raylim's library 88 articles Export

	Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. [My Copy] Molecular cell, Vol. 9, No. 2. (February 2002), pp. 279-289. by L. A. Cirillo, F. R. Lin, I. Cuesta, D. Friedman, M. Jarnik, K. S. Zaret posted to foxa transcription_factors by raylim on 2009-01-12 18:40:40 as
	Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 30. (24 July 2007), pp. 12377-12382. by J. Xu, S. D. Pope, A. R. Jazirehi, et al.J. L. Attema, P. Papathanasiou, J. A. Watts, K. S. Zaret, I. L. Weissman, S. T. Smale posted to enhancers by raylim on 2009-01-12 18:36:28 as
	Identifying tissue-selective transcription factor binding sites in vertebrate promoters. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 5. (1 February 2005), pp. 1560-1565. by A. D. Smith, P. Sumazin, M. Q. Zhang posted to motif_discovery motifs by raylim on 2008-12-18 17:49:53 as along with 2 people heliopais idonaldson
	WinBUGS - A Bayesian modelling framework: Concepts, structure, and extensibility [My Copy] Statistics and Computing, Vol. 10, No. 4. (1 October 2000), pp. 325-337. by David J. Lunn, Andrew Thomas, Nicky Best, David Spiegelhalter posted to mcmc by raylim on 2008-12-18 15:33:35 as along with 3 people renreff famuvie wnpx
	A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling [My Copy] Bioinformatics, Vol. 17, No. 12. (1 December 2001), pp. 1113-1122. by Gert Thijs, Magali Lescot, Kathleen Marchal, et al.Stephane Rombauts, Bart De Moor, Pierre Rouze, Yves Moreau posted to dna_background_model by raylim on 2008-12-18 13:38:35 as along with 7 people lusk Mehlhorn lyongu dquest natstreet nklee xili03
	STAMP: a web tool for exploring DNA-binding motif similarities. [My Copy] Nucleic acids research, Vol. 35, No. Web Server issue. (3 July 2007) by Shaun Mahony, Panayiotis V. Benos posted to motifs by raylim on 2008-12-18 11:44:58 as along with 3 people and 1 group yuslinaz aalibes dpollard EisenLab
	TRANSFAC: transcriptional regulation, from patterns to profiles. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 374-378. by V. Matys, E. Fricke, R. Geffers, et al.E. Gössling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A. E. Kel, O. V. Kel-Margoulis, D. U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, E. Wingender posted to database motifs by raylim on 2008-12-18 11:43:41 as along with 8 people and 1 group aprasad aalibes setar chad_davis GustavoLacerda marti Auger kmdaily Dead 60's
	Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding [My Copy] Genome Research, Vol. 18, No. 12. (3 December 2008), pp. 1906-1917. by A. Gordon Robertson, Mikhail Bilenky, Angela Tam, et al.Yongjun Zhao, Thomas Zeng, Nina Thiessen, Timothee Cezard, Anthony P. Fejes, Elizabeth D. Wederell, Rebecca Cullum, Ghia Euskirchen, Martin Krzywinski, Inanc Birol, Michael Snyder, Pamela A. Hoodless, Martin Hirst, Marco A. Marra, Steven J. M. Jones posted to histone_methylations histone_modifications by raylim on 2008-12-18 11:40:32 as along with 8 people tonamswish humburg gdb ewilban1 natstreet maximilianh jernst cpreviti
	Combinatorial patterns of histone acetylations and methylations in the human genome [My Copy] Nature Genetics, Vol. 40, No. 7. (15 June 2008), pp. 897-903. by Zhibin Wang, Chongzhi Zang, Jeffrey A. Rosenfeld, et al.Dustin E. Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q. Zhang, Keji Zhao posted to histone_modifications by raylim on 2008-12-14 04:36:06 as along with 16 people and 1 group akakak hagechouchin443 RyuOgawa suizifish tonamswish sebastien_vigneau gderwin oelemento coela jernst bpcusack kambiz caseybrown djkt kengg inesdesantiago Epigenetics
	High-Resolution Mapping and Characterization of Open Chromatin across the Genome. [My Copy] Cell, Vol. 132, No. 2. (25 January 2008), pp. 311-322. by A. P. Boyle, S. Davis, H. P. Shulha, et al.P. Meltzer, E. H. Margulies, Z. Weng, T. S. Furey, G. E. Crawford posted to histone_methylations by raylim on 2008-12-14 04:33:09 as along with 7 people and 1 group athma inesdesantiago Stew Eroslavochka djkt bootsy aprasad Bioinformatics - CRUK
