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Rosenberg lab publications
In press
M DeGiorgio, JH Degnan (2009) Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution in press.
2009
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]
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]
NA Rosenberg, JM VanLiere (2009) Replication of genetic associations as pseudoreplication due to shared genealogy. Genetic Epidemiology 33: 479-487. [Abstract]
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]
JH Degnan, NA Rosenberg (2009) Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 24: 332-340. [Abstract]
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]
M DeGiorgio, NA Rosenberg (2009) An unbiased estimator of gene diversity in samples containing related individuals. Molecular Biology and Evolution 26: 501-512. [Abstract]
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]
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: 281-291. [Abstract]
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]
NA Rosenberg, M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036. [Abstract]
JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology 74: 130-137. [Abstract]
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] [Data]
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]
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]
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]
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]
2007
K Zhang, NA Rosenberg (2007) On the genealogy of a duplicated microsatellite. Genetics 177: 2109-2122. [Abstract] [PDF]
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. [Abstract] [Full text at journal website] [PDF] [Supplement] [Data] [Readme for datafile]
M Jakobsson, NA Rosenberg (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806. [Abstract] [Full text at journal website] [PDF] [Software]
MGB Blum, NA Rosenberg (2007) Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling. Genetics 176: 1741-1757. [Abstract] [PDF]
NA Rosenberg (2007) Counting coalescent histories. Journal of Computational Biology 14: 360-377. [Abstract] [PDF]
NA Rosenberg, MGB Blum (2007) Sampling properties of homozygosity-based statistics for linkage disequilibrium. Mathematical Biosciences 208: 33-47. [Abstract] [PDF]
M Jakobsson, NA Rosenberg (2007) The probability distribution under a population divergence model of the number of genetic founding lineages of a population or species. Theoretical Population Biology 71: 502-523. [Abstract] [PDF]
L David, NA Rosenberg, U Lavi, MW Feldman, J Hillel (2007). Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L. Genetics Selection Evolution 39: 319-340. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplement]
NA Rosenberg (2007) Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61: 317-323. [Abstract] [PDF]
2006
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. [Abstract] [Full-text at journal website] [PDF] [Supplementary Tables 1-3 (DOC)] [Supplementary Tables 1-3 (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. [Abstract] [PDF] [Supplement (methods, note, and figures] [Supplementary Table 1] [Data]
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. [Abstract] [PDF] [Supplement] [Data] [Spreadsheet with recommended subsets (txt format)] [Spreadsheet with recommended subsets (xls format)]
NA Rosenberg, M Nordborg (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations. Genetics 173: 1665-1678. [Abstract] [PDF]
JH Degnan, NA Rosenberg (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics 2: 762-768. [Abstract] [Full-text at journal website] [PDF]
NA Rosenberg (2006) The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees. Annals of Combinatorics 10: 129-146. [Abstract] [PDF]
2005
NA Rosenberg, S Mahajan, S Ramachandran, C Zhao, JK Pritchard, MW Feldman (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: 660-671. [Abstract] [Full-text at journal website] [PDF] [Data]
NA Rosenberg (2005) Algorithms for selecting informative marker panels for population assignment. Journal of Computational Biology 12: 1183-1201. [Abstract] [PDF]
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. [Abstract] [PDF] [Supplementary Figure 6] [Supplementary Table 2] [Supplementary text] [Data]
NA Rosenberg (2005) A sharp minimum on the mean number of steps taken in adaptive walks. Journal of Theoretical Biology 237: 17-22. [Abstract] [PDF]
M Nordborg, TT Hu, Y Ishino, J Jhaveri, C Toomajian, H Zheng, E Bakker, P Calabrese, J Gladstone, R Goyal, M Jakobsson, S Kim, Y Morozov, B Padhukasahasram, V Plagnol, NA Rosenberg, C Shah, JD Wall, J Wang, K Zhao, T Kalbfleisch, V Schulz, M Kreitman, J Bergelson (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3: 1289-1299. [Abstract] [Full-text at journal website] [PDF]
2005
H Innan, K Zhang, P Marjoram, S Tavaré, NA Rosenberg (2005)
Statistical tests of the coalescent model based on the haplotype
frequency distribution and the number of segregating
sites. Genetics 169: 1763-1777. [Abstract] [PDF] [Software]
NA Rosenberg, PP Calabrese (2004) Polyploid and multilocus
extensions of the Wahlund inequality. Theoretical Population
Biology 66: 381-391. [Abstract] [PDF]
MM Tanaka, NA Rosenberg, PM Small (2004) The control of copy
number of IS6110 in Mycobacterium
tuberculosis. Molecular Biology and Evolution 21:
2195-2201. [Abstract] [PDF]
NA Rosenberg (2004) Review of Probability Models for DNA
Sequence Evolution by R Durrett. Journal of the American
Statistical Association 99: 560-561. [PDF]
S Ramachandran, NA Rosenberg, LA Zhivotovsky, MW Feldman
(2004) Robustness of the inference of human population structure: a
comparison of X-chromosomal and autosomal microsatellites. Human
Genomics 1: 87-97. [Abstract] [PDF]
NA Rosenberg (2004) Distruct: a program for the
graphical display of population structure. Molecular Ecology
Notes 4: 137-138. [Abstract] [PDF] [Software]
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.
