Rosenberg lab at Stanford University

Noah A Rosenberg
+1 650 721 2599 (office phone)
+1 650 724 5122 (lab phone)
+1 650 724 5114 (fax)


Mailing address
Department of Biology
Stanford University
371 Jane Stanford Way
Stanford, CA 94305-5020 USA

Last modified 9-20-2024

Lab alumni publications based on their time in the lab

[Postdocs] [PhD students] [Master's students]
[Undergraduates]

Postdocs

Nicolas Alcala (Oct 2014 - Mar 2017).

  • ML Morrison, N Alcala, NA Rosenberg (2022) FSTruct: an FST-based tool for measuring ancestry variation in inference of population structure. Molecular Ecology Resources 22: 2614-2626. [Abstract] [PDF] [Supplement]

  • N Alcala, NA Rosenberg (2022) Mathematical constraints on FST: multiallelic markers in arbitrarily many populations. Philosophical Transactions of the Royal Society B: Biological Sciences 377: 20200414. [Abstract] [PDF] [Supplement]

  • N Alcala, A Goldberg, U Ramakrishnan, NA Rosenberg (2019) Coalescent theory of migration network motifs. Molecular Biology and Evolution 36: 2358-2374. [Abstract] [PDF] [Supplement]

  • N Alcala, AE Launer, MF Westphal, R Seymour, EM Cole*, NA Rosenberg* (2019) Use of stochastic patch occupancy models in the California red-legged frog for Bayesian inference regarding past events and future persistence. Conservation Biology 33: 685-696. [Abstract] [PDF] [Supplement] [Data and Software]

  • N Alcala, NA Rosenberg (2019) G'ST, Jost's D, and FST are similarly constrained by allele frequencies: a mathematical, simulation, and empirical study. Molecular Ecology 28: 1624-1636. [Abstract] [PDF] [Supplement]

  • N Alcala, NA Rosenberg (2017) Mathematical constraints on FST: biallelic markers in arbitrarily many populations. Genetics 206: 1581-1600. [Abstract] [PDF] [File S1] [File S2]
Bridget Algee-Hewitt (Sep 2013 - June 2018).
  • J Kim, MD Edge, BFB Algee-Hewitt, JZ Li, NA Rosenberg (2018) Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell 175: 848-858. [Abstract] [PDF] [PDF] [Code]

  • 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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]
Michael Blum (Nov 2005 - Sep 2006).

  • 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]

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

  • 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] [PDF] [Supplementary Tables 1-3 (DOC)] [Supplementary Tables 1-3 (PDF)]
Erkan Buzbas (Jul 2009 - Aug 2012).

  • EO Buzbas, NA Rosenberg (2015) AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology 99: 31-42. [Abstract] [PDF]

  • 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]

  • 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).

  • 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]

  • 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]
James Degnan (Jul 2007 - Sep 2008).

  • A Kim, NA Rosenberg, JH Degnan (2020) Probabilities of unranked and ranked anomaly zones under birth-death models. Molecular Biology and Evolution 37: 1480-1494. [Abstract]

  • 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. [Abstract] [PDF] [Supplement]

  • 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]

  • JH Degnan, NA Rosenberg, T Stadler (2012) The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235: 45-55. [Abstract]

  • 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]

  • NA Rosenberg, JH Degnan (2010) Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151. [Abstract] [PDF]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • JH Degnan, NA Rosenberg (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics 2: 762-768. [Abstract] [PDF]
Filippo Disanto (Nov 2013 - Feb 2017).

