Rosenberg lab at Stanford University

Metadata for Rosenberg lab peer-reviewed publications (2008-present)

[2024] [2023] [2022] [2021] [2016-2020] [2011-2015] [2008-2010]


In press

EH Dickey, NA Rosenberg. Labeled histories with multifurcation and simultaneity. Philosophical Transactions of the Royal Society B Biological Sciences in press (2025).

EE Armstrong, JA Mooney, KA Solari, BY Kim, GS Barsh, VB Grant, G Greenbaum, C 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 in press (2024).


2024

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]
[PMID 39298482]
[PMCID (none)]
[Journal issue date: September 2024]
[Grant support: -]
[Access: -]

L Agranat-Tamir, M Fuchs, B Gittenberger, NA Rosenberg (2024) Asymptotic enumeration of rooted binary unlabeled galled trees with a fixed number of galls. 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: 27. Schloss Dagstuhl — Leibniz-Zentrum für Informatik. [Abstract] [PDF]
[PMID (none)]
[PMCID (none)]
[Proceedings publication date: July 2024]
[Grant support: NSF BCS-2116322]
[Access: open access]

M Doboli, H-K Hwang, NA Rosenberg (2024) 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. Schloss Dagstuhl — Leibniz-Zentrum für Informatik. [Abstract] [PDF]
[PMID (none)]
[PMCID (none)]
[Proceedings publication date: July 2024]
[Grant support: NIH R01 HG005855]
[Access: open access]

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]
[PMID 38289724]
[PMCID PMC10990421]
[Journal issue date: April 2024]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

L Agranat-Tamir, S Mathur, NA Rosenberg (2024) Enumeration of rooted binary unlabeled galled trees. Bulletin of Mathematical Biology 86: 45. [Abstract] [PDF]
[PMID 38519704]
[PMCID PMC10959814]
[Journal issue date: May 2024]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

TD Gress, NA Rosenberg (2024). Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy. BioSystems 237: 105153. [Abstract]
[PMID 38417692]
[PMCID PMC10972423]
[Journal issue date: March 2024]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 37972246]
[PMCID PMC10849319]
[Journal issue date: February 2024]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: open access journal]

E Lappo, NA Rosenberg (2024). Solving the Arizona search problem by imputation. iScience 27: 108831. [Abstract] [PDF] [Supplement]
[PMID 38323008]
[PMCID PMC10845060]
[Journal issue date: February 26, 2024]
[Grant support: NIH R01 HG005855]
[Access: open access journal]

X Liu, NM Kopelman, NA Rosenberg (2024) Clumppling: cluster matching and permutation program with integer linear programming. Bioinformatics 40: btad751. [Abstract] [PDF] [Supplement]
[PMID 38096585]
[PMCID PMC10766593]
[Journal issue date: January 2024]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: open access charge paid]

E Lappo, NA Rosenberg (2024) A lattice structure for ancestral configurations arising from the relationship between gene trees and species trees. Discrete Applied Mathematics 343: 65-81. [Abstract] [PDF]
[PMID 38078045]
[PMCID PMC10704929]
[Journal issue date: January 30, 2024]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

ARP Maranca, NA Rosenberg (2024) Bijections between the multifurcating unlabeled rooted trees and the positive integers. Advances in Applied Mathematics 153: 102612. [Abstract] [PDF].
[PMID]
[PMCID]
[Journal issue date: February 2024]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID]
[PMCID]
[Journal issue date: January 2024]
[Grant support: NIH R01 GM117590]
[Access: ]


2023

MC King, NA Rosenberg (2023) A mathematical connection between single-elimination sports tournaments and evolutionary trees. Mathematics Magazine 96: 484-497. [Abstract] [PDF]
[PMID]
[PMCID]
[Journal issue date: December 2023]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 38073574]
[PMCID PMC38073574]
[Journal issue date: December 12, 2023]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access charge paid]

