Noah A Rosenberg

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
    N A Rosenberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Genetics 159:699-713. 2001
  2. ncbi request reprint Polyploid and multilocus extensions of the Wahlund inequality
    Noah A Rosenberg
    Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1042 West 36th Place DRB 289, Los Angeles, CA 90089, USA
    Theor Popul Biol 66:381-91. 2004
  3. pmc Informativeness of genetic markers for inference of ancestry
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
    Am J Hum Genet 73:1402-22. 2003
  4. ncbi request reprint The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model
    Noah A Rosenberg
    Molecular and Computational Biology, University of Southern California, 1042 West 36th Place, DRB 289, Los Angeles, California 90089, USA
    Evolution 57:1465-77. 2003
  5. pmc On the use of star-shaped genealogies in inference of coalescence times
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, 1042 W 36th Pl, DRB 289, Los Angeles, CA 90089, USA
    Genetics 164:1677-82. 2003
  6. ncbi request reprint Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis
    Noah A Rosenberg
    Department of Biological Sciences, University of Southern California, 1042 W 36th Place DRB 289, Los Angeles, CA 90089, USA
    Theor Popul Biol 63:347-63. 2003
  7. ncbi request reprint The probability of topological concordance of gene trees and species trees
    Noah A Rosenberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Theor Popul Biol 61:225-47. 2002
  8. ncbi request reprint Genetic structure of human populations
    Noah A Rosenberg
    Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
    Science 298:2381-5. 2002
  9. pmc Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites
    Sohini Ramachandran
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    Hum Genomics 1:87-97. 2004
  10. pmc Genomic patterns of homozygosity in worldwide human populations
    Trevor J Pemberton
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Am J Hum Genet 91:275-92. 2012

Detail Information

Publications48

  1. pmc Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
    N A Rosenberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Genetics 159:699-713. 2001
    ..The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation...
  2. ncbi request reprint Polyploid and multilocus extensions of the Wahlund inequality
    Noah A Rosenberg
    Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1042 West 36th Place DRB 289, Los Angeles, CA 90089, USA
    Theor Popul Biol 66:381-91. 2004
    ..Using microsatellite genotypes from human populations, we demonstrate that the multilocus Wahlund inequality can explain a positive bias in "identity-in-state excess"...
  3. pmc Informativeness of genetic markers for inference of ancestry
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
    Am J Hum Genet 73:1402-22. 2003
    ..Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry...
  4. ncbi request reprint The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model
    Noah A Rosenberg
    Molecular and Computational Biology, University of Southern California, 1042 West 36th Place, DRB 289, Los Angeles, California 90089, USA
    Evolution 57:1465-77. 2003
    ..The results have potential applications for the testing of evolutionary hypotheses...
  5. pmc On the use of star-shaped genealogies in inference of coalescence times
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, 1042 W 36th Pl, DRB 289, Los Angeles, CA 90089, USA
    Genetics 164:1677-82. 2003
    ..The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr...
  6. ncbi request reprint Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis
    Noah A Rosenberg
    Department of Biological Sciences, University of Southern California, 1042 W 36th Place DRB 289, Los Angeles, CA 90089, USA
    Theor Popul Biol 63:347-63. 2003
    ..0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology...
  7. ncbi request reprint The probability of topological concordance of gene trees and species trees
    Noah A Rosenberg
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Theor Popul Biol 61:225-47. 2002
    ..Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation...
  8. ncbi request reprint Genetic structure of human populations
    Noah A Rosenberg
    Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
    Science 298:2381-5. 2002
    ..General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies...
  9. pmc Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites
    Sohini Ramachandran
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    Hum Genomics 1:87-97. 2004
    ..The dependence of the partitioning on the number of individuals sampled from each region and on the number of markers used is discussed...
  10. pmc Genomic patterns of homozygosity in worldwide human populations
    Trevor J Pemberton
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Am J Hum Genet 91:275-92. 2012
    ..These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases...
  11. pmc Haplotypic background of a private allele at high frequency in the Americas
    Kari B Schroeder
    Department of Anthropology, University of California, Davis, CA, USA
    Mol Biol Evol 26:995-1016. 2009
    ....
