Searching journal content for articles similar to Nievergelt et al. 14 (6): 1199.

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  1. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...prediction. We build on these data, implementing further filtering steps to remove families with homology with other species, to identify putative SSOGs in the gut microbiome and to study them systematically. By looking for patterns in large-scale comparisons, we attempt to disentangle the evolutionary...
  2. Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
    • Jeanlin Jourdain,
    • Harmonie Barasc,
    • Thomas Faraut,
    • Anne Calgaro,
    • Nathalie Bonnet,
    • Camille Marcuzzo,
    • Amandine Suin,
    • Anne Barbat,
    • Chris Hozé,
    • Florian Besnard,
    • Sébastien Taussat,
    • Cécile Grohs,
    • Claire Kuchly,
    • Carole Iampietro,
    • Cécile Donnadieu,
    • Alain Pinton,
    • Didier Boichard,
    • and Aurélien Capitan
    Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
    ...Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain,1,2 Harmonie Barasc,3 Thomas Faraut,3 Anne Calgaro,3 Nathalie Bonnet,3 Camille Marcuzzo,4 Amandine Suin,4 Anne Barbat,2 Chris Hozé,1...
  3. Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
    • Leslie O. Goodwin,
    • Erik Splinter,
    • Tiffany L. Davis,
    • Rachel Urban,
    • Hao He,
    • Robert E. Braun,
    • Elissa J. Chesler,
    • Vivek Kumar,
    • Max van Min,
    • Juliet Ndukum,
    • Vivek M. Philip,
    • Laura G. Reinholdt,
    • Karen Svenson,
    • Jacqueline K. White,
    • Michael Sasner,
    • Cathleen Lutz,
    • and Stephen A. Murray
    Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
    ...means to identify both the insertion site and content of transgenes through deep sequencing of genomic loci linked to specific known transgene cassettes. Here, we report the first large-scale analysis of transgene insertion sites from 40 highly used transgenic mouse lines. We show that the transgenes...
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  4. Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
    • Stephen J. Salipante,
    • David J. Roach,
    • Jacob O. Kitzman,
    • Matthew W. Snyder,
    • Bethany Stackhouse,
    • Susan M. Butler-Wu,
    • Choli Lee,
    • Brad T. Cookson,
    • and Jay Shendure
    Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
    ...of Washington, Seattle, Washington 98195, USA Large-scale bacterial sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole- sequencing and de novo assembly of 312...
  5. Research: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
    • David van Dijk,
    • Eilon Sharon,
    • Maya Lotan-Pompan,
    • Adina Weinberger,
    • Eran Segal,
    • and Lucas B. Carey
    Genome Res. January 2017 27: 87-94; Published in Advance December 13, 2016, doi:10.1101/gr.212316.116
    ...understood. To determine the mapping between promoter DNA sequence, TF concentration, and gene expression output, we have conducted in budding yeast a large-scale measurement of the activity of thousands of designed promoters at six different levels of TF. We observe that maximum promoter activity...
  6. Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    • Matthias H. Weissensteiner,
    • Andy W.C. Pang,
    • Ignas Bunikis,
    • Ida Höijer,
    • Olga Vinnere-Petterson,
    • Alexander Suh,
    • and Jochen B.W. Wolf
    Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
    ...assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM...
  7. Research: Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization
    • Kasper D. Hansen,
    • Sarven Sabunciyan,
    • Ben Langmead,
    • Noemi Nagy,
    • Rebecca Curley,
    • Georg Klein,
    • Eva Klein,
    • Daniel Salamon,
    • and Andrew P. Feinberg
    Genome Res. February 2014 24: 177-184; Published in Advance September 25, 2013, doi:10.1101/gr.157743.113
    ...Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization Kasper D. Hansen 1 , 2 , 3 , 8 , Sarven Sabunciyan 2 , 4 , 8 , Ben Langmead 2 , 5 , Noemi Nagy 6 , Rebecca Curley 2 , 7...
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  8. Perspective: Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
    • Ian A. Mellis and
    • Arjun Raj
    Genome Res. October 2015 25: 1466-1472; doi:10.1101/gr.190579.115
    ...Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? Ian A. Mellis 1 and Arjun Raj 2 1Perelman School of Medicine, Genomics and Computational Biology Graduate Group, University...
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  9. LETTER: Large-scale recombination rate patterns are conserved among human populations
    • David Serre,
    • Robert Nadon,
    • and Thomas J. Hudson
    Genome Res. November 2005 15: 1547-1552; doi:10.1101/gr.4211905
    ...in the overall length of the map and therefore in the species recombination rate (the physical map being of roughly constant size) ( Rogers et al. 2000 ). This suggests that large-scale recombination rates can also vary, which raises the question whether they differ among human populations. We currently do...
  10. RESOURCE: Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
    • Gwenn M. Hansen,
    • Diane C. Markesich,
    • Michael B. Burnett,
    • Qichao Zhu,
    • Karen M. Dionne,
    • Lizabeth J. Richter,
    • Richard H. Finnell,
    • Arthur T. Sands,
    • Brian P. Zambrowicz,
    • and Alejandro Abuin
    Genome Res. October 2008 18: 1670-1679; Published in Advance September 17, 2008, doi:10.1101/gr.078352.108
    ...Large-scale gene trapping in C57BL/6N mouse embryonic stem cells Gwenn M. Hansen 1 , 3 , 4 , Diane C. Markesich 1 , 3 , Michael B. Burnett 1 , Qichao Zhu 1 , Karen M. Dionne 1 , Lizabeth J. Richter 1 , Richard H. Finnell...
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