Noah Rosenberg laboratory at the University of Michigan

Rosenberg lab publications


In press

JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology in press.

O François, MGB Blum, M Jakobsson, NA Rosenberg (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics in press.

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 in press.


2008

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]

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]

NA Rosenberg (2007) Counting coalescent histories. Journal of Computational Biology 14: 360-377. [Abstract]

NA Rosenberg, MGB Blum (2007) Sampling properties of homozygosity-based statistics for linkage disequilibrium. Mathematical Biosciences 208: 33-47. [Abstract]

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]

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]

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]

NA Rosenberg (2007) Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61: 317-323. [Abstract]


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]


Noah Rosenberg's publications 1999-2005

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]


2004

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]


2003

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]


2002

NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2981-2985. [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]


2001

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]


2000

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]


1999

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]