PubMed

Studying chromosome-wide transcriptional networks: new insights into disease?

Kapranov P.

Genome Med. 2009 May 11;1(5):50.PMID: 19480644 [PubMed - in process]Related articlesFree article

[Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes]

Zhang DL, Ji L, Li YD.

Yi Chuan Xue Bao. 2004 May;31(5):431-43. Chinese. PMID: 15478601 [PubMed - indexed for MEDLINE]Related articles

Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury.

Maia RM, Valente V, Cunha MA, Sousa JF, Araujo DD, Silva WA Jr, Zago MA, Dias-Neto E, Souza SJ, Simpson AJ, Monesi N, Ramos RG, Espreafico EM, Paçó-Larson ML.

BMC Genomics. 2007 Jul 24;8:249.PMID: 17650329 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ.

BMC Biol. 2008 Jul 8;6:30.PMID: 18611272 [PubMed - indexed for MEDLINE]Related articlesFree article

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, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.

Science. 2007 Jun 8;316(5830):1484-8. Epub 2007 May 17.PMID: 17510325 [PubMed - indexed for MEDLINE]Related articlesFree article

The mouse genome: experimental examination of gene predictions and transcriptional start sites.

Dike S, Balija VS, Nascimento LU, Xuan Z, Ou J, Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR.

Genome Res. 2004 Dec;14(12):2424-9.PMID: 15574821 [PubMed - indexed for MEDLINE]Related articlesFree article

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. 2006;71:101-10.PMID: 17480199 [PubMed - indexed for MEDLINE]Related articles

Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.

He H, Wang J, Liu T, Liu XS, Li T, Wang Y, Qian Z, Zheng H, Zhu X, Wu T, Shi B, Deng W, Zhou W, Skogerbø G, Chen R.

Genome Res. 2007 Oct;17(10):1471-7. Epub 2007 Sep 4.PMID: 17785534 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR.

Science. 2005 May 20;308(5725):1149-54. Epub 2005 Mar 24.PMID: 15790807 [PubMed - indexed for MEDLINE]Related articlesFree article

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project.

Nature. 2009 Feb 19;457(7232):1028-32. Epub 2009 Jan 25.PMID: 19169241 [PubMed - indexed for MEDLINE]Related articlesFree article

A comprehensive transcript index of the human genome generated using microarrays and computational approaches.

Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, Svetnik V, Leonardson A, Hart KW, Russell A, Li G, Cavet G, Castle J, McDonagh P, Kan Z, Chen R, Kasarskis A, Margarint M, Caceres RM, Johnson JM, Armour CD, Garrett-Engele PW, Tsinoremas NF, Shoemaker DD.

Genome Biol. 2004;5(10):R73. Epub 2004 Sep 23.PMID: 15461792 [PubMed - indexed for MEDLINE]Related articlesFree article

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. 2009 Feb 19;457(7232):1033-7. Epub 2009 Jan 25.PMID: 19169243 [PubMed - indexed for MEDLINE]Related articlesFree 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.

Genome Res. 2007 Jun;17(6):746-59.PMID: 17567994 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide transcription and the implications for genomic organization.

Kapranov P, Willingham AT, Gingeras TR.

Nat Rev Genet. 2007 Jun;8(6):413-23. Epub 2007 May 8. Review.PMID: 17486121 [PubMed - indexed for MEDLINE]Related articles

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K.

BMC Biol. 2007 Jun 18;5:25.PMID: 17577407 [PubMed - indexed for MEDLINE]Related articlesFree article

A high-resolution map of transcription in the yeast genome.

David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM.

Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5. Epub 2006 Mar 28.PMID: 16569694 [PubMed - indexed for MEDLINE]Related articlesFree article

Origin of phenotypes: genes and transcripts.

Gingeras TR.

Genome Res. 2007 Jun;17(6):682-90. Review.PMID: 17567989 [PubMed - indexed for MEDLINE]Related articlesFree article

Antisense transcription: a critical look in both directions.

Beiter T, Reich E, Williams RW, Simon P.

Cell Mol Life Sci. 2009 Jan;66(1):94-112. Review.PMID: 18791843 [PubMed - indexed for MEDLINE]Related articles

Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise?

Guimarães AO, Motta FL, Alves VS, Castilho BA, Pesquero JB.

BMC Mol Biol. 2009 Feb 8;10:7.PMID: 19200403 [PubMed - indexed for MEDLINE]Related articlesFree article

Structure, 5'-flanking sequence, and chromosome location of the human N-formyl peptide receptor gene. A single-copy gene comprised of two exons on chromosome 19q.13.3 that yields two distinct transcripts by alternative polyadenylation.

Haviland DL, Borel AC, Fleischer DT, Haviland JC, Wetsel RA.

Biochemistry. 1993 Apr 27;32(16):4168-74.PMID: 7682842 [PubMed - indexed for MEDLINE]Related articles