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Yun S. Song, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
 Statistics University of California, Berkeley, Berkeley, CA, United States 
Area:
Biosystems & Computational Biology (BIO); Theory (THY); Applied Probability and Statistics
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78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Kamm J, Terhorst J, Durbin R, Song YS. Efficiently inferring the demographic history of many populations with allele count data. Journal of the American Statistical Association. 115: 1472-1487. PMID 33012903 DOI: 10.1080/01621459.2019.1635482  0.415
2019 Spence JP, Song YS. Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. Science Advances. 5: eaaw9206. PMID 31681842 DOI: 10.1126/Sciadv.Aaw9206  0.391
2019 Steinrücken M, Kamm J, Spence JP, Song YS. Inference of complex population histories using whole-genome sequences from multiple populations. Proceedings of the National Academy of Sciences of the United States of America. PMID 31387977 DOI: 10.1073/Pnas.1905060116  0.441
2018 Chan J, Perrone V, Spence JP, Jenkins PA, Mathieson S, Song YS. A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. Advances in Neural Information Processing Systems. 31: 8594-8605. PMID 33244210  0.324
2018 Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, ... ... Song YS, et al. Early human dispersals within the Americas. Science (New York, N.Y.). PMID 30409807 DOI: 10.1126/Science.Aav2621  0.348
2018 Palamara PF, Terhorst J, Song YS, Price AL. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nature Genetics. 50: 1311-1317. PMID 30104759 DOI: 10.1038/S41588-018-0177-X  0.379
2018 Rosen Z, Bhaskar A, Roch S, Song YS. Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference. Genetics. PMID 30064984 DOI: 10.1534/Genetics.118.300733  0.645
2018 Spence JP, Steinrücken M, Terhorst J, Song YS. Inference of population history using coalescent HMMs: review and outlook. Current Opinion in Genetics & Development. 53: 70-76. PMID 30056275 DOI: 10.1016/J.Gde.2018.07.002  0.434
2018 Steinrücken M, Spence JP, Kamm JA, Wieczorek E, Song YS. Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans. Molecular Ecology. PMID 29603507 DOI: 10.1111/Mec.14565  0.388
2018 Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature. 553: 203-207. PMID 29323294 DOI: 10.1038/Nature25173  0.344
2017 Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, ... ... Song YS, et al. Loci associated with skin pigmentation identified in African populations. Science (New York, N.Y.). PMID 29025994 DOI: 10.1126/Science.Aan8433  0.351
2017 Kamm JA, Terhorst J, Song YS. Efficient computation of the joint sample frequency spectra for multiple populations. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 26: 182-194. PMID 28239248 DOI: 10.1080/10618600.2016.1159212  0.475
2016 Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics. PMID 28024154 DOI: 10.1038/Ng.3748  0.44
2016 Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, ... ... Song YS, et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. PMID 27654912 DOI: 10.1038/Nature18964  0.372
2016 Luo S, Yu JA, Song YS. Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. Plos Computational Biology. 12: e1005117. PMID 27632220 DOI: 10.1371/Journal.Pcbi.1005117  0.36
2016 Jewett EM, Steinrücken M, Song YS. The effects of population size histories on estimates of selection coefficients from time-series genetic data. Molecular Biology and Evolution. PMID 27550904 DOI: 10.1093/Molbev/Msw173  0.413
2016 Song YS. Na Li and Matthew Stephens on Modeling Linkage Disequilibrium. Genetics. 203: 1005-1006. PMID 27384022 DOI: 10.1534/Genetics.116.191817  0.351
2016 Kamm JA, Spence JP, Chan J, Song YS. Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation. Genetics. PMID 27182948 DOI: 10.1534/Genetics.115.184820  0.427
