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Title
Functions of noncoding sequences in mammalian genomes
Authors
Keywords
noncoding sequences, pervasive transcription, transcription regulation, promoter, 5′-UTR, 3′-UTR, DNA methylation, CpG islands, intron, splicing, transcription enhancer, LCR, insulator, S/MAR, noncoding RNA, siRNA, miRNA, lncRNA, pseudogene, repeated sequences, MGE
Journal
BIOCHEMISTRY-MOSCOW
Volume 79, Issue 13, Pages 1442-1469
Publisher
Pleiades Publishing Ltd
Online
2015-01-06
DOI
10.1134/s0006297914130021
References
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- (2015) G. A. Romanov et al. Russian Journal of Developmental Biology
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- (2014) Miroslav Plohl et al. CHROMOSOMA
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- (2014) Michael T.Y. Lam et al. TRENDS IN BIOCHEMICAL SCIENCES
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- (2013) Alessandro Fatica et al. NATURE REVIEWS GENETICS
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- (2013) N. P. Blackledge et al. Cold Spring Harbor Perspectives in Biology
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- (2011) Ivan Krivega et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
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- (2011) Edward Hitti Frontiers in Bioscience-Landmark
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- The realm of microRNAs in cancers
- (2010) Nuray Varol et al. MOLECULAR BIOLOGY REPORTS
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- (2010) Richard M. Durbin et al. NATURE
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- (2010) A. M. Monteys et al. RNA
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- (2010) Tomoko Kawamata et al. TRENDS IN BIOCHEMICAL SCIENCES
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- (2009) Robert S. Illingworth et al. FEBS LETTERS
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- (2009) Thomas R. Gingeras NATURE
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- (2009) Nathaniel D. Heintzman et al. NATURE
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- (2009) Axel Visel et al. NATURE
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- (2009) Geoffrey J Faulkner et al. NATURE GENETICS
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- (2009) Rafael A Irizarry et al. NATURE GENETICS
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- Biogenesis of small RNAs in animals
- (2009) V. Narry Kim et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
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- (2009) Ahmad M. Khalil et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2009) E. Lieberman-Aiden et al. SCIENCE
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- (2008) Yasukazu Nakahata et al. BMC MOLECULAR BIOLOGY
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- (2008) Pavla Navratilova et al. DEVELOPMENTAL BIOLOGY
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- (2008) Jill M. Brown et al. JOURNAL OF CELL BIOLOGY
- Locus control region mediated regulation of adult β-globin gene expression
- (2008) Shermi Liang et al. JOURNAL OF CELLULAR BIOCHEMISTRY
- Alternative promoters in expression of genetic information
- (2008) E. V. Pankratova MOLECULAR BIOLOGY
- Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
- (2008) Toshiaki Watanabe et al. NATURE
- Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
- (2008) Oliver H. Tam et al. NATURE
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
- (2008) Ali Mortazavi et al. NATURE METHODS
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- Endogenous small interfering RNAs in animals
- (2008) Katsutomo Okamura et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
- (2008) R. Jothi et al. NUCLEIC ACIDS RESEARCH
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- (2008) Z. Wang et al. RNA
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- (2008) R. Sandberg et al. SCIENCE
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