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High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. Batut P, et al. Genome Res. 2013 Jan;23(1):169-80. doi: 10.1101/gr.139618.112. Epub 2012 Aug 30. Genome Res. 2013. PMID: 22936248 Free PMC article.
Temporal gene regulation during HIV-1 infection of human CD4+ T cells.
Corbeil J, Sheeter D, Genini D, Rought S, Leoni L, Du P, Ferguson M, Masys DR, Welsh JB, Fink JL, Sasik R, Huang D, Drenkow J, Richman DD, Gingeras T. Corbeil J, et al. Genome Res. 2001 Jul;11(7):1198-204. doi: 10.1101/ Genome Res. 2001. PMID: 11435401 Free PMC article.
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR. Kampa D, et al. Genome Res. 2004 Mar;14(3):331-42. doi: 10.1101/gr.2094104. Genome Res. 2004. PMID: 14993201 Free PMC article.
Origin of phenotypes: genes and transcripts.
Gingeras TR. Gingeras TR. Genome Res. 2007 Jun;17(6):682-90. doi: 10.1101/gr.6525007. Genome Res. 2007. PMID: 17567989 Review.
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. Rozowsky JS, et al. Genome Res. 2007 Jun;17(6):732-45. doi: 10.1101/gr.5696007. Genome Res. 2007. PMID: 17567993 Free PMC article.
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Denoeud F, et al. Genome Res. 2007 Jun;17(6):746-59. doi: 10.1101/gr.5660607. Genome Res. 2007. PMID: 17567994 Free PMC article.
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Zheng D, et al. Genome Res. 2007 Jun;17(6):839-51. doi: 10.1101/gr.5586307. Genome Res. 2007. PMID: 17568002 Free PMC article.
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