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Tag non-coding [60 articles]

Recent papers classified by the tag non-coding.
  • RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
    Science (17 May 2007), 1138341.
    by Philipp Kapranov, Jill Cheng, Sujit Dike, David A Nix, Radharani Duttagupta, Aarron T Willingham, Peter F Stadler, Jana Hertel, Joerg Hackermueller, Ivo L Hofacker, Ian Bell, Evelyn Cheung, Jorg Drenkow, Erica Dumais, Sandeep Patel, Gregg Helt, Madhavan Ganesh, Srinka Ghosh, Antonio Piccolboni, Victor Sementchenko, Hari Tammana, Thomas R Gingeras
    posted to non-coding rna transcriptome by xico on 2007-05-27 01:43:52 as *** along with 11 people and 4 groups xingxu marcius alexg dpollard mtagaya rdiaz djkt stajich mathijsv asddd elfar EisenLab WetBiology BioinfoCIPF SGU-CIPF
  • Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming.
    Nucleic Acids Res, Vol. 33, No. 10. (2005), pp. 3263-3270.
    by P Saetrom, R Sneve, KI Kristiansen, O Snøve, T Grünfeld, T Rognes, E Seeberg
    posted to genes genetic non-coding programming rna by ujh on 2005-06-25 13:03:58 as ** along with 2 people and 2 groups numata bsmagic Bioinformatics bioinplant
  • Ultraconserved elements in the human genome.
    Science, Vol. 304, No. 5675. (28 May 2004), pp. 1321-1325.
    by G Bejerano, M Pheasant, I Makunin, S Stephen, WJ Kent, JS Mattick, D Haussler
    posted to bioinformatics clustering dna non-coding by ujh on 2005-03-03 10:51:59 as read along with 13 people and 5 groups pradiptaray karbak barry alexisgallagher bpb aprasad balicea dchughes djkt sujaikumar blobbybirdman cisevol fpattyn structural_bioinformatics Bioinformatics G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Into the heart of darkness: large-scale clustering of human non-coding DNA.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by G Bejerano, D Haussler, M Blanchette
    posted to bioinformatics clustering dna non-coding by ujh on 2005-03-03 10:21:32 as read along with 1 person arcticrasta
  • Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing.
    Genome Res (17 May 2005)
    by Evgeny A A Glazov, Michael Pheasant, Elizabeth A A McGraw, Gill Bejerano, John S S Mattick
    posted to bioinformatics clustering dna insect non-coding by ujh on 2005-05-20 18:56:11 as **** along with 2 people and 1 group sujaikumar Stew EisenLab
  • Experimental approaches to identify non-coding RNAs.
    Nucleic Acids Res, Vol. 34, No. 2. (2006), pp. 635-646.
    by A Hüttenhofer, J Vogel
    posted to microarray non-coding noncoding by tabu on 2006-01-27 14:33:56 as ** along with 7 people and 7 groups marcius eweaver perrywoo dchughes mtagaya cdawson bsmagic Bioinformatics G4ID BioinfoCIPF bioinplant SGU-CIPF GIG Genetics-of-Gambling
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to cne comparative insects non-coding phastcons vertebrates worms yeast by sujaikumar on 2007-03-19 09:53:45 as *** along with 14 people and 2 groups pradiptaray bpb aprasad balajis eckart_bindewald indigoviolet brant adepace djkt olympos Stew cisevol dmc elfar EisenLab cis-regulatory-evolution
  • Into the heart of darkness: large-scale clustering of human non-coding DNA
    by Gill Bejerano
    posted to clustering non-coding by sujaikumar on 2007-07-31 18:30:39 as ***
  • notes Functional variation and evolution of non-coding DNA
    Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 559-564.
    by Christine P Bird, Barbara E Stranger, Emmanouil T Dermitzakis
    posted to cne evolution non-coding by sujaikumar on 2007-03-10 16:21:09 as read along with 7 people and 4 groups dpollard dchughes adepace lusk candypmcg Stew cisevol EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Fast-evolving non-coding sequences in the human genome
    Genome Biology, Vol. 8 (19 June 2007), R118.
