Rosenberg lab at Stanford University

Rosenberg lab peer-reviewed publications

[1999-2005] [2006-2010] [2011-2015] [2016-2020] [Review articles]

In press

X Liu, NM Kopelman, NA Rosenberg (2022) A Dirichlet model of alignment cost in mixed-membership unsupervised clustering. Journal of Computational and Graphical Statistics in press.

E Lappo, NA Rosenberg (2022) Approximations to the expectations and variances of ratios of tree properties under the coalescent. G3: Genes, Genomes, Genetics in press.

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 in press.


NA Rosenberg (2022) Mendel of mathematics. Notices of the American Mathematical Society 69: 1564-1565. [PDF]

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]

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]

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]

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]

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]

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]

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]

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

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]

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]

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]

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]

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]

A Harpak, N Garud, NA Rosenberg, DA Petrov, M Combs, PS Pennings, J Munshi-South (2021) Genetic adaptation in New York City rats. Genome Biology and Evolution 13: evaa247. [Abstract] [PDF] [Supplement]

NA Rosenberg (2021) On the Colijn-Plazzotta numbering scheme for unlabeled binary rooted trees. Discrete Applied Mathematics 291: 88-98. [Abstract] [PDF]


SM Boca, L Huang, NA Rosenberg (2020) On the heterozygosity of an admixed population. Journal of Mathematical Biology 81: 1217-1250. [Abstract]

J Kim, NA Rosenberg, JA Palacios (2020) Distance metrics for ranked evolutionary trees. Proceedings of the National Academy of Sciences USA 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]

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]

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

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

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]

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]

NA Rosenberg, DM Zulman (2020) Measures of care fragmentation: mathematical insights from population genetics. Health Services Research 55: 318-327. [Abstract]

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]


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]

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]

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]

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]

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]

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]

AL Severson, S Carmi, NA Rosenberg (2019) The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212: 305-316. [Abstract] [PDF]

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]

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]

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, 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]

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]

NA Rosenberg (2019) Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries. Advances in Applied Mathematics 102: 1-17. [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]

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

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

NA Rosenberg (2018) Variance-partitioning and classification in human population genetics. In RG Winther, ed. Phylogenetic Inference, Selection Theory, and History of Science: Selected Papers of A. W. F. Edwards with Commentaries, pp. 399-403. Cambridge: Cambridge University Press. [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]

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]


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]

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]

OK Kamneva, J Syring, A Liston, NA Rosenberg (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evolutionary Biology 17: 180. [Abstract] [PDF] [File S1 Table S1] [File S2 Sequences] [File S3 Table S2] [File S4 Figures S1-S11] [File S5 Table S3] [File S6 R code]

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]

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]

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]

OK Kamneva, NA Rosenberg (2017) Simulation-based evaluation of hybridization network reconstruction methods in the presence of incomplete lineage sorting. Evolutionary Bioinformatics 13: 1176934317691935. [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]

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]

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]

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]

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]

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]

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]

NA Rosenberg (2016) Admixture models and the breeding systems of H. S. Jennings: a GENETICS connection. Genetics 202: 9-13. [PDF]


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: 313-337. [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]

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

R Ronen*, G Tesler*, A Akbari*, S Zakov, NA Rosenberg, V Bafna (2015) Predicting carriers of ongoing selective sweeps without knowledge of the favored allele. PLoS Genetics 11: e1005527. [Abstract] [PDF] [Supplement]

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]

NA Rosenberg, JTL Kang (2015) Genetic diversity and societally important disparities. Genetics 201: 1-12. [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]

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]

NR Garud, NA Rosenberg (2015) Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps. Theoretical Population Biology 102: 94-101. [Abstract] [PDF]

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]

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

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

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]

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

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


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]

PJ Oefner, G Hölzl, P Shen, I Shpirer, D Gefel, T Lavi, E Woolf, J Cohen, C Cinnioglu, PA Underhill, NA Rosenberg, J Hochrein, JM Granka, J Hillel, MW Feldman (2013) Genetics and the history of the Samaritans: Y-chromosomal microsatellites and genetic affinity between Samaritans and Cohanim. Human Biology 85: 825-857. [Abstract] [PDF]

NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 1253-1262. [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]

NA Rosenberg (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution 30: 2709-2713. [Abstract] [Full-text at journal website] [PDF]

P Zhang, X Zhan, NA Rosenberg, S Zöllner (2013) Genotype imputation reference panel selection using maximal phylogenetic diversity. Genetics 195: 319-330. [Abstract] [PDF]

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

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]

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]

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]

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]

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]


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] [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). [PDF]

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, 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]

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

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] [PDF] [Main Supplement] [Supplementary Table 2 (.zip)] [Supplementary Table 3 (.zip)] [Supplementary Table 4 (.zip)] [Supplementary Table 5 (.zip)]

