Rosenberg lab at Stanford University

Metadata for Rosenberg lab peer-reviewed publications (2008-present)

[2014] [2013] [2012] [2011] [2010] [2009] [2008]


In press

EO Buzbas, NA Rosenberg (2014) AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology (in press).
[PMID]
[PMCID (none)]
[Journal issue date]
[Grant support]
[Access: -]

F Disanto, NA Rosenberg (2014) On the number of ranked species trees producing anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics (in press).
[PMID]
[PMCID (none)]
[Journal issue date]
[Grant support]
[Access: -]


2014

A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]
[PMID 25194159]
[PMCID (none)]
[Journal issue date: November 2014]
[Grant support: NSF BCS-1147534]
[Access: open access charge paid]

MD Edge, NA Rosenberg (2014) Upper bounds on FST in terms of the frequency of the most frequent allele and total homozygosity: the case of a specified number of alleles. Theoretical Population Biology 97: 20-34. [Abstract] [PDF]
[PMID 25132646]
[PMCID PMC4180022]
[Journal issue date: November 2014]
[Grant support: NIH R01 HG005855]
[Access: -]

P Verdu, TJ Pemberton, R Laurent, BM Kemp, A Gonzalez-Oliver, C Gorodezky, CE Hughes, MR Shattuck, B Petzelt, J Mitchell, H Harry, T William, R Worl, JS Cybulski, NA Rosenberg, RS Malhi (2014) Patterns of admixture and population structure in native populations of northwest North America. PLoS Genetics 10: e1004530. [Abstract] [PDF] [Supplement]
[PMID 25122539]
[PMCID PMC4133047]
[Journal issue date: 8-14-2014]
[Grant support: NSF BCS-1147534]
[Access: open access journal]

TJ Pemberton, NA Rosenberg (2014) Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Human Heredity 77: 37-48. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Table 3]
[PMID 25060268]
[PMCID PMC4154368]
[Journal issue date: July 2014]
[Grant support: BWF, NIH R01 HG005855]
[Access: -]

CV Than, NA Rosenberg (2014) Mean deep coalescence cost under exchangeable probability distributions. Discrete Applied Mathematics 174: 11-26. [Abstract] [PDF]
[PMID]
[PMCID (none)]
[Journal issue date: 9-10-2014]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

M DeGiorgio, J Syring, AJ Eckert, AI Liston, R Cronn, DB Neale, NA Rosenberg (2014) An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evolutionary Biology 14: 67. [Abstract] [PDF] [Supplementary File 1 (.xlsx, accession numbers)] [Supplementary File 2 (.pdf, supplementary analyses)] [Supplementary File 3 (.zip, data)]
[PMID 24678701]
[PMCID PMC4021425]
[Journal issue date: 3-29-2014]
[Grant support: NSF DBI-1146722]
[Access: open access journal]

EM Jewett, NA Rosenberg (2014) Theory and applications of a deterministic approximation to the coalescent model. Theoretical Population Biology 93: 14-29. [Abstract] [PDF]
[PMID 24412419]
[PMCID (none)]
[Journal issue date: May 2014]
[Grant support: BWF, NIH R01 HG005855, NSF DBI-1146722]
[Access: -]


2013

DM Behar*, M Metspalu*, Y Baran, NM Kopelman, B Yunusbayev, A Gladstein, S Tzur, H Sahakyan, A Bahmanimehr, L Yepiskoposyan, K Tambets, EK Khusnutdinova, A Kushniarevich, O Balanovsky, E Balanovsky, L Kovacevic, D Marjanovic, E Mihailov, A Kouvatsi, C Triantaphyllidis, RJ King, O Semino, A Torroni, MF Hammer, E Metspalu, K Skorecki, S Rosset, E Halperin, R Villems, NA Rosenberg (2013) No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews. Human Biology 85: 859-900. [Abstract] [PDF]
[PMID 25079123]
[PMCID (none)]
[Journal issue date: December 2013]
[Grant support: -]
[Access: -]

