Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

[1]  Lee E. Edsall,et al.  A map of the cis-regulatory sequences in the mouse genome , 2012, Nature.

[2]  A. Clark,et al.  Impact of microRNA regulation on variation in human gene expression , 2012, Genome research.

[3]  A. Ballabio,et al.  Identification of microRNA-regulated gene networks by expression analysis of target genes , 2012, Genome research.

[4]  Chris P Ponting,et al.  Wrangling for microRNAs provokes much crosstalk , 2011, Genome Biology.

[5]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[6]  E. M. Muro,et al.  Functional evidence of post-transcriptional regulation by pseudogenes. , 2011, Biochimie.

[7]  S. Bergmann,et al.  The evolution of gene expression levels in mammalian organs , 2011, Nature.

[8]  Xuerui Yang,et al.  An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma , 2011, Cell.

[9]  D. Cacchiarelli,et al.  A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA , 2011, Cell.

[10]  Ferdinando Di Cunto,et al.  Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs , 2011, Cell.

[11]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[12]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[13]  L. Poliseno,et al.  Deletion of PTENP1 pseudogene in human melanoma , 2011, The Journal of investigative dermatology.

[14]  Manolis Kellis,et al.  PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions , 2011, Bioinform..

[15]  E. Punch,et al.  Pseudogenes: pseudo-functional or key regulators in health and disease? , 2011, RNA.

[16]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[17]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[18]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[19]  M. Gerstein,et al.  Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates , 2010, Genome Biology.

[20]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[21]  Chung-I Wu,et al.  Evolution under canalization and the dual roles of microRNAs: a hypothesis. , 2009, Genome research.

[22]  Anton J. Enright,et al.  An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice , 2009, Nature Genetics.

[23]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[24]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[25]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[26]  C. Ponting,et al.  Variable Strength of Translational Selection Among 12 Drosophila Species , 2007, Genetics.

[27]  David Haussler,et al.  Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage , 2007, PLoS Comput. Biol..

[28]  M. Todesco,et al.  Target mimicry provides a new mechanism for regulation of microRNA activity , 2007, Nature Genetics.

[29]  Yong Zhang,et al.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..

[30]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[31]  M. Gerstein,et al.  What is a gene, post-ENCODE? History and updated definition. , 2007, Genome research.

[32]  Deyou Zheng,et al.  The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? , 2007, Trends in genetics : TIG.

[33]  Kunio Inoue [MicroRNA function in animal development]. , 2007, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[34]  Mark A McPeek,et al.  The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. , 2006, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[35]  Mark Gerstein,et al.  Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation , 2006, Nucleic Acids Res..

[36]  Laurent Duret,et al.  The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene , 2006, Science.

[37]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[38]  Kristin C. Gunsalus,et al.  microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets , 2005, PLoS Comput. Biol..

[39]  Mark Gerstein,et al.  Integrated pseudogene annotation for human chromosome 22: evidence for transcription. , 2005, Journal of molecular biology.

[40]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[41]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[42]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[43]  D. Bartel MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[44]  C. Ponting,et al.  Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. , 2003, Genome research.

[45]  V. Ambros MicroRNA Pathways in Flies and Worms Growth, Death, Fat, Stress, and Timing , 2003, Cell.

[46]  Michael O'Shea,et al.  Evolution of nitric oxide synthase regulatory genes by DNA inversion. , 2002, Molecular biology and evolution.

[47]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[48]  O. Smithies,et al.  A mouse α-globin-related pseudogene lacking intervening sequences , 1980, Nature.

[49]  G. Brownlee,et al.  A pseudogene structure in 5S DNA of Xenopus laevis , 1977, Cell.

[50]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[51]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[52]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[53]  O. Smithies,et al.  A mouse alpha-globin-related pseudogene lacking intervening sequences. , 1980, Nature.