    by Christine P Bird, Barbara E Stranger, Maureen Liu, Daryl J Thomas, Catherine E Ingle, Claude Beazley, Webb Miller, Matthew E Hurles, Emmanouil T Dermitzakis
    posted to chip conserved dermitzakis evolution human non-coding positive selection by Stew on 2007-07-27 23:07:05 as read along with 4 people and 2 groups djkt jlangdon cisevol iris42 EisenLab cis-regulatory-evolution
  • SEARCHING FOR FUNCTIONAL GENETIC VARIANTS IN NON-CODING DNA
    Clinical and Experimental Pharmacology and Physiology, Vol. 35, No. 4. (April 2008), pp. 372-375.
    by Cobb, Joanna, Busst, Cara, Petrou, Steven, Harrap, Stephen, Ellis, Justine
    posted to variation non-coding functional by Stew on 2008-06-02 10:54:59 as ***
  • Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila.
    Biology letters (27 May 2008)
    by Penelope R R Haddrill, Brian Charlesworth
    posted to nucleotide non-neutral non-coding drosophila composition base by Stew on 2008-06-02 10:52:39 as **
  • CONDOR: a database resource of developmentally associated conserved non-coding elements
    BMC Developmental Biology, Vol. 7 (30 August 2007), 100.
    by Adam Woolfe, Debbie K Goode, Julie Cooke, Heather Callaway, Sarah Smith, Phil Snell, Gayle K Mcewen, Greg Elgar
    posted to cis-regulatory conserved elgar evolution non-coding by Stew on 2007-09-04 16:17:41 as ***** along with 1 person and 1 group maximilianh EisenLab
  • Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans.
    Genome Biology, Vol. 8 (02 February 2007), R15.
    by Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar
    posted to conserved evolution human non-coding worm by Stew on 2007-09-18 01:17:38 as ** along with 7 people and 2 groups smbe2008 indigoviolet dpollard adepace djkt sujaikumar cisevol EisenLab cis-regulatory-evolution
  • Deletion of Ultraconserved Elements Yields Viable Mice
    PLoS Biology, Vol. 5, No. 9. (1 September 2007), e234.
    by Nadav Ahituv, Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A Pennacchio, Edward M Rubin
    posted to mice non-coding ultraconserved by Stew on 2007-09-18 00:51:14 as ** along with 7 people and 3 groups balicea dchughes cwbrown djkt lp2 cabbagezs gjuggler EisenLab G4ID Genetics-of-Gambling
  • Conserved noncoding sequences are selectively constrained and not mutation cold spots
    Nature Genetics, Vol. 38, No. 2. (25 December 2005), pp. 223-227.
    by Jared A Drake, Christine Bird, James Nemesh, Daryl J Thomas, Christopher Newton-Cheh, Alexandre Reymond, Laurent Excoffier, Homa Attar, Stylianos E Antonarakis, Emmanouil T Dermitzakis, Joel N Hirschhorn
    posted to cold-spot conserved dermitzakis mutation non-coding rate by Stew on 2007-07-29 22:06:38 as read along with 5 people and 2 groups bpcusack aprasad ccots ashandanj cisevol EisenLab cis-regulatory-evolution
  • Adaptive Evolution of Conserved Noncoding Elements in Mammals
    PLoS Genetics, Vol. 3, No. 9. (1 September 2007), e147.
    by Su Y Kim, Jonathan K Pritchard
    posted to cis-regulatory conserved evolution mammals non-coding by Stew on 2007-09-18 01:09:01 as ** along with 8 people and 5 groups mattjb livingthingdan djkt stajich Garamonfok cabbagezs cisevol rrhudson EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cis-regulatory-evolution
  • Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences.