PJ Oefner, G Hölzl, P Shen, I Shpirer, D Gefel, T Lavi, E Woolf, J Cohen, C Cinnioglu, PA Underhill, NA Rosenberg, J Hochrein, JM Granka, J Hillel, MW Feldman (2013) Genetics and the history of the Samaritans: Y-chromosomal microsatellites and genetic affinity between Samaritans and Cohanim. Human Biology 85: 825-857. [Abstract] [PDF]
[PMID 25079122]
[PMCID (none)]
[Journal issue date: December 2013]
[Grant support: -]
[Access: -]

NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 1253-1262. [Abstract]
[PDF]
[PMID 24524157]
[PMCID (none)]
[Journal issue date: September/October 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

MD Edge, P Gorroochurn, NA Rosenberg (2013) Windfalls and pitfalls: applications of population genetics to the search for disease genes. Evolution, Medicine, and Public Health 2013: 254-272. [Abstract] [Full-text at journal website] [PDF]
[PMID 24481204]
[PMCID PMC3868415]
[Journal issue date: 2013 (advance publication date 11-6-2013)]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

NA Rosenberg (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution 30: 2709-2713. [Abstract] [Full-text at journal website] [PDF]
[PMID 24030555]
[PMCID PMC3840310]
[Journal issue date: December 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: open access charge paid]

P Zhang, X Zhan, NA Rosenberg, S Zöllner (2013) Genotype imputation reference panel selection using maximal phylogenetic diversity. Genetics 195: 319-330. [Abstract] [PDF]
[PMID 23934887]
[PMCID PMC3781962]
[Journal issue date: October 2013]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

NA Rosenberg, TJ Pemberton, JZ Li, JW Belmont (2013) Runs of homozygosity and parental relatedness. Genetics in Medicine 15: 753-754. [PDF]
[PMID 24008258]
[PMCID (none)]
[Journal issue date: September 2013]
[Grant support: NIH R01 HG005855]
[Access: -]

L Huang, EO Buzbas, NA Rosenberg (2013) Genotype imputation in a coalescent model with infinitely-many-sites mutation. Theoretical Population Biology 87: 62-74. [Abstract] [PDF]
[PMID 23079542]
[PMCID PMC3587719]
[Journal issue date: August 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

ZA Szpiech, J Xu, TJ Pemberton, W Peng, S Zöllner, NA Rosenberg, JZ Li (2013) Long runs of homozygosity are enriched for deleterious variation. American Journal of Human Genetics 93: 90-102. [Abstract] [PDF] [Supplement] [Data]
[PMID 23746547]
[PMCID PMC3710769]
[Journal issue date: July 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: free highlighted article]

TJ Pemberton, M DeGiorgio, NA Rosenberg (2013) Population structure in a comprehensive data set on human microsatellite variation. G3: Genes, Genomes, Genetics 3: 891-907. [Abstract] [Full-text at journal website] [PDF] [Supplement] [Data (.zip) - File S1]
[PMID 23550135]
[PMCID PMC3656735]
[Journal issue date: May 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

CV Than, NA Rosenberg (2013) Mathematical properties of the deep coalescence cost. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 61-72. [Abstract] [PDF]
[PMID 23109533]
[PMCID (none)]
[Journal issue date: January/February 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

M Jakobsson, MD Edge, NA Rosenberg (2013) The relationship between FST and the frequency of the most frequent allele. Genetics 193: 515-528. [Abstract] [PDF]
[PMID 23172852]
[PMCID PMC3567740]
[Journal issue date: February 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

M DeGiorgio, NA Rosenberg (2013) Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis. Molecular Biology and Evolution 30: 480-488. [Abstract] [PDF]
[PMID 23051843]
[PMCID PMC3548310]
[Journal issue date: February 2013]
[Grant support: NIH R01 GM081441]
[Access: open access charge paid]

