Searching journal content for articles similar to Chaignat et al. 21 (1): 106.

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  1. Research: Variation in the fitness impact of translationally optimal codons among animals
    • Florian Bénitière,
    • Tristan Lefébure,
    • and Laurent Duret
    Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
    ...variation in the intensity in TS across animals, it is important to refer to population genetic principles (Ohta 1996). Indeed, the SCU in a given reflects a balance between selection favoring translationally optimal codons and the effects of mutation and drift, allowing the fixation of nonoptimal codons...
  2. Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
    • Aleix Palahí i Torres,
    • Lars Höök,
    • Karin Näsvall,
    • Daria Shipilina,
    • Christer Wiklund,
    • Roger Vila,
    • Peter Pruisscher,
    • and Niclas Backström
    Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
    ...on recombination rate variation along chromosomes here, exact estimates of r are not crucial, but caution is of course needed when comparing our results to estimates of -wide recombination rate obtained using different approaches. The ZW sex-chromosome system in Lepidoptera, where males are homogametic, coupled...
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  3. Research: Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
    • Meredith M. Course,
    • Arvis Sulovari,
    • Kathryn Gudsnuk,
    • Evan E. Eichler,
    • and Paul N. Valdmanis
    Genome Res. August 2021 31: 1313-1324; Published in Advance July 9, 2021, doi:10.1101/gr.275560.121
    ...long-read sequencing in a very large pedigree for the WDR7 VNTR (Course et al. 2020). It is also consistent with the negative relationship we observed between motif size and copy number (Fig. 1B), which indicates that the longer a motif length is, the less likely it is to expand rapidly. That said...
  4. Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
    • Ryan O'Hara,
    • Enzo Tedone,
    • Andrew Ludlow,
    • Ejun Huang,
    • Beatrice Arosio,
    • Daniela Mari,
    • and Jerry W. Shay
    Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
    ...be fully explained by cell cycle-dependent variations in mtDNA copy number (Supplemental Fig. 1D; Supplemental Table S5). Although we observed a significant increase in mtDNA copy number during the transition from G2 to M phase, and a significant decrease during the early G1 phase, these changes were...
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  5. Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
    • Wesley A. Brashear,
    • Terje Raudsepp,
    • and William J. Murphy
    Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
    ...family Felidae but show high transcript diversity, copy number variation, and structural rearrangement. Our analysis of ampliconic gene evolution unveils a complex pattern of long-term gene content stability despite extensive structural variation on a nonrecombining background.Advances in DNA sequencing...
  6. Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
    • Daniela S. Aliaga Goltsman,
    • Christine L. Sun,
    • Diana M. Proctor,
    • Daniel B. DiGiulio,
    • Anna Robaczewska,
    • Brian C. Thomas,
    • Gary M. Shaw,
    • David K. Stevenson,
    • Susan P. Holmes,
    • Jillian F. Banfield,
    • and David A. Relman
    Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
    ...) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity...
  7. Research: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
    • Elodie Gazave,
    • Fleur Darré,
    • Carlos Morcillo-Suarez,
    • Natalia Petit-Marty,
    • Angel Carreño,
    • Urko M. Marigorta,
    • Oliver A. Ryder,
    • Antoine Blancher,
    • Mariano Rocchi,
    • Elena Bosch,
    • Carl Baker,
    • Tomàs Marquès-Bonet,
    • Evan E. Eichler,
    • and Arcadi Navarro
    Genome Res. October 2011 21: 1626-1639; Published in Advance August 8, 2011, doi:10.1101/gr.117242.110
    ...Copy number variation analysis in the great apes reveals species-specific patterns of structural variation Elodie Gazave 1 , 10 , 11 , Fleur Darré 1 , 10 , 12 , Carlos Morcillo-Suarez 1 , 2 , Natalia Petit-Marty 1 , Angel Carreño 1...
  8. Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
    • Matthew B. Rogers,
    • James D. Hilley,
    • Nicholas J. Dickens,
    • Jon Wilkes,
    • Paul A. Bates,
    • Daniel P. Depledge,
    • David Harris,
    • Yerim Her,
    • Pawel Herzyk,
    • Hideo Imamura,
    • Thomas D. Otto,
    • Mandy Sanders,
    • Kathy Seeger,
    • Jean-Claude Dujardin,
    • Matthew Berriman,
    • Deborah F. Smith,
    • Christiane Hertz-Fowler,
    • and Jeremy C. Mottram
    Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
    ...Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania Matthew B. Rogers 1 , 2 , 9 , James D. Hilley 3 , 9 , Nicholas J. Dickens 3 , 9 , Jon Wilkes 3 , Paul A. Bates 4...
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  9. Research: Genetic and phenotypic intra-species variation in Candida albicans
    • Matthew P. Hirakawa,
    • Diego A. Martinez,
    • Sharadha Sakthikumar,
    • Matthew Z. Anderson,
    • Aaron Berlin,
    • Sharvari Gujja,
    • Qiandong Zeng,
    • Ethan Zisson,
    • Joshua M. Wang,
    • Joshua M. Greenberg,
    • Judith Berman,
    • Richard J. Bennett,
    • and Christina A. Cuomo
    Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
    ...is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number...
  10. Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
    • Barbara Dunn,
    • Chandra Richter,
    • Daniel J. Kvitek,
    • Tom Pugh,
    • and Gavin Sherlock
    Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
    ...interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate...
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