E Lappo, NA Rosenberg, MW Feldman (2023) Cultural transmission of move choice in chess. Proceedings of the Royal ` Society B: Biological Sciences 290: 37964528. [Abstract] [PDF] [Supplement]
[PMID 37964528]
[PMCID PMC10646474]
[Journal issue date: November 29, 2023]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 37567955]
[PMCID PMC10620386]
[Journal issue date: November 2023]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 37884812]
[PMCID PMC10603011]
[Journal issue date: November 2023]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 37982130]
[PMCID PMC10656040]
[Journal issue date: September 2023]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 37410594]
[PMCID PMC10324943]
[Journal issue date: July 2023]
[Grant support: NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 37096877]
[PMCID PMC10322156]
[Journal issue date: July 4, 2023]
[Grant support: -]
[Access: open access journal]

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]
[PMID 37075098]
[PMCID PMC10213490]
[Journal issue date: June 2023]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access charge paid]

S Mathur, NA Rosenberg (2023) All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees. Algorithms for Molecular Biology 18:1. [Abstract] [PDF]
[PMID 36782318]
[PMCID PMC9926779]
[Journal issue date: 2023]
[Grant support: NSF BCS-2116322]
[Access: open access journal]


2022

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]
[PMID]
[PMCID]
[Journal issue date: December 2022]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]

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]
[PMID 35951748]
[PMCID PMC9526068]
[Journal issue date: October 2022]
[Grant support: NIH R01 GM131404, NIH R01 HG005855, NSF BCS-2116322]
[Access: open access journal]

NA Rosenberg (2022) Mendel of mathematics. Notices of the American Mathematical Society 69: 1564-1565. [PDF]
[PMID]
[PMCID]
[Journal issue date: October 2022]
[Grant support: -]
[Access: open access journal]

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]
[PMID 35596736]
[PMCID PMC9544611]
[Journal issue date: October 2022]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 35973448]
[PMCID PMC9867987]
[Journal issue date: October 2022]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: -]

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]
[PMID 35544237]
[PMCID PMC9464369]
[Journal issue date: July 2022]
[Grant support: NIH R01 GM131404, NSF BCS-2116322]
[Access: -]

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]
[PMID 36276878]
[PMCID PMC9583705]
[Journal issue date: May 2022]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access journal]

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]
[PMID 35552538]
[PMCID PMC9098623]
[Journal issue date: May 2022]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]

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]
[PMID 35430885]
[PMCID PMC9014193]
[Journal issue date: June 6, 2022]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 35430889]
[PMCID PMC9014183]
[Journal issue date: June 6, 2022]
[Grant support: NIH R01 HG005855, NSF BCS-2116322]
[Access: open access charge paid]

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]
[PMID 35312358]
[PMCID PMC9060455]
[Journal issue date: March 29, 2022]
[Grant support: NSF BCS-2017956]
[Access: open access charge paid]

E Alimpiev, NA Rosenberg (2022) A compendium of covariances and correlation coefficients of coalescent tree properties. Theoretical Population Biology 143: 1-13. [Abstract] [PDF]
[PMID 34757022]
[PMCID PMC9731325]
[Journal issue date: February 2022]
[Grant support: NIH R01 GM131404, NIH R01 HG005855]
[Access: open access charge paid]


2021

MC King, NA Rosenberg 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 (2021). [PDF]
[PMID 34537229]
[PMCID PMC8629161]
[Journal issue date: December 2021]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]

E Alimpiev, NA Rosenberg Enumeration of coalescent histories for caterpillar species trees and p-pseudocaterpillar gene trees. Advances in Applied Mathematics 131: 102265 (2021). [Abstract] [PDF]
[PMID 34483422]
[PMCID PMC8415704]
[Journal issue date: October 2021]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]

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]
[PMID 33901539]
[PMCID PMC8378513]
[Journal issue date: August 2021]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: ]

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]
[PMID 33675872]
[PMCID PMC8489744]
[Journal issue date: June 2021]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: ]