D Bryant, R Bouckaert, J Felsenstein, NA Rosenberg, A RoyChoudhury (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29: 1917-1932. [Abstract] [PDF] [Supplement]

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]

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]

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] [PDF]

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


NA Rosenberg (2011) A population-genetic perspective on the similarities and differences among worldwide human populations. Human Biology 83: 659-684. [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]

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]

S Ramachandran, NA Rosenberg (2011) A test of the influence of continental axes of orientation on patterns of human gene flow. American Journal of Physical Anthropology 146: 515-529. [Abstract] [PDF] [Supplementary Figure 1] [Supplementary Figure 2] [Supplementary Tables]

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]

SM Boca, NA Rosenberg (2011) Mathematical properties of Fst between admixed populations and their parental source populations. Theoretical Population Biology 80: 208-216. [Abstract] [PDF]

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

Z Yang, M Rosenthal, NA Rosenberg, S Talarico, L Zhang, C Marrs, VO Thomsen, T Lillebaek, AB Andersen (2011) How dormant is Mycobacterium tuberculosis during latency? A study integrating genomics and molecular epidemiology. Infection, Genetics and Evolution 11: 1164-1167. [Abstract] [PDF]

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]

CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [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]

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]

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]

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]

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]

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]

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]

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]

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]

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

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]

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]

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]


S Ramachandran, NA Rosenberg, MW Feldman, J Wakeley (2008) Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theoretical Population Biology 74: 291-301. [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]

NA Rosenberg, M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036. [Abstract] [PDF]

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

JM Macpherson, J Gonzalez, DM Witten, JC Davis, NA Rosenberg, AE Hirsh, DA Petrov (2008) Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Molecular Biology and Evolution 25: 1025-1042. [Abstract] [PDF]

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]

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]


K Zhang, NA Rosenberg (2007) On the genealogy of a duplicated microsatellite. Genetics 177: 2109-2122. [Abstract] [PDF]

S Wang*, CM Lewis Jr*, M Jakobsson*, S Ramachandran, N Ray, G Bedoya, W Rojas, MV Parra, JA Molina, C Gallo, G Mazzotti, G Poletti, K Hill, AM Hurtado, D Labuda, W Klitz, R Barrantes, MC Bortolini, FM Salzano, ML Petzl-Erler, LT Tsuneto, E Llop, F Rothhammer, L Excoffier, MW Feldman, NA Rosenberg, A Ruiz-Linares (2007) Genetic variation and population structure in Native Americans. PLoS Genetics 3: 2049-2067. [Abstract] [PDF] [Supplement] [Data] [Readme for datafile]

M Jakobsson, NA Rosenberg (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806. [Abstract] [Full text at journal website] [PDF] [Software]

MGB Blum, NA Rosenberg (2007) Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling. Genetics 176: 1741-1757. [Abstract] [PDF]

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

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

M Jakobsson, NA Rosenberg (2007) The probability distribution under a population divergence model of the number of genetic founding lineages of a population or species. Theoretical Population Biology 71: 502-523. [Abstract] [PDF]

L David, NA Rosenberg, U Lavi, MW Feldman, J Hillel (2007) Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L. Genetics Selection Evolution 39: 319-340. [Abstract] [PDF]

KB Schroeder, TG Schurr, JC Long, NA Rosenberg, MH Crawford, LA Tarskaia, LP Osipova, SI Zhadanov, DG Smith (2007) A private allele ubiquitous in the Americas. Biology Letters 3: 218-223. [Abstract] [PDF] [Supplement]

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


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)]

DF Conrad*, M Jakobsson*, G Coop*, X Wen, JD Wall, NA Rosenberg, JK Pritchard (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38: 1251-1260. [Abstract] [PDF] [Supplement (methods, note, and figures)] [Supplementary Table 1] [Data]

NA Rosenberg (2006) Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Annals of Human Genetics 70: 841-847. [Abstract] [PDF] [Supplement] [Data] [Spreadsheet with recommended subsets (txt format)] [Spreadsheet with recommended subsets (xls format)]

NA Rosenberg (2006) Gene genealogies. Chapter 12 in CW Fox and JB Wolf, eds. Evolutionary Genetics: Concepts and Case Studies. Oxford: Oxford University Press, pp. 173-189. [PDF of final version]

NA Rosenberg, M Nordborg (2006) A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations. Genetics 173: 1665-1678. [Abstract] [PDF]

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

NA Rosenberg (2006) The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees. Annals of Combinatorics 10: 129-146. [Abstract] [PDF]


NA Rosenberg, S Mahajan, S Ramachandran, C Zhao, JK Pritchard, MW Feldman (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: 660-671. [Abstract] [PDF] [Data]

NA Rosenberg (2005) Algorithms for selecting informative marker panels for population assignment. Journal of Computational Biology 12: 1183-1201. [Abstract] [PDF]

S Ramachandran, O Deshpande, CC Roseman, NA Rosenberg, MW Feldman, LL Cavalli-Sforza (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences USA 102: 15942-15947. [Abstract] [PDF] [Supplementary Figure 6] [Supplementary Table 2] [Supplementary text] [Data]