NM Kopelman, L Stone, O Gascuel, NA Rosenberg (2013) The behavior of admixed populations in neighbor-joining inference of population trees. Pacific Symposium on Biocomputing 18: 263-274. [Abstract] [PDF]
[PMID 23424132]
[PMCID PMC3597466]
[Journal issue date: January 2013]
[Grant support: BWF, NIH R01 GM081441, NSF BCS-1024627, NSF DBI-1146722]
[Access: freely available online]


2012

JH Degnan, NA Rosenberg, T Stadler (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 1558-1568. [Abstract] [PDF]
[PMID 22868677]
[PMCID (none)]
[Journal issue date: November/December 2012]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

EO Buzbas (2012) On the article titled "Estimating species trees using approximate Bayesian computation" (Fan and Kubatko, Molecular Phylogenetics and Evolution 59:354-363). Molecular Phylogenetics and Evolution 65: 1014-1016 (2012). [PDF]
[PMID 22981955]
[PMCID (none)]
[Journal issue date: December 2012]
[Grant support: NSF DBI-1146722]
[Access: -]

C Wang, KB Schroeder, NA Rosenberg (2012) A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes. Genetics 192: 651-669. [Abstract] [Full-text at journal website] [PDF] [Supplement] [Software]
[PMID 22851645]
[PMCID PMC3360999]
[Journal issue date: October 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

C Wang, S Zöllner, NA Rosenberg (2012) A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genetics 8: e1002886. [Abstract] [Full-text at journal website] [PDF] [Supplement]
[PMID 22927824]
[PMCID PMC3426559]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

TJ Pemberton, F-Y Li, EK Hanson, NU Mehta, S Choi, J Ballantyne, JW Belmont, NA Rosenberg, C Tyler-Smith, PI Patel (2012) Impact of restricted marital practices on genetic variation in an endogamous Gujarati group. American Journal of Physical Anthropology 149: 92-103. [Abstract] [PDF] [Supplement (.docx)] [Data]
[PMID 22729696]
[PMCID PMC3436606]
[Journal issue date: September 2012]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

EM Jewett*, M Zawistowski*, NA Rosenberg, S Zöllner (2012) A coalescent model for genotype imputation. Genetics 191: 1239-1255. [Abstract] [PDF]
[PMID 22595242]
[PMCID PMC3416004]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

TJ Pemberton, D Absher, MW Feldman, RM Myers, NA Rosenberg, JZ Li (2012) Genomic patterns of homozygosity in worldwide human populations. American Journal of Human Genetics 91: 275-292. [Abstract] [PDF] [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]
[PMID 22883143]
[PMCID PMC3415543]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

D Bryant, R Bouckaert, J Felsenstein, NA Rosenberg, A RoyChoudhury (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29: 1917-1932. [Abstract] [PDF] [Supplement]
[PMID 22422763]
[PMCID PMC3408069]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NSF DBI-1146722]
[Access: -]

LJ Helmkamp, EM Jewett, NA Rosenberg (2012) Improvements to a class of distance matrix methods for inferring species trees from gene trees. Journal of Computational Biology 19: 632-649. [Abstract] [PDF]
[PMID 22697239]
[PMCID PMC3400268]
[Journal issue date: June 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: open access charge paid]

EM Jewett, NA Rosenberg (2012) iGLASS: an improvement to the GLASS method for estimating species trees from gene trees. Journal of Computational Biology 19: 293-315. [Abstract] [PDF]
[PMID 22216756]
[PMCID PMC3298679]
[Journal issue date: March 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: open access charge paid]

SB Reddy, NA Rosenberg (2012) Refining the relationship between homozygosity and the frequency of the most frequent allele. Journal of Mathematical Biology 64: 87-108. [Abstract] [PDF]
[PMID 21305294]
[PMCID PMC3636777]
[Journal issue date: January 2012]
[Grant support: BWF, NIH R01 GM081441]
[Access: open access charge paid]

FA San Lucas, NA Rosenberg, P Scheet (2012) Haploscope: a tool for the graphical display of haplotype structure in populations. Genetic Epidemiology 35: 17-21. [Abstract] [PDF]
[PMID 22147662]
[PMCID PMC3725725]
[Journal issue date: January 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

