Experience

Software Engineer, Academia.edu, September 2013 - Present

• Full Stack Development, wrote and rewrote multiple major features.
• Worked on product, design, recruiting, interviewing, and hiring.

Co-Founder, Plasmyd.com, October 2011 - September 2013

• Acquired by Academia.edu.
• K5 Launch, Winter 2012.

Graduate Research Assistant, Briggs Lab, Sept 2011 - Present

• Developed a novel protein quant method using mass spec data.
• Wrote the Maize Protein Atlas.

Intern, Google Summer of Code, Su Lab, Summer 2012
Genelist storage system and enrichment score computation engine.

• Developed a RESTful API to for genelists.
• Parallelized enrichment score calculations for statistical tests.

Intern, NSF REU, Ware Lab, Summer 2011
Maize De Novo Assembly and Annotation in the Cloud

• Experimented with de novo assembly using three assemblers.
• Assemblies were run using a resources on Amazon Web Services.
• Determined the “best” assembler and evaulated AWS pricing.

Undergraduate Research Assistant, Saier Lab, Sept 2010 - Jun 2011

• Developed methods and software to run mass scale comparisons of known transport protein families by creating an in-house distributed system.

Intern, Calit2 Summer Scholarship, Wilfred Li, Summer 2009

• Developed a COVISE plugin for the Tiled Display Wall and Cave Automatic Virtual Enviroment using OpenSceneGraph to display simulation results in real time.

Undergraduate Research Assistant, Wilfred Li, Sept 2008 - Oct 2010

• In silico discovery of small molecule inhibitors of influenza hemagglutinin using computer aided drug discovery.
• Analysis of molecular dynamics simulations on multiple subtypes of hemagglutinin.

Intern, PRIME, Wilfred Li, Summer 2008
Discovery of small molecule inhibitors of H5N1

• Conducted molecular docking and virtual screening experiments to find a small molecule inhibitor for influenza H5N1 subtype in Beijing, China.

Undergraduate Research Assistant Ryan Lab, Sept 2007 - Mar 2008

• Optimization of cellular growth protocol of Organ of Corti cells.

Noteable Open Source Contributions

• KEGG REST Module, Biopython
• Genelist Enrichment Score and Calculation Engine, GSoC 2012

Notable Projects

GraphTV

Visualize IMDb ratings of any TV series. Featured in Wired, Gizmodo, AV Club, Flowing Data, Fast Company, Time, and others. A v2 of this site is "coming soon".

Tessellate (Code)

Triangles are my favourite shape
Three points where two lines meet
∆ (Alt-J) - Tessellate

Generate tessellated equilateral triangles with pleasant colors onto a canvas. Used to generate the landing graphic above as well as the dividers.

What Would PG Do?

Currently defunct. Search all of Paul Graham's essays and comments on Hacker News for startup related advice. Got called out on TechCrunch and Inc for making something so stupid.

UI Styleguides (Code)

A curated list of UI styleguides. At Academia.edu, we were trying to come up with a reference of design patterns and UI components to standardize on. This is a list of companies who have made beautiful, public references that I often draw inspiration from.

hypepy

Hypepy (pronounced hyphy) is an python wrapper around Hype Machine. Has support to fetch playlists and related metadata, but I mostly use it to download music from Hype Machine. Adds metadata and album art so it shows a nice image on my phone.

See more open source projects on Github.

Publications

JW Walley, Z Shen, R Sartor, KJ Wu, J Osborn, LG Smith, SP Briggs. Reconstruction of protein networks from an atlas of maize seed proteotypes. PNAS. 2013, 110 (49), E4808-E4817. 10.1073/pnas.1319113110.

Newhouse, E.I., D. Xu, P.R.L. Markwick, H.C. Pao, K.J. Wu, R.E. Amaro, M. Alam, J.A. McCammon, P.W.Arzberger, W.W. Li. Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective. J. Am. Chem. Soc., 2009, 131 (47), pp 17430–17442. 10.1021/ja904052q.

Education

M.S., Biology, In Progress
University of California, San Diego

B.S., Biochemistry and Cell Biology, June 2011
University of California, San Diego

B.S., Computer Science, June 2011
University of California, San Diego

Teaching

Biology

• BIBC 103. Biochemical Techniques
  Lara Soowal. Spring 2012

• BICD 100. Genetics
  Debbie Yelon. Winter 2011

• BILD 10. Fundamental Concepts of Biology
  Par Towb. Winter 2008

• BILD 3. Organismic and Evolutionary Biology
  Christopher Wills. Spring 2010

Computer Science

• CSE 3. Fluency in Information Technology
  Gary Gillespie. Winter 2010, Spring 2010

• CSE 5A. Introduction to Programming
  Gary Gillespie. Spring 2010; Susan Marx. Summer 2010

• CSE 12. Basic Data Structures and Object-Oriented Design
  Gary Gillespie. Fall, Winter, Spring, Summer 2009, Winter 2010

• CSE 15L. Software Tools and Techniques Laboratory
  Charles Elkan. Fall 2010

Graduate Coursework

• PHYS 244. Parallel Computing. (Michael Norman)
• BGGN 216. Graduate Biostatistics. (Raffi Aroian)
• BGGN 227. Plant Postgenomics & Systems Biology. (Julian Schroeder)
• PHARM 201. Structural Bioinformatics. (Philip Bourne)
• CSE 280A. Advanced Topics in Computational Molecular Biology (Vineet Bafna)
• CSE 181. Molecular Sequence Analysis. (Pavel Pevzner)
• CSE 182. Biological Data Analysis. (Vineet Bafna)
• CSE 184. Computational Molecular Biology. (Wei Wang)
• BENG 183. Applied Genomic Technologies. (Trey Ideker)

Interests

Rubik’s Cubing

• Fastest Solve of 15.60s. Top 100 in America in 2006 and 2007.
• Vice President, Rubik’s Cube Club at UCSD, 2008 - 2010

Photography

Staff Photographer, The Guardian (Campus Newspaper), 2009 - 2011

• Photographer for the largest student publication on campus. Photographed various events and submitted photos for publication.

Photographer and Owner, Kevin Wu Photography

• Freelance wedding, portrait, and event photographer.