TY - JOUR AU - Amaral, P. P. AU - Dinger, M. E. AU - Mercer, T. R. AU - Mattick, J. S. PY - 2008 DA - 2008// TI - The eukaryotic genome as an RNA machine JO - Science VL - 319 UR - https://doi.org/10.1126/science.1155472 DO - 10.1126/science.1155472 ID - Amaral2008 ER - TY - JOUR AU - Askarian-Amiri, M. E. AU - Crawford, J. AU - French, J. D. AU - Smart, C. E. AU - Smith, M. A. AU - Clark, M. B. AU - Mattick, J. S. PY - 2011 DA - 2011// TI - SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer JO - RNA VL - 17 UR - https://doi.org/10.1261/rna.2528811 DO - 10.1261/rna.2528811 ID - Askarian-Amiri2011 ER - TY - JOUR AU - Baillie, J. K. AU - Barnett, M. W. AU - Upton, K. R. AU - Gerhardt, D. J. AU - Richmond, T. A. AU - De Sapio, F. AU - Faulkner, G. J. PY - 2011 DA - 2011// TI - Somatic retrotransposition alters the genetic landscape of the human brain JO - Nature VL - 479 UR - https://doi.org/10.1038/nature10531 DO - 10.1038/nature10531 ID - Baillie2011 ER - TY - CHAP AU - Behe, M. J. PY - 2003 DA - 2003// BT - A functional pseudogene: an open letter to Nature ID - Behe2003 ER - TY - JOUR AU - Birney, E. AU - Stamatoyannopoulos, J. A. AU - Dutta, A. AU - Guigo, R. AU - Gingeras, T. R. AU - Margulies, E. H. AU - de Jong, P. J. PY - 2007 DA - 2007// TI - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project JO - Nature VL - 447 UR - https://doi.org/10.1038/nature05874 DO - 10.1038/nature05874 ID - Birney2007 ER - TY - JOUR AU - Brosius, J. PY - 1999 DA - 1999// TI - RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00227-9 DO - 10.1016/S0378-1119(99)00227-9 ID - Brosius1999 ER - TY - JOUR AU - Carninci, P. AU - Kasukawa, T. AU - Katayama, S. AU - Gough, J. AU - Frith, M. C. AU - Maeda, N. AU - Hayashizaki, Y. PY - 2005 DA - 2005// TI - The transcriptional landscape of the mammalian genome JO - Science VL - 309 UR - https://doi.org/10.1126/science.1112014 DO - 10.1126/science.1112014 ID - Carninci2005 ER - TY - JOUR AU - Carroll, S. B. PY - 2008 DA - 2008// TI - Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution JO - Cell VL - 134 UR - https://doi.org/10.1016/j.cell.2008.06.030 DO - 10.1016/j.cell.2008.06.030 ID - Carroll2008 ER - TY - JOUR AU - Cheng, J. AU - Kapranov, P. AU - Drenkow, J. AU - Dike, S. AU - Brubaker, S. AU - Patel, S. AU - Gingeras, T. R. PY - 2005 DA - 2005// TI - Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution JO - Science VL - 308 UR - https://doi.org/10.1126/science.1108625 DO - 10.1126/science.1108625 ID - Cheng2005 ER - TY - JOUR AU - Clark, M. B. AU - Amaral, P. P. AU - Schlesinger, F. J. AU - Dinger, M. E. AU - Taft, R. J. AU - Rinn, J. L. AU - Mattick, J. S. PY - 2011 DA - 2011// TI - The reality of pervasive transcription JO - PLoS Biol VL - 9 UR - https://doi.org/10.1371/journal.pbio.1000625 DO - 10.1371/journal.pbio.1000625 ID - Clark2011 ER - TY - BOOK AU - Collins, F. S. PY - 2006 DA - 2006// TI - The Language of God: a Scientist Presents Evidence for Belief PB - Free Press CY - New York ID - Collins2006 ER - TY - BOOK AU - Dawkins, R. PY - 1986 DA - 1986// TI - The Blind Watchmaker: Why the evidence of Evolution Reveals a Universe without Design PB - Company, Inc CY - New York ID - Dawkins1986 