2016 Sheehan S, Song YS. Deep Learning for Population Genetic Inference. Plos Computational Biology. 12: e1004845. PMID 27018908 DOI: 10.1371/Journal.Pcbi.1004845  0.376
2016 Spence JP, Kamm JA, Song YS. The Site Frequency Spectrum for General Coalescents. Genetics. PMID 26883445 DOI: 10.1534/Genetics.115.184101  0.379
2015 Jenkins PA, Fearnhead P, Song YS. TRACTABLE DIFFUSION AND COALESCENT PROCESSES FOR WEAKLY CORRELATED LOCI. Electronic Journal of Probability. 20. PMID 27375350 DOI: 10.1214/Ejp.V20-3564  0.395
2015 Steinrücken M, Jewett EM, Song YS. SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes. Bioinformatics (Oxford, England). PMID 26556388 DOI: 10.1093/Bioinformatics/Btv627  0.395
2015 Zou JY, Park DS, Burchard EG, Torgerson DG, Pino-Yanes M, Song YS, Sankararaman S, Halperin E, Zaitlen N. Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns. Proceedings of the National Academy of Sciences of the United States of America. 112: 13621-6. PMID 26483472 DOI: 10.1073/Pnas.1501741112  0.37
2015 Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, ... ... Song YS, et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science (New York, N.Y.). PMID 26198033 DOI: 10.1126/Science.Aab3884  0.345
2015 Terhorst J, Song YS. Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proceedings of the National Academy of Sciences of the United States of America. 112: 7677-82. PMID 26056264 DOI: 10.1073/Pnas.1503717112  0.438
2015 Živkovi? D, Steinrücken M, Song YS, Stephan W. Transition Densities and Sample Frequency Spectra of Diffusion Processes with Selection and Variable Population Size. Genetics. 200: 601-17. PMID 25873633 DOI: 10.1534/Genetics.115.175265  0.417
2015 Terhorst J, Schlötterer C, Song YS. Multi-locus analysis of genomic time series data from experimental evolution. Plos Genetics. 11: e1005069. PMID 25849855 DOI: 10.1371/Journal.Pgen.1005069  0.437
2015 Bhaskar A, Wang YX, Song YS. Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data. Genome Research. 25: 268-79. PMID 25564017 DOI: 10.1101/Gr.178756.114  0.66
2014 Bhaskar A, Song YS. DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA. Annals of Statistics. 42: 2469-2493. PMID 28018011 DOI: 10.1214/14-Aos1264  0.662
2014 Steinrücken M, Bhaskar A, Song YS. A NOVEL SPECTRAL METHOD FOR INFERRING GENERAL DIPLOID SELECTION FROM TIME SERIES GENETIC DATA. The Annals of Applied Statistics. 8: 2203-2222. PMID 25598858 DOI: 10.1214/14-Aoas764  0.63
2014 Harris K, Sheehan S, Kamm JA, Song YS. Decoding coalescent hidden Markov models in linear time. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 8394: 100-114. PMID 25340178 DOI: 10.1007/978-3-319-05269-4_8  0.341
2014 Tataru P, Nirody JA, Song YS. diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinformatics (Oxford, England). 30: 3430-1. PMID 25147361 DOI: 10.1093/Bioinformatics/Btu563  0.355
2014 Talwalkar A, Liptrap J, Newcomb J, Hartl C, Terhorst J, Curtis K, Bresler M, Song YS, Jordan MI, Patterson D. SMaSH: a benchmarking toolkit for human genome variant calling. Bioinformatics (Oxford, England). 30: 2787-95. PMID 24894505 DOI: 10.1093/Bioinformatics/Btu345  0.353
2014 Bhaskar A, Clark AG, Song YS. Distortion of genealogical properties when the sample is very large. Proceedings of the National Academy of Sciences of the United States of America. 111: 2385-90. PMID 24469801 DOI: 10.1073/Pnas.1322709111  0.622
2014 Jenkins PA, Mueller JW, Song YS. General triallelic frequency spectrum under demographic models with variable population size. Genetics. 196: 295-311. PMID 24214345 DOI: 10.1534/Genetics.113.158584  0.399
2014 Bhaskar A, Song YS. Descartes' rule of signs and the identifiability of population demographic models from genomic variation data Annals of Statistics. 42: 2469-2493. DOI: 10.1214/14-AOS1264  0.576
2013 Rohlfs RV, Murphy E, Song YS, Slatkin M. The influence of relatives on the efficiency and error rate of familial searching. Plos One. 8: e70495. PMID 23967076 DOI: 10.1371/Journal.Pone.0070495  0.303