  12. pmc A population-genetic perspective on the similarities and differences among worldwide human populations
    Noah A Rosenberg
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Hum Biol 83:659-84. 2011
    ..The collection of answers obtained provides an introductory perspective for understanding key results on the features of worldwide human genetic variation...
  13. pmc Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa
    Sohini Ramachandran
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:15942-7. 2005
    ..Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation...
  14. pmc A coalescent model for genotype imputation
    Ethan M Jewett
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Genetics 191:1239-55. 2012
    ..Our approach can be extended to understand additional factors that affect imputation accuracy in complex population-genetic settings, and the results can ultimately facilitate improvements in imputation study designs...
  15. pmc iGLASS: an improvement to the GLASS method for estimating species trees from gene trees
    Ethan M Jewett
    Department of Biology, Stanford University, Stanford, California 94305 5020, USA
    J Comput Biol 19:293-315. 2012
    ..Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree...
  16. pmc Nonadaptive explanations for signatures of partial selective sweeps in Drosophila
    J Michael Macpherson
    Department of Biological Sciences, Stanford University, USA
    Mol Biol Evol 25:1025-42. 2008
    ....
  17. pmc Long runs of homozygosity are enriched for deleterious variation
    Zachary A Szpiech
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
    Am J Hum Genet 93:90-102. 2013
    ..Thus, just as inbreeding can elevate the occurrence of rare recessive diseases that represent homozygotes for strongly deleterious mutations, inbreeding magnifies the occurrence of mildly deleterious variants as well. ..
  18. pmc Impact of restricted marital practices on genetic variation in an endogamous Gujarati group
    Trevor J Pemberton
    Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Am J Phys Anthropol 149:92-103. 2012
    ....
  19. pmc On the genealogy of a duplicated microsatellite
    Kangyu Zhang
    Department of Mathematics, University of Southern California, Los Angeles 90089 1113, USA
    Genetics 177:2109-22. 2007
    ..Our results can be useful for helping to interpret genetic variation at microsatellite loci in species with a very recent history of gene and genome duplication...
  20. ncbi request reprint Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, 835 West 37th Street, SHS172, Los Angeles, California 90089 1340, USA
    Nat Rev Genet 3:380-90. 2002
    ..Traditional analysis methods do not take this into account. A stochastic process known as the 'coalescent' presents a coherent statistical framework for analysis of genetic polymorphisms...
  21. pmc The pattern of polymorphism in Arabidopsis thaliana
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Biol 3:e196. 2005
    ..Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics...
  22. pmc Population structure in a comprehensive genomic data set on human microsatellite variation
    Trevor J Pemberton
    Department of Biology, Stanford University, Stanford, California 94305, USA
    G3 (Bethesda) 3:891-907. 2013
    ..Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies...
  23. pmc Genetic variation and population structure in native Americans
    Sijia Wang
    The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
    PLoS Genet 3:e185. 2007
    ..These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas...
  24. doi request reprint Genotype, haplotype and copy-number variation in worldwide human populations
    Mattias Jakobsson
    Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 451:998-1003. 2008
    ..Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations...
  25. pmc Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, 77030, USA
    Genetics 169:1763-77. 2005
    ..For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster...
  26. pmc Demographic history of european populations of Arabidopsis thaliana
    Olivier Francois
    Institut National Polytechnique de Grenoble, Grenoble, France
    PLoS Genet 4:e1000075. 2008
    ..However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition...
  27. pmc The relationship between homozygosity and the frequency of the most frequent allele
    Noah A Rosenberg
    Department of Human Genetics, Center for Computational Medicine and Biology, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    Genetics 179:2027-36. 2008
    ....
  28. pmc ADZE: a rarefaction approach for counting alleles private to combinations of populations
    Zachary A Szpiech
    Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Bioinformatics 24:2498-504. 2008
    ..However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups...
  29. ncbi request reprint The control of copy number of IS6110 in Mycobacterium tuberculosis
    Mark M Tanaka
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    Mol Biol Evol 21:2195-201. 2004
    ..Specifically, our analysis points to the interaction of separate copies of the element causing lethal effects. We discuss the implications of these findings for genome evolution and molecular epidemiology...
  30. pmc Low levels of genetic divergence across geographically and linguistically diverse populations from India
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 2:e215. 2006
    ....
