Searching journal content for articles similar to Peterson et al. 9 (9): 844.

Displaying results 1-10 of 4233
For checked items
  1. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...variants into causal and noncausal, referring to variants neither truly associated with the phenotype nor in linkage disequilibrium (LD) with causal variants. We assumed that any systematic differences in calculated P-values or effect sizes of noncausal variants in between the two models are likely owing...
    OPEN ACCESS ARTICLE
  2. Research: Most chromatin interactions are not in linkage disequilibrium
    • Sean Whalen and
    • Katherine S. Pollard
    Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
    ...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
    OPEN ACCESS ARTICLE
  3. Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    ...). However, because MGEs are vehicles for the exchange of beneficial accessory genes, defense systems could consequently impede rapid adaptation in microbial populations. Here, we study how defense systems impact horizontal gene transfer (HGT) in the short term and long term. By combining comparative...
    OPEN ACCESS ARTICLE
  4. Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
    • Paige A. Byerly,
    • Alina von Thaden,
    • Evgeny Leushkin,
    • Leon Hilgers,
    • Shenglin Liu,
    • Sven Winter,
    • Tilman Schell,
    • Charlotte Gerheim,
    • Alexander Ben Hamadou,
    • Carola Greve,
    • Christian Betz,
    • Hanno J. Bolz,
    • Sven Büchner,
    • Johannes Lang,
    • Holger Meinig,
    • Evax Marie Famira-Parcsetich,
    • Sarah P. Stubbe,
    • Alice Mouton,
    • Sandro Bertolino,
    • Goedele Verbeylen,
    • Thomas Briner,
    • Lídia Freixas,
    • Lorenzo Vinciguerra,
    • Sarah A. Mueller,
    • Carsten Nowak,
    • and Michael Hiller
    Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
    ...samples with a mean per site depth of 14.75× and mean frequency of missingness of 0.11 (Supplemental Table S2). For analyses dependent on allele frequencies, such as principal component analysis (PCA)-based analyses, we pruned SNPs based on linkage disequilibrium (LD), resulting in a data set of 19...
  5. Research: Worldwide patterns of genomic variation and admixture in gray wolves
    • Zhenxin Fan,
    • Pedro Silva,
    • Ilan Gronau,
    • Shuoguo Wang,
    • Aitor Serres Armero,
    • Rena M. Schweizer,
    • Oscar Ramirez,
    • John Pollinger,
    • Marco Galaverni,
    • Diego Ortega Del-Vecchyo,
    • Lianming Du,
    • Wenping Zhang,
    • Zhihe Zhang,
    • Jinchuan Xing,
    • Carles Vilà,
    • Tomas Marques-Bonet,
    • Raquel Godinho,
    • Bisong Yue,
    • and Robert K. Wayne
    Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
    ...was performed using the pairwise allele-sharing genetic distance. Following vonHoldt et al. (2011), sites exhibiting apparent strong local linkage disequilibrium (R2 > 0.5) were filtered using the –indep option in PLINK (–indep 50 5 0.2) (Purcell et al. 2007). To improve resolution among wolves, the two golden...
  6. Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
    • Yueying He,
    • Yue Xue,
    • Jingyao Wang,
    • Yupeng Huang,
    • Lu Liu,
    • Yanyi Huang,
    • and Yi Qin Gao
    Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
    ...is a painfully crowded and complex environment for proteins to find and associate with each other faithfully in a timely and well-organized manner, as required by signal transduction, especially if the population and distribution of individual proteins were entirely random or independent...
  7. Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
    • Greta Bellinzona,
    • Tiago Nardi,
    • Michele Castelli,
    • Gherard Batisti Biffignandi,
    • Karim Adjou,
    • Martha Betson,
    • Yannick Blanchard,
    • Ioana Bujila,
    • Rachel Chalmers,
    • Rebecca Davidson,
    • Nicoletta D'Avino,
    • Tuulia Enbom,
    • Jacinto Gomes,
    • Gregory Karadjian,
    • Christian Klotz,
    • Emma Östlund,
    • Judith Plutzer,
    • Ruska Rimhanen-Finne,
    • Guy Robinson,
    • Anna Rosa Sannella,
    • Jacek Sroka,
    • Christen Rune Stensvold,
    • Karin Troell,
    • Paolo Vatta,
    • Barbora Zalewska,
    • Claudio Bandi,
    • Davide Sassera,
    • and Simone M. Cacciò
    Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
    ....Within-population genetic indicesTo gain further insight into the genetic differentiation of the two populations in the “Western” lineage (i.e., populations 2 and 3), we calculated linkage disequilibrium (LD) decay, Tajima's D values, and nucleotide diversity (π).We found that population 3 had a slower...
    OPEN ACCESS ARTICLE
  8. Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
    • Nathan LaPierre,
    • Boyang Fu,
    • Steven Turnbull,
    • Eleazar Eskin,
    • and Sriram Sankararaman
    Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
    ...for standard MR methods (Supplemental Fig. S2). We observed inflated FPR for standard MR methods even when there is no confounding (stratification) for large values of FST (Supplemental Fig. S2) likely owing to correlation or linkage disequilibrium (LD) among the genetic variants induced by population...
  9. Research: Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs
    • Brian P. McEvoy,
    • Joseph E. Powell,
    • Michael E. Goddard,
    • and Peter M. Visscher
    Genome Res. June 2011 21: 821-829; Published in Advance April 25, 2011, doi:10.1101/gr.119636.110
    ...Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs Brian P. McEvoy 1 , 4 , Joseph E. Powell 1 , 4 , 5 , Michael E. Goddard 2 , 3 and Peter M. Visscher 1 1Queensland...
  10. Methods: Recent human effective population size estimated from linkage disequilibrium
    • Albert Tenesa,
    • Pau Navarro,
    • Ben J. Hayes,
    • David L. Duffy,
    • Geraldine M. Clarke,
    • Mike E. Goddard,
    • and Peter M. Visscher
    Genome Res. April 2007 17: 520-526; Published in Advance March 9, 2007, doi:10.1101/gr.6023607
    ...Recent human effective population size estimated from linkage disequilibrium Albert Tenesa 1 , 2 , 3 , Pau Navarro 3 , Ben J. Hayes 4 , David L. Duffy 5 , Geraldine M. Clarke 6 , Mike E. Goddard 4 , 7 , and Peter M...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research