2013 Sheehan S, Harris K, Song YS. Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach. Genetics. 194: 647-62. PMID 23608192 DOI: 10.1534/Genetics.112.149096  0.463
2013 Steinrücken M, Wang YX, Song YS. An explicit transition density expansion for a multi-allelic Wright-Fisher diffusion with general diploid selection. Theoretical Population Biology. 83: 1-14. PMID 23127866 DOI: 10.1016/J.Tpb.2012.10.006  0.374
2013 Steinrücken M, Paul JS, Song YS. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology. 87: 51-61. PMID 23010245 DOI: 10.1016/J.Tpb.2012.08.004  0.647
2012 Bhaskar A, Kamm JA, Song YS. APPROXIMATE SAMPLING FORMULAS FOR GENERAL FINITE-ALLELES MODELS OF MUTATION. Advances in Applied Probability. 44: 408-428. PMID 24634516 DOI: 10.1239/Aap/1339878718  0.594
2012 Jenkins PA, Song YS. PADÉ APPROXIMANTS AND EXACT TWO-LOCUS SAMPLING DISTRIBUTIONS. The Annals of Applied Probability : An Official Journal of the Institute of Mathematical Statistics. 22: 576-607. PMID 23788830 DOI: 10.1214/11-Aap780  0.402
2012 Chan AH, Jenkins PA, Song YS. Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. Plos Genetics. 8: e1003090. PMID 23284288 DOI: 10.1371/Journal.Pgen.1003090  0.413
2012 Jenkins PA, Song YS, Brem RB. Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. Plos One. 7: e46947. PMID 23226196 DOI: 10.1371/Journal.Pone.0046947  0.428
2012 Bresler M, Sheehan S, Chan AH, Song YS. Telescoper: de novo assembly of highly repetitive regions. Bioinformatics (Oxford, England). 28: i311-i317. PMID 22962446 DOI: 10.1093/Bioinformatics/Bts399  0.337
2012 Bhaskar A, Song YS. CLOSED-FORM ASYMPTOTIC SAMPLING DISTRIBUTIONS UNDER THE COALESCENT WITH RECOMBINATION FOR AN ARBITRARY NUMBER OF LOCI. Advances in Applied Probability. 44: 391-407. PMID 22859863 DOI: 10.1239/Aap/1339878717  0.593
2012 Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, ... Song YS, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 192: 533-98. PMID 22673804 DOI: 10.1534/Genetics.112.142018  0.415
2012 Paul JS, Song YS. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics (Oxford, England). 28: 2008-15. PMID 22641715 DOI: 10.1093/Bioinformatics/Bts314  0.672
2012 Song YS, Steinrücken M. A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection. Genetics. 190: 1117-29. PMID 22209899 DOI: 10.1534/Genetics.111.136929  0.395
2011 Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nature Reviews. Genetics. 12: 443-51. PMID 21587300 DOI: 10.1038/Nrg2986  0.616
2011 Jenkins PA, Song YS. The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele. Theoretical Population Biology. 80: 158-73. PMID 21550359 DOI: 10.1016/J.Tpb.2011.04.001  0.383
2011 Kao WC, Chan AH, Song YS. ECHO: a reference-free short-read error correction algorithm. Genome Research. 21: 1181-92. PMID 21482625 DOI: 10.1101/Gr.111351.110  0.606
2011 Lam F, Langley CH, Song YS. On the genealogy of asexual diploids. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 415-28. PMID 21385044 DOI: 10.1089/Cmb.2010.0270  0.334
2011 Kao WC, Song YS. naiveBayesCall: an efficient model-based base-calling algorithm for high-throughput sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 365-77. PMID 21385040 DOI: 10.1089/Cmb.2010.0247  0.603
2011 Paul JS, Steinrücken M, Song YS. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics. 187: 1115-28. PMID 21270390 DOI: 10.1534/Genetics.110.125534  0.681
2011 Malaspinas AS, Slatkin M, Song YS. Match probabilities in a finite, subdivided population. Theoretical Population Biology. 79: 55-63. PMID 21266180 DOI: 10.1016/J.Tpb.2011.01.003  0.424
2010 Jenkins PA, Song YS. AN ASYMPTOTIC SAMPLING FORMULA FOR THE COALESCENT WITH RECOMBINATION. The Annals of Applied Probability : An Official Journal of the Institute of Mathematical Statistics. 20: 1005-1028. PMID 20671802 DOI: 10.1214/09-Aap646  0.408
2010 Paul JS, Song YS. A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics. 186: 321-38. PMID 20592264 DOI: 10.1534/Genetics.110.117986  0.693
