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 12-8-2025

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, Z Ahsan, NA Rosenberg (2025) Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities. Theoretical Population Biology 166: 116-137. [Abstract] [PDF]

  • 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]
Maike Morrison (Sep 2020 - Aug 2025).

  • ML Morrison, KS Xue, NA Rosenberg (2025) Quantifying compositional variability in microbial communities with FAVA. Proceedings of the National Academy of Sciences USA 122: e2413211122. [Abstract] [PDF] [Supplement]

  • ML Morrison, NA Rosenberg (2023) Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon. Journal of Mathematical Biology 87: 76. [Abstract] [PDF] [Supplement]

  • 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]
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

Zarif Ahsan (Jun 2022 - Jun 2025).

  • X Liu, Z Ahsan, NA Rosenberg (2025) Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities. Theoretical Population Biology 166: 116-137. [Abstract] [PDF]

  • 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]
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]
Emily Dickey (Apr 2023 - Aug 2025)

  • EH Dickey, NA Rosenberg (2025) Labeled histories with multifurcation and simultaneity. Philosophical Transactions of the Royal Society B Biological Sciences 380: 20230307. [Abstract] [PDF]
Michael Doboli (Apr 2023 - Aug 2025)

  • L Devroye, MR Doboli, NA Rosenberg, S Wagner (2025) Tree height and the asymptotic mean of the Colijn-Plazzotta rank of unlabeled binary rooted trees. Bulletin of Mathematical Biology 87: 172. [Abstract] [PDF]

  • M Doboli, H-K Hwang, NA Rosenberg. Periodic behavior of the minimal Colijn-Plazzotta rank for trees with a fixed number of leaves. In C. Mailler, S. Wild, eds. Proceedings of the 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs) 302: 18 (2024). Schloss Dagstuhl — Leibniz-Zentrum für Informatik. [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]
Egor Lappo (Oct 2018 - Jun 2022).
  • E Lappo, NA Rosenberg (2022) Approximations to the expectations and variances of ratios of tree properties under the coalescent. G3: Genes, Genomes, Genetics 12: jkac205. [Abstract] [PDF]

  • E Alimpiev, NA Rosenberg (2022) A compendium of covariances and correlation coefficients of coalescent tree properties. Theoretical Population Biology 143: 1-13. [Abstract] [PDF]

  • E Alimpiev, NA Rosenberg (2021) Enumeration of coalescent histories for caterpillar species trees and p-pseudocaterpillar gene trees. Advances in Applied Mathematics 131: 102265. [Abstract] [PDF]

    Publications from the PhD period are not listed here.

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]
Tarun Martheswaran (Jun 2022 - Aug 2022, Sep 2024 - Jun 2025)

  • 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]
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]