembled Monolayers Devaraj, N. K.; Miller, G. P.; Ebina, W.; Kakaradov, B.; Collman, J. P.; Kool, E. T.; Chidsey, C. E. D.; Journal of the American Chemical Society. 2004 Ultra-Fast Matrix Multiplication: An Empirical Analysis of Highly Optimized Vector Algorithms Boyko Kakaradov; Stanford Undergraduate Research Journal. PEER REVIEWED CONFERENCE PROCEEDINGS 2007 “Identifying Protein Complexes in Saccharomyces cerevisiae”; Boyko Kakaradov; Haidong Wang; Sean Collins; Nevan Krogan; Daphne Koller; BCATS, Stanford. 2006 “Effect of Colony Size and Surrounding Substrate on Corals Experiencing a Mild Bleaching Event on Heron Island Reef Flat”; Juan Carlos Ortiz; Zubin Agarwal; Boyko Kakaradov; Rahul Vasavada; ACRS: Australian Coral Reef Society. Mission Beach, Queensland, Australia. 2006 "ButterflyNet: A Mobile Capture and Access System for Field Biology Research"; Ron B. Yeh; Chunyuan Liao; Scott R. Klemmer; Francois Guimbretiere; Brian Lee; Boyko Kakaradov; Jeannie Stamberger; Andreas Paepcke; CHI: ACM Conference on Human Factors in Computing Systems. Montreal, Quebec, Canada. 2004 “Clicking Functionality to Azide-Terminated Monolayers on Silica Surfaces” Boyko Kakaradov; Neal Devaraj; Chris Chidsey; SURP: Symposium of Undergraduate Research in Progress. Stanford University RESEARCH AND TEACHING EXPERIENCE 2009 - Research Assistant, Bioinformatics Program, University of California, San Diego Rotation Advisers: Professors Pavel Pevzner and Glenn Tesler Adapted an existing genome assembly tool to the problem of transcriptome assembly from RNA-Seq reads of human samples. Proposed the existence and estimated the expression of 63 novel transcripts that would not be captured by mapping to a reference genome/transcriptome. 2008 - Research Assistant, SMARTer Lab, University of California, San Diego Rotation Adviser: Professor Yoav Freund, Collaborator: Dr. Ce Liu (MIT, Microsoft Research) Developing a high-performance system for measuring fluorescent protein dynamics in time- lapse microscopy. Constructed a hierarchical segmentation using adaptive filters trained with RobustBoost in an active learning setting. Currently improving the tracking with SIFTflow. 2008 - Research Assistant, Network Systems Biology Lab, University of California, San Diego Rotation Adviser: Professor Trey Ideker, Collaborator: Professor Stephen Kay Reconstructed a network from time-series expression measurements of arabidopsis thaliana genes specific to the circadian cycle. Currently, expanding my cross-correlation analysis method to the entire genome of a. thaliana and of s. cerevisiae, where validation is easier due to the existence of double knockout results and other high throughput genetic interaction assays. 2006 - 2008 Research Assistant, Stanford Artificial Intelligence Lab, Stanford University Adviser: Professor Daphne Koller 1. Predicted protein-protein interactions using markov network models with approximate inference based on graph cuts (generalized to quadratic pseudo-boolean optimization) 2. Identified protein complexes in Saccharomyces cerevisiae using boosted decision trees for evidence integration and agglomerative clustering for complex identification. Produced high- confidence reference set and collaborative visualization tools for evaluation of predictions. 2006 , 2007 Teaching Assistant, Computer Science Department, Stanford University Course: CS107 Programming Paradigms, Lecturer: Jerry Cain Held weekly office hours and led weekly discussion section for 110 students. 2005 - 2006 Lead Programmer & Web Developer, EveryTrail.net, Stanford, CA Co-founded an outdoor enthusiast online community driven by Google -Maps and -Earth. Designed and implemented a prototype GPS-based trail sharing site in a fast-paced startup environment. Web technologies learned on the fly: AJAX, PHP, MySQL. 2005 - 2006 Research Assistant, Human Computer Interaction Lab, Stanford University Advisers: Professors Scott Klemmer and Ove Hoegh-Guldberg (University of Queensland) Conducted a usability study of ButterflyNet, a novel field biology research browser. Deployed a wireless sensor network along the field research browser to facilitate novel marine biology study of coral bleaching at the Great Barrier Reef with collaborators. 2004 - 2005 Research Assistant, Virtual Human Interaction Lab, Stanford University Advisers: Professor Jeremy Bailenson Created virtual worlds using various tools for content creation (3D objects, face-mapping, 3D sound), project management, and interactive object scripting (C++/Python). Implemented a networked perspective-shifting virtual world that explores social interaction principles in negotiation. Showed link between poor negotiation skills to empathy (in virtual perspective). 2004 Research Assistant, Chidsey Surface Chemistry Lab, Stanford University Adviser: Professor Christopher Chidsey Conducted original research in semiconductor chemistry and molecular electronics. Co- authored an internal technical report titled “Clicking Functionality to Azide-Terminated Self- Assembled Silane Monolayers on Silica Surfaces.” 2003 Computer Science Teacher, Maine School of Science and Mathematics Adviser: Mr. Patrick Farrell Taught the second semester of a Computer Science Fundamentals course based with practice in LISP (Dr. Scheme) programming. Topics included: Induction, Primary Functions, Numerical Calculus, Fractals, and MapReduce. Prepared lectures and facilitated student interaction in the programming lab. Taught and evaluated 15 students. HONORS AND AWARDS 2008 – 2013 National Science Foundation Graduate Research Fellowship 2007 Solon E. Summerfield Scholarship 2005 - 2007 CURIS: Undergraduate Research Internship in Computer Science Three competitive summer research grants 2004 Chemistry Department Summer Research Grant Competitive funding won by individually-designed summer research proposal. 2003 - 2007 MBNA Maine Scholars Program Scholarship 2003 - 2007 M. Alton French Scholarship Fund 2003 U.S. Presidential Award for Excellence .