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]
[PMID 33772750]
[PMCID PMC8202736]
[Journal issue date: June 2021]
[Grant support: NIH R01 HG005855]
[Access: ]

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]
[PMID 33630838]
[PMCID PMC7943199]
[Journal issue date: February 2021]
[Grant support: NIH R01 HG005855]
[Access: open access journal]

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]
[PMID 33211096]
[PMCID PMC7851592]
[Journal issue date: January 2021]
[Grant support: NSF DBI-1458059]
[Access: open access journal]

NA Rosenberg (2021) On the Colijn-Plazzotta numbering scheme for unlabeled binary rooted trees. Discrete Applied Mathematics 291: 88-98. [Abstract] [PDF]
[PMID 33364668]
[PMCID PMC7751944]
[Journal issue date: 3-11-2021]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]


2020

NA Rosenberg (2020) A population-genetic perspective on the similarities and differences among worldwide human populations. Human Biology 92: 135-152. [Abstract]
[PMID 34057327]
[PMCID (none)]
[Journal issue date: Summer 2020]
[Grant support: -]
[Access: -]

SM Boca, L Huang, NA Rosenberg (2020) On the heterozygosity of an admixed population. Journal of Mathematical Biology 81: 1217-1250. [Abstract]
[PMID 33034736]
[PMCID PMC7710588]
[Journal issue date: December 2020]
[Grant support: NIH R01 HG005855, NSF BCS-1515127]
[Access: -]

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]
[PMID 33139566]
[PMCID PMC7682335]
[Journal issue date: 11-17-2020]
[Grant support: NIH R01 GM131404]
[Access: open access charge paid]

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]
[PMID 32586848]
[PMCID PMC7407470]
[Journal issue date: August 2020]
[Grant support: NIH R01 HG005855]
[Access: open access journal]

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]
[PMID 32275920]
[PMCID PMC7387155]
[Journal issue date: August 2020]
[Grant support: NIH R01 HG005855, NSF BCS-1515127]
[Access: -]

RS Mehta, NA Rosenberg (2020) Modelling anti-vaccine sentiment as a cultural pathogen. Evolutionary Human Sciences 2: e21. [Abstract] [PDF] [Supplement]
[PMID]
[PMCID (none)]
[Journal issue date: May 2020]
[Grant support: -]
[Access: open access journal]

IM Arbisser, NA Rosenberg (2020) FST and the triangle inequality for biallelic markers. Theoretical Population Biology 133: 117-129. [Abstract]
[PMID 31132375]
[PMCID PMC8448291]
[Journal issue date: June 2020]
[Grant support: NIH R01 GM117590, NIH R01 GM131404, NIH R01 HG005855]
[Access: -]

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]
[PMID 31919450]
[PMCID PMC7253422]
[Journal issue date: June 2020]
[Grant support: -]
[Access: -]

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]
[PMID 31860090]
[PMCID PMC7182218]
[Journal issue date: May 2020]
[Grant support: NIH R01 GM117590, NIH R01 GM131404]
[Access: -]

NA Rosenberg, DM Zulman (2020) Measures of care fragmentation: mathematical insights from population genetics. Health Services Research 55: 318-327. [Abstract]
[PMID 31970757]
[PMCID PMC7080386]
[Journal issue date: April 2020]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 32863514]
[PMCID PMC7450691]
[Journal issue date: February 2020]
[Grant support: NIH R01 GM117590, NIH R01 GM131404]
[Access: -]


2019

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]
[PMID 32045910]
[PMCID PMC7199518]
[Journal issue date: March 2020]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 31694865]
[PMCID PMC6886512]
[Journal issue date: December 2019]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 31676766]
[PMCID PMC6825168]
[Journal issue date: 11-1-2019]
[Grant support: NSF BCS-1515127]
[Access: open access journal]

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]
[PMID 29729946]
[PMCID PMC6215533]
[Journal issue date: October 2019]
[Grant support: NIH R01 GM117590]
[Access: -]

