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Research

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  The influence of genomic context on mutation patterns in the human genome inferred from rare variants

  • Valerie M. Schaibley,
  • Matthew Zawistowski,
  • Daniel Wegmann,
  • Margaret G. Ehm,
  • Matthew R. Nelson,
  • Pamela L. St. Jean,
  • Gonçalo R. Abecasis,
  • John Novembre,
  • Sebastian Zöllner,
  • and Jun Z. Li

  Genome Res. December 2013 23: 1974-1984; Published in Advance August 29, 2013, doi:10.1101/gr.154971.113
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  Derived variants at six genes explain nearly half of size reduction in dog breeds

  • Maud Rimbault,
  • Holly C. Beale,
  • Jeffrey J. Schoenebeck,
  • Barbara C. Hoopes,
  • Jeremy J. Allen,
  • Paul Kilroy-Glynn,
  • Robert K. Wayne,
  • Nathan B. Sutter,
  • and Elaine A. Ostrander

  Genome Res. December 2013 23: 1985-1995; Published in Advance September 11, 2013, doi:10.1101/gr.157339.113
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  Identifying multiple causative genes at a single GWAS locus

  • Michael J. Flister,
  • Shirng-Wern Tsaih,
  • Caitlin C. O'Meara,
  • Bradley Endres,
  • Matthew J. Hoffman,
  • Aron M. Geurts,
  • Melinda R. Dwinell,
  • Jozef Lazar,
  • Howard J. Jacob,
  • and Carol Moreno

  Genome Res. December 2013 23: 1996-2002; Published in Advance September 4, 2013, doi:10.1101/gr.160283.113
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  The shared genomic architecture of human nucleolar organizer regions

  • Ioanna Floutsakou,
  • Saumya Agrawal,
  • Thong T. Nguyen,
  • Cathal Seoighe,
  • Austen R.D. Ganley,
  • and Brian McStay

  Genome Res. December 2013 23: 2003-2012; Published in Advance August 29, 2013, doi:10.1101/gr.157941.113
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  Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs

  • Phuc-Loi Luu,
  • Hans R. Schöler,
  • and Marcos J. Araúzo-Bravo

  Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
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  DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation

  • Anne Y. Lai,
  • Deepak Mav,
  • Ruchir Shah,
  • Sara A. Grimm,
  • Dhiral Phadke,
  • Katerina Hatzi,
  • Ari Melnick,
  • Cissy Geigerman,
  • Steve E. Sobol,
  • David L. Jaye,
  • and Paul A. Wade

  Genome Res. December 2013 23: 2030-2041; Published in Advance September 6, 2013, doi:10.1101/gr.155473.113
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  Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

  • Alexej Abyzov,
  • Rebecca Iskow,
  • Omer Gokcumen,
  • David W. Radke,
  • Suganthi Balasubramanian,
  • Baikang Pei,
  • Lukas Habegger,
  • The 1000 Genomes Project Consortium,
  • Charles Lee,
  • and Mark Gerstein

  Genome Res. December 2013 23: 2042-2052; Published in Advance September 11, 2013, doi:10.1101/gr.154625.113
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  H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

  • Gillian C.A. Taylor,
  • Ragnhild Eskeland,
  • Betül Hekimoglu-Balkan,
  • Madapura M. Pradeepa,
  • and Wendy A. Bickmore

  Genome Res. December 2013 23: 2053-2065; Published in Advance August 29, 2013, doi:10.1101/gr.155028.113
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  Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

  • Vlad C. Seitan,
  • Andre J. Faure,
  • Ye Zhan,
  • Rachel Patton McCord,
  • Bryan R. Lajoie,
  • Elizabeth Ing-Simmons,
  • Boris Lenhard,
  • Luca Giorgetti,
  • Edith Heard,
  • Amanda G. Fisher,
  • Paul Flicek,
  • Job Dekker,
  • and Matthias Merkenschlager

  Genome Res. December 2013 23: 2066-2077; Published in Advance September 3, 2013, doi:10.1101/gr.161620.113
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  3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

  • Noah Spies,
  • Christopher B. Burge,
  • and David P. Bartel

  Genome Res. December 2013 23: 2078-2090; Published in Advance September 26, 2013, doi:10.1101/gr.156919.113
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  Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations

  • Daniel M. Ibrahim,
  • Peter Hansen,
  • Christian Rödelsperger,
  • Asita C. Stiege,
  • Sandra C. Doelken,
  • Denise Horn,
  • Marten Jäger,
  • Catrin Janetzki,
  • Peter Krawitz,
  • Gundula Leschik,
  • Florian Wagner,
  • Till Scheuer,
  • Mareen Schmidt-von Kegler,
  • Petra Seemann,
  • Bernd Timmermann,
  • Peter N. Robinson,
  • Stefan Mundlos,
  • and Jochen Hecht

  Genome Res. December 2013 23: 2091-2102; Published in Advance August 30, 2013, doi:10.1101/gr.157610.113
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  The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

  • Julia Oh,
  • Alexandra F. Freeman,
  • NISC Comparative Sequencing Program,
  • Morgan Park,
  • Robert Sokolic,
  • Fabio Candotti,
  • Steven M. Holland,
  • Julia A. Segre,
  • and Heidi H. Kong

  Genome Res. December 2013 23: 2103-2114; Published in Advance October 29, 2013, doi:10.1101/gr.159467.113
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