    Trends Genet, Vol. 21, No. 8. (August 2005), pp. 436-440.
    by K Walter, I Abnizova, G Elgar, WR Gilks
    posted to base bias cne composition conserved elgar fugu human non-coding by Stew on 2007-07-27 21:47:10 as read along with 2 people and 2 groups aprasad cisevol EisenLab cis-regulatory-evolution
  • Non-coding RNAs, epigenetics and complexity
    Gene, Vol. 410, No. 1. (29 February 2008), pp. 9-17.
    by Fabricio F Costa
    posted to epigenetics non-coding rna by paulcartwright on 2008-03-03 12:53:32 as read along with 2 people and 1 group pradiptaray dchughes BergmanLab
  • MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
    BMC Bioinformatics, Vol. 7 (08 June 2006), 292.
    by Jun Wang, Peter D Keightley, Toby Johnson
    posted to alignment non-coding by papamicd on 2006-06-28 17:41:01 as ** along with 2 people and 1 group Ayest dpollard EisenLab
  • Adaptive evolution of non-coding DNA in Drosophila
    Nature, Vol. 437, No. 7062. (20 October 2005), pp. 1149-1152.
    by Peter Andolfatto
    posted to adaptive dna drosophila evolution non-coding by mimulus_99 on 2007-09-13 08:20:58 as read along with 12 people and 4 groups pradiptaray stevanspringer bpb aprasad jmeppley balicea jimmithy emilyhare cdawson adepace Stew cisevol EisenLab FAB-lab GIG cis-regulatory-evolution
  • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
    Nat Genet, Vol. 39, No. 9. (2007), pp. 1140-1144.
    by Ralph Haygood, Olivier Fedrigo, Brian Hanson, Ken-Daigoro Yokoyama, Gregory A Wray
    posted to non-coding selection by mimulus_99 on 2007-09-13 22:04:15 as ***** along with 6 people and 4 groups mjoach candypmcg dchughes djkt Garamonfok cisevol G4ID Genetics-of-Gambling cis-regulatory-evolution Fasting, food and evolution
  • Raising the estimate of functional human sequences.
    Genome Res (9 August 2007)
    by Michael Pheasant, John S S Mattick
    posted to functional human non-coding sequence by mimulus_99 on 2007-11-07 23:51:03 as ** along with 9 people and 2 groups jyuh jfr andersbj djkt grahamc lp2 cabbagezs nklee ljs microRNA ParkinsonLab_at_MaRS
  • An RNA gene expressed during cortical development evolved rapidly in humans
    Nature (16 August 2006)
    by Katherine S Pollard, Sofie R Salama, Nelle Lambert, Marie-Alexandra Lambot, Sandra Coppens, Jakob S Pedersen, Sol Katzman, Bryan King, Courtney Onodera, Adam Siepel, Andrew D Kern, Colette Dehay, Haller Igel, Manuel Ares, Pierre Vanderhaeghen, David Haussler
    posted to brain evolution gene genomics non-coding rna by larios on 2006-09-20 05:49:55 as read along with 11 people and 3 groups bpcusack brian bpb marcius nickluscombe joshuashen ealloza ce2benna lusk nolodie rrhudson EBI-regulation BioinfoCIPF SGU-CIPF
  • Non-coding RNAs in imprinted gene clusters.
    Biol Cell, Vol. 100, No. 3. (March 2008), pp. 149-166.
    by H Royo, J Cavaillé
    posted to imprinting non-coding rna by kjglennie on 2008-02-24 05:56:34 as ** along with 1 person rschulz
  • Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model.
    PLoS Comput Biol, Vol. 2, No. 1. (13 January 2006)
    by Gerton Lunter, Chris P P Ponting, Jotun Hein
    posted to dna functional non-coding by juliettecolinas on 2006-05-18 16:04:54 as *** along with 8 people and 2 groups aprasad eckart_bindewald eweaver lhonigberg acidwizard Stew cisevol mailund EisenLab cis-regulatory-evolution
  • Ultraconserved Regions Encoding ncRNAs Are Altered in Human Leukemias and Carcinomas.
    Cancer Cell, Vol. 12, No. 3. (September 2007), pp. 215-229.
    by GA Calin, CG Liu, M Ferracin, T Hyslop, R Spizzo, C Sevignani, M Fabbri, A Cimmino, EJ Lee, SE Wojcik, M Shimizu, E Tili, S Rossi, C Taccioli, F Pichiorri, X Liu, S Zupo, V Herlea, L Gramantieri, G Lanza, H Alder, L Rassenti, S Volinia, TD Schmittgen, TJ Kipps, M Negrini, CM Croce
    posted to mirna non-coding by jfr on 2008-04-09 12:56:36 as **** along with 3 people and 1 group andersbj maximilianh fpattyn microRNA
  • Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA.