  • F Disanto, M Fuchs, C-Y Huang, AR Paningbatan, NA Rosenberg (2024) The distributions under two species-tree models of the total number of ancestral configurations for matching gene trees and species trees. Advances in Applied Mathematics 152: 102594. [Abstract]

  • F Disanto, M Fuchs, AR Paningbatan, NA Rosenberg (2022) The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees. Annals of Applied Probability 32: 4426-4458. [Abstract] [PDF]

  • JA Palacios, A Bhaskar, F Disanto, NA Rosenberg (2022) Enumeration of binary trees compatible with a perfect phylogeny. Journal of Mathematical Biology 84: 54. [Abstract] [PDF]

  • F Disanto, NA Rosenberg (2019) Enumeration of compact coalescent histories for matching gene trees and species trees. Journal of Mathematical Biology 78: 155-188. [Abstract] [PDF]

  • J Kim, F Disanto, NM Kopelman, NA Rosenberg (2019) Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm. Bulletin of Mathematical Biology 81: 452-493. [Abstract] [PDF] [Supplement]

  • F Disanto, NA Rosenberg (2019) On the number of non-equivalent ancestral configurations for matching gene trees and species trees. Bulletin of Mathematical Biology 81: 384-407. [Abstract] [PDF]

  • F Disanto, NA Rosenberg (2017) Enumeration of ancestral configurations for matching gene trees and species trees. Journal of Computational Biology 24: 831-850. [Abstract] [PDF]

  • F Disanto, NA Rosenberg (2016) Asymptotic properties of the number of matching coalescent histories for caterpillar-like families of species trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13: 913-925. [Abstract] [PDF]

  • F Disanto, NA Rosenberg (2015) Coalescent histories for lodgepole species trees. Journal of Computational Biology 22: 918-929. [Abstract] [PDF]

  • F Disanto, NA Rosenberg (2014) On the number of ranked species trees producing anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 11: 1229-1238. [Abstract] [PDF]
Gili Greenbaum (Sep 2017 - Aug 2020).

  • EE Armstrong*, JA Mooney*, KA Solari, BY Kim, GS Barsh, VB Grant, G Greenbaum, CB Kaelin, K Panchenko, JK Pickrell, NA Rosenberg, OA Ryder, T Yokoyama, U Ramakrishnan, DA Petrov, EA Hadly. Unraveling the genomic diversity and admixture history of captive tigers in the United States. Proceedings of the National Academy of Sciences USA 121: e2402924121 (2024). [Abstract] [PDF] [Supplementary Appendix ]

  • X Liu, NA Rosenberg, G Greenbaum (2022) Extracting hierarchical features of cultural variation using network-based clustering. Evolutionary Human Sciences 4: e18. [Abstract] [PDF] [Supplement] [Supplementary code] [Supplementary data]

  • G Greenbaum, MW Feldman, NA Rosenberg, J Kim (2021) Designing gene drives to limit spillover to non-target populations. PLoS Genetics 17: e1009278. [Abstract] [PDF] [Supplement]

  • G Greenbaum, A Rubin, AR Templeton, NA Rosenberg (2019) Network-based hierarchical population structure analysis for large genomic datasets. Genome Research 29: 2020-2033. [Abstract] [PDF] [Supplement]

  • G Greenbaum, WM Getz, NA Rosenberg, MW Feldman, E Hovers, O Kolodny (2019) Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals. Nature Communications 10: 5003. [Abstract] [PDF] [Supplement]
Mattias Jakobsson (Sep 2005 - Mar 2008).

  • A Goldberg, T Günther, NA Rosenberg, M Jakobsson (2017). Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe. Proceedings of the National Academy of Sciences USA 114: E3875-E3877. [PDF]

  • 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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement] [Software]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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] [PDF]

  • 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]

  • 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]

  • 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]

  • 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] [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]

  • 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]

  • 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]
Olga Kamneva (Jul 2013 - Jul 2016).
Jaehee Kim (Oct 2015 - Dec 2021).