  31. pmc Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers
    Lev A Zhivotovsky
    Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
    Am J Hum Genet 72:1171-86. 2003
    ..The features of population subdivision and growth are discussed in the context of the ancient expansion of modern humans...
  32. ncbi request reprint Algorithms for selecting informative marker panels for population assignment
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 2218, USA
    J Comput Biol 12:1183-201. 2005
    ..Although none of the approaches necessarily chooses the panel with optimal performance, the algorithms all likely select panels with performance near enough to the maximum that they all are suitable for practical use...
  33. ncbi request reprint Counting coalescent histories
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    J Comput Biol 14:360-77. 2007
    ....
  34. pmc Clines, clusters, and the effect of study design on the inference of human population structure
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
    PLoS Genet 1:e70. 2005
    ....
  35. pmc A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program and the Life Sciences Institute, University of Michigan, Michigan 48109 2218, USA
    Genetics 173:1665-78. 2006
    ..This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations...
  36. pmc Discordance of species trees with their most likely gene trees
    James H Degnan
    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
    PLoS Genet 2:e68. 2006
    ..We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies...
  37. ncbi request reprint Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, 2017 Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI 48109 2218, USA
    Ann Hum Genet 70:841-7. 2006
    ..Together with information on atypical and duplicated samples, the inferred relative pairs suggest standardized subsets of the panel for use in future population-genetic studies...
  38. ncbi request reprint A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
    Donald F Conrad
    Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
    Nat Genet 38:1251-60. 2006
    ..Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations...
  39. ncbi request reprint Sampling properties of homozygosity-based statistics for linkage disequilibrium
    Noah A Rosenberg
    Department of Human Genetics, University of Michigan, 1241 East Catherine Street, Ann Arbor, MI 48109 0618, USA
    Math Biosci 208:33-47. 2007
    ....
  40. ncbi request reprint A sharp minimum on the mean number of steps taken in adaptive walks
    Noah A Rosenberg
    Department of Human Genetics and Bioinformatics Program, University of Michigan, 2017 Palmer Commons, Box 2218, 100 Washtenaw Avenue, Ann Arbor, MI 48109 2218, USA
    J Theor Biol 237:17-22. 2005
    ....
  41. ncbi request reprint Statistical tests for taxonomic distinctiveness from observations of monophyly
    Noah A Rosenberg
    Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    Evolution 61:317-23. 2007
    ..The results suggest minimal sample sizes required for inferences to be made about taxonomic distinctiveness from observations of monophyly...
  42. pmc Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L
    Lior David
    Department of Animal Sciences, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P O Box 12, Rehovot, 76100, Israel
    Genet Sel Evol 39:319-40. 2007
    ..Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication...
  43. pmc Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling
    Michael G B Blum
    Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 176:1741-57. 2007
    ..Our estimates support a view that the proportion of the modern population consisting of Neanderthal contributions must be relatively small, less than approximately 5%, if the admixture happened as recently as 30,000 years ago...
  44. ncbi request reprint CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    Mattias Jakobsson
    Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1801-6. 2007
    ....
  45. pmc Mathematical properties of the r2 measure of linkage disequilibrium
    Jenna M VanLiere
    Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Theor Popul Biol 74:130-7. 2008
    ..Our results concerning the properties of r(2) have the potential to inform the interpretation of unusual LD behavior and to assist in the design of LD-based association-mapping studies...
  46. ncbi request reprint Read all about it: The Lancet's Paper of the Year, 2003
    Richard Horton
    The Lancet, 32 Jamestown Road, London NW1 7BY, UK
    Lancet 362:2101-3. 2003
  47. ncbi request reprint The probability distribution under a population divergence model of the number of genetic founding lineages of a population or species
    Mattias Jakobsson
    Bioinformatics Program, Department of Human Genetics, University of Michigan, 2017 Palmer Commons, 100 Washtenaw Ave, Ann Arbor, MI 48109 2218, USA
    Theor Popul Biol 71:502-23. 2007
    ....
  48. doi request reprint Discordance of species trees with their most likely gene trees: the case of five taxa
    Noah A Rosenberg
    Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109 2218, USA
    Syst Biol 57:131-40. 2008
    ....