Searching journal content for articles similar to Clark et al. 15 (11): 1496.

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  1. Research: Genome-wide analysis of differential RNA editing in epilepsy
    • Prashant Kumar Srivastava,
    • Marta Bagnati,
    • Andree Delahaye-Duriez,
    • Jeong-Hun Ko,
    • Maxime Rotival,
    • Sarah R. Langley,
    • Kirill Shkura,
    • Manuela Mazzuferi,
    • Bénédicte Danis,
    • Jonathan van Eyll,
    • Patrik Foerch,
    • Jacques Behmoaras,
    • Rafal M. Kaminski,
    • Enrico Petretto,
    • and Michael R. Johnson
    Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
    ...mouse SNP database version 137. Additional biases such as strand and variant distance bias were removed as described in Danecek et al. (2012). VDB evaluates the likelihood of the mean pairwise distance of the variant bases in the aligned portion of the reads; it was calculated using SAMtools...
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  2. Resource: Genome-wide discovery of human splicing branchpoints
    • Tim R. Mercer,
    • Michael B. Clark,
    • Stacey B. Andersen,
    • Marion E. Brunck,
    • Wilfried Haerty,
    • Joanna Crawford,
    • Ryan J. Taft,
    • Lars K. Nielsen,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
    ...Genome-wide discovery of human splicing branchpoints Tim R. Mercer 1 , 2 , 8 , Michael B. Clark 1 , 3 , 8 , Stacey B. Andersen 4 , Marion E. Brunck 4 , Wilfried Haerty 3 , Joanna Crawford 5 , Ryan J...
  3. LETTER: Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
    • Mikael Brandström and
    • Hans Ellegren
    Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
    ...Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias Mikael Brandström and Hans Ellegren 1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala...
  4. Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
    • Vera B. Kaiser,
    • Lana Talmane,
    • Yatendra Kumar,
    • Fiona Semple,
    • Marie MacLennan,
    • Deciphering Developmental Disorders Study,
    • David R. FitzPatrick,
    • Martin S. Taylor,
    • and Colin A. Semple
    Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
    .... The same TFBSs appear to be somewhat more important features in models that specifically predict damage at active brain enhancers (Supplemental Fig. S9). Genome-wide, deletion breakpoints and 5- to 20-bp insertions were enriched in early replicating DNA (Spearman's rank correlation with replication timing...
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  5. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  6. Method: Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease
    • Snehit Prabhu and
    • Itsik Pe'er
    Genome Res. November 2012 22: 2230-2240; Published in Advance July 5, 2012, doi:10.1101/gr.137885.112
    ...Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease Snehit Prabhu and Itsik Pe'er 1 Department of Computer Science, Columbia University, New York, New York 10027, USA Abstract Long-range gene–gene interactions...
  7. Research: 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
    ...A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids Bridgett M. vonHoldt 1 , John P. Pollinger 1 , Dent A. Earl 2 , James C. Knowles 1 , Adam R. Boyko 3 , Heidi Parker 4 , Eli Geffen 5...
  8. Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
    • Viola Nolte,
    • Ram Vinay Pandey,
    • Robert Kofler,
    • and Christian Schlötterer
    Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
    ...melanogaster . Based on a new, annotated genome sequence, we characterized the genome-wide polymorphism by sequencing pooled individuals (Pool-seq). We show that the interplay between selection and recombination results in a genome-wide polymorphism pattern characteristic for D. mauritiana . Two large genomic...
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  9. Next-Generation DNA Sequencing/Review: Finding the fifth base: Genome-wide sequencing of cytosine methylation
    • Ryan Lister and
    • Joseph R. Ecker
    Genome Res. June 2009 19: 959-966; Published in Advance March 9, 2009, doi:10.1101/gr.083451.108
    ...Finding the fifth base: Genome-wide sequencing of cytosine methylation Ryan Lister 1 , 2 and Joseph R. Ecker 1 , 2 , 3 1 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; 2 Plant...
  10. LETTER: The genome-wide determinants of human and chimpanzee microsatellite evolution
    • Yogeshwar D. Kelkar,
    • Svitlana Tyekucheva,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. January 2008 18: 30-38; Published in Advance November 21, 2007, doi:10.1101/gr.7113408
    ...The genome-wide determinants of human and chimpanzee microsatellite evolution Yogeshwar D. Kelkar 1 , 2 , Svitlana Tyekucheva 2 , 3 , Francesca Chiaromonte 2 , 3 , and Kateryna D. Makova 1 , 2 , 4 1 Department of Biology, Penn...
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