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  Extensive relationship between antisense transcription and alternative splicing in the human genome

  • A. Sorana Morrissy,
  • Malachi Griffith,
  • and Marco A. Marra

  Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
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  Genetic analysis of complex traits in the emerging Collaborative Cross

  • David L. Aylor,
  • William Valdar,
  • Wendy Foulds-Mathes,
  • Ryan J. Buus,
  • Ricardo A. Verdugo,
  • Ralph S. Baric,
  • Martin T. Ferris,
  • Jeff A. Frelinger,
  • Mark Heise,
  • Matt B. Frieman,
  • Lisa E. Gralinski,
  • Timothy A. Bell,
  • John D. Didion,
  • Kunjie Hua,
  • Derrick L. Nehrenberg,
  • Christine L. Powell,
  • Jill Steigerwalt,
  • Yuying Xie,
  • Samir N.P. Kelada,
  • Francis S. Collins,
  • Ivana V. Yang,
  • David A. Schwartz,
  • Lisa A. Branstetter,
  • Elissa J. Chesler,
  • Darla R. Miller,
  • Jason Spence,
  • Eric Yi Liu,
  • Leonard McMillan,
  • Abhishek Sarkar,
  • Jeremy Wang,
  • Wei Wang,
  • Qi Zhang,
  • Karl W. Broman,
  • Ron Korstanje,
  • Caroline Durrant,
  • Richard Mott,
  • Fuad A. Iraqi,
  • Daniel Pomp,
  • David Threadgill,
  • Fernando Pardo-Manuel de Villena,
  • and Gary A. Churchill

  Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
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  Genetic analysis in the Collaborative Cross breeding population

  • Vivek M. Philip,
  • Greta Sokoloff,
  • Cheryl L. Ackert-Bicknell,
  • Martin Striz,
  • Lisa Branstetter,
  • Melissa A. Beckmann,
  • Jason S. Spence,
  • Barbara L. Jackson,
  • Leslie D. Galloway,
  • Paul Barker,
  • Ann M. Wymore,
  • Patricia R. Hunsicker,
  • David C. Durtschi,
  • Ginger S. Shaw,
  • Sarah Shinpock,
  • Kenneth F. Manly,
  • Darla R. Miller,
  • Kevin D. Donohue,
  • Cymbeline T. Culiat,
  • Gary A. Churchill,
  • William R. Lariviere,
  • Abraham A. Palmer,
  • Bruce F. O'Hara,
  • Brynn H. Voy,
  • and Elissa J. Chesler

  Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
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  Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection

  • Caroline Durrant,
  • Hanna Tayem,
  • Binnaz Yalcin,
  • James Cleak,
  • Leo Goodstadt,
  • Fernando Pardo-Manuel de Villena,
  • Richard Mott,
  • and Fuad A. Iraqi

  Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
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  High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation

  • E. Josephine Clowney,
  • Angeliki Magklara,
  • Bradley M. Colquitt,
  • Nidhi Pathak,
  • Robert P. Lane,
  • and Stavros Lomvardas

  Genome Res. August 2011 21: 1249-1259; Published in Advance June 24, 2011, doi:10.1101/gr.120162.110
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  Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

  • Sharmistha Pal,
  • Ravi Gupta,
  • Hyunsoo Kim,
  • Priyankara Wickramasinghe,
  • Valérie Baubet,
  • Louise C. Showe,
  • Nadia Dahmane,
  • and Ramana V. Davuluri

  Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
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  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

  • Gabriel E. Zentner,
  • Paul J. Tesar,
  • and Peter C. Scacheri

  Genome Res. August 2011 21: 1273-1283; Published in Advance June 1, 2011, doi:10.1101/gr.122382.111
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  Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells

  • Hong-Bing Yu,
  • Rory Johnson,
  • Galih Kunarso,
  • and Lawrence W. Stanton

  Genome Res. August 2011 21: 1284-1293; Published in Advance June 1, 2011, doi:10.1101/gr.114488.110
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  A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

  • Bridgett M. vonHoldt,
  • John P. Pollinger,
  • Dent A. Earl,
  • James C. Knowles,
  • Adam R. Boyko,
  • Heidi Parker,
  • Eli Geffen,
  • Malgorzata Pilot,
  • Wlodzimierz Jedrzejewski,
  • Bogumila Jedrzejewska,
  • Vadim Sidorovich,
  • Claudia Greco,
  • Ettore Randi,
  • Marco Musiani,
  • Roland Kays,
  • Carlos D. Bustamante,
  • Elaine A. Ostrander,
  • John Novembre,
  • and Robert K. Wayne

  Genome Res. August 2011 21: 1294-1305; Published in Advance May 12, 2011, doi:10.1101/gr.116301.110
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  Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

  • Stephen R. Voss,
  • D. Kevin Kump,
  • Srikrishna Putta,
  • Nathan Pauly,
  • Anna Reynolds,
  • Rema J. Henry,
  • Saritha Basa,
  • John A. Walker,
  • and Jeramiah J. Smith

  Genome Res. August 2011 21: 1306-1312; Published in Advance April 11, 2011, doi:10.1101/gr.116491.110
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  Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

  • Ozren Bogdanović,
  • Steven W. Long,
  • Simon J. van Heeringen,
  • Arie B. Brinkman,
  • Jose Luis Gómez-Skarmeta,
  • Hendrik G. Stunnenberg,
  • Peter L. Jones,
  • and Gert Jan C. Veenstra

  Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
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  Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

  • Håvard Aanes,
  • Cecilia L. Winata,
  • Chi Ho Lin,
  • Jieqi P. Chen,
  • Kandhadayar G. Srinivasan,
  • Serene G.P. Lee,
  • Adrian Y.M. Lim,
  • Hajira Shreen Hajan,
  • Philippe Collas,
  • Guillaume Bourque,
  • Zhiyuan Gong,
  • Vladimir Korzh,
  • Peter Aleström,
  • and Sinnakaruppan Mathavan

  Genome Res. August 2011 21: 1328-1338; Published in Advance May 9, 2011, doi:10.1101/gr.116012.110
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  The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming

  • Sanne Nygaard,
  • Guojie Zhang,
  • Morten Schiøtt,
  • Cai Li,
  • Yannick Wurm,
  • Haofu Hu,
  • Jiajian Zhou,
  • Lu Ji,
  • Feng Qiu,
  • Morten Rasmussen,
  • Hailin Pan,
  • Frank Hauser,
  • Anders Krogh,
  • Cornelis J.P. Grimmelikhuijzen,
  • Jun Wang,
  • and Jacobus J. Boomsma

  Genome Res. August 2011 21: 1339-1348; Published in Advance June 30, 2011, doi:10.1101/gr.121392.111
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