[ Recent ] [ Math/Physics ] [ Theses ]

Publications Related to Biology

• Jenkins, P.A. and Song, Y.S. An asymptotic sampling formula for the coalescent with recombination. Annals of Applied Probability, in press, 2009.
  (Technical Report 775, Department of Statistics, University of California, Berkeley, 2009.)
  [ PDF ] [ Tech Report Version ]
• Jenkins, P.A. and Song, Y.S. Closed-form two-locus sampling distributions: accuracy and universality Genetics, 183 (2009) 1087-1103.
  [ Abstract ] [ PDF ] [ Software ]
• Kao, W.C., Stevens, K. and Song, Y.S. BayesCall: A model-based basecalling algorithm for high-throughput short-read sequencing. Genome Research, 19 (2009) 1884-1895.
  [ Abstract ] [ Software ]
• Bhaskar, A. and Song, Y.S. Multi-locus match probability in a finite population: A fundamental difference between the Moran and Wright-Fisher models. Proceedings of ISMB 2009, Bioinformatics, 25 (2009) i187-i195.
  [ Abstract ] [ PDF ] [ Software ]
• Yin, J., Jordan, M.I., and Song, Y.S. Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Proceedings of ISMB 2009, Bioinformatics, 25 (2009) i231-i239.
  [ Abstract ] [ PDF ] [ Software ]
• Song, Y.S., Patil, A., Murphy, E.E., and Slatkin, M. Average probability that a "cold hit" in a DNA database search results in an erroneous attribution. J. Forensic Sciences, 54 (2009) 22-27.
  [ Abstract ]
• Ding, Z., Mailund, T., and Song, Y.S. Efficient whole-genome association mapping using local phylogenies for unphased genotype data. Bioinformatics, 24 (2008) 2215-2221.
  [ Abstract ]
• Griffiths, R.C, Jenkins, P.A., and Song, Y.S. Importance sampling and the two-locus model with subdivided population structure. Advances in Applied Probability, 40 (2008) 473-500.
  [ Abstract ] [ PDF ]
• Lyngsø, R., Song, Y.S., and Hein, J. Accurate computation of likelihoods in the coalescent with recombination via parsimony. Proc. 12th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2008), Lecture Notes in Computer Science 4955, pages 463--477.
  [ Abstract ] [ PDF ] [ Software ]
• Anderson, J.A., Song, Y.S., and Langley, C.H. Molecular population genetics of Drosophila subtelomeric DNA. Genetics, 178 (2008) 477-487.
  [ Abstract ]
• Gusfield, D, Bansal, V., Bafna, V., and Song, Y.S. A decomposition theory for phylogenetic networks and incompatible characters. J. Comput. Biol., 14 (2007) 1247-1272.
  [ Abstract ] [ PDF ]
• Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y. Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. J. Comput. Biol., 14 (2007) 1273-1286.
  (Extended journal version of our RECOMB 2006 conference paper.)
  [ Abstract ] [ PDF ] [ Software ]
• Song, Y.S. and Slatkin, M. A graphical approach to multi-locus match probability computation: revisiting the product rule. Theoretical Population Biology, 72 (2007) 96-110.
  [ Abstract ] [ PDF ]
• Song, Y.S. and Song, J.S. Analytic computation of the expectation of the linkage disequilibrium coefficient r². Theoretical Population Biology, 71 (2007) 49-60.
  [ Abstract ] [ PDF ]
• Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y. Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. Proc. 10th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2006). Lecture Notes in Computer Science 3909, (2006) 231-245.
  [ Abstract ] [ PDF ] [ Software ]
• Stephan, W., Song, Y.S., and Langley, C.H. The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172, (2006) 2647-2663.
  [ Abstract ] [ PDF ]
