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タグ: noncoding [132 articles]

Recent papers classified by the tag noncoding.
  • 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 evolution noncoding by xingxu on 2007-12-27 00:52:06 as ** along with 1 group EvolutionaryComputation
  • Fewer Genes, More Noncoding RNA
    Science, Vol. 309, No. 5740. (02 September 2005), pp. 1529-1530.
    by Jean-Michel Claverie
    posted to dna gene jund noncoding rna by tvdbulck on 2008-03-27 10:58:27 as ** along with 4 people inbetweener lyongu janisa olympos
  • Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    Nature Biotechnology, Vol. 23, No. 11. (04 November 2005), pp. 1383-1390.
    by Stefan Washietl, Ivo L Hofacker, Melanie Lukasser, Alexander Hüttenhofer, Peter F Stadler
    posted to noncoding by tabu on 2006-02-14 04:22:48 as ** along with 6 people and 3 groups marcius eckart_bindewald tardigrade cdawson ilh raylim BioinfoCIPF SGU-CIPF GIG
  • 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
  • Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis.
    Genome Res (13 March 2006)
    by Gayle K K McEwen, Adam Woolfe, Debbie Goode, Tanya Vavouri, Heather Callaway, Greg Elgar
    posted to conserved genome noncoding by tabu on 2006-03-21 23:41:55 as ** along with 4 people and 3 groups dpollard dchughes sujaikumar maximilianh EisenLab G4ID Genetics-of-Gambling
  • Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock.
    Mol Cell, Vol. 29, No. 4. (29 February 2008), pp. 499-509.
    by PD Mariner, RD Walters, CA Espinoza, LF Drullinger, SD Wagner, JF Kugel, JA Goodrich
    posted to jc noncoding rna by stoffreg on 2008-03-21 16:29:38 as ** along with 1 person elfar
  • Distinguishing protein-coding and noncoding genes in the human genome
    Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.
    by Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S Lander
    posted to annotation comparative_genomics gene_finding genome_annotation human noncoding by stajich on 2007-12-09 07:18:24 as ** along with 15 people and 3 groups Ema tmmurali rvosa balicea sebastien_vigneau giovanni neils cjeans cabbagezs maximilianh oelemento gjuggler slroberd renatomilani gracio EisenLab FAB-lab Berkeley Mycology
  • Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe.
    Nucleic Acids Res, Vol. 29, No. 11. (1 June 2001), pp. 2327-2337.
    by T Watanabe, K Miyashita, TT Saito, T Yoneki, Y Kakihara, K Nabeshima, YA Kishi, C Shimoda, H Nojima
    posted to development noncoding noncoding_rna pombe by stajich on 2008-03-10 04:28:17 as ** along with 1 group Berkeley Mycology
  • Beyond Mfold: Recent advances in RNA bioinformatics.
    J Biotechnol (9 March 2006)
    by Jens Reeder, Matthias Höchsmann, Marc Rehmsmeier, Björn Voss, Robert Giegerich
    posted to analysis gene_prediction genome noncoding noncoding_rna rna rna_gene software by stajich on 2008-03-10 23:24:36 as read along with 12 people and 4 groups reyez marcius eckart_bindewald tardigrade andersbj arcticrasta mtagaya condon Hosna Eonwe cthachuk physics microRNA beta BioinfoCIPF SGU-CIPF
  • Strategies for measuring evolutionary conservation of RNA secondary structures
    BMC Bioinformatics, Vol. 9 (26 February 2008), 122.
    by Andreas R Gruber, Stefan H Bernhart, Ivo L Hofacker, Stefan Washietl
    posted to gene_finding noncoding noncoding_rna rna rna_gene by stajich on 2008-04-01 06:25:37 as ** along with 3 people and 1 group eckart_bindewald ilh gresillaud Berkeley Mycology
  • 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 conserved noncoding selection selection_test by stajich on 2007-09-07 17:14:36 as ** along with 8 people and 5 groups mattjb livingthingdan djkt Garamonfok cabbagezs Stew cisevol rrhudson EisenLab ComplexAdaptiveSystems DSTO-CAS livingthing cis-regulatory-evolution
  • Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics
    Physical Review E, Vol. 52, No. 3. (1995), 2939.
    by RN Mantegna, SV Buldyrev, AL Goldberger, S Havlin, CK Peng, M Simons, HE Stanley
    posted to noncoding dna coding by soramame_0518 on 2007-04-18 09:57:33 as ****
  • Adaptive evolution of non-coding DNA in Drosophila
    Nature, Vol. 437, No. 7062. (20 October 2005), pp. 1149-1152.
    by Peter Andolfatto
    posted to selection noncoding evolution drosophila by pradiptaray on 2008-07-01 02:18:12 as ** along with 12 people and 4 groups stevanspringer bpb aprasad jmeppley balicea jimmithy emilyhare cdawson adepace Stew mimulus_99 cisevol EisenLab FAB-lab GIG cis-regulatory-evolution
  • A Long-Term Evolutionary Pressure on the Amount of Non-Coding DNA.