JH Degnan, NA Rosenberg, T Stadler (2012) The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235: 45-55. [Abstract] [PDF]
[PMID 22075548]
[PMCID (none)]
[Journal issue date: January/February 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: -]


2011

NA Rosenberg (2011) A population-genetic perspective on the similarities and differences among worldwide human populations. Human Biology 83: 659-684. [Abstract] [PDF]
[PMID 22276967]
[PMCID PMC3531797]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

L Huang*, M Jakobsson*, TJ Pemberton, M Ibrahim, T Nyambo, S Omar, JK Pritchard, SA Tishkoff, NA Rosenberg (2011) Haplotype variation and genotype imputation in African populations. Genetic Epidemiology 35: 766-780. [Abstract] [PDF] [Supplement] [Data]
[PMID 22125220]
[PMCID PMC3568705]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

P Verdu, NA Rosenberg (2011) A general mechanistic model for admixture histories of hybrid populations. Genetics 189: 1413-1426. [Abstract] [PDF] [Supplementary Text] [Supplementary Figure 1] [Supplementary Table 1]
[PMID 21968194]
[PMCID PMC3241432]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855, NSF BCS-1147534]
[Access: open access charge paid]

S Ramachandran, NA Rosenberg (2011) A test of the influence of continental axes of orientation on patterns of human gene flow. American Journal of Physical Anthropology 146: 515-529. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]
[PMID 21913175]
[PMCID PMC3538872]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

M DeGiorgio, JH Degnan, NA Rosenberg (2011) Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics 189: 579-593. [Abstract] [PDF]
[PMID 21775469]
[PMCID PMC3189793]
[Journal issue date: October 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: open access charge paid]

SM Boca, NA Rosenberg (2011) Mathematical properties of Fst between admixed populations and their parental source populations. Theoretical Population Biology 80: 208-216. [Abstract] [PDF]
[PMID 21640742]
[PMCID PMC3206961]
[Journal issue date: November 2011]
[Grant support: BWF, NIH R01 GM081441, NSF BCS-1024627]
[Access: -]

ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]
[PMID 21514313]
[PMCID PMC3143247]
[Journal issue date: September 2011]
[Grant support: BWF, NIH R01 GM081441, NSF DEB-0716904]
[Access: -]

Z Yang, M Rosenthal, NA Rosenberg, S Talarico, L Zhang, C Marrs, VO Thomsen, T Lillebaek, AB Andersen (2011) How dormant is Mycobacterium tuberculosis during latency? A study integrating genomics and molecular epidemiology. Infection, Genetics and Evolution 11: 1164-1167. [Abstract] [PDF]
[PMID 21315848]
[PMCID PMC3104100]
[Journal issue date: July 2011]
[Grant support: -]
[Access: -]

EO Buzbas, P Joyce, NA Rosenberg (2011) Inference on the strength of balancing selection for epistatically interacting loci. Theoretical Population Biology 79: 102-113. [Abstract] [PDF]
[PMID 21277883]
[PMCID PMC3070424]
[Journal issue date: May 2011]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [Abstract] [PDF]
[PMID 21210728]
[PMCID (none)]
[Journal issue date: January 2011]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]


2010

M DeGiorgio*, I Jankovic*, NA Rosenberg (2010) Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy. Genetics 186: 1367-1387. [Abstract] [PDF]
[PMID 20923981]
[PMCID PMC2998318]
[Journal issue date: December 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

TJ Pemberton, C Wang, JZ Li, NA Rosenberg (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. American Journal of Human Genetics 87: 457-464. [Abstract] [PDF] [Supplement]
[PMID 20869033]
[PMCID PMC2948801]
[Journal issue date: October 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