ER - TY - JOUR AU - Dinger, M. E. AU - Amaral, P. P. AU - Mercer, T. R. AU - Pang, K. C. AU - Bruce, S. J. AU - Gardiner, B. B. AU - Mattick, J. S. PY - 2008 DA - 2008// TI - Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.078378.108 DO - 10.1101/gr.078378.108 ID - Dinger2008 ER - TY - JOUR AU - Dinger, M. E. AU - Amaral, P. P. AU - Mercer, T. R. AU - Mattick, J. S. PY - 2009 DA - 2009// TI - Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications JO - Brief Funct Genomics Proteomics VL - 8 UR - https://doi.org/10.1093/bfgp/elp038 DO - 10.1093/bfgp/elp038 ID - Dinger2009 ER - TY - JOUR AU - Doolittle, W. F. PY - 2013 DA - 2013// TI - Is junk DNA bunk? A critique of ENCODE JO - Proc Natl Acad Sci USA VL - 110 UR - https://doi.org/10.1073/pnas.1221376110 DO - 10.1073/pnas.1221376110 ID - Doolittle2013 ER - TY - JOUR AU - Dunham, I. AU - Kundaje, A. AU - Aldred, S. F. AU - Collins, P. J. AU - Davis, C. A. AU - Doyle, F. AU - Birney, E. PY - 2012 DA - 2012// TI - An integrated encyclopedia of DNA elements in the human genome JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11247 DO - 10.1038/nature11247 ID - Dunham2012 ER - TY - JOUR AU - Faulkner, G. J. AU - Kimura, Y. AU - Daub, C. O. AU - Wani, S. AU - Plessy, C. AU - Irvine, K. M. AU - Carninci, P. PY - 2009 DA - 2009// TI - The regulated retrotransposon transcriptome of mammalian cells JO - Nat Genet VL - 41 UR - https://doi.org/10.1038/ng.368 DO - 10.1038/ng.368 ID - Faulkner2009 ER - TY - JOUR AU - Fisher, S. AU - Grice, E. A. AU - Vinton, R. M. AU - Bessling, S. L. AU - McCallion, A. S. PY - 2006 DA - 2006// TI - Conservation of RET regulatory function from human to zebrafish without sequence similarity JO - Science VL - 312 UR - https://doi.org/10.1126/science.1124070 DO - 10.1126/science.1124070 ID - Fisher2006 ER - TY - JOUR AU - Frith, M. C. AU - Ponjavic, J. AU - Fredman, D. AU - Kai, C. AU - Kawai, J. AU - Carninci, P. AU - Sandelin, A. PY - 2006 DA - 2006// TI - Evolutionary turnover of mammalian transcription start sites JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.5031006 DO - 10.1101/gr.5031006 ID - Frith2006 ER - TY - JOUR AU - Graur, D. AU - Zheng, Y. AU - Price, N. AU - Azevedo, R. B. AU - Zufall, R. A. AU - Elhaik, E. PY - 2013 DA - 2013// TI - On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE JO - Genome Biol Evol VL - 5 UR - https://doi.org/10.1093/gbe/evt028 DO - 10.1093/gbe/evt028 ID - Graur2013 ER - TY - JOUR AU - Gupta, R. A. AU - Shah, N. AU - Wang, K. C. AU - Kim, J. AU - Horlings, H. M. AU - Wong, D. J. AU - Chang, H. Y. PY - 2010 DA - 2010// TI - Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08975 DO - 10.1038/nature08975 ID - Gupta2010 ER - TY - JOUR AU - Guttman, M. AU - Donaghey, J. AU - Carey, B. W. AU - Garber, M. AU - Grenier, J. K. AU - Munson, G. AU - Lander, E. S. PY - 2011 DA - 2011// TI - lincRNAs act in the circuitry controlling pluripotency and differentiation JO - Nature VL - 477 UR - https://doi.org/10.1038/nature10398 DO - 10.1038/nature10398 ID - Guttman2011 ER - TY - JOUR AU - Khaitan, D. AU - Dinger, M. E. AU - Mazar, J. AU - Crawford, J. AU - Smith, M. A. AU - Mattick, J. S. AU - Perera, R. J. PY - 2011 DA - 2011// TI - The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion JO - Cancer Res VL - 71 UR - https://doi.org/10.1158/0008-5472.CAN-10-4460 DO - 10.1158/0008-5472.CAN-10-4460 ID - Khaitan2011 ER - TY - JOUR AU - Khalil, A. M. AU - Guttman, M. AU - Huarte, M. AU - Garber, M. AU - Raj, A. AU - Rivea Morales, D. AU - Rinn, J. L. PY - 2009 DA - 2009// TI - Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression JO - Proc Natl Acad Sci USA VL - 106 UR - https://doi.org/10.1073/pnas.0904715106 DO - 10.1073/pnas.0904715106 ID - Khalil2009 ER - TY - JOUR AU - Koziol, M. J. AU - Rinn, J. L. PY - 2010 DA - 2010// TI - RNA traffic control of chromatin complexes JO - Curr Opin Genet Dev VL - 20 UR - https://doi.org/10.1016/j.gde.2010.03.003 DO - 10.1016/j.gde.2010.03.003 ID - Koziol2010 ER - TY - JOUR AU - Lewejohann, L. AU - Skryabin, B. V. AU - Sachser, N. AU - Prehn, C. AU - Heiduschka, P. AU - Thanos, S. AU - Prior, H. PY - 2004 DA - 2004// TI - Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice JO - Behav Brain Res VL - 154 UR - https://doi.org/10.1016/j.bbr.2004.02.015 DO - 10.1016/j.bbr.2004.02.015 ID - Lewejohann2004 ER - TY - JOUR AU - Liu, G. AU - Mattick, J. S. AU - Taft, R. J. PY - 2013 DA - 2013// TI - A meta-analysis of the genomic and transcriptomic composition of complex life JO - Cell Cycle VL - 12 ID - Liu2013 ER - TY - JOUR AU - Lunter, G. AU - Ponting, C. P. AU - Hein, J. PY - 2006 DA - 2006// TI - Genome-wide identification of human functional DNA using a neutral indel model JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020005 DO - 10.1371/journal.pcbi.0020005 ID - Lunter2006 ER - TY - JOUR AU - Mattick, J. S. PY - 1994 DA - 1994// TI - Introns: evolution and function JO - Curr Opin Genet Dev VL - 4 UR - https://doi.org/10.1016/0959-437X(94)90066-3 DO - 10.1016/0959-437X(94)90066-3 ID - Mattick1994 ER - TY - JOUR AU - Mattick, J. S. PY - 2004 DA - 2004// TI - RNA regulation: a new genetics? JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1321 DO - 10.1038/nrg1321 ID - Mattick2004 ER - TY - JOUR AU - Mattick, J. S. PY - 2007 DA - 2007// TI - A new paradigm for developmental biology JO - J Exp Biol VL - 210 UR - https://doi.org/10.1242/jeb.005017 DO - 10.1242/jeb.005017 ID - Mattick2007 ER - TY - JOUR AU - Mattick, J. S. PY - 2009 DA - 2009// TI - Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms JO - Ann N Y Acad Sci VL - 1178 UR - https://doi.org/10.1111/j.1749-6632.2009.04991.x DO - 10.1111/j.1749-6632.2009.04991.x ID - Mattick2009 ER - TY - JOUR AU - Mattick, J. S. PY - 2009 DA - 2009// TI - The genetic signatures of noncoding RNAs JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000459 DO - 10.1371/journal.pgen.1000459 ID - Mattick2009 ER - TY - JOUR AU - Mattick, J. S. PY - 2009 DA - 2009// TI - Has evolution learnt how to learn? JO - EMBO Rep VL - 10 UR - https://doi.org/10.1038/embor.2009.135 DO - 10.1038/embor.2009.135 ID - Mattick2009 ER - TY - JOUR AU - Mattick, J. S. PY - 2011 DA - 2011// TI - The central role of RNA in human development and cognition JO - FEBS Lett VL - 585 UR - https://doi.org/10.1016/j.febslet.2011.05.001 DO - 10.1016/j.febslet.2011.05.001 ID - Mattick2011 ER - TY - JOUR AU - Mattick, J. S. AU - Gagen, M. J. PY - 2001 DA - 2001// TI - The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003951 DO - 10.1093/oxfordjournals.molbev.a003951 ID - Mattick2001 ER - TY - JOUR AU - Mattick, J. S. AU - Amaral, P. P. AU - Dinger, M. E. AU - Mercer, T. R. AU - Mehler, M. F. PY - 2009 DA - 2009// TI - RNA regulation of epigenetic processes JO - Bioessays VL - 31 UR - https://doi.org/10.1002/bies.080099 DO - 10.1002/bies.080099 ID - Mattick2009 ER - TY - JOUR AU - Mattick, J. S. AU - Taft, R. J. AU - Faulkner, G. J. PY - 2010 DA - 2010// TI - A global view of genomic information–moving beyond the gene and the master regulator JO - Trends Genet VL - 26 UR - https://doi.org/10.1016/j.tig.2009.11.002 DO - 10.1016/j.tig.2009.11.002 ID - Mattick2010 ER - TY - JOUR AU - Mercer, T. R. AU - Dinger, M. E. AU - Sunkin, S. M. AU - Mehler, M. F. AU - Mattick, J. S. PY - 2008 DA - 2008// TI - Specific expression of long noncoding RNAs in the mouse brain JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0706729105 DO - 10.1073/pnas.0706729105 ID - Mercer2008 ER - TY - JOUR AU - Mercer, T. R. AU - Qureshi, I. A. AU - Gokhan, S. AU - Dinger, M. E. AU - Li, G. AU - Mattick, J. S. AU - Mehler, M. F. PY - 2010 DA - 2010// TI - Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation JO - BMC Neurosci VL - 11 UR - https://doi.org/10.1186/1471-2202-11-14 DO - 10.1186/1471-2202-11-14 ID - Mercer2010 ER - TY - JOUR AU - Mercer, T. R. AU - Gerhardt, D. J. AU - Dinger, M. E. AU - Crawford, J. AU - Trapnell, C. AU - Jeddeloh, J. A. AU - Rinn, J. L. PY - 2012 DA - 2012// TI - Targeted RNA sequencing reveals the deep complexity of the human transcriptome JO - Nat Biotech VL - 30 UR - https://doi.org/10.1038/nbt.2024 DO - 10.1038/nbt.2024 ID - Mercer2012 ER - TY - JOUR AU - Nagano, T. AU - Mitchell, J. A. AU - Sanz, L. A. AU - Pauler, F. M. AU - Ferguson-Smith, A. C. AU - Feil, R. AU - Fraser, P. PY - 2008 DA - 2008// TI - The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin JO - Science VL - 322 UR - https://doi.org/10.1126/science.1163802 DO - 10.1126/science.1163802 ID - Nagano2008 ER - TY - JOUR AU - Ng, S. Y. AU - Johnson, R. AU - Stanton, L. W. PY - 2012 DA - 2012// TI - Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors JO - Embo J VL - 31 UR - https://doi.org/10.1038/emboj.2011.459 DO - 10.1038/emboj.2011.459 ID - Ng2012 ER - TY - JOUR AU - Niu, D. K. AU - Jiang, L. PY - 2013 DA - 2013// TI - Can ENCODE tell us how much junk DNA we carry in our genome? JO - Biochem Biophys Res Commun VL - 430 UR - https://doi.org/10.1016/j.bbrc.2012.12.074 DO - 10.1016/j.bbrc.2012.12.074 ID - Niu2013 ER - TY - JOUR AU - Oldmeadow, C. AU - Mengersen, K. AU - Mattick, J. S. AU - Keith, J. M. PY - 2010 DA - 2010// TI - Multiple evolutionary rate classes in animal genome evolution JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp299 DO - 10.1093/molbev/msp299 ID - Oldmeadow2010 ER - TY - JOUR AU - Pandey, R. R. AU - Mondal, T. AU - Mohammad, F. AU - Enroth, S. AU - Redrup, L. AU - Komorowski, J. AU - Kanduri, C. PY - 2008 DA - 2008// TI - Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation JO - Mol Cell VL - 32 UR - https://doi.org/10.1016/j.molcel.2008.08.022 