Applied Probability/Statistics and Population Genetics

• Kamm, J.A.*, Spence, J.P.*, Chan, J., and Song, Y.S. Two-locus likelihoods under variable population size and fine-scale recombination rate estimation. Genetics, Vol. 203 No. 3 (2016) 1381-1399.  *These authors contributed equally to this work.
  [ Journal ] [ Preprint ] [ Software: LDpop ]
• Spence, J.P., Kamm, J.A., and Song, Y.S. The site frequency spectrum for general coalescents. Genetics, Vol. 202 No. 4 (2016) 1549-1561.
  [ Journal ] [ Preprint ]
• Sheehan, S. and Song, Y.S. Deep learning for population genetic inference. PLoS Comput Biol, Vol. 12, No. 5 (2016) e1004845.
  [ Journal ] [ Preprint ] [ Software: evoNet ]
• Steinrücken, M., Jewett, E.M., and Song, Y.S. SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes. Bioinformatics, Vol. 32, No. 5 (2016) 795-797.
  [ Journal ] [ Preprint ] [ Software: spectralTDF ]
• Zou, J.Y., Park, D.S., Burchard, E.G., Torgerson, D.G., Pino-Yanes, M., Song, Y.S., Sankararaman, S., Halperin, E., and Zaitlen, N. Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns. PNAS, Vol. 112, No. 44 (2015) 13621-13626.
  [ Journal ]
• Raghavan, M.*, Steinrücken, M.*, Harris, K.*, Schiffels, S.*, ...(94 authors)... , Song, Y.S.^†, Nielsen, R.^†, Willerslev, E.^† Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015). ^† Corresponding authors; * These authors contributed equally to this work.
  [ Journal ] Media Coverage articles
• Terhorst, J. and Song, Y.S. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. PNAS, Vol. 112, No. 25 (2015) 7677-7682.
  [ Journal ] [ Preprint ]
• Živković, D., Steinrücken, M., Song, Y.S., and Stephan, W. Transition densities and sample frequency spectra of diffusion processes with selection and variable population size. Genetics, Vol. 200, No. 2 (2015) 601-617.
  [ Journal ] [ PDF ] [ Preprint ]
• Jenkins, P.A., Fearnhead, P., and Song, Y.S. Tractable diffusion and coalescent processes for weakly correlated loci. Electronic Journal of Probability, Vol. 20, No. 58 (2015) 1-26.
  [ Journal ] [ Preprint ]
• Terhorst, J., Schlötterer, C., Song, Y.S. Multi-locus analysis of genomic time series data from experimental evolution. PLoS Genetics, Vol. 11, No. 4 (2015) e1005069.
  [ Journal ] [ Preprint ]
• Bhaskar, A., Wang, Y.X.R. and Song, Y.S. Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data. Genome Research, Vol. 25, No. 2 (2015) 268-279.
  [ Journal ] [ Preprint ] [ Software: fastNeutrino ]
• Bhaskar, A. and Song, Y.S. Descartes' rule of signs and the identifiability of population demographic models from genomic variation data. Annals of Statistics, Vol. 42, No. 6 (2014) 2469-2493.
  [ Abstract ] [ PDF ] [ Preprint ]
• Steinrücken, M., Bhaskar, A. and Song, Y.S. A novel spectral method for inferring general diploid selection from time series genetic data. Annals of Applied Statistics, Vol. 8, No. 4 (2014) 2203-2222.
  [ Abstract ] [ PDF ] [ Preprint ] [ Software: spectralHMM ]
• Tataru, P., Nirody, J.A., and Song, Y.S. diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinformatics, Vol. 30, No. 23 (2014) 3430-3431.
  [ Abstract & PDF ] [ Preprint ] [ Software: diCal-IBD ]
• Bhaskar, A., Clark, A.G., and Song, Y.S. Distortion of genealogical properties when the sample is very large. PNAS, vol. 111 no. 6 (2014) 2385-2390.
  [ Abstract & PDF ] [ arXiv ]
• Harris, K., Sheehan, S., Kamm, J.A., Song, Y.S., Decoding coalescent hidden Markov models in linear time, Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB), LNBI Vol. 8394, 2014, pp 100-114.
  [ Abstract & PDF ] [ arXiv ]
• Jenkins, P.A., Mueller, J.W, and Song, Y.S. General triallelic frequency spectrum under demographic models with variable population size. Genetics, 196 (2014) 295-311.
  [ Abstract & PDF ] [ Preprint ] Research Highlight by Nature Reviews Genetics
• Sheehan, S.*, Harris, K.*, Song, Y.S. Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach. Genetics, 194 (2013) 647-662.
  *These authors contributed equally to this work.
  [ Abstract & PDF ] [ Ahead of Print ] [ Software: diCal ]
• Steinrücken, M., Paul, J.S., and Song, Y.S. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology, 87 (2013), 51-61.
  [ Abstract ] [ PDF ] [ arXiv ]
• Steinrücken, M., Wang, Y.X.R., and Song, Y.S. An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection. Theoretical Population Biology, 83 (2013) 1-14.
  [ Abstract ] [ PDF ] [ arXiv ]
• Chan, A.H.*, Jenkins, P.A.*, and Song, Y.S. Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, vol. 8 no. 12 (2012) e1003090.
  *These authors contributed equally to this work.
  [ Abstract & PDF ] [ Supporting Information ] [ Software: LDhelmet ]
• Jenkins, P.A., Song, Y.S., and Brem, R. Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. PLoS ONE, vol. 7 no. 11 (2012) e46947.
  [ Abstract & PDF ]
• Paul, J.S. and Song, Y.S. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics, 28 (2012) 2008-2015.
  [ Abstract ] [ PDF ]
• Langley, C.H., Stevens, K., Cardeno, C., Lee, Y.C.G, Schrider, D.R., Pool, J.E., Langley, S.A., Suarez, C. Corbett-Detig, R.B., Kolaczkowski, B., Fang, S., Nista, P.M., Holloway, A.K., Kern, A.D., Dewey, C.N., Song, Y.S., Hahn, M.W., Begun, D.J. Genomic variation in natural populations of Drosophila melanogaster. Genetics, vol. 192 no. 2 (2012) 533-598.
  [ Abstract ] [ PDF ]
• Song, Y.S. and Steinrücken, M. A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection. Genetics, 190 (2012) 1117-1129.
  [ Abstract ] [ PDF ]
• Bhaskar, A. and Song, Y.S. Closed-form asymptotic sampling distributions under the coalescent with recombination for an arbitrary number of loci. Advances in Applied Probability, 44 (2012) 391-407
  [ Abstract ] [ PDF ] [ arXiv ]
• Bhaskar, A., Kamm, J.A., and Song, Y.S. Approximate sampling formulae for general finite-alleles models of mutation. Advances in Applied Probability, 44 (2012) 408-428.
  [ Abstract ] [ PDF ] [ arXiv ]
• Jenkins, P.A. and Song, Y.S. Padé approximants and exact two-locus sampling distributions. Annals of Applied Probability, 22 (2012) 576-607.
  (Technical Report 793, Department of Statistics, University of California, Berkeley, 2010.)
  [ Abstract ] [ PDF ] [ arXiv ]
• Jenkins, P.A. and Song, Y.S. The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele. Theoretical Population Biology, 80 (2011) 158-173.
  [ Abstract ] [ PDF ]
• Paul, J.S., Steinrücken, M., and Song, Y.S. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics, 187 (2011) 1115-1128
  [ Abstract ] [ PDF ] [ Proof of Proposition 1]
• Paul, J.S. and Song, Y.S. A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics, 186 (2010) 321-338.
  [ Abstract ] [ PDF ]
• Jenkins, P.A. and Song, Y.S. An asymptotic sampling formula for the coalescent with recombination. Annals of Applied Probability, 20 (2010) 1005-1028.
  (Technical Report 775, Department of Statistics, University of California, Berkeley, 2009.)
  [ Abstract ] [ PDF ] [ arXiv ] [ 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 ]
• 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 ]
• 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 ]
• Anderson, J.A., Song, Y.S., and Langley, C.H. Molecular population genetics of Drosophila subtelomeric DNA. Genetics, 178 (2008) 477-487.
  [ Abstract ]
• 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 ]
• 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 ]
• 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 ]