E Borràs*, M Pineda*, I Blanco, EM Jewett, F Wang, A Teulé, T Caldés, M Urioste, C Martínez-Bouzas, J Brunet, J Balmaña, A Torres, T Ramón y Cajal, J Sanz, L Pérez-Cabornero, S Castellví-Bel, A Alonso, A Lanas, S González, V Moreno, SB Gruber, NA Rosenberg, B Mukherjee, C Lázaro, G Capellá (2010) MLH1 founder mutations with moderate penetrance in Spanish Lynch syndrome families. Cancer Research 70: 7379-7391. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Methods]
[PMID 20858721]
[PMCID (none)]
[Journal issue date: October 1, 2010]
[Grant support: -]
[Access: -]

I Jankovic, BM vonHoldt, NA Rosenberg (2010) Heterozygosity of the Yellowstone wolves. Molecular Ecology 19: 3246-3249. [PDF]
[PMID 20670367]
[PMCID PMC2924148]
[Journal issue date: August 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

NA Rosenberg, L Huang*, EM Jewett*, ZA Szpiech*, I Jankovic*, M Boehnke (2010) Genome-wide association studies in diverse populations. Nature Reviews Genetics 11: 356-366. [Abstract] [PDF]
[PMID 20395969]
[PMCID PMC3079573]
[Journal issue date: May 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

NA Rosenberg, JH Degnan (2010) Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151. [Abstract] [PDF]
[PMID 20064540]
[PMCID (none)]
[Journal issue date: May 2010]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

M DeGiorgio, JH Degnan (2010) Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution 27: 552-569. [Abstract] [PDF]
[PMID 19833741]
[PMCID PMC2877557]
[Journal issue date: March 2010]
[Grant support: NSF DEB-0716904]
[Access: -]

C Wang, ZA Szpiech, JH Degnan, M Jakobsson, TJ Pemberton, JA Hardy, AB Singleton, NA Rosenberg (2010) Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology 9: 13. [Abstract] [PDF]
[PMID 20196748]
[PMCID PMC2861313]
[Journal issue date: January 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

JT Mosher, TJ Pemberton, K Harter, C Wang, EO Buzbas, P Dvorak, C Simon, SJ Morrison, NA Rosenberg (2010) Lack of population diversity in commonly used human embryonic stem-cell lines. New England Journal of Medicine 362: 183-185. [PDF] [Supplement]
[PMID 20018958]
[PMCID (none)]
[Journal issue date: January 14, 2010]
[Grant support: Sloan Fdn]
[Access: -]


2009

TJ Pemberton, CI Sandefur, M Jakobsson, NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics 10: 612. [Abstract] [Full-text at journal website] [PDF] [Supplementary table 1 (XLS)] [Supplementary table 2 (XLS)] [Supplementary tables 3-6 (PDF)] [Data]
[PMID 20015383]
[PMCID PMC2806349]
[Journal issue date: December 16, 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access journal]

NM Kopelman, L Stone, C Wang, D Gefel, MW Feldman, J Hillel, NA Rosenberg (2009) Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genetics 10: 80. [Abstract] [Full-text at journal website] [PDF]
[PMID 19995433]
[PMCID PMC2797531]
[Journal issue date: December 8, 2009]
[Grant support: BWF, Sloan Fdn]
[Access: open access journal]

L Huang, C Wang, NA Rosenberg (2009) The relationship between imputation error and statistical power in genetic association studies in diverse populations. American Journal of Human Genetics 85: 692-698. [Abstract] [PDF] [Supplement]
[PMID 19853241]
[PMCID PMC2775841]
[Journal issue date: November 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

M DeGiorgio, M Jakobsson, NA Rosenberg (2009) Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences USA 106: 16057-16062. [Abstract] [PDF] [Supplement]
[PMID 19706453]
[PMCID PMC2752555]
[Journal issue date: September 22, 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: special open access section]

NA Rosenberg, JM VanLiere (2009) Replication of genetic associations as pseudoreplication due to shared genealogy. Genetic Epidemiology 33: 479-487. [Abstract] [PDF]
[PMID 19191270]
[PMCID PMC2766236]
[Journal issue date: September 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