DO - 10.1016/j.molcel.2008.08.022 ID - Pandey2008 ER - TY - JOUR AU - Pang, K. C. AU - Frith, M. C. AU - Mattick, J. S. PY - 2006 DA - 2006// TI - Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function JO - Trends Genet VL - 22 UR - https://doi.org/10.1016/j.tig.2005.10.003 DO - 10.1016/j.tig.2005.10.003 ID - Pang2006 ER - TY - JOUR AU - Pang, K. C. AU - Dinger, M. E. AU - Mercer, T. R. AU - Malquori, L. AU - Grimmond, S. M. AU - Chen, W. AU - Mattick, J. S. PY - 2009 DA - 2009// TI - Genome-wide identification of long noncoding RNAs in CD8+ T cells JO - J Immunol VL - 182 UR - https://doi.org/10.4049/jimmunol.0900603 DO - 10.4049/jimmunol.0900603 ID - Pang2009 ER - TY - JOUR AU - Pheasant, M. AU - Mattick, J. S. PY - 2007 DA - 2007// TI - Raising the estimate of functional human sequences JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6406307 DO - 10.1101/gr.6406307 ID - Pheasant2007 ER - TY - JOUR AU - Roberts, A. AU - Pachter, L. PY - 2011 DA - 2011// TI - RNA-Seq and find: entering the RNA deep field JO - Genome Med VL - 3 UR - https://doi.org/10.1186/gm290 DO - 10.1186/gm290 ID - Roberts2011 ER - TY - CHAP AU - Scanlan, J. PY - 2012 DA - 2012// TI - The Designer’s Detritus: ENCODE, Junk DNA, and Intelligent Design Creationists BT - Scitable (Nature Education) ID - Scanlan2012 ER - TY - JOUR AU - Smith, N. G. AU - Brandstrom, M. AU - Ellegren, H. PY - 2004 DA - 2004// TI - Evidence for turnover of functional noncoding DNA in mammalian genome evolution JO - Genomics VL - 84 UR - https://doi.org/10.1016/j.ygeno.2004.07.012 DO - 10.1016/j.ygeno.2004.07.012 ID - Smith2004 ER - TY - JOUR AU - Spitale, R. C. AU - Tsai, M. C. AU - Chang, H. Y. PY - 2011 DA - 2011// TI - RNA templating the epigenome: Long noncoding RNAs as molecular scaffolds JO - Epigenetics VL - 6 UR - https://doi.org/10.4161/epi.6.5.15221 DO - 10.4161/epi.6.5.15221 ID - Spitale2011 ER - TY - JOUR AU - Sunwoo, H. AU - Dinger, M. E. AU - Wilusz, J. E. AU - Amaral, P. P. AU - Mattick, J. S. AU - Spector, D. L. PY - 2009 DA - 2009// TI - MEN ϵ/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.087775.108 DO - 10.1101/gr.087775.108 ID - Sunwoo2009 ER - TY - JOUR AU - Taft, R. J. AU - Pheasant, M. AU - Mattick, J. S. PY - 2007 DA - 2007// TI - The relationship between non-protein-coding DNA and eukaryotic complexity JO - Bioessays VL - 29 UR - https://doi.org/10.1002/bies.20544 DO - 10.1002/bies.20544 ID - Taft2007 ER - TY - JOUR AU - Taylor, M. S. AU - Kai, C. AU - Kawai, J. AU - Carninci, P. AU - Hayashizaki, Y. AU - Semple, C. A. PY - 2006 DA - 2006// TI - Heterotachy in mammalian promoter evolution JO - PLoS Genet VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020030 DO - 10.1371/journal.pgen.0020030 ID - Taylor2006 ER - TY - JOUR AU - van Bakel, H. AU - Nislow, C. AU - Blencowe, B. J. AU - Hughes, T. R. PY - 2010 DA - 2010// TI - Most “dark matter” transcripts are associated with known genes JO - PLoS Biol VL - 8 UR - https://doi.org/10.1371/journal.pbio.1000371 DO - 10.1371/journal.pbio.1000371 ID - van Bakel2010 ER - TY - BOOK AU - Wells, J. PY - 2011 DA - 2011// TI - The Myth of Junk DNA PB - Discovery Institute Press CY - Seattle ID - Wells2011 ER -