Yun S Song

Yun S Song

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Yun S Song

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Inference of complex population histories using whole-genome sequences from multiple populations.

Proc Natl Acad Sci U S A 2019 Aug 6;116(34):17115-17120. Epub 2019 Aug 6.

Department of Statistics, University of California, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1905060116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708337PMC
August 2019

Differences in the path to exit the ribosome across the three domains of life.

Nucleic Acids Res 2019 May;47(8):4198-4210

Computer Science Division, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkz106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486554PMC
May 2019

Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans.

Life Sci Alliance 2019 04 26;2(2). Epub 2019 Feb 26.

Computer Science Division, University of California, Berkeley, Berkeley, CA, USA

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http://www.life-science-alliance.org/lookup/doi/10.26508/lsa
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http://dx.doi.org/10.26508/lsa.201800221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391684PMC
April 2019

Inference of population history using coalescent HMMs: review and outlook.

Curr Opin Genet Dev 2018 12 26;53:70-76. Epub 2018 Jul 26.

Computer Science Division and Department of Statistics, University of California, Berkeley, United States; Chan Zuckerberg Biohub, San Francisco, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2018.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296859PMC
December 2018

Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans.

Mol Ecol 2018 10 17;27(19):3873-3888. Epub 2018 Apr 17.

Department of EECS, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1111/mec.14565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165692PMC
October 2018

Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference.

Genetics 2018 10 31;210(2):665-682. Epub 2018 Jul 31.

Department of Statistics, University of California, Berkeley, California 94720

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http://dx.doi.org/10.1534/genetics.118.300733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6216588PMC
October 2018

High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability.

Nat Genet 2018 09 13;50(9):1311-1317. Epub 2018 Aug 13.

Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41588-018-0177-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6145075PMC
September 2018

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.

PLoS Genet 2018 01 16;14(1):e1007166. Epub 2018 Jan 16.

Computer Science Division, University of California Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786338PMC
January 2018

Theoretical analysis of the distribution of isolated particles in totally asymmetric exclusion processes: Application to mRNA translation rate estimation.

Phys Rev E 2018 Jan;97(1-1):012106

Computer Science Division and Department of Statistics, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1103/PhysRevE.97.012106DOI Listing
January 2018

Establishment of Cell-Based Neuroglobin Promoter Reporter Assay for Neuroprotective Compounds Screening.

CNS Neurol Disord Drug Targets 2016 ;15(5):629-39

Neuroprotection Research Laboratory, Departments of Neurology and Radiology, Massachusetts General Hospital, 149 13th Street, Room 2411A, Charlestown, MA 02129, USA.

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October 2017

Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics.

Cell Syst 2017 06 31;4(6):636-644.e9. Epub 2017 May 31.

Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546878PMC
June 2017

OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

Linear Algebra Appl 2017 May 17;520:44-66. Epub 2017 Jan 17.

Department of Mathematics, University of Pennsylvania; Department of Statistics, University of California, Berkeley; Computer Science Division, University of California, Berkeley.

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http://dx.doi.org/10.1016/j.laa.2017.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340277PMC
May 2017

Robust and scalable inference of population history from hundreds of unphased whole genomes.

Nat Genet 2017 Feb 26;49(2):303-309. Epub 2016 Dec 26.

Department of Statistics, University of California, Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1038/ng.3748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470542PMC
February 2017

Efficient computation of the joint sample frequency spectra for multiple populations.

J Comput Graph Stat 2017 16;26(1):182-194. Epub 2017 Feb 16.

Departments of EECS, Statistics, and Integrative Biology, University of California, Berkeley.

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http://dx.doi.org/10.1080/10618600.2016.1159212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319604PMC
February 2017

The Effects of Population Size Histories on Estimates of Selection Coefficients from Time-Series Genetic Data.

Mol Biol Evol 2016 11 22;33(11):3002-3027. Epub 2016 Aug 22.

Department of EECS, University of California, Berkeley, CA Department of Statistics, University of California, Berkeley, CA Department of Integrative Biology, University of California, Berkeley, CA Department of Biology, University of Pennsylvania, Philadelphia, PA Department of Mathematics, University of Pennsylvania, Philadelphia, PA

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http://dx.doi.org/10.1093/molbev/msw173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062326PMC
November 2016

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Nature 2016 Oct 21;538(7624):201-206. Epub 2016 Sep 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature18964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557PMC
October 2016

Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads.