    Genome Res (6 December 2006)
    by Eva K K Freyhult, Jonathan P P Bollback, Paul P P Gardner
    posted to software non-coding methodology evaluation by jfr on 2007-01-16 17:59:48 as * along with 9 people and 2 groups evaf eckart_bindewald ppgardne gpalidwor dchughes aswin bjhaugen jayster4 yoanjacquemin G4ID Genetics-of-Gambling
  • Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila.
    Mol Biol Evol (23 July 2007)
    by Sònia Casillas, Antonio Barbadilla, Casey M M Bergman
    posted to selection non-coding drosophila dna by emilyhare to the group EisenLab on 2007-08-04 00:28:09 as ** along with 7 people and 1 group brant operon dpollard Garamonfok Stew cisevol emptyhb cis-regulatory-evolution
  • Genome-wide assessment of coding and non-coding conserved sequence tags in human and mouse genomes
    BMC Genomics, Vol. 9 (11 June 2008), 277.
    by Flavio Mignone, Anna Anselmo, Giacinto Donvito, Giorgio P Maggi, Giorgio Grillo, Graziano Pesole
    posted to tags sequence non-coding mouse human genome conserved conservation coding by fpattyn on 2008-06-19 07:02:07 as **
  • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
    BMC Genomics, Vol. 5, No. 1. (2004)
    by A Sandelin, P Bailey, S Bruce, PG Engström, JM Klos, WW Wasserman, J Ericson, B Lenhard
    posted to algorithm element non-coding ultraconserved by fpattyn on 2008-02-28 13:58:52 as ** along with 1 person sujaikumar
  • Fast and reliable prediction of noncoding RNAs.
    Proc Natl Acad Sci U S A, Vol. 102, No. 7. (15 February 2005), pp. 2454-2459.
    by S Washietl, IL Hofacker, PF Stadler
    posted to non-coding rna by evaf on 2005-03-10 21:23:10 as ** along with 9 people and 3 groups gangli dayjm marcius eckart_bindewald tardigrade dquest Eonwe ilh raylim tulip BioinfoCIPF SGU-CIPF
  • Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.
    Nucleic Acids Res, Vol. 31, No. 14. (15 July 2003), pp. 4119-4128.
    by JP McCutcheon, SR Eddy
    posted to comparative non-coding rna yeast by evaf on 2005-03-10 21:18:35 as **
  • Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.
    Nucleic Acids Res, Vol. 28, No. 8. (15 April 2000), pp. 1808-1818.
    by J van Helden, AF Rios, J Collado-Vides
    posted to non-coding regulatory_element rna by evaf on 2005-03-10 21:22:50 as **
  • Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs.
    Bioessays, Vol. 26, No. 8. (August 2004), pp. 833-843.
    by M Suzuki, Y Hayashizaki
    posted to coding non-coding rna by evaf on 2005-03-10 21:22:25 as **
  • Non-coding RNA genes and the modern RNA world.
    Nat Rev Genet, Vol. 2, No. 12. (December 2001), pp. 919-929.
    by SR Eddy
    posted to non-coding rna by evaf on 2005-03-10 21:12:37 as ** along with 3 people and 2 groups eckart_bindewald arcticrasta bsmagic Bioinformatics bioinplant
  • Noncoding RNA genes.
    Curr Opin Genet Dev, Vol. 9, No. 6. (December 1999), pp. 695-699.
    by SR Eddy
    posted to non-coding rna by evaf on 2005-03-10 21:12:25 as ** along with 5 people and 3 groups marcius arcticrasta mtagaya cmm blobbybirdman FAB-lab BioinfoCIPF SGU-CIPF
  • Computational identification of noncoding RNAs in E. coli by comparative genomics.
    Curr Biol, Vol. 11, No. 17. (4 September 2001), pp. 1369-1373.
    by E Rivas, RJ Klein, TA Jones, SR Eddy
    posted to non-coding rna by evaf on 2005-03-10 21:20:47 as ** along with 5 people and 4 groups marcius eckart_bindewald arcticrasta dquest bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
  • Noncoding RNA gene detection using comparative sequence analysis.