  • J Kim, NA Rosenberg (2023) Record-matching of STR profiles with fragmentary genomic SNP data. European Journal of Human Genetics 31: 1283-1290. [Abstract] [PDF] [Supplement]

  • J Kim, MD Edge, A Goldberg, NA Rosenberg (2021) Skin deep: the decoupling of genetic admixture levels from phenotypes that differed between source populations. American Journal of Physical Anthropology 175: 406-421 (2021). [Abstract]

  • J Kim, NA Rosenberg, JA Palacios (2020) Distance metrics for ranked evolutionary trees. Proceedings of the National Academy of Sciences 117: 28876-28886. [Abstract] [PDF] [Supplement]

  • AL Fortier, J Kim, NA Rosenberg (2020) Human-genetic ancestry inference and false positives in forensic familial searching. G3: Genes, Genomes, Genetics 10: 2893-2902. [Abstract] [PDF] [Supplement]

  • J Kim, F Disanto, NM Kopelman, NA Rosenberg (2019) Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm. Bulletin of Mathematical Biology 81: 452-493. [Abstract] [PDF]

  • J Kim, MD Edge, BFB Algee-Hewitt, JZ Li, NA Rosenberg (2018) Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell 175: 848-858. [Abstract] [PDF] [Supplement] [Code]

  • 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. [Abstract] [PDF] [Supplement]
Jazlyn Mooney (Sep 2020 - Dec 2021).

  • EE Armstrong*, JA Mooney*, KA Solari, BY Kim, GS Barsh, VB Grant, G Greenbaum, CB Kaelin, K Panchenko, JK Pickrell, NA Rosenberg, OA Ryder, T Yokoyama, U Ramakrishnan, DA Petrov, EA Hadly. Unraveling the genomic diversity and admixture history of captive tigers in the United States. Proceedings of the National Academy of Sciences USA 121: e2402924121 (2024). [Abstract] [PDF] [Supplementary Appendix ]

  • L Agranat-Tamir, JA Mooney, NA Rosenberg (2024). Counting the genetic ancestors from source populations in members of an admixed population. Genetics 226: iyae011. [Abstract] [PDF] [Supplement]

  • JA Mooney, L Agranat-Tamir, JK Pritchard, NA Rosenberg (2023) On the number of genealogical ancestors tracing to the source groups of an admixed population. Genetics 224: iyad079. [Abstract] [PDF] [Supplement]
Trevor Pemberton (Mar 2008 - Dec 2012).

  • TJ Pemberton*, P Verdu*, NS Becker, CJ Willer, BS Hewlett, S Le Bomin, A Froment, NA Rosenberg, E Heyer (2018) A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers. Human Genetics 137: 487-509. [Abstract] [PDF] [Supplement]

  • 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. [Abstract] [PDF] [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. [Abstract] [PDF] [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. [Abstract] [PDF] [Supplement]

  • 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]

  • NA Rosenberg, TJ Pemberton, JZ Li, JW Belmont (2013) Runs of homozygosity and parental relatedness. Genetics in Medicine 15: 753-754. [PDF]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]
Paul Scheet (Sep 2006 - Jul 2008).

  • 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]

  • 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]

  • 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]
Cuong Than (Nov 2009 - Sep 2012).

  • CV Than, NA Rosenberg (2014) Mean deep coalescence cost under exchangeable probability distributions. Discrete Applied Mathematics 174: 11-26. [Abstract] [PDF]

  • 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]

  • CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [Abstract] [PDF]
Lawrence Uricchio (May 2015 - Dec 2018).

  • AL Severson*, LH Uricchio*, IM Arbisser*, EC Glassberg, NA Rosenberg (2019) Analysis of author gender in TPB, 1991-2018. Theoretical Population Biology 127: 1-6. [PDF] [Supplement]

  • A Goldberg, LH Uricchio, NA Rosenberg (2018) Natural selection in human populations. Oxford Bibliographies in Evolutionary Biology doi:10.1093/OBO/9780199941728-0112. [PDF]

  • LH Uricchio, T Warnow, NA Rosenberg (2016) An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. BMC Bioinformatics 17: 417. [Abstract] [PDF]
Paul Verdu (Sep 2009 - Sep 2012).

