 |
|
Metadata for Rosenberg lab peer-reviewed publications (2008-present)
[2024] [2023] [2022] [2021] [2016-2020] [2011-2015] [2008-2010]
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: ]
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]
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]
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]
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: -]
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]
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: -]
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]
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: -]
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: -]
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: -]
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]
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: -]
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: -]
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: -]
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: -]
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: -]