Searching journal content for articles similar to Cutter and Choi 20 (8): 1103.

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  1. Research: Natural variation in C. elegans short tandem repeats
    • Gaotian Zhang,
    • Ye Wang,
    • and Erik C. Andersen
    Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
    ...been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1–6 bp in the reference of C. elegans. Of these STRs, 27,667 harbored polymorphisms across 540 wild strains and only...
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  2. Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
    • Cristel G. Thomas,
    • Wei Wang,
    • Richard Jovelin,
    • Rajarshi Ghosh,
    • Tatiana Lomasko,
    • Quang Trinh,
    • Leonid Kruglyak,
    • Lincoln D. Stein,
    • and Asher D. Cutter
    Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
    ...- sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans...
  3. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...be overlooked in traditional pairwise comparative analyses relying on a single reference per population or species.The nematode species pair Caenorhabditis briggsae and Caenorhabditis nigoni has emerged as a powerful model for dissecting the genetic and genomic bases of speciation. Although both species...
  4. Research: Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans
    • Moein Rajaei,
    • Ayush Shekhar Saxena,
    • Lindsay M. Johnson,
    • Michael C. Snyder,
    • Timothy A. Crombie,
    • Robyn E. Tanny,
    • Erik C. Andersen,
    • Joanna Joyner-Matos,
    • and Charles F. Baer
    Genome Res. September 2021 31: 1602-1613; Published in Advance August 17, 2021, doi:10.1101/gr.275372.121
    ...selection biases the standing genetic variation.The nematode Caenorhabditis elegans is an important model organism in many areas of biology and was the first metazoan organism to have its mutational process characterized at the genomic level (Denver et al. 2000, 2004b). As genomic sequence data from C...
  5. Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
    • Owen Thompson,
    • Mark Edgley,
    • Pnina Strasbourger,
    • Stephane Flibotte,
    • Brent Ewing,
    • Ryan Adair,
    • Vinci Au,
    • Iasha Chaudhry,
    • Lisa Fernando,
    • Harald Hutter,
    • Armelle Kieffer,
    • Joanne Lau,
    • Norris Lee,
    • Angela Miller,
    • Greta Raymant,
    • Bin Shen,
    • Jay Shendure,
    • Jon Taylor,
    • Emily H. Turner,
    • LaDeana W. Hillier,
    • Donald G. Moerman,
    • and Robert H. Waterston
    Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
    ..., Robert H Armelle Hutter, H Vinci Au Donald Strasbourger Pnina Angela Miller Pnina Chaudhry 10.1101/gr.157651.113 1088-9051 genome;gr.157651.113 The million mutation project: A new approach to genetics in Caenorhabditis elegans Resource The million mutation project: A new approach to genetics...
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  6. Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
    • Christina A. Cuomo,
    • Christopher A. Desjardins,
    • Malina A. Bakowski,
    • Jonathan Goldberg,
    • Amy T. Ma,
    • James J. Becnel,
    • Elizabeth S. Didier,
    • Lin Fan,
    • David I. Heiman,
    • Joshua Z. Levin,
    • Sarah Young,
    • Qiandong Zeng,
    • and Emily R. Troemel
    Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
    ...address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed...
  7. Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
    • Ignacio Maeso,
    • Manuel Irimia,
    • Juan J. Tena,
    • Esther González-Pérez,
    • David Tran,
    • Vydianathan Ravi,
    • Byrappa Venkatesh,
    • Sonsoles Campuzano,
    • José Luis Gómez-Skarmeta,
    • and Jordi Garcia-Fernàndez
    Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
    ...An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement Ignacio Maeso 1 , 6 , 8 , 9 , Manuel Irimia 1 , 7 , 8 , 9 , Juan J. Tena 2 , 8 , Esther González-Pérez 3 , 8...
  8. LETTER: The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    • Linda Z. Holland,
    • Ricard Albalat,
    • Kaoru Azumi,
    • Èlia Benito-Gutiérrez,
    • Matthew J. Blow,
    • Marianne Bronner-Fraser,
    • Frederic Brunet,
    • Thomas Butts,
    • Simona Candiani,
    • Larry J. Dishaw,
    • David E.K. Ferrier,
    • Jordi Garcia-Fernàndez,
    • Jeremy J. Gibson-Brown,
    • Carmela Gissi,
    • Adam Godzik,
    • Finn Hallböök,
    • Dan Hirose,
    • Kazuyoshi Hosomichi,
    • Tetsuro Ikuta,
    • Hidetoshi Inoko,
    • Masanori Kasahara,
    • Jun Kasamatsu,
    • Takeshi Kawashima,
    • Ayuko Kimura,
    • Masaaki Kobayashi,
    • Zbynek Kozmik,
    • Kaoru Kubokawa,
    • Vincent Laudet,
    • Gary W. Litman,
    • Alice C. McHardy,
    • Daniel Meulemans,
    • Masaru Nonaka,
    • Robert P. Olinski,
    • Zeev Pancer,
    • Len A. Pennacchio,
    • Mario Pestarino,
    • Jonathan P. Rast,
    • Isidore Rigoutsos,
    • Marc Robinson-Rechavi,
    • Graeme Roch,
    • Hidetoshi Saiga,
    • Yasunori Sasakura,
    • Masanobu Satake,
    • Yutaka Satou,
    • Michael Schubert,
    • Nancy Sherwood,
    • Takashi Shiina,
    • Naohito Takatori,
    • Javier Tello,
    • Pavel Vopalensky,
    • Shuichi Wada,
    • Anlong Xu,
    • Yuzhen Ye,
    • Keita Yoshida,
    • Fumiko Yoshizaki,
    • Jr-Kai Yu,
    • Qing Zhang,
    • Christian M. Zmasek,
    • Pieter J. de Jong,
    • Kazutoyo Osoegawa,
    • Nicholas H. Putnam,
    • Daniel S. Rokhsar,
    • Noriyuki Satoh,
    • and Peter W.H. Holland
    Genome Res. July 2008 18: 1100-1111; Published in Advance June 18, 2008, doi:10.1101/gr.073676.107
    ..., including those of protostomes, such as nematodes ( C. elegans Sequencing Consortium 1998 ; Stein et al. 2003 ) and insects ( Adams et al. 2000 ; Mongin et al. 2004 ; The Honeybee Genome Sequencing Consortium 2006 ), and deuterostomes, such as the urochordate Ciona intestinalis ( Dehal et al. 2002...
  9. Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
    • Itai Yanai and
    • Craig P. Hunter
    Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
    ...or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species—Caenorhabditis elegans and C. briggsae—that share a near-identical developmental...
  10. ARTICLE: The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
    • Cristian I. Castillo-Davis,
    • Fyodor A. Kondrashov,
    • Daniel L. Hartl,
    • and Rob J. Kulathinal
    Genome Res. May 2004 14: 802-811; doi:10.1101/gr.2195604
    ...annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components...
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