Rosenberg lab at Stanford University

Online supplements

[2017] [2016] [2015] [2014] [2013] [2012] [2011] [2010] [2009] [2008] [2007] [2006] [1999-2005]


P Verdu*, EM Jewett*, TJ Pemberton, NA Rosenberg, M Baptista (2017) Parallel trajectories of genetic and linguistic admixture in a genetically admixed creole population. Current Biology 27: 2529-2535. [Supplement]

OK Kamneva, J Syring, A Liston, NA Rosenberg (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evolutionary Biology 17: 180. [File S1 Table S1] [File S2 Sequences] [File S3 Table S2] [File S4 Figures S1-S11] [File S5 Table S3] [File S6 R code]

N Alcala, NA Rosenberg (2017) Mathematical constraints on FST: biallelic markers in arbitrarily many populations. Genetics 206: 1581-1600. [File S1] [File S2]

MD Edge, BFB Algee-Hewitt, TJ Pemberton, JZ Li, NA Rosenberg (2017) Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. Proceedings of the National Academy of Sciences USA 114: 5671-5676. [Supplement]

A Goldberg, T Günther, NA Rosenberg, M Jakobsson (2017) Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age migrations. Proceedings of the National Academy of Sciences USA 114: 2657-2662. [Supplement]

OK Kamneva, NA Rosenberg (2017) Simulation-based evaluation of hybridization network reconstruction methods in the presence of incomplete lineage sorting. Evolutionary Bioinformatics 13: 1176934317691935. [Supplement]


RS Mehta, D Bryant, NA Rosenberg (2016) The probability of monophyly of a sample of gene lineages on a species tree. Proceedings of the National Academy of Sciences 113: 8002-8009. [Supplement]

T Stadler, JH Degnan, NA Rosenberg (2016) Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times? Systematic Biology 65: 628-639. [Supplement]

BFB Algee-Hewitt*, MD Edge*, J Kim, JZ Li, NA Rosenberg (2016) Individual identifiability predicts population identifiability in forensic microsatellite markers. Current Biology 26: 935-942. [Supplement]


R Ronen*, G Tesler*, A Akbari*, S Zakov, NA Rosenberg, V Bafna (2015) Predicting carriers of ongoing selective sweeps without knowledge of the favored allele. PLoS Genetics 11: e1005527. [Fig S1] [Fig S2] [Fig S3] [Fig S4] [Fig S5] [Fig S6] [Fig S7] [Fig S8] [Fig S9] [Fig S10] [Fig S11] [Fig S12] [Fig S13] [Fig S14] [Fig S15] [Table S1] [Text S1] [Source code]

NA Rosenberg, JTL Kang (2015) Genetic diversity and societally important disparities. Genetics 201: 1-12. [Supplement]

NM Kopelman, J Mayzel, M Jakobsson, NA Rosenberg, I Mayrose (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15: 1179-1191. [Supplement]

N Creanza, M Ruhlen, T Pemberton, NA Rosenberg, MW Feldman, S Ramachandran (2015) Comparison of worldwide phonemic and genetic variation in human populations. Proceedings of the National Academy of Sciences USA 112: 1265-1272. [Supplementary Appendix] [Supplementary Data S1] [Supplementary Data S2] [Supplementary Data S3]


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. [Supplementary Figure 1 (.tif)] [Supplementary Figure 2 (.tif)] [Supplementary Figure 3 (.tif)] [Supplementary Figure 4 (.tif)] [Supplementary Figure 5 (.tif)] [Supplementary Figure 6 (.tif)] [Supplementary Figure 7 (.tif)] [Supplementary Figure 8 (.tif)] [Supplementary Figure 9 (.tif)] [Supplementary Figure 10 (.tif)] [Supplementary Table 1 (.docx)] [Supplementary Table 2 (.txt)]

TJ Pemberton, NA Rosenberg (2014) Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Human Heredity 77: 37-48. [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Table 3]

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. [Supplementary File 1 (.xlsx, accession numbers)] [Supplementary File 2 (.pdf, supplementary analyses)] [Supplementary File 3 (.zip, data)]


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. [Supplement]

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. [Supplement] [Data (.zip) - File S1]


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. [Supplement]

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. [Supplement]

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. [Supplement (.docx)]

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. [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]

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. [Supplement]


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. [Supplement]

P Verdu, NA Rosenberg (2011) A general mechanistic model for admixture histories of hybrid populations. Genetics 189: 1413-1426. [Supplementary Text] [Supplementary Figure 1] [Supplementary Table 1]

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. [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]


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. [Supplement]

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. [Supplementary Figure 1] [Supplementary Table 1] [Supplementary Table 2] [Supplementary Methods]

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. [Supplement]


TJ Pemberton, CI Sandefur, M Jakobsson, NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics 10: 612. [Supplementary table 1 (XLS)] [Supplementary table 1 (TXT)] [Supplementary table 2 (XLS)] [Supplementary table 2 (TXT)] [Supplementary tables 3-6 (PDF)]

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. [Supplement]

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. [Supplement]

JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Supplement]

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. [Supplement]

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. [Supplement]


O François, MGB Blum, M Jakobsson, NA Rosenberg (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics 4: e1000075. [Supplement]

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. [Supplement]

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. [Supplement]


S Wang*, CM Lewis Jr*, M Jakobsson*, S Ramachandran, N Ray, G Bedoya, W Rojas, MV Parra, JA Molina, C Gallo, G Mazzotti, G Poletti, K Hill, AM Hurtado, D Labuda, W Klitz, R Barrantes, MC Bortolini, FM Salzano, ML Petzl-Erler, LT Tsuneto, E Llop, F Rothhammer, L Excoffier, MW Feldman, NA Rosenberg, A Ruiz-Linares (2007) Genetic variation and population structure in Native Americans. PLoS Genetics 3: 2049-2067. [Supplement]

KB Schroeder, TG Schurr, JC Long, NA Rosenberg, MH Crawford, LA Tarskaia, LP Osipova, SI Zhadanov, DG Smith (2007). A private allele ubiquitous in the Americas. Biology Letters 3: 218-223. [Supplement]


NA Rosenberg, S Mahajan, C Gonzalez-Quevedo, MGB Blum, L Nino-Rosales, V Ninis, P Das, M Hegde, L Molinari, G Zapata, JL Weber, JW Belmont, PI Patel (2006) Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genetics 2: 2052-2061. [Supplement (DOC)] [Supplement (PDF)]

DF Conrad*, M Jakobsson*, G Coop*, X Wen, JD Wall, NA Rosenberg, JK Pritchard (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38: 1251-1260. [Supplement (methods, note, and figures)] [Supplementary Table 1]

NA Rosenberg (2006) Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Annals of Human Genetics 70: 841-847. [Supplement]


S Ramachandran, O Deshpande, CC Roseman, NA Rosenberg, MW Feldman, LL Cavalli-Sforza (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences USA 102: 15942-15947. [Supplementary Figure 6] [Supplementary Table 2] [Supplementary text]


NA Rosenberg, LM Li, R Ward, JK Pritchard (2003) Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics 73: 1402-1422. [Supplement]


NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2381-2385. [Supplement]