PLoS Comput Biol 2016 09 15;12(9):e1005117. Epub 2016 Sep 15.

Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025152PMC
September 2016

Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.

Genetics 2016 07 10;203(3):1381-99. Epub 2016 May 10.

Department of Statistics, University of California, Berkeley, California 94720 Computer Science Division, University of California, Berkeley, California 94720 Department of Integrative Biology, University of California, Berkeley, California 94720 Departments of Mathematics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104

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http://dx.doi.org/10.1534/genetics.115.184820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937484PMC
July 2016

Na Li and Matthew Stephens on Modeling Linkage Disequilibrium.

Authors:
Yun S Song

Genetics 2016 07;203(3):1005-6

Computer Science Division and Department of Statistics, University of California, Berkeley, California 94720, Department of Mathematics and Department of Biology and University of Pennsylvania, Philadelphia, Pennsylvania 19104

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http://dx.doi.org/10.1534/genetics.116.191817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937133PMC
July 2016

TRACTABLE DIFFUSION AND COALESCENT PROCESSES FOR WEAKLY CORRELATED LOCI.

Electron J Probab 2015;20. Epub 2016 Jun 4.

Department of Statistics and Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929886PMC
June 2016

Prediction of ribosome footprint profile shapes from transcript sequences.

Bioinformatics 2016 06;32(12):i183-i191

Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Electrical Engineering and Computer Sciences Department of Statistics and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908337PMC
June 2016

Riches of phenotype computationally extracted from microbial colonies.

Proc Natl Acad Sci U S A 2016 May 2;113(20):E2822-31. Epub 2016 May 2.

Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1523295113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878510PMC
May 2016

The Site Frequency Spectrum for General Coalescents.

Genetics 2016 Apr 16;202(4):1549-61. Epub 2016 Feb 16.

Department of Statistics, University of California, Berkeley, California 94720 Computer Science Division, University of California, Berkeley, California 94720 Department of Integrative Biology, University of California, Berkeley, California 94720 Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104

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http://dx.doi.org/10.1534/genetics.115.184101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827730PMC
April 2016

SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes.

Bioinformatics 2016 03 9;32(5):795-7. Epub 2015 Nov 9.

Department of Statistics, Department of EECS, Department of Integrative Biology, University of California, Berkeley, CA 94720, USA, Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907395PMC
March 2016

Deep Learning for Population Genetic Inference.

PLoS Comput Biol 2016 Mar 28;12(3):e1004845. Epub 2016 Mar 28.

Computer Science Division, UC Berkeley, Berkeley, California, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004845
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http://dx.doi.org/10.1371/journal.pcbi.1004845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809617PMC
March 2016

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns.

Proc Natl Acad Sci U S A 2015 Nov 19;112(44):13621-6. Epub 2015 Oct 19.

Department of Medicine, University of California, San Francisco, CA 94143;

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http://dx.doi.org/10.1073/pnas.1501741112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640764PMC
November 2015

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Authors:
Maanasa Raghavan Matthias Steinrücken Kelley Harris Stephan Schiffels Simon Rasmussen Michael DeGiorgio Anders Albrechtsen Cristina Valdiosera María C Ávila-Arcos Anna-Sapfo Malaspinas Anders Eriksson Ida Moltke Mait Metspalu Julian R Homburger Jeff Wall Omar E Cornejo J Víctor Moreno-Mayar Thorfinn S Korneliussen Tracey Pierre Morten Rasmussen Paula F Campos Peter de Barros Damgaard Morten E Allentoft John Lindo Ene Metspalu Ricardo Rodríguez-Varela Josefina Mansilla Celeste Henrickson Andaine Seguin-Orlando Helena Malmström Thomas Stafford Suyash S Shringarpure Andrés Moreno-Estrada Monika Karmin Kristiina Tambets Anders Bergström Yali Xue Vera Warmuth Andrew D Friend Joy Singarayer Paul Valdes Francois Balloux Ilán Leboreiro Jose Luis Vera Hector Rangel-Villalobos Davide Pettener Donata Luiselli Loren G Davis Evelyne Heyer Christoph P E Zollikofer Marcia S Ponce de León Colin I Smith Vaughan Grimes Kelly-Anne Pike Michael Deal Benjamin T Fuller Bernardo Arriaza Vivien Standen Maria F Luz Francois Ricaut Niede Guidon Ludmila Osipova Mikhail I Voevoda Olga L Posukh Oleg Balanovsky Maria Lavryashina Yuri Bogunov Elza Khusnutdinova Marina Gubina Elena Balanovska Sardana Fedorova Sergey Litvinov Boris Malyarchuk Miroslava Derenko M J Mosher David Archer Jerome Cybulski Barbara Petzelt Joycelynn Mitchell Rosita Worl Paul J Norman Peter Parham Brian M Kemp Toomas Kivisild Chris Tyler-Smith Manjinder S Sandhu Michael Crawford Richard Villems David Glenn Smith Michael R Waters Ted Goebel John R Johnson Ripan S Malhi Mattias Jakobsson David J Meltzer Andrea Manica Richard Durbin Carlos D Bustamante Yun S Song Rasmus Nielsen Eske Willerslev