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]
[PMID 31165149]
[PMCID PMC6759081]
[Journal issue date: October 2019]
[Grant support: NSF DBI-1458059]
[Access: open access charge paid]

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]
[PMID 31285255]
[PMCID PMC6727796]
[Journal issue date: September 2019]
[Grant support: NIH R01 HG005855, NSF DBI-1458059]
[Access: -]

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]
[PMID 30019427]
[PMCID (none)]
[Journal issue date: June 2019]
[Grant support: -]
[Access: open access charge paid]

AL Severson, S Carmi, NA Rosenberg (2019) The effect of consanguinity on between-individual identity-by-descent sharing. Genetics 212: 305-316. [Abstract] [PDF]
[PMID 30926583]
[PMCID PMC6499533]
[Journal issue date: May 2019]
[Grant support: BSF 2017024, NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 30589985]
[PMCID PMC6821915]
[Journal issue date: April 2019]
[Grant support: NIH R01 HG005855]
[Access: -]

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] [Supplement]
[PMID 30116881]
[PMCID PMC7661175]
[Journal issue date: January-February 2019]
[Grant support: NIH R01 GM117590]
[Access: -]

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]
[PMID 30838127]
[PMCID PMC6393779]
[Journal issue date: January 2019]
[Grant support: NIH R01 HG005855, NSF DBI-1458059]
[Access: open access journal]

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]
[PMID 29876842]
[PMCID PMC7723469]
[Journal issue date: February 2019]
[Grant support: NIH R01 GM117590, NSF BCS-1515127]
[Access: -]

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]
[PMID 28913585]
[PMCID PMC5851864]
[Journal issue date: February 2019]
[Grant support: NIH R01 GM117590]
[Access: -]

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]
[PMID 30983650]
[PMCID PMC6456302]
[Journal issue date: January 2019]
[Grant support: NIH R01 GM117590]
[Access: open access charge paid]


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]
[PMID 30318150]
[PMCID PMC6240431]
[Journal issue date: 10-16-2018]
[Grant support: NIH R01 HG005855, NIJ 2014-DN-BX-K015]
[Access: -]

AJ Aw, NA Rosenberg (2018) Bounding measures of genetic similarity and diversity using majorization. Journal of Mathematical Biology 77: 711-737. [Abstract] [PDF]
[PMID 29569105]
[PMCID PMC6133051]
[Journal issue date: September 2018]
[Grant support: NIH R01 HG005855, NSF DBI-1458059]
[Access: -]

A Goldberg, LH Uricchio, NA Rosenberg (2018) Natural selection in human populations. Oxford Bibliographies in Evolutionary Biology doi:10.1093/OBO/9780199941728-0112. [PDF]
[PMID (none)]
[PMCID (none)]
[Journal issue date: 8-28-2018]
[Grant support: -]
[Access: -]

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]
[PMID (none)]
[PMCID (none)]
[Book publication date: 7-19-2018]
[Grant support: -]
[Access: -]

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]
[PMID 30008065]
[PMCID (none)]
[Journal issue date: July 2018]
[Grant support: -]
[Access: -]

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]
[PMID 29132923]
[PMCID PMC5945353]
[Journal issue date: July 2018]
[Grant support: NIH R01 GM117590, NSF DBI-1458059]
[Access: -]


2017

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]
[PMID 28437136]
[PMCID PMC5610458]
[Journal issue date: September 2017]
[Grant support: NIH R01 GM117590]
[Access: -]

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.
[PMID 28803872]
[PMCID (none)]
[Journal issue date: 8-21-2017]
[Grant support: -]
[Access: -]

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]
[PMID 28778145]
[PMCID PMC5543553]
[Journal issue date: 8-4-2017]
[Grant support: NIH R01 GM117590, NSF DBI-1458059]
[Access: open access journal]

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]
[PMID 28476869]
[PMCID PMC5500152]
[Journal issue date: July 2017]
[Grant support: NIJ 2014-DN-BX-K015, NSF BCS-1515127, NSF DBI-1458059]
[Access: -]