	High-resolution profiling of histone methylations in the human genome. [My Copy] Cell, Vol. 129, No. 4. (18 May 2007), pp. 823-837. by Artem Barski, Suresh Cuddapah, Kairong Cui, et al.Tae-Young Y. Roh, Dustin E. Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, Keji Zhao posted to dhs enhancers histone_methylations by raylim on 2008-12-14 04:31:24 as along with 22 people and 2 groups rsaito darian tonamswish stubrown fpattyn hagechouchin443 absterga ewilban1 suizifish jochenG caseybrown jernst giovenko guhjy kengg sebastien_vigneau jackjackjjj ghattem epigenetics ksha inesdesantiago dquest JLab Plantandetc
	Dynamics of Enhancer-Promoter Communication during Differentiation-Induced Gene Activation [My Copy] Molecular Cell, Vol. 10, No. 6. (December 2002), pp. 1467-1477. by Pantelis Hatzis, Iannis Talianidis posted to enhancers p300 by raylim on 2008-12-14 03:54:57 as along with 1 person and 1 group wrowell Cline_lab
	CBP and p300: HATs for different occasions [My Copy] Biochemical Pharmacology, Vol. 68, No. 6. (15 September 2004), pp. 1145-1155. by Eric Kalkhoven posted to enhancers p300 by raylim on 2008-12-14 03:52:56 as along with 2 people guhjy Piggeldi
	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome [My Copy] Nat Genet, Vol. 39, No. 3. (04 February 2007), pp. 311-318. by Nathaniel D. Heintzman, Rhona K. Stuart, Gary Hon, et al.Yutao Fu, Christina W. Ching, R. David Hawkins, Leah O. Barrera, Sara Van Calcar, Chunxu Qu, Keith A. Ching, Wei Wang, Zhiping Weng, Roland D. Green, Gregory E. Crawford, Bing Ren posted to enhancers by raylim on 2008-12-14 03:51:04 as along with 12 people and 2 groups tonamswish hagechouchin443 suizifish absterga kengg djkt mgaldzic olympos skoch3 epigenetics caseybrown inesdesantiago CHIP Plantandetc
	Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? [My Copy] Journal of Cellular Biochemistry, Vol. 94, No. 5. (2005), pp. 890-898. by David N. Arnosti, Meghana M. Kulkarni posted to enhancers by raylim on 2008-12-14 03:47:55 as along with 2 people lusk olympos
	The role of enhancers as centres for general transcription factor recruitment [My Copy] Trends in Biochemical Sciences, Vol. 30, No. 11. (November 2005), pp. 593-599. by H. Szutorisz, N. Dillon, L. Tora posted to enhancers by raylim on 2008-12-14 01:50:09 as along with 1 person siebert
	Comparing functional annotation analyses with Catmap. [My Copy] BMC bioinformatics [electronic resource]. , Vol. 5, No. 1. (9 December 2004) by Thomas Breslin, Patrik Edén, Morten Krogh posted to gene_scoring roc by raylim on 2008-06-14 02:10:10 as along with 3 people and 3 groups jperkins ana ealloza structural_bioinformatics Bioinformatics BioinfoCIPF
	ErmineJ: tool for functional analysis of gene expression data sets. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by H. K. Lee, W. Braynen, K. Keshav, P. Pavlidis posted to gene_ontology microarray by raylim on 2008-06-12 00:17:52 as along with 3 people and 1 group oliviawi ealloza jdiggans BioinfoCIPF
	Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms [My Copy] Nucleic Acids Research, Vol. 33, No. 18. (2005), pp. 5914-5923. by Michael Barnes, Johannes Freudenberg, Susan Thompson, Bruce Aronow, Paul Pavlidis posted to affy illumina microarray by raylim on 2008-06-10 21:44:52 as along with 2 people daforerog heliopais
	beadarray: R classes and methods for Illumina bead-based data. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 16. (15 August 2007), pp. 2183-2184. by Mark J. Dunning, Mike L. Smith, Matthew E. Ritchie, Simon Tavaré posted to illumina microarray r by raylim on 2008-06-07 01:05:47 as along with 7 people daforerog dswan ptrobajo heliopais srp33 guhjy Stew
