| Date |
Title |
Authors |
Source |
| 2006 |
Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. |
Willingham AT, Dike S, Cheng J, Manak JR, Bell I, Cheung E, Drenkow J, Dumais E, Duttagupta R, Ganesh M, Ghosh S, Helt G, Nix D, Piccolboni A, Sementchenko V, Tammana H, Kapranov P; ENCODE Genes And Transcripts Group, Gingeras TR. |
Cold Spring Harb Symp Quant Biol. 71:101-10. |
| 2007-02 |
Transcriptional noise and the fidelity of initiation by RNA polymerase II |
Struhl K |
Nature Structural & Molecular Biology, 14(2):103-5 |
| 2007-05-08 |
Genome-wide transcription and the implications for genomic organization |
Kapranov P, Willingham AT, Gingeras TR |
Nat Rev Genet 8 (6): 413-23 |
| 2007-05-17 |
RNA maps reveal new RNA classes and a possible function for pervasive transcription |
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. |
Science 316 (5830): 1484-8 |
| 2007-06-14 |
Identification and analysis of
functional elements in 1% of the human genome by the
ENCODE pilot project |
The ENCODE Project Consortium |
Nature 447, 799-816 |
| 2007-06 |
Genome Biology ENCODE pilot project companion issue |
(Assorted articles and authors) |
Genome Biol 17(6) |
| 2007-07-13 |
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells |
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA |
Cell 130, 77-88 |
| 2008-05-30 |
Mapping and quantifying mammalian transcriptomes by RNA-Seq; (supplementary materials) |
Mortazavi A, Williams BA, McCue1 K, Schaeffer L, Wold B |
Nature Methods 5:621-628. |
| 2008-06-06 |
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing |
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M |
Science 320 (5881): 1344-1349 |
| 2009 |
Pervasive transcription in the human genome |
Choudhuri S, Carlson DB |
Genomics: Fundamentals and Applications, Section 4.1.10.1, pp.80-82. |
| 2009-01 |
RNA-Seq: a revolutionary tool for transcriptomics |
Wang Z, Gerstein M, Snyder M. |
Nat Rev Genet. 10(1):57-63. |
| 2009-02-19 |
Bidirectional promoters generate pervasive transcription in yeast. |
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. |
Nature 457(7232):1033-7. |
| 2009-05-11 |
Studying chromosome-wide transcriptional networks: new insights into disease? |
Kapranov, K |
Genome Medicine 1:50 |
| 2009-06-17 |
Unlocking the secrets of the genome |
Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH, and the modENCODE Consortium. |
Nature 459: 927-930 |
| 2009-08-14 |
Pervasive transcription constitutes a new level of eukaryotic genome regulation (review) |
Berretta J and Morillon A |
EMBO reports 10(9): 973–982 |
| 2009-09-21 |
Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications |
Dinger ME, Amaral PP, Mercer TR, Mattick JS |
Briefings in Functional Genomics and Proteomics, Advance Access |
| 2009-12 |
The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs |
Jacquier A |
Nat Rev Genet 10: 833-844 |
| 2010-12-21 |
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA |
Kapranov P, St. Laurent G, Raz T,
Ozsolak F, Reynolds C, Sorensen P, Reaman G, Milos P,
Arceci R, Thompson J, Triche T |
BMC Biology 8: 149 |
| 2011-09 |
Regulatory Variation Within and Between Species |
Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M |
Annual Review of Genomics and Human Genetics, vol 12 |
