Biblio

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2009
Johansson, J., M. H. S. Amin, A. J. Berkley, P. Bunyk, V. Choi, R. Harris, M. W. Johnson, T. M. Lanting, S. Lloyd, and G. Rose, Landau-Zener Transitions in an Adiabatic Quantum Computer, , vol. Phys. Rev. B, 80(1), 2009.
Amin, M. H. S., and V. Choi, "First-order quantum phase transition in adiabatic quantum computation", Physical Review A, vol. 80, issue 6, 12/2009.
Choi, V., "Fundamental Algorithmic Problems in Adiabatic Quantum Computation", The 3rd International Workshop on Solid-State Quantum Computing & the Hong Kong Forum on Quantum Control, 12/2009.
2008
Zhu, Q., Z. Adam, V. Choi, and D. Sankoff, "Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution", RECOMB’08, 2008.
2007
Choi, V., C. Zheng, Q. Zhu, and D. Sankoff, "Algorithms enabling extraction of syteny blocks from comparative maps.", The 7th Workshop on Algorithms in Bioinformatics, 2007.
Choi, V., and N. Goyal, "Alogirthmic Approaches to the Identification of Rigid Domains in Proteins", Special issue of Algorithmica on algorithms for processing protein structures, 2007.
Choi, V., "Faster Algorithms for Constructing Galois Lattice", DIMACS book on Clustering Challenges in Biological Networks, 2007.
Choi, V., Y. Huang, V. Lam, R. Laubenbacher, and K. Duca, "Using Formal Concept Analysis for Microarray Data Comparison", The Fifth Asia-Pacific Bioinformatics Conference, APBC2007, 2007.
2006
Choi, V., and N. Goyal, "An Efficient Approximation Algorithm for Point Pattern Matching Under Noise", The 7th International Symposium, Latin American Theoretical Informatics (LATIN 2006), 2006.
Choi, V., "On Updating Torsion Angles of Molecular Conformations", Journal of Chemical Information and Modeling, vol. 46, no. 1, pp. pp438 – 444, 2006.
2005
Choi, V., "YUCCA: An Efficient Small Molecule Docking Algorithm", Chemistry and Biodiversity, vol. 11, pp. 1517 – 1524, 2005.
2004
Choi, V., and N. Goyal, "A Combinatorial Shape Matching Algorithm for Rigid Protein Docking", The Fifteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2004), vol. 3109, pp. pp 285-296, 2004.
Choi, V., P. K. Agarwal, H. Edelsbrunner, and J. Rudolph, "Local Search Heuristic for Rigid Protein Docking", The 4th Workshop on Algorithms in Bioinformatics (WABI 2004), vol. 3240, pp. pp. 218–229, 2004.
2003
Bespamaytnikh, S., V. Choi, H. Edelsbrunner, and J. Rudolph, "Accurate Rigid Protein Docking by Shape Complementarity Alone", Technical Report, Department of Computer Science, Duke University, 2003.
Choi, V., and M. Farach-Colton, "BARNACLE: An Assembly Algorithm for Clone-based Sequences of Whole Genomes", Gene, vol. 320, pp. 165-176, 2003.
2002
Choi, V., J. Bailey, G. Schuler, Z. Gu, P. Li, M. Farach-Colton, and E. Eichler, "The Sequence and Assembly of Highly Duplicated Regions in the Human Genome", Genome Sequencing & Biology meeting , Cold Spring Harbor Laboratory, 2002.
2001
Choi, V., and M. Golin, "Lopsided Trees, I: Analyses", Algorithmica, vol. 31, pp. 240-290, 2001.
Choi, V., and M. Golin, "Lopsided Trees, II: Algorithms and Applications", Technical Report, HKUST, 2001.
Choi, V., and M. Farach-Colton, "A Simple Sequence Assembly Algorithm for the Human Genome", RECOMB Satellite Meeting on DNA Sequence Assembly , 2001.
1996
Choi, V., and M. Golin, Lopsided Trees: Analyses, Algorithms, and Applications, , pp. pages 538-549, 1996.