2009 Jenkins PA, Song YS. Closed-form two-locus sampling distributions: accuracy and universality. Genetics. 183: 1087-103. PMID 19737744 DOI: 10.1534/Genetics.109.107995  0.408
2009 Kao WC, Stevens K, Song YS. BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing. Genome Research. 19: 1884-95. PMID 19661376 DOI: 10.1101/Gr.095299.109  0.613
2009 Yin J, Jordan MI, Song YS. Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinformatics (Oxford, England). 25: i231-9. PMID 19477993 DOI: 10.1093/Bioinformatics/Btp229  0.368
2009 Bhaskar A, Song YS. Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. Bioinformatics (Oxford, England). 25: i187-95. PMID 19477986 DOI: 10.1093/Bioinformatics/Btp227  0.619
2009 Song YS, Patil A, Murphy EE, Slatkin M. Average probability that a "cold hit" in a DNA database search results in an erroneous attribution. Journal of Forensic Sciences. 54: 22-7. PMID 19040670 DOI: 10.1111/J.1556-4029.2008.00917.X  0.383
2008 Griffiths RC, Jenkins PA, Song YS. IMPORTANCE SAMPLING AND THE TWO-LOCUS MODEL WITH SUBDIVIDED POPULATION STRUCTURE. Advances in Applied Probability. 40: 473-500. PMID 19936262 DOI: 10.1239/Aap/1214950213  0.416
2008 Ding Z, Mailund T, Song YS. Efficient whole-genome association mapping using local phylogenies for unphased genotype data. Bioinformatics (Oxford, England). 24: 2215-21. PMID 18667442 DOI: 10.1093/Bioinformatics/Btn406  0.358
2008 Anderson JA, Song YS, Langley CH. Molecular population genetics of Drosophila subtelomeric DNA. Genetics. 178: 477-87. PMID 18202389 DOI: 10.1534/Genetics.107.083196  0.34
2007 Gusfield D, Bansal V, Bafna V, Song YS. A decomposition theory for phylogenetic networks and incompatible characters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1247-72. PMID 18047426 DOI: 10.1089/Cmb.2006.0137  0.322
2007 Song YS, Ding Z, Gusfield D, Langley CH, Wu Y. Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1273-86. PMID 18047424 DOI: 10.1089/Cmb.2007.0096  0.378
2007 Song YS, Slatkin M. A graphical approach to multi-locus match probability computation: revisiting the product rule. Theoretical Population Biology. 72: 96-110. PMID 17239909 DOI: 10.1016/J.Tpb.2006.11.005  0.409
2007 Song YS, Song JS. Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theoretical Population Biology. 71: 49-60. PMID 17069867 DOI: 10.1016/J.Tpb.2006.09.001  0.31
2006 Song YS, Lyngsø R, Hein J. Counting all possible ancestral configurations of sample sequences in population genetics. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 239-51. PMID 17048462 DOI: 10.1109/Tcbb.2006.31  0.37
2006 Song YS. A concise necessary and sufficient condition for the existence of a galled-tree. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 186-91. PMID 17048404 DOI: 10.1109/Tcbb.2006.15  0.305
2006 Song YS. A sufficient condition for reducing recursions in hidden Markov models. Bulletin of Mathematical Biology. 68: 361-84. PMID 16794935 DOI: 10.1007/S11538-005-9045-9  0.304
2006 Stephan W, Song YS, Langley CH. The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics. 172: 2647-63. PMID 16452153 DOI: 10.1534/Genetics.105.050179  0.334
2005 Song YS, Wu Y, Gusfield D. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics (Oxford, England). 21: i413-22. PMID 15961486 DOI: 10.1093/Bioinformatics/Bti1033  0.364
2005 Song YS, Hein J. Constructing minimal ancestral recombination graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 147-69. PMID 15767774 DOI: 10.1089/Cmb.2005.12.147  0.334
2004 Song YS, Hein J. On the minimum number of recombination events in the evolutionary history of DNA sequences. Journal of Mathematical Biology. 48: 160-86. PMID 14745509 DOI: 10.1007/S00285-003-0227-5  0.313
2000 Silverstein E, Song YS. On the critical behavior of D1-brane theories Journal of High Energy Physics. 4: 1-20. DOI: 10.1088/1126-6708/2000/03/029  0.495
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