Genome Biology

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This article is part of the supplement: EGASP '05: ENCODE Genome Annotation Assessment Project

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A computational approach for identifying pseudogenes in the ENCODE regions

Deyou Zheng and Mark B Gerstein*

Genome Biology 2006, 7(Suppl 1):S13 doi:10.1186/gb-2006-7-s1-s13

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Research article   Open Access

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity

Yuen-Jong Liu, Deyou Zheng, Suganthi Balasubramanian, Nicholas Carriero, Ekta Khurana, Rebecca Robilotto, Mark B Gerstein BMC Genomics 2009, 10:480 (16 October 2009)

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Asymmetric histone modifications between the original and derived loci of human segmental duplications

Deyou Zheng Genome Biology 2008, 9:R105 (3 July 2008)

A systematic analysis of histone modifications between human segmental duplications shows that two seemingly identical genomic copies have distinct epigenomic properties.

Research article   Open Access

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

Flavio Mignone, Anna Anselmo, Giacinto Donvito, Giorgio P Maggi, Giorgio Grillo, Graziano Pesole BMC Genomics 2008, 9:277 (11 June 2008)

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EGASP: the human ENCODE Genome Annotation Assessment Project

Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese Genome Biology 2006, 7(Suppl 1):S2 (7 August 2006)