Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Keywords

ENCODE, Genome, Human genome, Computational biology, Biology

References

• Large-Scale Transcriptional Activity in Chromosomes 21 and 22尹亦辉 — 2002
• Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.浩作 潮田, 英男 大曾根, 光延 阿部 — 2003
• Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers.Teresa Blanch Bofill — 2004
• Integrated pseudogene annotation for human chromosome 22: evidence for transcription.Deyou Zheng, Zhaolei Zhang, Paul M. Harrison — 2005
• A computational approach for identifying pseudogenes in the ENCODE regionsGemma Benavides Gil, Fermín Martínez‐Zaragoza, José P. Espada — 2006
• Spatial organization of gene expression: the active chromatin hubWouter de Laat, Frank Grosveld — 2003
• Primer3 on the WWW for general users and for biologist programmers.Steve Rozen, Helen Skaletsky — 2000
• Replication program of active and inactive multigene families in mammalian cellsK S Hatton, Veena Dhar, E H Brown — 1988
• High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays.Matthew J. Oberley, Julissa Tsao, Patrick Yau — 2004
• Conserved non-genic sequences — an unexpected feature of mammalian genomesEmmanouil T. Dermitzakis, Alexandre Reymond, Stylianos E. Antonarakis — 2005
• From The Cover: An algorithm for progressive multiple alignment of sequences withAri Löytynoja, Nick Goldman — 2005
• Antisense Transcription in the Mammalian TranscriptomeShintaro Katayama, Yuji Tomaru, Takeya Kasukawa — 2005
• Initial sequence of the chimpanzee genome and comparison with the human genomeTarjei S. Mikkelsen — 2005
• Intensely punctate meiotic recombination in the class II region of the major histocompatibility complexAlec J. Jeffreys, Liisa Kauppi, Rita Neumann — 2001
• Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.Michael Ludwig, Martin Kreitman — 1995
• Statistical significance for genomewide studiesJohn D. Storey, Robert Tibshirani — 2003
• CAGE: cap analysis of gene expressionRimantas Kodzius, Miki Kojima, Hiromi Nishiyori — 2006
• A bivalent chromatin structure marks key developmental genes in embryonic stem cells.B Bernstein, Tarjei S. Mikkelsen, Xiaohui Xie — 2006
• DNA microarrays for comparative genomic hybridization based on DOP‐PCR amplification of BAC and PAC clonesHeike Fiegler, Philippa Carr, Eleanor Douglas — 2003
• A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MSChunming Ding, Charles R. Cantor — 2003

Cited by

• Functional analysis of human enhancers using the zebrafish embryoIrene Miguel Escalada — 2014
• Chromatin Immunoprecipitation in Adult Zebrafish Red CellsEirini Trompouki, Teresa V. Bowman, Anthony DiBiase — 2011
• Identification and Characterization of Novel Sir3/MeCP2-Chromatin InteractionsNicholas L. Adkins — 2009
• Interactions of transcription factors with chromatin.Harm van Bakel — 2011
• Ancient roles of non-coding RNAs in eukaryotic evolutionLotta Avesson — 2011
• The role of noncoding RNA in thyroid cancer.Xinying Li, Zhiming Wang — 2012
• Establishing a screen for enhancers active in Drosophila embryogenesisGerald Stampfel — 2011
• Exploiting Drosophila genetics to understand microRNA function and regulationQi Dai, Peter Smibert, Eric C. Lai — 2012
• Word-Based Characterization of the Bidirectional Promoters from the Human DNA-Repair PathwayJens Lichtenberg, Edwin Jacox, Mary Qu Yang — 2008
• New links to the pathogenesis of Crohn disease provided by genome-wide association scansLixian Qin — 2008
• Extrapolating ENCODE data to the whole human genome.Albert Fabà — 2008
• Transcription induces strand-specific mutations at the 5' end of human genes.Pascale Dupuy Brun — 2008
• Phenotype-defining functions of multiple non-coding RNA pathways公恵 中川 — 2008
• Revisiting the Saccharomyces cerevisiae predicted ORFeome.Robert T. Reville, Seth A. Seabury, Frank Neuhauser — 2008
• Genomic Organization of Zebrafish microRNAs加奈子 山田, 知恵 椿, 美穂 古山 — 2008
• Genome-wide nucleotide-level mammalian ancestor reconstruction.Mathew Zachariah — 2008
• Annotation of tertiary interactions in RNA structures reveals variations and correlations.純子 小川, 数江 遠藤, 友 金丸 — 2008
• Sharing Data between LSDBs and Central RepositoriesDavid J. Whitin — 2009
• Regulation of Ubx Expression by Epigenetic Enhancer Silencing in Response to Ubx Levels and Genetic VariationArturo Martín Alonso — 2009
• An overview of recent developments in genomics and associated statistical methods光子 浅井, 清 小牟田, 誠一 延山 — 2009

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