  • R Laurent, ZA Szpiech, SS da Cosa, V Thouzeau, CA Fortes-Lima, F Dessarps-Freichey, L Lémée, J Utgé, NA Rosenberg, M Baptista, P Verdu (2023) A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde. eLife 12: e79827. [Abstract] [PDF]

  • TJ Pemberton*, P Verdu*, NS Becker, CJ Willer, BS Hewlett, S Le Bomin, A Froment, NA Rosenberg, E Heyer (2018) A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers. Human Genetics 137: 487-509. [Abstract] [PDF] [Supplement]

  • 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. [Abstract] [PDF] [Supplement]

  • A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]

  • 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]

  • 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]


PhD students

Ilana Arbisser (Aug 2014 - Dec 2018).

  • IM Arbisser, NA Rosenberg (2020) FST and the triangle inequality for biallelic markers. Theoretical Population Biology 133: 117-129. [Abstract]

  • AL Severson*, LH Uricchio*, IM Arbisser*, EC Glassberg, NA Rosenberg (2019) Analysis of author gender in TPB, 1991-2018. Theoretical Population Biology 127: 1-6. [PDF] [Supplement]

  • IM Arbisser, EM Jewett, NA Rosenberg (2018) On the joint distribution of tree height and tree length under the coalescent. Theoretical Population Biology 122: 46-56. [Abstract] [PDF]
Daniel Cotter (Jan 2019 - Sep 2023).

  • DJ Cotter, AL Severson, JTL Kang, HN Godrej, S Carmi, NA Rosenberg (2024) Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes, Genomes, Genetics 14: jkad264. [Abstract] [PDF] [Supplement]

  • DJ Cotter, EF Hofgard, J Novembre, ZA Szpiech, NA Rosenberg (2023) A rarefaction approach for measuring population differences in rare and common variation. Genetics 224: iyad070. [Abstract] [PDF] [Supplement]

  • DJ Cotter, AL Severson, S Carmi, NA Rosenberg (2022) Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating. Theoretical Population Biology 147: 1-15. [Abstract]

  • DJ Cotter, AL Severson, NA Rosenberg (2021) The effect of consanguinity on coalescence times on the X chromosome. Theoretical Population Biology 140: 32-43. [Abstract]
Mike DeGiorgio (Apr 2007 - Aug 2011).

  • AL Severson, BF Byrd, EK Mallott, AC Owings, M DeGiorgio, A de Flamingh, C, Nijmeh, MV Arellano, A Leventhal, NA Rosenberg, RS Malhi (2022) Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences USA 119: e2111533119. [Abstract] [PDF] [Supplement]

  • M DeGiorgio, NA Rosenberg (2016) Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure. Theoretical Population Biology 110: 12-24. [Abstract] [PDF]

  • 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)]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]
Doc Edge (Jul 2012 - Feb 2017).

  • MD Edge, S Ramachandran, NA Rosenberg (2022) Celebrating 50 years since Lewontin's apportionment of human diversity. Philosophical Transactions of the Royal Society of London B: Biological Sciences 377: 20200405. [PDF]

  • J Kim, MD Edge, A Goldberg, NA Rosenberg (2021) Skin deep: the decoupling of genetic admixture levels from phenotypes that differed between source populations. American Journal of Physical Anthropology 175: 406-421 (2021). [Abstract]
  • NA Rosenberg, MD Edge, JK Pritchard, MW Feldman (2019) Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evolution, Medicine, and Public Health 2019: 26-34. [Abstract] [PDF]

  • J Kim, MD Edge, BFB Algee-Hewitt, JZ Li, NA Rosenberg (2018) Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell 175: 848-858. [Abstract] [PDF] [PDF]

  • 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. [Abstract] [PDF] [Supplement]

  • JTL Kang, A Goldberg, MD Edge, DM Behar, NA Rosenberg (2016) Consanguinity rates predict long runs of homozygosity in Jewish populations. Human Heredity 82: 87-102. [Abstract] [PDF]

  • 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. [Abstract] [PDF] [Supplement]

  • MD Edge, NA Rosenberg (2015) A general model of the relationship between the apportionment of human genetic diversity and the apportionment of human phenotypic diversity. Human Biology 87: 317-337. [Abstract] [PDF]

  • 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 52: 32-45. [Abstract] [PDF]

  • 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]

  • 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]

  • 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]
Amy Goldberg (Sep 2012 - Jun 2017).