    Mol Biol Evol (19 August 2007)
    by Carole Knibbe, Antoine Coulon, Olivier Mazet, Jean-Michel M Fayard, Guillaume Beslon
    posted to selection noncoding evolution by pradiptaray on 2008-07-01 02:05:15 as ** along with 5 people and 2 groups operon bpb aprasad cisevol coldmeadow cis-regulatory-evolution BergmanLab
  • Non-coding RNAs, epigenetics and complexity
    Gene, Vol. 410, No. 1. (29 February 2008), pp. 9-17.
    by Fabricio F Costa
    posted to rna noncoding epigenetics by pradiptaray on 2008-07-01 16:37:52 as ** along with 2 people and 1 group dchughes paulcartwright BergmanLab
  • 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 drosophila evolution noncoding phylogenetics selection by operon on 2007-07-26 14:46:52 as *** along with 7 people and 2 groups brant dpollard emilyhare Garamonfok Stew cisevol emptyhb EisenLab cis-regulatory-evolution
  • notes What controls the length of noncoding DNA?
    Curr Opin Genet Dev, Vol. 11, No. 6. (December 2001), pp. 652-659.
    by JM Comeron
    posted to evolution genome noncoding by miniprep on 2007-03-13 09:35:14 as **** along with 3 people and 1 group aprasad penka lilou Nie
  • Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.
    BMC Bioinformatics, Vol. 7, No. 1. (16 March 2006)
    by Rahul Siddharthan
    posted to alignment noncoding by lilou on 2007-06-08 09:24:23 as ** along with 1 person and 1 group dpollard EisenLab
  • 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 bioinformatics noncoding by lhonigberg on 2006-01-28 23:04:46 as ** along with 8 people and 2 groups aprasad eckart_bindewald eweaver acidwizard juliettecolinas Stew cisevol mailund EisenLab cis-regulatory-evolution
  • The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells.
    Mol Cell Biol, Vol. 26, No. 4. (February 2006), pp. 1445-1451.
    by JM Park, MJ Kohn, MW Bruinsma, C Vech, RV Intine, S Fuhrmann, A Grinberg, I Mukherjee, PE Love, MS Ko, ML DePamphilis, RJ Maraia
    posted to biogenesis cell cells cerevisiae development embryonic erythematosus eukaryote gene la lupus mice mrna noncoding polymerase pombe protein ribosome rna saccharomyces schizosaccharomyces sjogrens snornas trna yeast by jonathanjacobs on 2008-03-31 21:28:15 as *** along with 1 person and 1 group miguel The La Autoantigen.
  • High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e96.
    by Kevin A Wilkinson, Robert J Gorelick, Suzy M Vasa, Nicolas Guex, Alan Rein, David H Mathews, Morgan C Giddings, Kevin M Weeks
    posted to virus trna transcriptome transcriptase structure shape sequence rnaprotein rna ribosome retroviral protein primer nucleotide nucleocapsid noncoding native nascent motif human homolog hiv genomics genome function fold dna by jonathanjacobs on 2008-05-08 16:40:11 as ***** along with 1 person and 1 group kieran101 Molecular Biology
  • 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 evolution noncoding by jlangdon on 2008-01-18 16:39:45 as ** along with 4 people and 2 groups djkt Stew cisevol iris42 EisenLab cis-regulatory-evolution
  • Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.
    Genome Biol, Vol. 3, No. 12. (2002)
    by CM Bergman, BD Pfeiffer, DE Rincón-Limas, RA Hoskins, A Gnirke, CJ Mungall, AM Wang, B Kronmiller, J Pacleb, S Park, M Stapleton, K Wan, RA George, PJ de Jong, J Botas, GM Rubin, SE Celniker
    posted to comparative conserved enhancer noncoding sequence by indigoviolet on 2007-11-24 09:23:33 as ** along with 4 people and 2 groups brant dpollard nklee cisevol EisenLab cis-regulatory-evolution
  • Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements
    BMC Bioinformatics, Vol. 8 (15 March 2007), 94.