JH Degnan, M DeGiorgio, D Bryant, NA Rosenberg (2009) Properties of consensus methods for inferring species trees from gene trees. Systematic Biology 58: 35-54. [Abstract] [PDF]
[PMID 20525567]
[PMCID PMC2909780]
[Journal issue date: February 2009]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Abstract] [PDF] [Supplement]
[PMID 19307040]
[PMCID (none)]
[Journal issue date: June 2009]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

KB Schroeder, M Jakobsson, MH Crawford, TG Schurr, SM Boca, DF Conrad, RY Tito, LP Osipova, LA Tarskaia, SI Zhadanov, JD Wall, JK Pritchard, RS Malhi, DG Smith, NA Rosenberg (2009) Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution 26: 995-1016. [Abstract] [PDF] [Supplement]
[PMID 19221006]
[PMCID PMC2734135]
[Journal issue date: May 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

M DeGiorgio, NA Rosenberg (2009) An unbiased estimator of gene diversity in samples containing related individuals. Molecular Biology and Evolution 26: 501-512. [Abstract] [PDF]
[PMID 18988687]
[PMCID PMC2915906]
[Journal issue date: March 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access charge paid]

L Huang, Y Li, AB Singleton, JA Hardy, G Abecasis, NA Rosenberg, P Scheet (2009) Genotype-imputation accuracy across worldwide human populations. American Journal of Human Genetics 84: 235-250. [Abstract] [PDF] [Supplement]
[PMID 19215730]
[PMCID PMC2668016]
[Journal issue date: February 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]


2008

S Ramachandran, NA Rosenberg, MW Feldman, J Wakeley (2008) Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theoretical Population Biology 74: 291-301. [Abstract] [PDF]
[PMID 18817799]
[PMCID PMC2630000]
[Journal issue date: December 2008]
[Grant support: NIH R01 GM081441]
[Access: -]

ZA Szpiech, M Jakobsson, NA Rosenberg (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504. [Abstract] [Full text at journal website] [PDF] [Software]
[PMID 18779233]
[PMCID PMC2732282]
[Journal issue date: November 1, 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access charge paid]

NA Rosenberg, M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036. [Abstract] [PDF]
[PMID 18689892]
[PMCID PMC2516077]
[Journal issue date: August 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology 74: 130-137. [Abstract] [PDF]
[PMID 18572214]
[PMCID PMC2580747]
[Journal issue date: August 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

TJ Pemberton*, M Jakobsson*, DF Conrad, G Coop, JD Wall, JK Pritchard, PI Patel, NA Rosenberg (2008) Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Annals of Human Genetics 72: 535-546. [Abstract] [PDF] [Data]
[PMID 18513279]
[PMCID PMC2495051]
[Journal issue date: July 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

O François, MGB Blum, M Jakobsson, NA Rosenberg (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics 4: e1000075. [Abstract] [Full text at journal website] [PDF] [Supplement]
[PMID 18483550]
[PMCID PMC2364639]
[Journal issue date: May 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access journal]

JM Macpherson, J Gonzalez, DM Witten, JC Davis, NA Rosenberg, AE Hirsh, DA Petrov (2008) Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Molecular Biology and Evolution 25: 1025-1042. [Abstract] [PDF]
[PMID 18199829]
[PMCID PMC3299400]
[Journal issue date: June 2008]
[Grant support: -]
[Access: -]

NA Rosenberg, R Tao (2008) Discordance of species trees with their most likely gene trees: the case of five taxa. Systematic Biology 57: 131-140. [Abstract] [Full-text at journal website] [PDF] [Supplement]
[PMID 18300026]
[Journal issue date: February 2008]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

M Jakobsson*, SW Scholz*, P Scheet*, JR Gibbs, JM VanLiere, H-C Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, DG Hernandez, BJ Traynor, J Simon-Sanchez, M Matarin, A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg, AB Singleton (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003. [Abstract] [PDF] [Supplement]
[PMID 18288195]
[Journal issue date: February 21, 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]