Vicky Choi Assistant Professor Department of Computer Science Virginia Tech Office: KnowledgeworkII 2222 Phone: (540) 231-2919; Fax: (540) 231-6075 Email: vchoi@(virginia tech's email address)

Research Interest:

Quantum Computation. Design, analysis and implementation of algorithms in bioinformatics, computational biology, computational chemistry, computational geometry, and discrete mathematics.

Teaching:

• Spring 2009: CS4104 Data and Algorithm Analysis, CS6104 Quantum Computation
• Fall 2006: CS5124 Algorithms in Bioinformatics
• Spring 2006: CS5984 Algorithms in Structural Bioinformatics
• Fall 2005: CS5114 Theory of Algorithms
• Spring 2005: CS6104 Algorithms in Structural Bioinformatics
• Fall 2004: CS4104 Data and Algorithm Analysis

Current Research on Quantum Computation:

• Minor-Embedding in Adiabatic Quantum Computation.
  • Minor-Embedding in Adiabatic Quantum Computation: I. The Parameter Setting Problem. Quantum Information Processing, Volume 7, Number 5, 2008, page 193 -- 209.
• Spectral Gaps in Adiabatic Quantum Computation (with Mohammad Amin).
  • First Order Quantum Phase Transition in Adiabatic Quantum Computation. arXiv:quant-ph/0904.1387.

Some Earlier Work:

Microarray Data Analysis using Galois (Concept) Lattice:

• Faster Algorithms for Constructing a Galois/Concept Lattice. Presented at SIAM Conference on Discrete Mathematics 2006, University of Victoria, Canada. [(pdf)](arXiv:cs.DM/0602069)
• Microarray Data Analysis (with Reinhard Laubenbacher, Karen Duca, Vy Lam and Yang Huang) [(pdf)]. Presented at DIMACS Workshop on Clustering Problems in Biological Networks, Piscataway, NJ, May 9--11, 2006. APBC 2007. Journal of Bioinformatics and Computational Biology, Vol 6, No.1, 2008.

Protein Small-Molecule Docking and Conformation Analysis:

• V. Choi. Yucca: An efficient algorithm for small molecule docking. Chemistry and Biodiversity, Issue 11, 2005, pp1517 -- 1524. [preprint(pdf)] Presented at the Symposium on Computational Methods in Drug Design, Switzerland, 2005. [presentation(ppt)]
• V. Choi. On Updating Torsion Angles of Molecular Conformations. DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition, June 13-14 2005. Journal of Chemical Information and Modeling (formerly JCICS) 46 (1), 2006, pp438 -- 444. [preprint(pdf)] [presentation(ppt)]

Sequence Assembly of the Human Genome

• BARNACLE's assembly of December 2001 freeze of the human genome
• The Sequence and Assembly of Highly Duplicated Regions in the Human Genome. Genome Sequencing & Biology meeting at Cold Spring Harbor Laboratory 2002.  
• Barnacle: An Assembly Algorithm for Clone-based Sequences of Whole Genomes. Gene,  320, 165-176, 2003.