Science 2015 Aug 21;349(6250):aab3884. Epub 2015 Jul 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.aab3884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733658PMC
August 2015

Transition Densities and Sample Frequency Spectra of Diffusion Processes with Selection and Variable Population Size.

Genetics 2015 Jun 14;200(2):601-17. Epub 2015 Apr 14.

Section of Evolutionary Biology, Department of Biology, Ludwig-Maximilian University Munich, 82152 Munich, Germany.

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http://dx.doi.org/10.1534/genetics.115.175265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492383PMC
June 2015

Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum.

Proc Natl Acad Sci U S A 2015 Jun 8;112(25):7677-82. Epub 2015 Jun 8.

Department of Statistics, University of California, Berkeley, CA 94720; Computer Science Division, University of California, Berkeley, CA 94720; Department of Integrative Biology, University of California, Berkeley, CA 94720

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http://dx.doi.org/10.1073/pnas.1503717112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485089PMC
June 2015

Multi-locus analysis of genomic time series data from experimental evolution.

PLoS Genet 2015 Apr 7;11(4):e1005069. Epub 2015 Apr 7.

Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America; Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America; Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388667PMC
April 2015

Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

Genome Res 2015 Feb 6;25(2):268-79. Epub 2015 Jan 6.

Simons Institute for the Theory of Computing, Berkeley, California 94720, USA; Computer Science Division, University of California, Berkeley, California 94720, USA; Department of Statistics, University of California, Berkeley, California 94720, USA; Department of Integrative Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.178756.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315300PMC
February 2015

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.

Bioinformatics 2014 Dec 21;30(23):3430-1. Epub 2014 Aug 21.

Bioinformatics Research Centre, Department of Computer Science, Aarhus University, 8000 Aarhus C, Denmark, Biophysics Graduate Group, Computer Science Division, Department of Statistics and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA Bioinformatics Research Centre, Department of Computer Science, Aarhus University, 8000 Aarhus C, Denmark, Biophysics Graduate Group, Computer Science Division, Department of Statistics and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA Bioinformatics Research Centre, Department of Computer Science, Aarhus University, 8000 Aarhus C, Denmark, Biophysics Graduate Group, Computer Science Division, Department of Statistics and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296155PMC
December 2014

A NOVEL SPECTRAL METHOD FOR INFERRING GENERAL DIPLOID SELECTION FROM TIME SERIES GENETIC DATA.

Ann Appl Stat 2014 Dec;8(4):2203-2222

University of California, Berkeley.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4295721PMC
December 2014

DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA.

Ann Stat 2014 20;42(6):2469-2493. Epub 2014 Oct 20.

University of California, Berkeley.

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http://dx.doi.org/10.1214/14-AOS1264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175586PMC
October 2014

SMaSH: a benchmarking toolkit for human genome variant calling.

Bioinformatics 2014 Oct 3;30(19):2787-95. Epub 2014 Jun 3.

Department of Electrical Engineering and Computer Science, UC Berkeley, Berkeley, CA 94720, USA, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA and Department of Statistics, UC Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173010PMC
October 2014

The influence of relatives on the efficiency and error rate of familial searching.

PLoS One 2013 14;8(8):e70495. Epub 2013 Aug 14.

Department of Integrative Biology, University of California, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070495PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743829PMC
March 2014

Distortion of genealogical properties when the sample is very large.

Proc Natl Acad Sci U S A 2014 Feb 27;111(6):2385-90. Epub 2014 Jan 27.

Computer Science Division and Department of Statistics, University of California, Berkeley, CA 94720.