  • J Kim, MD Edge, A Goldberg, NA Rosenberg (2021) Skin deep: the decoupling of genetic admixture levels from phenotypes that differed between source populations. American Journal of Physical Anthropology 175: 406-421 (2021). [Abstract]

  • A Goldberg, A Rastogi, NA Rosenberg (2020) Assortative mating by population of origin in a mechanistic model of admixture. Theoretical Population Biology 134: 129-146. [Abstract]

  • N Alcala, A Goldberg, U Ramakrishnan, NA Rosenberg (2019) Coalescent theory of migration network motifs. Molecular Biology and Evolution 36: 2358-2374. [Abstract] [PDF] [Supplement]

  • A Goldberg, LH Uricchio, NA Rosenberg (2018) Natural selection in human populations. Oxford Bibliographies in Evolutionary Biology doi:10.1093/OBO/9780199941728-0112. [PDF]

  • A Goldberg, T Günther, NA Rosenberg, M Jakobsson (2017) Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe. Proceedings of the National Academy of Sciences USA 114: E3875-E3877. [PDF]

  • 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. [Abstract] [PDF] [Supplement]

  • JTL Kang, A Goldberg, MD Edge, DM Behar, NA Rosenberg (2016) Consanguinity rates predict long runs of homozygosity in Jewish populations. Human Heredity 82: 87-102. [Abstract] [PDF]

  • A Goldberg, NA Rosenberg (2015) Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome. Genetics 201: 263-279. [Abstract] [PDF]

  • A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]
Lucy Huang (Nov 2006 - Dec 2011).

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]
Ethan Jewett (Jan 2010 - Sep 2014).

  • IM Arbisser, EM Jewett, NA Rosenberg (2018) On the joint distribution of tree height and tree length under the coalescent. Theoretical Population Biology 122: 46-56. [Abstract] [PDF]

  • 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. [Abstract] [PDF] [Supplement]

  • EM Jewett, NA Rosenberg (2014) Theory and applications of a deterministic approximation to the coalescent model. Theoretical Population Biology 93: 14-29. [Abstract] [PDF]

  • EM Jewett*, M Zawistowski*, NA Rosenberg, S Zöllner (2012) A coalescent model for genotype imputation. Genetics 191: 1239-1255. [Abstract] [PDF]

  • 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]

  • 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]

  • 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]

  • 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]
Jonathan Kang (Sep 2013 - Aug 2018).

  • DJ Cotter, AL Severson, JTL Kang, HN Godrej, S Carmi, NA Rosenberg (2024) Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes, Genomes, Genetics 14: jkad264. [Abstract] [PDF] [Supplement]

  • JTL Kang, NA Rosenberg (2019) Mathematical properties of linkage disequilibrium statistics defined by normalization of the coefficient D=pAB-pApB. Human Heredity 84: 127-143. [Abstract] [PDF]

  • JTL Kang, A Goldberg, MD Edge, DM Behar, NA Rosenberg (2016) Consanguinity rates predict long runs of homozygosity in Jewish populations. Human Heredity 82: 87-102. [Abstract] [PDF]

  • JTL Kang, P Zhang, S Zöllner, NA Rosenberg (2015) Choosing subsamples for sequencing studies by minimizing the average distance to the closest leaf. Genetics 201: 499-511. [Abstract] [PDF]

  • NA Rosenberg, JTL Kang (2015) Genetic diversity and societally important disparities. Genetics 201: 1-12. [Abstract] [PDF] [Supplement]
Naama Kopelman (Jul 2007 - Feb 2014).

