Background


I am currently a PhD student in the Biomolecular Engineering department at UCSC. My studies are focused on the interdisciplinary field of Bioinformatics.



Current Research


-Detection of Protein Interactions Using Electrostatics (Fall 2012 Rotation)

-Symbiotic Horizontal Gene Transfer (Carnegie Institution)

-Tandem Repeat Visualization (Carnegie Institution)



Previous Research


-Repeat Detection Pipeline (SFSU)

-Protein Structure Alignment (SFSU)



Publications


Repeat Detection Pipeline

  • Suen G. et al. The genome sequence of the leaf cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 2011. Feb 10;7(2):e1002007. PMID: 21347285

  • Smith C. R. et al. A draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci USA. 2011, Jan 31. PMID: 21282651

  • Smith C. D. et al. A draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci USA. 2011, Jan 31. PMID: 21282631


Protein Structure Alignment

  • J. W. Kim and R. Singh. “Residue Contexts: Non-Sequential Protein Structure Matching using Structural and Biochemical Features”, in Proceedings of the 6th International Symposium on Bioinformatics Research and Applications (ISBRA), 2010, p77-88.


Genome Annotation

  • Werren et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010 Jan 15;327(5963):343-8. PMID: 20075255



Software


TRAViS - A web-based tool for visualizing tandem repeats

(Under Construction)


Residue Context - Flexible and Non-sequential alignment of protein structures

(Under Construction)




Past and Current Affiliations


University of California, Santa Cruz


Carnegie Institution for Science


San Francisco State University


University of California, Los Angeles


University of California, Davis