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http://dx.doi.org/10.1073/pnas.1322709111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926037PMC
February 2014

General triallelic frequency spectrum under demographic models with variable population size.

Genetics 2014 Jan 8;196(1):295-311. Epub 2013 Nov 8.

Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom.

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http://dx.doi.org/10.1534/genetics.113.158584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872192PMC
January 2014

Decoding coalescent hidden Markov models in linear time.

Res Comput Mol Biol 2014 ;8394:100-114

Department of Integrative Biology, University of California, Berkeley.

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http://dx.doi.org/10.1007/978-3-319-05269-4_8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203418PMC
January 2014

Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.

Genetics 2013 Jul 22;194(3):647-62. Epub 2013 Apr 22.

Computer Science Division, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1534/genetics.112.149096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697970PMC
July 2013

Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.

PLoS Genet 2012 20;8(12):e1003090. Epub 2012 Dec 20.

Computer Science Division, University of California Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527307PMC
May 2013

Telescoper: de novo assembly of highly repetitive regions.

Bioinformatics 2012 Sep;28(18):i311-i317

Department of EECS, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436826PMC
September 2012

Blockwise HMM computation for large-scale population genomic inference.

Bioinformatics 2012 Aug 28;28(15):2008-15. Epub 2012 May 28.

Computer Science Division and Department of Statistics, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400961PMC
August 2012

PADÉ APPROXIMANTS AND EXACT TWO-LOCUS SAMPLING DISTRIBUTIONS.

Ann Appl Probab 2012 Apr;22(2):576-607

Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, Berkeley USA.

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http://projecteuclid.org/euclid.aoap/1333372008
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http://dx.doi.org/10.1214/11-AAP780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685441PMC
April 2012

A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.

Genetics 2012 Mar 29;190(3):1117-29. Epub 2011 Dec 29.

Department of Statistics, University of California, Berkeley, California 94720, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.111.136929
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http://dx.doi.org/10.1534/genetics.111.136929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296246PMC
March 2012

ECHO: a reference-free short-read error correction algorithm.

Genome Res 2011 Jul 11;21(7):1181-92. Epub 2011 Apr 11.

Computer Science Division, University of California-Berkeley, CA 94721, USA.

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http://dx.doi.org/10.1101/gr.111351.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129260PMC
July 2011

Genotype and SNP calling from next-generation sequencing data.

Nat Rev Genet 2011 Jun;12(6):443-51

Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1038/nrg2986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722PMC
June 2011

Match probabilities in a finite, subdivided population.

Theor Popul Biol 2011 May 23;79(3):55-63. Epub 2011 Jan 23.

Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.tpb.2011.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065509PMC
May 2011

An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination.

Genetics 2011 Apr 26;187(4):1115-28. Epub 2011 Jan 26.

Computer Science Division, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1534/genetics.110.125534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070520PMC
April 2011

naiveBayesCall: an efficient model-based base-calling algorithm for high-throughput sequencing.

J Comput Biol 2011 Mar;18(3):365-77

Department of EECS, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1089/cmb.2010.0247DOI Listing
March 2011

On the genealogy of asexual diploids.

J Comput Biol 2011 Mar;18(3):415-28

Department of Computer Science, University of California, Davis, California, USA.

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http://dx.doi.org/10.1089/cmb.2010.0270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123918PMC
March 2011

General epistatic models of the risk of complex diseases.

Genetics 2010 Dec 20;186(4):1467-73. Epub 2010 Sep 20.

Department of Electrical Engineering, University of California, Berkeley, California 94720-3140, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.110.119008
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http://dx.doi.org/10.1534/genetics.110.119008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998324PMC
December 2010

AN ASYMPTOTIC SAMPLING FORMULA FOR THE COALESCENT WITH RECOMBINATION.

Ann Appl Probab 2010 Jun;20(3):1005-1028

Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://projecteuclid.org/euclid.aoap/1276867305
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http://dx.doi.org/10.1214/09-AAP646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910927PMC
June 2010

Closed-form two-locus sampling distributions: accuracy and universality.

Genetics 2009 Nov 7;183(3):1087-103. Epub 2009 Sep 7.

Computer Science Division, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1534/genetics.109.107995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778962PMC
November 2009

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing.

Genome Res 2009 Oct 6;19(10):1884-95. Epub 2009 Aug 6.