Next-Generation Sequencing

• Talwalkar, A., Liptrap, J., Newcomb, J. Hartl, C., Terhorst, T., Curtis, K., Bresler, M., Song, Y.S., Jordan, M.I., and Patterson, D. SMaSH: A benchmarking toolkit for human genome variant calling. Bioinformatics, vol. 30 no. 19 (2014) 2787-2795.
  [ Abstract & PDF ] [ Preprint ] [ Software ]
• Bloniarz, A., Talwalkar, A., Terhorst, J., Jordan, M.I., Patterson, D., Yu, B., and Song, Y.S. Changepoint analysis for efficient variant calling, Proc. 18th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB), LNBI Vol. 8394, 2014, pp. 20-34.
  [ Abstract & PDF ]
• Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S. Telescoper: De novo Assembly of Highly Repetitive Regions. ECCB'12 Special Issue, Bioinformatics, 28 (2012) i311-i317.
  [ Abstract ] [ PDF ]
• Nielsen, R., Paul, J.S., Albrechtsen, A., and Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12 (2011) 443-451.
  [ Abstract ]
• Kao, W.-C., Chan, A.H., and Song, Y.S. ECHO: A reference-free short-read error correction algorithm Genome Research, 21 (2011) 1181-1192
  [ Abstract ] [ PDF ] [ Software ]
• Stevens, K., Chen, H., Filiba, T., McMahon, P., Song, Y.S. SeqHive: A reconfigurable computer cluster for genome re-sequencing. IEEE Proceedings of the 20th International Conference on Field Programmable Logic and Applications (FPL 2010), pages 442-447, 2010.
  [ Abstract ] [ PDF ]
• Kao, W.-C. and Song, Y.S. naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing. Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2010), Lecture Notes in Computer Science 6044, pages 233-247, 2010.
  (A new base-calling algorithm that builds on our previous method BayesCall to achieve scalability.)
  [ Abstract ] [ PDF ] [ Software ]
  Extended Journal version: J. Comput. Biol., 18 (2011) 365-377.
  [ Abstract ] [ PDF ]
• 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 ] [ PDF ] [ Software ]