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]
[PMID 28507140]
[PMCID PMC5465933]
[Journal issue date: May 30, 2017]
[Grant support: NIH R01 HG005855, NIJ 2014-DN-BX-K015]
[Access: -]

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]
[PMID 28476765]
[PMCID (none)]
[Journal issue date: May 16, 2017]
[Grant support:]
[Access: -]

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]
[PMID 28223527]
[PMCID PMC5347611]
[Journal issue date: March 7, 2017]
[Grant support: NSF BCS-1515127]
[Access: -]

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]
[PMID 28469378]
[PMCID PMC5395256]
[Journal issue date: March 2017]
[Grant support: NIH R01 GM117590]
[Access: open access journal]


2016

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]
[PMID 28910803]
[PMCID PMC5698150]
[Journal issue date: November 2017]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 28185570]
[PMCID PMC5123308]
[Journal issue date: November 2016]
[Grant support: NIH R01 GM117590, NSF DBI-1146722, NSF DBI-1458059]
[Access: open access journal]

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]
[PMID 26452289]
[PMCID PMC5096406]
[Journal issue date: September/October 2016]
[Grant support: NIH R01 GM117590, NSF DBI-1146722]
[Access: -]

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 113: 8002-8009.
[PMID 27432988]
[PMCID PMC4961160]
[Journal issue date: July 19, 2016]
[Grant support: NIH R01 GM117590, NSF DBI-1458059]
[Access: open access special issue]

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]
[PMID 26968785]
[PMCID PMC4911941]
[Journal issue date: July 2016]
[Grant support: NIH R01 GM117590]
[Access: open access charge paid]

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]
[PMID 27086043]
[PMCID PMC4947426]
[Journal issue date: August 2016]
[Grant support: NIH R01 GM117590]
[Access: -]

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]
[PMID 26996508]
[PMCID (none)]
[Journal issue date: April 4, 2016]
[Grant support: NIJ 2014-DN-BX-K015]
[Access: -]

NA Rosenberg (2016) Admixture models and the breeding systems of H. S. Jennings: a GENETICS connection. Genetics 202: 9-13. [PDF]
[PMID 26733663]
[PMCID PMC4701105]
[Journal issue date: January 2016]
[Grant support: -]
[Access: -]


2015

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]
[PMID 27737590]
[PMCID PMC8504698]
[Journal issue date: October 2015]
[Grant support: NIH R01 HG005855, NSF DBI-1458059]
[Access:]

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]
[PMID 26307072]
[PMCID PMC4596665]
[Journal issue date: October 2015]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

F Disanto, NA Rosenberg (2015) Coalescent histories for lodgepole species trees. Journal of Computational Biology 22: 918-929. [Abstract] [PDF]
[PMID 25973633]
[PMCID (none)]
[Journal issue date: October 2015]
[Grant support: NSF DBI-1146722]
[Access: -]

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]
[PMID 26402243]
[PMCID PMC4581834]
[Journal issue date: September 2015]
[Grant support: NSF DBI-1458059]
[Access: open access journal]

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]
[PMID 26209245]
[PMCID PMC4566268]
[Journal issue date: September 2015]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

NA Rosenberg, JTL Kang (2015) Genetic diversity and societally important disparities. Genetics 201: 1-12. [Abstract] [PDF] [Supplement]
[PMID 26354973]
[PMCID PMC4566256]
[Journal issue date: September 2015]
[Grant support:]
[Access: open access charge paid]

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]
[PMID 25684545]
[PMCID PMC4534335]
[Journal issue date: September 2015]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 25677859]
[PMCID PMC4516610]
[Journal issue date: August 2015]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 25891325]
[PMCID PMC4447712]
[Journal issue date: June 2015]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 25605893]
[PMCID PMC4321277]
[Journal issue date: 2-3-2015]
[Grant support:]
[Access: -]