• Song, Y.S. A concise necessary and sufficient condition for the existence of a galled-tree. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, (2006) 186-191.
  [ Abstract ] [ PDF ]
• Song, Y.S., Lyngsø, R., and Hein, J. Counting all possible ancestral configurations of sample sequences in population genetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, (2006) 239-251.
  [ Abstract ] [ PDF ]
• Song, Y.S. A sufficient condition for reducing recursions in hidden Markov models. Bulletin of Mathematical Biology 68, (2006) 361-384.
  [ Abstract ] [ PDF ]
• Song, Y.S. Properties of subtree-prune-and-regraft operations on totally-ordered phylogenetic trees. Annals of Combinatorics 10, (2006) 129-146.
  [ Abstract ] [ PDF ]
• Lyngsø, R., Song, Y.S., and Hein, J. Minimum recombination histories by branch and bound. Proceedings of Workshop on Algorithms in Bioinformatics 2005, Lecture Notes in Computer Science 3692, (2005) 239-250.
  [ Abstract ] [ PDF ] [ Software ]
• Song, Y.S., Wu, Y. and Gusfield, D. Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event. Proceedings of Workshop on Algorithms in Bioinformatics 2005, Lecture Notes in Computer Science 3692, (2005) 152-164.
  [ Abstract ] [ PDF ]
• Song, Y.S., Wu, Y. and Gusfield, D. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Proceedings of ISMB 2005. Bioinformatics 21, Suppl.1, (2005) i413-i422.
  [ Abstract ] [ PDF ] [ Software ]
• Song, Y.S. and Hein, J. Constructing minimal ancestral recombination graphs. J. Comput. Biol. 12, (2005) 147-169.
  [ Abstract ] [ PDF ]
• Song, Y.S. and Hein, J. Phylogenetics. (Review of Charles Semple and Mike Steel's book.) Systematic Biology 53, No.6 (2004) 1003-1006.
  [ PDF ]
• Song, Y.S. and Hein, J. On the minimum number of recombination events in the evolutionary history of DNA sequences. J. Math. Biol. 48, (2004) 160-186.
  [ Abstract ] [ PDF ]
• Lunter, G.A, Miklós, I., Song, Y.S. and Hein, J. An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J. Comput. Biol. 10, (2003) 869-889.
  [ Abstract ] [ PDF ]
• Song, Y.S. and Hein, J. Parsimonious reconstruction of sequence evolution and haplotype blocks. Algorithms in Bioinformatics, Proceedings of Workshop on Algorithms in Bioinformatics 2003, Lecture Notes in Computer Science 2812, (2003) 287-302.
  [ Abstract ] [ PDF ]
• Song, Y.S. On the combinatorics of rooted binary phylogenetic trees. Annals of Combinatorics 7, (2003) 365-379.
  [ Abstract ] [ PDF ]

Publications in Physics/Mathematics

• Jun Li and Yun S. Song Open string instantons and relative stable morphisms. Geometry and Topology Monographs 8, (2006) 49-72. (Invited reprint of the 2001 paper shown below.)
  [ Link ]
• Jun S. Song and Yun S. Song. On a conjecture of Givental. J. Math. Phys. 45, (2004) 4539-4550.
  [ Abstract ] [ PDF ]
• Stefano Monni, Jun S. Song, and Yun S. Song The Hurwitz enumeration problem of branched covers and Hodge integrals. J. Geometry and Physics 50, (2004) 223-256.
  [ Abstract ] [ PDF ]
• Jun Li and Yun S. Song. Open string instantons and relative stable morphisms. Adv. Theor. Math. Phys. 5, (2001) 67-91.
  [ Link ]
  
• Eva Silverstein and Yun S. Song. On the critical behavior of D1-brane theories. J. High Energy Phys. 03 (2000) 029.
  [ Abstract & PDF ]

Theses

• Ph.D. Thesis. Physics, Stanford University, 2001.
  Topological String Theory and Enumerative Geometry
• B.S. Thesis. Physics, MIT, 1996.
  Differential Renormalization of Supersymmetric Gauge Theories in Superspace