    by Sung T Doh, Yunyu Zhang, Matthew H Temple, Li Cai
    posted to algorithm homology noncoding by indigoviolet on 2007-11-29 02:50:27 as ** along with 1 person and 1 group jyuh EisenLab
  • 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 constraints drosophila noncoding by hugoparker on 2007-11-12 12:49:53 as ** along with 4 people and 2 groups brant penka adijr cisevol Nie cis-regulatory-evolution
  • Fruitfly genome is not junk
    Nature, Vol. 437, No. 7062. (19 October 2005), pp. 1106-1106.
    by Alexey S Kondrashov
    posted to -drosophila noncoding selection summary by stevanspringer to the group FAB-lab on 2005-10-24 21:14:41 as ** along with 3 people and 2 groups dayjm ogcruz marcius BioinfoCIPF SGU-CIPF
  • Adaptations to fluctuating selection in Drosophila.
    Proc Natl Acad Sci U S A (7 February 2007)
    by Ville Mustonen, Michael Lässig
    posted to noncoding evolution drosophila adaptation by dpollard to the group EisenLab on 2007-02-10 01:21:39 as *** along with 1 person lusk
  • Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations
    BMC Genomics, Vol. 7 (15 September 2006), 235.
    by Debraj Guhathakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susana Wang, Eric E Schadt
    posted to cis gene linkage mouse noncoding polymorphism regulation variation by dpollard to the group EisenLab on 2006-09-30 00:25:03 as *** along with 2 people adepace natstreet
  • Conserved distances between vertebrate highly conserved elements.
    Hum Mol Genet (21 August 2006)
    by Hong Sun, Geir Skogerbø, Runsheng Chen
    posted to conserved noncoding spacing by dpollard to the group EisenLab on 2006-08-25 18:22:00 as ** along with 1 person aprasad
  • The regulatory content of intergenic DNA shapes genome architecture.
    Genome Biol, Vol. 5, No. 4. (2004)
    by CE Nelson, BM Hersh, SB Carroll
    posted to drosophila gene_expression genome_architecture nematode noncoding by dpollard to the group EisenLab on 2007-11-14 21:21:28 as read along with 4 people and 2 groups madhadron elzodw blobbybirdman cisevol cis-regulatory-evolution BergmanLab
  • Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments.
    Proc Natl Acad Sci U S A (21 August 2006)
    by William Salerno, Paul Havlak, Jonathan Miller
    posted to conserved constraint evolution length noncoding by dpollard to the group EisenLab on 2006-08-25 17:47:37 as ** along with 1 person jmeppley
  • Rapid sequence turnover at an intergenic locus in Drosophila.
    Mol Biol Evol, Vol. 21, No. 4. (April 2004), pp. 670-680.
    by ND Singh, DA Petrov
    posted to drosophila genome_architecture genome_size indels noncoding by dpollard to the group EisenLab on 2007-11-14 21:13:48 as read
  • Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.
    BMC Genomics, Vol. 6 (27 November 2005)
    by S Lee, I Kohane, S Kasif
    posted to conserved development expression gene intergenic noncoding rate by dpollard to the group EisenLab on 2006-03-21 20:26:29 as ** along with 2 people balicea Garamonfok
  • Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland ESTs.
    Genetics (16 December 2005)
    by David Begun, Heather Lindfors, Melissa Thompson, Alisha Holloway
    posted to adaptive drosophila evolution gene noncoding by dpollard to the group EisenLab on 2006-03-21 19:56:01 as ****
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to alignment noncoding by dpollard to the group EisenLab on 2006-11-07 01:53:28 as read along with 12 people Neeperando operon balajis xwbcn dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee
  • Position specific variation in the rate of evolution in transcription factor binding sites.
    BMC Evol Biol, Vol. 3, No. 1. (28 August 2003)
    by AM Moses, DY Chiang, M Kellis, ES Lander, MB Eisen
    posted to binding conserved constraint evolution noncoding pattern phylogeny prediction pwm rate selection specific transcription by dpollard to the group EisenLab on 2006-11-07 00:22:07 as read along with 6 people and 1 group emptyhb briann adepace lusk nklee cisevol cis-regulatory-evolution
  • Housekeeping genes tend to show reduced upstream sequence conservation
    Genome Biology, Vol. 8 (13 July 2007), R140.