EO Buzbas, NA Rosenberg (2015) AABC: approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology 99: 31-42. [Abstract] [PDF]
[PMID 25261426]
[PMCID PMC4429919]
[Journal issue date: February 2015]
[Grant support: NIH R01 HG005855, NSF DBI-1146722]
[Access: -]


2014

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.
[PMID 26357058]
[PMCID (none)]
[Journal issue date: November/December 2014]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

A Goldberg, P Verdu, NA Rosenberg (2014) Autosomal admixture levels are informative about sex bias in admixed populations. Genetics 198: 1209-1229. [Abstract] [PDF]
[PMID 25194159]
[PMCID PMC4224161]
[Journal issue date: November 2014]
[Grant support: NSF BCS-1147534]
[Access: open access charge paid]

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]
[PMID 25132646]
[PMCID PMC4180022]
[Journal issue date: November 2014]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 25122539]
[PMCID PMC4133047]
[Journal issue date: 8-14-2014]
[Grant support: NSF BCS-1147534]
[Access: open access journal]

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]
[PMID 25060268]
[PMCID PMC4154368]
[Journal issue date: July 2014]
[Grant support: BWF, NIH R01 HG005855]
[Access: -]

CV Than, NA Rosenberg (2014) Mean deep coalescence cost under exchangeable probability distributions. Discrete Applied Mathematics 174: 11-26. [Abstract] [PDF]
[PMID (none)]
[PMCID (none)]
[Journal issue date: 9-10-2014]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

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)]
[PMID 24678701]
[PMCID PMC4021425]
[Journal issue date: 3-29-2014]
[Grant support: NSF DBI-1146722]
[Access: open access journal]

EM Jewett, NA Rosenberg (2014) Theory and applications of a deterministic approximation to the coalescent model. Theoretical Population Biology 93: 14-29. [Abstract] [PDF]
[PMID 24412419]
[PMCID PMC4425369]
[Journal issue date: May 2014]
[Grant support: BWF, NIH R01 HG005855, NSF DBI-1146722]
[Access: -]


2013

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]
[PMID 25079123]
[PMCID (none)]
[Journal issue date: December 2013]
[Grant support: -]
[Access: -]

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]
[PMID 25079122]
[PMCID (none)]
[Journal issue date: December 2013]
[Grant support: -]
[Access: -]

NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10: 1253-1262. [Abstract]
[PDF]
[PMID 24524157]
[PMCID (none)]
[Journal issue date: September/October 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

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]
[PMID 24481204]
[PMCID PMC3868415]
[Journal issue date: 2013 (advance publication date 11-6-2013)]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

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]
[PMID 24030555]
[PMCID PMC3840310]
[Journal issue date: December 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: open access charge paid]

P Zhang, X Zhan, NA Rosenberg, S Zöllner (2013) Genotype imputation reference panel selection using maximal phylogenetic diversity. Genetics 195: 319-330. [Abstract] [PDF]
[PMID 23934887]
[PMCID PMC3781962]
[Journal issue date: October 2013]
[Grant support: NIH R01 HG005855]
[Access: open access charge paid]

NA Rosenberg, TJ Pemberton, JZ Li, JW Belmont (2013) Runs of homozygosity and parental relatedness. Genetics in Medicine 15: 753-754. [PDF]
[PMID 24008258]
[PMCID (none)]
[Journal issue date: September 2013]
[Grant support: NIH R01 HG005855]
[Access: -]

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]
[PMID 23079542]
[PMCID PMC3587719]
[Journal issue date: August 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

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]
[PMID 23746547]
[PMCID PMC3710769]
[Journal issue date: July 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: free highlighted article]

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]
[PMID 23550135]
[PMCID PMC3656735]
[Journal issue date: May 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

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]
[PMID 23109533]
[PMCID (none)]
[Journal issue date: January/February 2013]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

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]
[PMID 23172852]
[PMCID PMC3567740]
[Journal issue date: February 2013]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 23051843]
[PMCID PMC3548310]
[Journal issue date: February 2013]
[Grant support: NIH R01 GM081441]
[Access: open access charge paid]