University of California, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.095299.109
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http://dx.doi.org/10.1101/gr.095299.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765266PMC
October 2009

Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models.

Bioinformatics 2009 Jun;25(12):i187-95

Computer Science Division and Department of Statistics, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687981PMC
June 2009

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data.

Bioinformatics 2009 Jun;25(12):i231-9

Computer Science Division and Department of Statistics, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687983PMC
June 2009

Average probability that a "cold hit" in a DNA database search results in an erroneous attribution.

J Forensic Sci 2009 Jan 21;54(1):22-7. Epub 2008 Nov 21.

Departments of EECS and Statistics, University of California, Berkeley, CA 94720-3140, USA.

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http://dx.doi.org/10.1111/j.1556-4029.2008.00917.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124364PMC
January 2009

Efficient whole-genome association mapping using local phylogenies for unphased genotype data.

Bioinformatics 2008 Oct 30;24(19):2215-21. Epub 2008 Jul 30.

Department of Computer Science, University of California, Davis, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553438PMC
October 2008

Molecular population genetics of Drosophila subtelomeric DNA.

Genetics 2008 Jan;178(1):477-87

Section of Evolution and Ecology, University of California, Davis 95616, USA.

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http://dx.doi.org/10.1534/genetics.107.083196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206096PMC
January 2008

A decomposition theory for phylogenetic networks and incompatible characters.

J Comput Biol 2007 Dec;14(10):1247-72

Department of Computer Science, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1089/cmb.2006.0137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581772PMC
December 2007

A graphical approach to multi-locus match probability computation: revisiting the product rule.

Theor Popul Biol 2007 Aug 15;72(1):96-110. Epub 2006 Dec 15.

Department of Computer Science, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1016/j.tpb.2006.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268388PMC
August 2007

Analytic computation of the expectation of the linkage disequilibrium coefficient r2.

Theor Popul Biol 2007 Feb 23;71(1):49-60. Epub 2006 Sep 23.

Department of Computer Science, University of California at Davis, 2063 Kemper Hall, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1016/j.tpb.2006.09.001DOI Listing
February 2007

A concise necessary and sufficient condition for the existence of a galled-tree.

Authors:
Yun S Song

IEEE/ACM Trans Comput Biol Bioinform 2006 Apr-Jun;3(2):186-91

Department of Computer Science, University of California at Davis, Davis, CA 95616, USA.

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http://dx.doi.org/10.1109/TCBB.2006.15DOI Listing
November 2006

Counting all possible ancestral configurations of sample sequences in population genetics.

IEEE/ACM Trans Comput Biol Bioinform 2006 Jul-Sep;3(3):239-51

Department of Computer Science, University of California at Davis, 2063 Kemper Hall, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1109/TCBB.2006.31DOI Listing
November 2006

The hitchhiking effect on linkage disequilibrium between linked neutral loci.

Genetics 2006 Apr 1;172(4):2647-63. Epub 2006 Feb 1.

Section of Evolutionary Biology, Biocenter, University of Munich, Planegg-Martinsried, Germany.

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http://dx.doi.org/10.1534/genetics.105.050179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456384PMC
April 2006

A sufficient condition for reducing recursions in hidden Markov models.

Authors:
Yun S Song

Bull Math Biol 2006 Feb 29;68(2):361-84. Epub 2006 Mar 29.

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.

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http://dx.doi.org/10.1007/s11538-005-9045-9DOI Listing
February 2006

Oxidative stress transiently decreases the IKK complex (IKKalpha, beta, and gamma), an upstream component of NF-kappaB signaling, after transient focal cerebral ischemia in mice.

J Cereb Blood Flow Metab 2005 Oct;25(10):1301-11

Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/sj.jcbfm.9600123DOI Listing
October 2005

Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution.

Bioinformatics 2005 Jun;21 Suppl 1:i413-22

Department of Computer Science, University of California Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti1033DOI Listing
June 2005

Constructing minimal ancestral recombination graphs.

J Comput Biol 2005 Mar;12(2):147-69

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.

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http://dx.doi.org/10.1089/cmb.2005.12.147DOI Listing
March 2005

On the minimum number of recombination events in the evolutionary history of DNA sequences.

J Math Biol 2004 Feb 20;48(2):160-86. Epub 2003 Aug 20.

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK.

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http://dx.doi.org/10.1007/s00285-003-0227-5DOI Listing
February 2004