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COMMENTARY: ENCODE: More genomic empowerment
- George M. Weinstock
Genome Res. June 2007 17: 667-668; doi:10.1101/gr.6534207
.... , et al. ( 2007 ) The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci . Genome Res. doi: 10.1101/gr.5696007 , (this issue) . ↵ Ruan, Y. , Ooi, H.S. , Choo, S.W. , Chiu, K.P. , Zhao, X.D. , Srinivasan, K.G. , Yao, F. , Choo...
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PERSPECTIVE: What is a gene, post-ENCODE? History and updated definition
- Mark B. Gerstein,
- Can Bruce,
- Joel S. Rozowsky,
- Deyou Zheng,
- Jiang Du,
- Jan O. Korbel,
- Olof Emanuelsson,
- Zhengdong D. Zhang,
- Sherman Weissman,
- and Michael Snyder
Genome Res. June 2007 17: 669-681; doi:10.1101/gr.6339607
...number of unannotated transcription start sites (TSSs) identified by either sequencing of the 5′ end of transcribed mRNAs or the mapping of promoter-associated transcription factors via ChIP–chip or ChIP–PET ( The ENCODE Project Consortium 2007 ). Furthermore, the consortium found that many known protein...
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Methods: Generic eukaryotic core promoter prediction using structural features of DNA
- Thomas Abeel,
- Yvan Saeys,
- Eric Bonnet,
- Pierre Rouzé,
- and Yves Van de Peer
Genome Res. February 2008 18: 310-323; Published in Advance December 20, 2007, doi:10.1101/gr.6991408
...that some of the FP in the setting are actually missed genes or missed TSSs. To test this last claim, we retrieved datasets from the ENCODE project for Affymetrix Transcribed Fragments, Yale Transcriptionally Active Regions (TARs), and novel TARs from the DART system ( Rozowsky et al. 2007 ). We combined...
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PERSPECTIVE: Origin of phenotypes: Genes and transcripts
- Thomas R. Gingeras
Genome Res. June 2007 17: 682-690; doi:10.1101/gr.6525007
...term may not be as useful as it once was. Currently, “gene” has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity...
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Methods: Transcriptional and post-transcriptional profile of human chromosome 21
- Sergey I. Nikolaev,
- Samuel Deutsch,
- Raphael Genolet,
- Christelle Borel,
- Leila Parand,
- Catherine Ucla,
- Frederic Schütz,
- Genevieve Duriaux Sail,
- Yann Dupré,
- Pascale Jaquier-Gubler,
- Tanguy Araud,
- Beatrice Conne,
- Patrick Descombes,
- Jean-Dominique Vassalli,
- Joseph Curran,
- and Stylianos E. Antonarakis
Genome Res. August 2009 19: 1471-1479; Published in Advance July 6, 2009, doi:10.1101/gr.089425.108
...T, et al. 2002. An iron-responsive element type II in the 59-untranslated region of the Alzheimer’s amyloid precursor protein transcript. J Biol Chem 277: 45518–45528. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigo R, et al. 2007. The DART...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...discernible location preferences (Supplemental Fig. 5B), and are associated with a wide range of functions (Fig. 3C). A particularly notable finding was the identification of two distinct sites of ASM on the Armc10 transcript, which encodes a protein involved in mitochondrial dynamics (Serrat et al. 2014...

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