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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
...Functional transcriptomics in the post-ENCODE era Jonathan M. Mudge 1 , Adam Frankish and Jennifer Harrow Department of Informatics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom Abstract The last decade has seen...
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Research: Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
- Dorothee Pflueger,
- Stéphane Terry,
- Andrea Sboner,
- Lukas Habegger,
- Raquel Esgueva,
- Pei-Chun Lin,
- Maria A. Svensson,
- Naoki Kitabayashi,
- Benjamin J. Moss,
- Theresa Y. MacDonald,
- Xuhong Cao,
- Terrence Barrette,
- Ashutosh K. Tewari,
- Mark S. Chee,
- Arul M. Chinnaiyan,
- David S. Rickman,
- Francesca Demichelis,
- Mark B. Gerstein,
- and Mark A. Rubin
Genome Res. January 2011 21: 56-67; Published in Advance October 29, 2010, doi:10.1101/gr.110684.110
...(Maher et al. 2009a; Rickman et al. 2009). Although this analysis does not completely rule out possible contamination by epithelial cancer cells in the benign tissue, our data provide evidence for an extended complexity of the cellular transcriptome and support a broader definition of a gene thatmight...
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Resource: mGene: Accurate SVM-based gene finding with an application to nematode genomes
- Gabriele Schweikert,
- Alexander Zien,
- Georg Zeller,
- Jonas Behr,
- Christoph Dieterich,
- Cheng Soon Ong,
- Petra Philips,
- Fabio De Bona,
- Lisa Hartmann,
- Anja Bohlen,
- Nina Krüger,
- Sören Sonnenburg,
- and Gunnar Rätsch
Genome Res. November 2009 19: 2133-2143; Published in Advance June 29, 2009, doi:10.1101/gr.090597.108
...methods in general is to assess their accuracy in comparison to previously published ones with as little bias as possible. This is particularly true for gene finders, since even the very definition of a gene is still under discussion (Gerstein et al. 2007). Even subtle differences in evaluation routines...
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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
...is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion...
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Perspective: Understanding the regulatory and transcriptional complexity of the genome through structure
- Tim R. Mercer and
- John S. Mattick
Genome Res. July 2013 23: 1081-1088; doi:10.1101/gr.156612.113
..., Weissman S, Snyder M. 2007. What is a gene, postENCODE? History and updated definition. Genome Res 17: 669–681. Gingeras TR. 2007. Origin of phenotypes: Genes and transcripts.Genome Res 17: 682–690. Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager...
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Methods: Targeted discovery of novel human exons by comparative genomics
- Adam Siepel,
- Mark Diekhans,
- Broňa Brejová,
- Laura Langton,
- Michael Stevens,
- Charles L.G. Comstock,
- Colleen Davis,
- Brent Ewing,
- Shelly Oommen,
- Christopher Lau,
- Hung-Chun Yu,
- Jianfeng Li,
- Bruce A. Roe,
- Phil Green,
- Daniela S. Gerhard,
- Gary Temple,
- David Haussler,
- and Michael R. Brent
Genome Res. December 2007 17: 1763-1773; Published in Advance November 7, 2007, doi:10.1101/gr.7128207
...2004 ). These discoveries point to an unanticipated level of complexity in the way the encodes functional molecules, and they call into question our working definition of the gene ( Gerstein et al. 2007 ). Nevertheless, for its day-to-day work, the research community depends on sets of gene annotations...
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Perspective: Toward mapping the biology of the genome
- Stephen Chanock
Genome Res. September 2012 22: 1612-1615; doi:10.1101/gr.144980.112
...is a gene, postENCODE? History and updated definition. Genome Res 17: 669–681. Gingeras TR. 2007. Origin of phenotypes: Genes and transcripts.Genome Res 17: 682–690. Greally JM. 2007. Encyclopedia of humble DNA. Nature 447: 782–783. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
....B. , Bruce, C. , Rozowsky, J.S. , Zheng, D. , Du, J. , Korbel, J.O. , Emanuelsson, O. , Zhang, Z.D. , Weissman, S. , Snyder, M. ( 2007 ) What is a gene, post-ENCODE? History and updated definition . Genome Res. 17 : 669 – 681 . ↵ Ginger, M.R. , Shore, A.N. , Contreras, A. , Rijnkels, M. , Miller, J...
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LETTER: Impacts of protein–protein interaction domains on organism and network complexity
- Kai Xia,
- Zheng Fu,
- Lei Hou,
- and Jing-Dong J. Han
Genome Res. September 2008 18: 1500-1508; Published in Advance August 7, 2008, doi:10.1101/gr.068130.107
...is a gene, post-ENCODE? History and updated definition . Genome Res. 17 : 669 – 681 . ↵ Graveley, B.R. ( 2001 ) Alternative splicing: Increasing diversity in the proteomic world . Trends Genet. 17 : 100 – 107 . ↵ Kirschner, M. , Gerhart, J. ( 1998 ) Evolvability . Proc. Natl. Acad. Sci. 95 : 8420 – 8427...

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