[Abstract] [PDF] [Supplement] [Microsatellite data] [SNP data] [SNP data readme] [Solution to Problem 11039 required in
appendix of paper (American Mathematical Monthly 112:
572-573, 2005)] [Software]
NA Rosenberg, AE Hirsh (2003) On the use of star-shaped
genealogies in inference of coalescence times. Genetics 164:
1677-1682. [Abstract]
[PDF]
NA Rosenberg (2003) The shapes of neutral gene genealogies
in two species: probabilities of monophyly, paraphyly, and polyphyly
in a coalescent model. Evolution 57: 1465-1477. [Abstract] [PDF]
NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA
Zhivotovsky, MW Feldman (2003) Response to comment on "Genetic
structure of human populations." Science 300: 1877. [Abstract] [PDF] [Data]
NA Rosenberg, AG Tsolaki, MM Tanaka (2003) Estimating change
rates of genetic markers using serial samples: applications to the
transposon IS6110 in Mycobacterium tuberculosis.
Theoretical Population Biology 63: 347-363. [Abstract] [PDF]
LA Zhivotovsky, NA Rosenberg, MW Feldman (2003)
Features of evolution and expansion of modern humans, inferred from
genomewide microsatellite markers. American Journal of Human
Genetics 72: 1171-1186. [Abstract] [PDF] [Data]
NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA
Zhivotovsky, MW Feldman (2002) Genetic structure of human
populations. Science 298: 2381-2385. [Abstract] [Full
Text at Science website] [PDF] [Supplement] [Data
in Excel] [Data in structure and
NEXUS formats] [Software for drawing
figures] [Español]
NA Rosenberg, D Nettle (2002) Joining forces to uncover
human evolutionary history. Trends in Ecology and Evolution
17: 301-302. (report on Genes, Peoples, and Languages conference) [PDF]
NA Rosenberg, M Nordborg (2002) Genealogical trees,
coalescent theory, and the analysis of genetic polymorphisms.
Nature Reviews Genetics 3: 380-390. [Abstract] [PDF] [article
at NRG website (includes "bullet point" summary)]
NA Rosenberg (2002) The probability of topological
concordance of gene trees and species trees. Theoretical
Population Biology 61: 225-247. [Abstract] [PDF]
NA Rosenberg, MW Feldman (2002) The relationship between
coalescence times and population divergence times. Chapter 9 in M
Slatkin and M Veuille, eds. Modern Developments in Theoretical
Population Genetics. Oxford: Oxford University Press,
pp. 130-164. [Abstract] [PDF of final version]
NA Rosenberg, T Burke, K Elo, MW Feldman, P Friedlin,
MAM Groenen, J Hillel, A Mäki-Tanila, M Tixier-Boichard, A Vignal, K
Wimmers, S Weigend (2001) Empirical evaluation of genetic clustering
methods using multilocus genotypes from 20 chicken breeds.
Genetics 159: 699-713. [Abstract] [PDF] [Data] [Photo]
MM Tanaka, NA Rosenberg (2001) Optimal estimation of
transposition rates of insertion sequences for molecular epidemiology.
Statistics in Medicine 20: 2409-2420. [Abstract] [PDF]
NA Rosenberg, E Woolf, JK Pritchard, T Schaap, D Gefel,
I Shpirer, U Lavi, B Bonné-Tamir, J Hillel, MW Feldman (2001)
Distinctive genetic signatures in the Libyan Jews. Proceedings of
the National Academy of Sciences, USA 98: 858-863. [Abstract] [PDF] [Data]
L Jin , ML Baskett, LL Cavalli-Sforza, LA Zhivotovsky, MW Feldman,
NA Rosenberg (2000) Microsatellite evolution in modern humans:
a comparison of two data sets from the same populations. Annals of
Human Genetics 64: 117-134. [Abstract] [PDF] [Data]
JK Pritchard, M Stephens, NA Rosenberg, P Donnelly
(2000) Association mapping in structured populations. American
Journal of Human Genetics 67: 170-181. [Abstract] [PDF]
JK Pritchard, NA Rosenberg (1999) Use of unlinked genetic
markers to detect population stratification in association studies.
American Journal of Human Genetics 65: 220-228. [Abstract] [PDF]
Noah Rosenberg's publications 1999-2005
2004
2003
2002
2001
2000
1999