  • X Liu, NM Kopelman, NA Rosenberg (2024) Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics 40: btad751. [Abstract] [PDF] [Supplement]

  • X Liu, NM Kopelman, NA Rosenberg (2023) A Dirichlet model of alignment cost in mixed-membership unsupervised clustering. Journal of Computational and Graphical Statistics 32: 1145-1159. [Abstract] [PDF] [Supplement]

  • NM Kopelman, L Stone, DG Hernandez, D Gefel, AB Singleton, E Heyer, MW Feldman, J Hillel, NA Rosenberg (2020) High-resolution inference of genetic relationships among Jewish populations. European Journal of Human Genetics 28: 804-814. [Abstract]

  • J Kim, F Disanto, NM Kopelman, NA Rosenberg (2019) Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm. Bulletin of Mathematical Biology 81: 452-493. [Abstract] [PDF]

  • 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. [Abstract] [PDF] [Supplement] [Software]

  • 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]

  • 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: 273-284. [Abstract] [PDF]

  • 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] [Data]

Xiran Liu (Jun 2019 - Sep 2023).

  • X Liu, NM Kopelman, NA Rosenberg (2024) Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics 40: btad751. [Abstract] [PDF] [Supplement]

  • X Liu, Z Ahsan, TK Martheswaran, NA Rosenberg (2023) When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself? Statistical Applications in Genetics and Molecular Biology 22: 2023004. [Abstract] [PDF]

  • X Liu, NM Kopelman, NA Rosenberg (2023) A Dirichlet model of alignment cost in mixed-membership unsupervised clustering. Journal of Computational and Graphical Statistics 32: 1145-1159. [Abstract] [PDF] [Supplement]

  • X Liu, NA Rosenberg, G Greenbaum (2022) Extracting hierarchical features of cultural variation using network-based clustering. Evolutionary Human Sciences 4: e18. [Abstract] [PDF] [Supplement] [Supplementary code] [Supplementary data]
Rohan Mehta (Sep 2013 - Dec 2018).

  • RS Mehta, M Steel, NA Rosenberg (2022) The probability of joint monophyly of samples of gene lineages for all species in an arbitrary species tree. Journal of Computational Biology 27: 679-703. [Abstract]

  • RS Mehta, NA Rosenberg (2020) Modelling anti-vaccine sentiment as a cultural pathogen. Evolutionary Human Sciences 2: e21. [Abstract] [PDF] [Supplement]

  • RS Mehta, NA Rosenberg (2019) The probability of reciprocal monophyly of gene lineages in three and four species. Theoretical Population Biology 129: 133-147. [Abstract] [PDF]

  • RS Mehta, AF Feder, SM Boca, NA Rosenberg (2019) The relationship between haplotype-based FST and haplotype length. Genetics 213: 281-295. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Figure 3] [Supplementary Figure 4]

  • 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 USA 113: 8002-8009. [Abstract] [PDF] [Supplement] [Software]
Alissa Severson (Jan 2017 - Sep 2021).

  • DJ Cotter, AL Severson, JTL Kang, HN Godrej, S Carmi, NA Rosenberg (2024) Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes, Genomes, Genetics 14: jkad264. [Abstract] [PDF] [Supplement]

  • DJ Cotter, AL Severson, S Carmi, NA Rosenberg (2022) Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating. Theoretical Population Biology 147: 1-15. [Abstract]

  • AL Severson, BF Byrd, EK Mallott, AC Owings, M DeGiorgio, A de Flamingh, C, Nijmeh, MV Arellano, A Leventhal, NA Rosenberg, RS Malhi (2022) Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences USA 119: e2111533119. [Abstract] [PDF] [Supplement]

  • DJ Cotter, AL Severson, NA Rosenberg The effect of consanguinity on coalescence times on the X chromosome. Theoretical Population Biology 140: 32-43 (2021). [Abstract]

  • AL Severson, S Carmi, NA Rosenberg (2021) Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population. Theoretical Population Biology 139: 50-65. [Abstract]

  • AL Severson*, LH Uricchio*, IM Arbisser*, EC Glassberg, NA Rosenberg (2019) Analysis of author gender in TPB, 1991-2018. Theoretical Population Biology 127: 1-6. [PDF] [Supplement]

  • AL Severson, S Carmi, NA Rosenberg (2019) The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212: 305-316. [Abstract]
Zachary Szpiech (Dec 2007 - Sep 2012).