    BMC Bioinformatics, Vol. 2, No. 1. (2001)
    by E Rivas, SR Eddy
    posted to comparative non-coding rna by evaf on 2005-03-10 21:20:43 as ** along with 4 people and 2 groups marcius eckart_bindewald arcticrasta jarasch BioinfoCIPF SGU-CIPF
  • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
    Genome Res, Vol. 9, No. 9. (September 1999), pp. 815-824.
    by N Jareborg, E Birney, R Durbin
    posted to comparative non-coding rna by evaf on 2005-03-10 21:15:43 as **
  • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
    Cell, Vol. 116, No. 4. (20 February 2004), pp. 499-509.
    by S Cawley, S Bekiranov, HH Ng, P Kapranov, EA Sekinger, D Kampa, A Piccolboni, V Sementchenko, J Cheng, AJ Williams, R Wheeler, B Wong, J Drenkow, M Yamanaka, S Patel, S Brubaker, H Tammana, G Helt, K Struhl, TR Gingeras
    posted to non-coding rna by evaf on 2005-03-10 21:10:44 as ** along with 5 people and 1 group bertelsen brant mtagaya kengg olympos Plantandetc
  • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 2911-2917.
    by E Bonnet, J Wuyts, P Rouzé, Y Van de Peer
    posted to mirna mirna_precursor non-coding rna by evaf on 2005-03-10 21:10:32 as ** along with 6 people and 2 groups tardigrade andersbj arcticrasta mtagaya cdawson erbon microRNA GIG
  • RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA.
    Proc Natl Acad Sci U S A, Vol. 99, No. 12. (11 June 2002), pp. 7906-7911.
    by DP Morse, PJ Aruscavage, BL Bass
    posted to mrna non-coding regulatory_element rna by evaf on 2005-03-10 21:18:58 as **
  • Conserved noncoding sequences are reliable guides to regulatory elements
    Trends in Genetics, Vol. 16, No. 9. (1 September 2000), pp. 369-372.
    by Ross C Hardison
    posted to comparative conserved enhancer_finding genomic non-coding by brant on 2008-02-19 01:14:38 as **
  • Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.
    Mol Biol Evol, Vol. 20, No. 5. (May 2003), pp. 703-714.
    by ET Dermitzakis, CM Bergman, AG Clark
    posted to non-coding molecular evolution by brant on 2008-05-13 19:00:46 as ** along with 2 people and 1 group cisevol emptyhb cis-regulatory-evolution
  • Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.
    Genome Res, Vol. 11, No. 8. (August 2001), pp. 1335-1345.
    by CM Bergman, M Kreitman
    posted to non-coding molecular evolution by brant on 2008-05-13 19:00:14 as ** along with 4 people and 2 groups penka adijr cisevol hugoparker Nie cis-regulatory-evolution
  • Computational genomics of noncoding RNA genes.
    Cell, Vol. 109, No. 2. (19 April 2002), pp. 137-140.
    by SR Eddy
    posted to bioinformatics non-coding rna by arcticrasta on 2006-02-01 13:46:44 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 335-340.
    by G Pesole, S Liuni, G Grillo, F Licciulli, F Mignone, C Gissi, C Saccone
    posted to database non-coding rna by arcticrasta on 2006-02-01 12:40:50 as **
  • Noncoding regulatory RNAs database
    Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 429-431.
    by Maciej Szymanski, Volker A Erdmann, Jan Barciszewski
    posted to database non-coding rna by arcticrasta on 2006-02-01 12:37:29 as ** along with 2 people and 2 groups mtagaya bsmagic Bioinformatics bioinplant
  • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
    Bioinformatics, Vol. 16, No. 7. (July 2000), pp. 583-605.
    by E Rivas, SR Eddy
    posted to bioinformatics non-coding rna secondary structure by arcticrasta on 2006-03-12 13:05:43 as ** along with 9 people and 3 groups evaf marcius eckart_bindewald eweaver andersbj mtagaya dquest Eonwe ilh microRNA BioinfoCIPF SGU-CIPF
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