    by Domenec Farre, Nicolas Bellora, Loris Mularoni, Xavier Messeguer, Mar
    posted to cis-regulatory mammals noncoding by cisevol to the group BergmanLab on 2007-10-23 19:01:52 as ** along with 3 people and 2 groups djkt Garamonfok gjuggler Bioinformatics cis-regulatory-evolution
  • Local conservation scores without a priori assumptions on neutral substitution rates
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Janis Dingel, Pavol Hanus, Niccolo Leonardi, Joachim Hagenauer, Juergen Zech, Jakob Mueller
    posted to model noncoding by cisevol to the group BergmanLab on 2008-04-13 16:34:32 as ** along with 3 people and 1 group aprasad maximilianh RamuAnandakrishnan cis-regulatory-evolution
  • Maintenance of transposon-free regions throughout vertebrate evolution
    BMC Genomics, Vol. 8 (20 December 2007), 470.
    by Cas Simons, Igor V Makunin, Michael Pheasant, John S Mattick
    posted to mammals noncoding transposon by cisevol to the group BergmanLab on 2007-12-22 13:26:58 as ** along with 2 people and 1 group blobbybirdman idonaldson cis-regulatory-evolution
  • A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e176.
    by Erika M Kvikstad, Svitlana Tyekucheva, Francesca Chiaromonte, Kateryna D Makova
    posted to indel mammals noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-28 18:28:58 as ** along with 2 people aprasad djkt
  • Patterns and rates of intron divergence between humans and chimpanzees
    Genome Biology, Vol. 8 (19 February 2007), R21.
    by Elodie Gazave, Tomas Marques-Bonet, Olga Fernando, Brian Charlesworth, Arcadi Navarro
    posted to mammals noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-21 18:32:03 as ** along with 3 people and 1 group hdopazo nickluscombe lilou EBI-regulation
  • Multiple sequence alignment accuracy and evolutionary distance estimation.
    BMC Bioinformatics, Vol. 6 (2005)
    by MS Rosenberg
    posted to noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-20 11:37:24 as ** along with 2 people and 1 group aprasad dpollard EisenLab
  • Sequences conserved by selection across mouse and human malaria species
    BMC Genomics, Vol. 8 (15 October 2007), 372.
    by Hideo Imamura, Jason H Persampieri, Jeffrey H Chuang
    posted to noncoding plasmodium by cisevol to the group cis-regulatory-evolution on 2007-10-21 22:37:57 as **
  • 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 fish noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-20 11:34:31 as ** along with 2 people and 1 group aprasad Stew EisenLab
  • 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 flies mammals noncoding worms by cisevol to the group cis-regulatory-evolution on 2007-10-20 11:34:23 as ** along with 14 people and 1 group pradiptaray bpb aprasad balajis eckart_bindewald indigoviolet brant adepace djkt olympos sujaikumar Stew dmc elfar EisenLab
  • 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 mammals noncoding by cisevol to the group cis-regulatory-evolution on 2007-10-24 23:35:41 as ** along with 13 people and 4 groups pradiptaray karbak barry ujh alexisgallagher bpb aprasad balicea dchughes djkt sujaikumar blobbybirdman fpattyn structural_bioinformatics Bioinformatics G4ID Genetics-of-Gambling
  • Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae.
    Nucleic Acids Res, Vol. 30, No. 5. (1 March 2002), pp. 1233-1239.
    by CT Webb, SA Shabalina, AY Ogurtsov, AS Kondrashov
    posted to noncoding worms by cisevol to the group cis-regulatory-evolution on 2007-10-21 18:27:49 as **
  • The strength of selection on ultraconserved elements in the human genome.
    Am J Hum Genet, Vol. 80, No. 4. (April 2007), pp. 692-704.
    by CT Chen, JC Wang, BA Cohen
    posted to mammals noncoding variation by cisevol to the group cis-regulatory-evolution on 2007-10-24 23:35:13 as ** along with 1 person gjuggler
  • Human Genome Ultraconserved Elements Are Ultraselected
    Science, Vol. 317, No. 5840. (17 August 2007), 915.
    by Sol Katzman, Andrew D Kern, Gill Bejerano, Ginger Fewell, Lucinda Fulton, Richard K Wilson, Sofie R Salama, David Haussler
    posted to mammals noncoding variation by cisevol to the group cis-regulatory-evolution on 2007-10-24 23:34:48 as ** along with 8 people aprasad balicea djkt lp2 cabbagezs Minty fpattyn gjuggler
  • Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time
    BMC Genomics, Vol. 8, No. 1. (2007)
    by Dorota Retelska, Emmanuel Beaudoing, Cedric Notredame, Victor C Jongeneel, Philipp Bucher
    posted to mammals noncoding by cisevol to the group cis-regulatory-evolution on 2007-11-01 10:17:24 as ** along with 1 person maximilianh
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