  • R Laurent, ZA Szpiech, SS da Cosa, V Thouzeau, CA Fortes-Lima, F Dessarps-Freichey, L Lémée, J Utgé, NA Rosenberg, M Baptista, P Verdu (2023) A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde. eLife 12: e79827. [Abstract] [PDF]

  • DJ Cotter, EF Hofgard, J Novembre, ZA Szpiech, NA Rosenberg (2023) A rarefaction approach for measuring population differences in rare and common variation. Genetics 224: iyad070. [Abstract] [PDF] [Supplement]

  • 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]

  • ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]

  • 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]

  • 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]

  • 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]

  • 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]
Chaolong Wang (Jan 2009 - Sep 2012).

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]

  • 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]


Master's students

Laura Helmkamp (Aug 2010 - Aug 2011).

  • 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]
Jenna VanLiere (Sep 2006 - Apr 2008).

  • NA Rosenberg, JM VanLiere (2009) Replication of genetic associations as pseudoreplication due to shared genealogy. Genetic Epidemiology 33: 479-487. [Abstract] [PDF]

  • JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology 74: 130-137. [Abstract] [PDF]

  • 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]


Undergraduates

Alan Aw (Aug 2015 - Aug 2018).

  • AJ Aw, NA Rosenberg (2018) Bounding measures of genetic similarity and diversity using majorization. Journal of Mathematical Biology 77: 711-737. [Abstract] [PDF]
Hormazd Godrej (Sep 2016 - Dec 2018)

  • DJ Cotter, AL Severson, JTL Kang, HN Godrej, S Carmi, NA Rosenberg (2024) Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing. G3: Genes, Genomes, Genetics 14: jkad264. [Abstract] [PDF] [Supplement]
Amy Goldberg (Apr 2011 - Aug 2011).

  • A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]

    Publications from the PhD period are listed under PhD students

Zoe Himwich (Apr 2017 - Jun 2019).

  • ZM Himwich, NA Rosenberg (2020) Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees. Advances in Applied Mathematics 113: 101939. [Abstract]
Elyssa Hofgard (Mar 2021 - Sep 2021).

  • DJ Cotter, EF Hofgard, J Novembre, ZA Szpiech, NA Rosenberg (2023) A rarefaction approach for measuring population differences in rare and common variation. Genetics 224: iyad070. [Abstract] [PDF] [Supplement]
Ivana Jankovic (Apr 2008 - May 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]

  • I Jankovic, BM vonHoldt, NA Rosenberg (2010) Heterozygosity of the Yellowstone wolves. Molecular Ecology 19: 3246-3249. [PDF]

  • 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]
Matthew King (Mar 2021 - Jun 2022).

  • MC King, NA Rosenberg (2023) A mathematical connection between single-elimination sports tournaments and evolutionary trees. Mathematics Magazine 96: 484-497. [Abstract] [PDF]

  • MC King, NA Rosenberg (2021) A simple derivation of the mean of the Sackin index of tree balance under the uniform model on rooted binary labeled trees. Mathematical Biosciences 342: 108688. [PDF]
Alessandra Maranca (Feb 2021 - Aug 2021).

  • ARP Maranca, NA Rosenberg (2024) Bijections between the multifurcating unlabeled rooted trees and the positive integers. Advances in Applied Mathematics 153: 102612. [Abstract] [PDF]
Ananya Rastogi (May 2014 - Jul 2014).

  • A Goldberg, A Rastogi, NA Rosenberg (2020) Assortative mating by population of origin in a mechanistic model of admixture. Theoretical Population Biology 134: 129-146. [Abstract]
Shashir Reddy (Sep 2008 - Jan 2010).

  • 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]
Zachary Szpiech (Sep 2006 - Aug 2007).
Randa Tao (Feb 2006 - Jun 2006).

  • 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] [PDF] [Supplement]