PubMed

The regulatory content of intergenic DNA shapes genome architecture.

Nelson CE, Hersh BM, Carroll SB.

Genome Biol. 2004;5(4):R25. Epub 2004 Mar 15.PMID: 15059258 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R.

BMC Genomics. 2009 Feb 25;10:92.PMID: 19243610 [PubMed - indexed for MEDLINE]Related articlesFree article

Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

BMC Bioinformatics. 2004 Jan 21;5:6.PMID: 14736341 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

Bergman CM, Kreitman M.

Genome Res. 2001 Aug;11(8):1335-45.PMID: 11483574 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin.

Fontanillas P, Hartl DL, Reuter M.

PLoS Genet. 2007 Nov;3(11):e210. Epub 2007 Oct 10.PMID: 18081425 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D.

Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.PMID: 16024819 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

Maglich JM, Sluder A, Guan X, Shi Y, McKee DD, Carrick K, Kamdar K, Willson TM, Moore JT.

Genome Biol. 2001;2(8):RESEARCH0029. Epub 2001 Jul 24.PMID: 11532213 [PubMed - indexed for MEDLINE]Related articlesFree article

Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes.

Marais G, Piganeau G.

Mol Biol Evol. 2002 Sep;19(9):1399-406.PMID: 12200468 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila.

Costas J, Vieira CP, Casares F, Vieira J.

BMC Genomics. 2003 Dec 16;4(1):52.PMID: 14675495 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic regulatory blocks underlie extensive microsynteny conservation in insects.

Engström PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B.

Genome Res. 2007 Dec;17(12):1898-908. Epub 2007 Nov 7.PMID: 17989259 [PubMed - indexed for MEDLINE]Related articlesFree article

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans.

Chen N, Stein LD.

Genome Res. 2006 May;16(5):606-17. Epub 2006 Apr 10.PMID: 16606698 [PubMed - indexed for MEDLINE]Related articlesFree article

Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans.

Duret L, Marais G, Biémont C.

Genetics. 2000 Dec;156(4):1661-9.PMID: 11102365 [PubMed - indexed for MEDLINE]Related articlesFree article

Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans.

Barnes TM, Kohara Y, Coulson A, Hekimi S.

Genetics. 1995 Sep;141(1):159-79.PMID: 8536965 [PubMed - indexed for MEDLINE]Related articlesFree article

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

Kuntz SG, Schwarz EM, DeModena JA, De Buysscher T, Trout D, Shizuya H, Sternberg PW, Wold BJ.

Genome Res. 2008 Dec;18(12):1955-68. Epub 2008 Nov 3.PMID: 18981268 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessment of SAGE in transcript identification.

Pleasance ED, Marra MA, Jones SJ.

Genome Res. 2003 Jun;13(6A):1203-15. Epub 2003 May 12.PMID: 12743019 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene finding in novel genomes.

Korf I.

BMC Bioinformatics. 2004 May 14;5:59.PMID: 15144565 [PubMed - indexed for MEDLINE]Related articlesFree article

A gateway-compatible yeast one-hybrid system.

Deplancke B, Dupuy D, Vidal M, Walhout AJ.

Genome Res. 2004 Oct;14(10B):2093-101.PMID: 15489331 [PubMed - indexed for MEDLINE]Related articlesFree article

Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes.

Lercher MJ, Blumenthal T, Hurst LD.

Genome Res. 2003 Feb;13(2):238-43.PMID: 12566401 [PubMed - indexed for MEDLINE]Related articlesFree article

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Borkova D, Miñana B, Kafatos FC, Bolshakov S, Sidén-Kiamos I, Papagiannakis G, Spanos L, Louis C, Madueño E, de Pablos B, Modolell J, Peter A, Schöttler P, Werner M, Mourkioti F, Beinert N, Dowe G, Schäfer U, Jäckle H, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Glover DM, Ashburner M.

Genome Res. 2001 May;11(5):710-30.PMID: 11337470 [PubMed - indexed for MEDLINE]Related articlesFree article

Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression.

Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9935-9. Epub 2006 Jun 15.PMID: 16777968 [PubMed - indexed for MEDLINE]Related articlesFree article