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] [Data]
[PMID 23424132]
[PMCID PMC3597466]
[Journal issue date: January 2013]
[Grant support: BWF, NIH R01 GM081441, NSF BCS-1024627, NSF DBI-1146722]
[Access: freely available online]


2012

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]
[PMID 22868677]
[PMCID (none)]
[Journal issue date: November/December 2012]
[Grant support: BWF, NSF DBI-1146722]
[Access: -]

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]
[PMID 22981955]
[PMCID (none)]
[Journal issue date: December 2012]
[Grant support: NSF DBI-1146722]
[Access: -]

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]
[PMID 22851645]
[PMCID PMC3660999]
[Journal issue date: October 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

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]
[PMID 22927824]
[PMCID PMC3426559]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access journal]

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]
[PMID 22729696]
[PMCID PMC3436606]
[Journal issue date: September 2012]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

EM Jewett*, M Zawistowski*, NA Rosenberg, S Zöllner (2012) A coalescent model for genotype imputation. Genetics 191: 1239-1255. [Abstract] [PDF]
[PMID 22595242]
[PMCID PMC3416004]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: open access charge paid]

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)]
[PMID 22883143]
[PMCID PMC3415543]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

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]
[PMID 22422763]
[PMCID PMC3408069]
[Journal issue date: August 2012]
[Grant support: BWF, NIH R01 GM081441, NSF DBI-1146722]
[Access: -]

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]
[PMID 22697239]
[PMCID PMC3400268]
[Journal issue date: June 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: open access charge paid]

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]
[PMID 22216756]
[PMCID PMC3298679]
[Journal issue date: March 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: open access charge paid]

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]
[PMID 21305294]
[PMCID PMC3636777]
[Journal issue date: January 2012]
[Grant support: BWF, NIH R01 GM081441]
[Access: open access charge paid]

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]
[PMID 22147662]
[PMCID PMC3725725]
[Journal issue date: January 2012]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

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]
[PMID 22075548]
[PMCID (none)]
[Journal issue date: January/February 2012]
[Grant support: BWF, NSF DBI-1146722, NSF DEB-0716904]
[Access: -]


2011

NA Rosenberg (2011) A population-genetic perspective on the similarities and differences among worldwide human populations. Human Biology 83: 659-684. [Abstract] [PDF]
[PMID 22276967]
[PMCID PMC3531797]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

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]
[PMID 22125220]
[PMCID PMC3568705]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855]
[Access: -]

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]
[PMID 21968194]
[PMCID PMC3241432]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441, NIH R01 HG005855, NSF BCS-1147534]
[Access: open access charge paid]

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]
[PMID 21913175]
[PMCID PMC3538872]
[Journal issue date: December 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: -]

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]
[PMID 21775469]
[PMCID PMC3189793]
[Journal issue date: October 2011]
[Grant support: BWF, NIH R01 GM081441]
[Access: open access charge paid]

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]
[PMID 21640742]
[PMCID PMC3206961]
[Journal issue date: November 2011]
[Grant support: BWF, NIH R01 GM081441, NSF BCS-1024627]
[Access: -]

ZA Szpiech, NA Rosenberg (2011) On the size distribution of private microsatellite alleles. Theoretical Population Biology 80: 100-113. [Abstract] [PDF]
[PMID 21514313]
[PMCID PMC3143247]
[Journal issue date: September 2011]
[Grant support: BWF, NIH R01 GM081441, NSF DEB-0716904]
[Access: -]

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]
[PMID 21315848]
[PMCID PMC3104100]
[Journal issue date: July 2011]
[Grant support: -]
[Access: -]

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]
[PMID 21277883]
[PMCID PMC3070424]
[Journal issue date: May 2011]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [Abstract] [PDF]
[PMID 21210728]
[PMCID (none)]
[Journal issue date: January 2011]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]


