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Metadata for Rosenberg lab peer-reviewed publications (2008-present)
[2023] [2022] [2021] [2016-2020] [2011-2015] [2008-2010]
L Agranat-Tamir, JA Mooney, NA Rosenberg (2024).
Counting the genetic ancestors from source populations in members of
an admixed population. Genetics in press
[PMID 38289724]
[PMCID (none)]
[Journal issue date: ]
[Grant support: NSF BCS-2116322]
[Access: ]
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 in press.
[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: -]