The regulatory content of intergenic DNA shapes genome architecture.

Nelson CE, Hersh BM, Carroll SB.

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PMID: 15059258 [PubMed - indexed for MEDLINE]

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Benchmarking tools for the alignment of functional noncoding DNA.

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

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PMID: 14736341 [PubMed - indexed for MEDLINE]

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

Bergman CM, Kreitman M.

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PMID: 11483574 [PubMed - indexed for MEDLINE]

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

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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.

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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]

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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]

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Genomic regulatory blocks underlie extensive microsynteny conservation in insects.

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

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

Chen N, Stein LD.

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The Release 5.1 annotation of Drosophila melanogaster heterochromatin.

Smith CD, Shu S, Mungall CJ, Karpen GH.

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Korf I.

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