NA Rosenberg (2005) A sharp minimum on the mean number of steps taken in adaptive walks. Journal of Theoretical Biology 237: 17-22. [Abstract] [PDF]

M Nordborg, TT Hu, Y Ishino, J Jhaveri, C Toomajian, H Zheng, E Bakker, P Calabrese, J Gladstone, R Goyal, M Jakobsson, S Kim, Y Morozov, B Padhukasahasram, V Plagnol, NA Rosenberg, C Shah, JD Wall, J Wang, K Zhao, T Kalbfleisch, V Schulz, M Kreitman, J Bergelson (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3: 1289-1299. [Abstract] [PDF]

Noah Rosenberg's publications 1999-2005


H Innan, K Zhang, P Marjoram, S Tavaré, NA Rosenberg (2005) Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 169: 1763-1777. [Abstract] [PDF] [Software]


NA Rosenberg, PP Calabrese (2004) Polyploid and multilocus extensions of the Wahlund inequality. Theoretical Population Biology 66: 381-391. [Abstract] [PDF]

MM Tanaka, NA Rosenberg, PM Small (2004) The control of copy number of IS6110 in Mycobacterium tuberculosis. Molecular Biology and Evolution 21: 2195-2201. [Abstract] [PDF]

S Ramachandran, NA Rosenberg, LA Zhivotovsky, MW Feldman (2004) Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Human Genomics 1: 87-97. [Abstract] [PDF]

NA Rosenberg (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137-138. [Abstract] [PDF] [Software]


NA Rosenberg, LM Li, R Ward, JK Pritchard (2003) Informativeness of genetic markers for inference of ancestry. American Journal of Human Genetics 73: 1402-1422. [Abstract] [PDF] [Supplement] [Microsatellite data] [SNP data] [SNP data readme] [Solution to Problem 11039 required in appendix of paper (American Mathematical Monthly 112: 572-573, 2005)] [Software]

NA Rosenberg, AE Hirsh (2003) On the use of star-shaped genealogies in inference of coalescence times. Genetics 164: 1677-1682. [Abstract] [PDF]

NA Rosenberg (2003) The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57: 1465-1477. [Abstract] [PDF]

NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2003) Response to comment on "Genetic structure of human populations." Science 300: 1877. [Abstract] [PDF] [Data]

NA Rosenberg, AG Tsolaki, MM Tanaka (2003) Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis. Theoretical Population Biology 63: 347-363. [Abstract] [PDF]

LA Zhivotovsky, NA Rosenberg, MW Feldman (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. American Journal of Human Genetics 72: 1171-1186. [Abstract] [PDF] [Data]


NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2381-2385. [Abstract] [Full Text at Science website] [PDF] [Supplement] [Data in structure and NEXUS formats] [Software for drawing figures] [Español]

NA Rosenberg, M Nordborg (2002) Genealogical trees, coalescent theory, and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380-390. [Abstract] [PDF]

NA Rosenberg (2002) The probability of topological concordance of gene trees and species trees. Theoretical Population Biology 61: 225-247. [Abstract] [PDF]

NA Rosenberg, MW Feldman (2002) The relationship between coalescence times and population divergence times. Chapter 9 in M Slatkin and M Veuille, eds. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press, pp. 130-164. [Abstract] [PDF of final version]


NA Rosenberg, T Burke, K Elo, MW Feldman, P Friedlin, MAM Groenen, J Hillel, A Mäki-Tanila, M Tixier-Boichard, A Vignal, K Wimmers, S Weigend (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713. [Abstract] [PDF] [Data] [Photo]

MM Tanaka, NA Rosenberg (2001) Optimal estimation of transposition rates of insertion sequences for molecular epidemiology. Statistics in Medicine 20: 2409-2420. [Abstract] [PDF]

NA Rosenberg, E Woolf, JK Pritchard, T Schaap, D Gefel, I Shpirer, U Lavi, B Bonné-Tamir, J Hillel, MW Feldman (2001) Distinctive genetic signatures in the Libyan Jews. Proceedings of the National Academy of Sciences, USA 98: 858-863. [Abstract] [PDF] [Data]


L Jin, ML Baskett, LL Cavalli-Sforza, LA Zhivotovsky, MW Feldman, NA Rosenberg (2000) Microsatellite evolution in modern humans: a comparison of two data sets from the same populations. Annals of Human Genetics 64: 117-134. [Abstract] [PDF] [Data]

JK Pritchard, M Stephens, NA Rosenberg, P Donnelly (2000) Association mapping in structured populations. American Journal of Human Genetics 67: 170-181. [Abstract] [PDF]


JK Pritchard, NA Rosenberg (1999) Use of unlinked genetic markers to detect population stratification in association studies. American Journal of Human Genetics 65: 220-228. [Abstract] [PDF]