Complex Traits

• Song, Y.S., Wang, F., and Slatkin, M. General epistatic models of the risk of complex diseases. Genetics, 186 (2010) 1467-1473.
  [ Abstract ] [ PDF ]
• 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 ] [ PDF ]

Forensic Science

• Rohlfs, R.V., Murphy, E., Song, Y.S., and Slatkin, M. The influence of relatives on the efficiency and error rate of familial searching. PLoS ONE, vol. 8 no. 8 (2013) e70495
  [ Abstract & PDF ] Media Coverage: LA Times, LiveScience
• Malaspinas, A.-S., Slatkin, M., and Song, Y.S. Match probabilities in a finite, subdivided population. Theoretical Population Biology, 79 (2011) 55-63
  [ Abstract ]
• 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 ]
• 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 ]
• 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 ]

Recombination Networks and Phylogenetics

• Lam, F., Langley, C.H., and Song, Y.S. On the genealogy of asexual diploids. Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2010), Lecture Notes in Computer Science 6044, pages 325-340, 2010.
  [ Abstract ] [ PDF ]
  Extended Journal version: J. Comput. Biol., 18 (2011) 415-428.
  [ Abstract ] [ PDF ]
• 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. 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 ]
  Extended Journal version: J. Comput. Biol., 14 (2007) 1273-1286.
  [ Abstract ] [ PDF ] [ Software ]
• 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) 147-163.
  [ 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. 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 ]

Letters and Book Reviews

• Krane DE, Bahn V, Balding D, Barlow B, Cash H, Desportes BL, D'Eustachio P, Devlin K, Doom TE, Dror I, Ford S, Funk C, Gilder J, Hampikian G, Inman K, Jamieson A, Kent PE, Koppl R, Kornfield I, Krimsky S, Mnookin J, Mueller L, Murphy E, Paoletti DR, Petrov DA, Raymer M, Risinger DM, Roth A, Rudin N, Shields W, Siegel JA, Slatkin M, Song YS, Speed T, Spiegelman C, Sullivan P, Swienton AR, Tarpey T, Thompson WC, Ungvarsky E, Zabell S. Time for DNA disclosure. Science 326, No.5960 (2009) 1631-1632.
  [ 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 ]

Physics/Mathematics

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

Theses

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

Publications by Group Members

• Steinrücken, M. , Birkner, M., Blath, J. Analysis of DNA sequence variation within marine species using Beta-coalescents, Theor. Popul. Biol. , in press.
• Jenkins, P.A. Stopping-time resampling and population genetic inference under coalescent models. Statistical Applications in Genetics and Molecular Biology, Vol. 11: Iss. 1, Article 9 (2012).
  [ Abstract ]
• Nielsen, J. A Coarse-to-Fine Approach to Computing the k-Best Viterbi Paths. Proceedings of Combinatorial Pattern Matching 2011, Lecture Notes in Computer Science 6661, pages 376-387, 2011.
  [ Abstract ]
• Birkner, M., Blath, J., and Steinrücken, M. Importance sampling for Lambda-coalescents in the infinitely many sites model. Theoretical Population Biology, 79 (2011) 155-173.
  [ Abstract ]
• Jenkins, P.A. and Griffiths, R.C. Inference from samples of DNA sequences using a two-locus model. Journal of Computational Biology 18, (2011) 109-127.
  [ Abstract ]
• Liachko, I., Bhaskar, A., Lee, C., Chung, S.C.C., Tye, B.-K. and Keich, U. A comprehensive genome-wide map of autonomously replicating sequences in a naive genome. PLoS Genetics, (2010) May; 6(5): e1000946.
  [ Abstract ]
• Bhaskar, A. and Keich, U. Confidently estimating the number of DNA replication origins. Statistical Applications in Genetics and Molecular Biology, Vol. 9, Iss. 1 (2010) Article 28.
  [ Abstract ]