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]
[PMID 20923981]
[PMCID PMC2998318]
[Journal issue date: December 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 20869033]
[PMCID PMC2948801]
[Journal issue date: October 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 20858721]
[PMCID (none)]
[Journal issue date: October 1, 2010]
[Grant support: -]
[Access: -]

I Jankovic, BM vonHoldt, NA Rosenberg (2010) Heterozygosity of the Yellowstone wolves. Molecular Ecology 19: 3246-3249. [PDF]
[PMID 20670367]
[PMCID PMC2924148]
[Journal issue date: August 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 20395969]
[PMCID PMC3079573]
[Journal issue date: May 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

NA Rosenberg, JH Degnan (2010) Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151. [Abstract] [PDF]
[PMID 20064540]
[PMCID (none)]
[Journal issue date: May 2010]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

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]
[PMID 19833741]
[PMCID PMC2877557]
[Journal issue date: March 2010]
[Grant support: NSF DEB-0716904]
[Access: -]

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]
[PMID 20196748]
[PMCID PMC2861313]
[Journal issue date: January 2010]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 20018958]
[PMCID (none)]
[Journal issue date: January 14, 2010]
[Grant support: Sloan Fdn]
[Access: -]


2009

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]
[PMID 20015383]
[PMCID PMC2806349]
[Journal issue date: December 16, 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access journal]

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]
[PMID 19995433]
[PMCID PMC2797531]
[Journal issue date: December 8, 2009]
[Grant support: BWF, Sloan Fdn]
[Access: open access journal]

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]
[PMID 19853241]
[PMCID PMC2775841]
[Journal issue date: November 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 19706453]
[PMCID PMC2752555]
[Journal issue date: September 22, 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: special open access section]

NA Rosenberg, JM VanLiere (2009) Replication of genetic associations as pseudoreplication due to shared genealogy. Genetic Epidemiology 33: 479-487. [Abstract] [PDF]
[PMID 19191270]
[PMCID PMC2766236]
[Journal issue date: September 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 20525567]
[PMCID PMC2909780]
[Journal issue date: February 2009]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

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]
[PMID 19307040]
[PMCID (none)]
[Journal issue date: June 2009]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

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]
[PMID 19221006]
[PMCID PMC2734135]
[Journal issue date: May 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 18988687]
[PMCID PMC2915906]
[Journal issue date: March 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access charge paid]

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]
[PMID 19215730]
[PMCID PMC2668016]
[Journal issue date: February 2009]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]


2008

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]
[PMID 18817799]
[PMCID PMC2630000]
[Journal issue date: December 2008]
[Grant support: NIH R01 GM081441]
[Access: -]

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]
[PMID 18779233]
[PMCID PMC2732282]
[Journal issue date: November 1, 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access charge paid]

NA Rosenberg, M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036. [Abstract] [PDF]
[PMID 18689892]
[PMCID PMC2516077]
[Journal issue date: August 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

JM VanLiere, NA Rosenberg (2008) Mathematical properties of the r2 measure of linkage disequilibrium. Theoretical Population Biology 74: 130-137. [Abstract] [PDF]
[PMID 18572214]
[PMCID PMC2580747]
[Journal issue date: August 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 18513279]
[PMCID PMC2495051]
[Journal issue date: July 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]

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]
[PMID 18483550]
[PMCID PMC2364639]
[Journal issue date: May 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: open access journal]

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]
[PMID 18199829]
[PMCID PMC3299400]
[Journal issue date: June 2008]
[Grant support: -]
[Access: -]

NA Rosenberg, R Tao (2008) Discordance of species trees with their most likely gene trees: the case of five taxa. Systematic Biology 57: 131-140. [Abstract] [Full-text at journal website] [PDF] [Supplement]
[PMID 18300026]
[Journal issue date: February 2008]
[Grant support: BWF, NSF DEB-0716904, Sloan Fdn]
[Access: -]

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]
[PMID 18288195]
[Journal issue date: February 21, 2008]
[Grant support: BWF, NIH R01 GM081441, Sloan Fdn]
[Access: -]