Rosenberg lab at Stanford University

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

[2015] [2014] [2013] [2012] [2011] [2010] [2009] [2008]


In press

MD Edge, NA Rosenberg (2015) Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity. Studies in History and Philosophy of Biological and Biomedical Sciences in press.
[PMID (none)]
[PMCID (none)]
[Journal issue date:]
[Grant support: NIH R01 HG005855]
[Access: -]


2015

EO Buzbas, NA Rosenberg (2015) AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology 99: 31-42. [Abstract] [PDF]
[PMID 25261426]
[PMCID (none)]
[Journal issue date: February 2015]
[Grant support: NIH R01 HG005855, NSF DBI-1146722]
[Access: -]


2014

F Disanto, NA Rosenberg (2015) 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: November/December 2014]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

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 4224161]
[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: -]