Lawrence Lee

University of California, San Francisco
Program in Biological and Medical Informatics
Cohen Lab

Contact Info:

Address UCSF Genentech Hall MC 2240
600 16th St.
San Francisco, CA 94143-2240
Email lawrence (at) cmpharm.ucsf.edu
Phone (415)502-5649

Interests:

I am interested in how functional protein information found in biomedical literature can be identified, extracted, and processed on a computational level. As the volume of scientific literature increases - and publications move towards open access formats - an unprescedented amount of processable information about protein function becomes available. While domain experts in certain protein families or disease systems read and assimilate all there is to know about their area of interest, identifying publications of interest and reading them takes an inordinate amount of time. Information retrieval and extraction systems can help identify articles of interest and extract relevant information in a fraction of the time, albeit in a less accurate manner.

Protein point mutations are an easily accessible type of functional protein information. Their regulararity in format and representation, mapping to protein sequences, and utility in exporing protein function make point mutations an ideal type of extractable information. My research focuses on:

  1. Identifying and extracting protein and DNA mutations from biomedical literature.
  2. Associating protein point mutations to their protein of origin.
  3. Identifying sentences which describe a functional protein change due to a point mutation.
  4. Extracting the functional changes.

Publications:

  1. Lee LC, Horn F, Cohen FE (2007) Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association. PLoS Comput Biol 3(2): e16 doi:10.1371/journal.pcbi.0030016
  2. Lee LC, Cohen FE (2008) Using Dependency Tree Kernels in Support Vector Machines to Identify and Extract the Functional Effects of Point Mutations (in preparation)

Presentations:

  1. NLM Training Conference, 6/2007 | PDF

Posters:

  1. Pacific Symposium Biology, 1/2007 | PDF
  2. NLM Training Conference, 7/2006 | PNG
  3. Intelligent Systems on Molecular Biology, 8/2003 | PDF

Curriculum Vitae: PDF | TXT