	affy--analysis of Affymetrix GeneChip data at the probe level. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 3. (12 February 2004), pp. 307-315. by Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry posted to affy microarray r by raylim on 2008-06-07 00:53:31 as along with 6 people and 1 group daforerog gupton RMGraze kengg bertelsen heliopais Plantandetc
	Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. [My Copy] Nature, Vol. 391, No. 6669. (19 February 1998), pp. 806-811. by A. Fire, S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver, C. C. Mello posted to c_elegans rnai by raylim on 2008-03-09 01:56:31 as along with 12 people and 2 groups duncan742 schmidtm thegoose2 micromassive czeller tharris dayjm tardigrade mtagaya shizhao benlin elfar C. elegans / WormBase Wikipedia
	Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. [My Copy] PLoS Genet, Vol. 2, No. 4. (April 2006) by N. Maeda, T. Kasukawa, R. Oyama, et al.J. Gough, M. Frith, P. G. Engström, B. Lenhard, R. N. Aturaliya, S. Batalov, K. W. Beisel, C. J. Bult, C. F. Fletcher, A. R. Forrest, M. Furuno, D. Hill, M. Itoh, M. Kanamori-Katayama, S. Katayama, M. Katoh, T. Kawashima, J. Quackenbush, T. Ravasi, B. Z. Ring, K. Shibata, K. Sugiura, Y. Takenaka, R. D. Teasdale, C. A. Wells, Y. Zhu, C. Kai, J. Kawai, D. A. Hume, P. Carninci, Y. Hayashizaki posted to annotation cdna genome-wide mouse transcriptome by raylim on 2008-03-08 23:22:51 as along with 1 person xiaobeizhao
	Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs [My Copy] Nature, Vol. 420 (December 2002), pp. 563-573. by Y. Okazaki, M. Furuno, T. Kasukawa, et al.J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki, I. Yamanaka, H. Kiyosawa, K. Yagi, Y. Tomaru, Y. Hasegawa, A. Nogami, C. Schönbach, T. Gojobori, R. Baldarelli, D. P. Hill, C. Bult, D. A. Hume, J. Quackenbush, L. M. Schriml, A. Kanapin, H. Matsuda, S. Batalov, K. W. Beisel, J. A. Blake, D. Bradt, V. Brusic, C. Chothia, L. E. Corbani, S. Cousins, E. Dalla, T. A. Dragani, C. F. Fletcher, A. Forrest, K. S. Frazer, T. Gaasterland, M. Gariboldi, C. Gissi, A. Godzik, J. Gough, S. Grimmond, S. Gustincich, N. Hirokawa, I. J. Jackson, E. D. Jarvis, A. Kanai, H. Kawaji, Y. Kawasawa, R. M. Kedzierski, B. L. King, A. Konagaya, I. V. Kurochkin, Y. Lee, B. Lenhard, P. A. Lyons, D. R. Maglott, L. Maltais, L. Marchionni, L. Mckenzie, H. Miki, T. Nagashima, K. Numata, T. Okido, W. J. Pavan, G. Pertea, G. Pesole, N. Petrovsky, R. Pillai, J. U. Pontius, D. Qi, S. Ramachandran, T. Ravasi, J. C. Reed, D. J. Reed, J. Reid, B. Z. Ring, M. Ringwald, A. Sandelin, C. Schneider, C. A. M. Semple, M. Setou, K. Shimada, R. Sultana, Y. Takenaka, M. S. Taylor, R. D. Teasdale, M. Tomita, R. Verardo, L. Wagner, C. Wahlestedt, Y. Wang, Y. Watanabe, C. Wells, L. G. Wilming, A. Wynshaw-Boris, M. Yanagisawa, I. Yang, L. Yang, Z. Yuan, M. Zavolan, Y. Zhu, A. Zimmer posted to annotation cdna genome-wide mouse transcriptome by raylim on 2008-03-08 23:20:00 as
	Integrative annotation of 21,037 human genes validated by full-length cDNA clones. [My Copy] PLoS Biol, Vol. 2, No. 6. (June 2004) by T. Imanishi, T. Itoh, Y. Suzuki, et al.C. O'Donovan, S. Fukuchi, K. O. Koyanagi, R. A. Barrero, T. Tamura, Y. Yamaguchi-Kabata, M. Tanino, K. Yura, S. Miyazaki, K. Ikeo, K. Homma, A. Kasprzyk, T. Nishikawa, M. Hirakawa, J. Thierry-Mieg, D. Thierry-Mieg, J. Ashurst, L. Jia, M. Nakao, M. A. Thomas, N. Mulder, Y. Karavidopoulou, L. Jin, S. Kim, T. Yasuda, B. Lenhard, E. Eveno, Y. Suzuki, C. Yamasaki, J. Takeda, C. Gough, P. Hilton, Y. Fujii, H. Sakai, S. Tanaka, C. Amid, M. Bellgard, M. d. e. . F. Bonaldo, H. Bono, S. K. Bromberg, A. J. Brookes, E. Bruford, P. Carninci, C. Chelala, C. Couillault, S. J. de Souza, M. A. Debily, M. D. Devignes, I. Dubchak, T. Endo, A. Estreicher, E. Eyras, K. Fukami-Kobayashi, G. R. Gopinath, E. Graudens, Y. Hahn, M. Han, Z. G. Han, K. Hanada, H. Hanaoka, E. Harada, K. Hashimoto, U. Hinz, M. Hirai, T. Hishiki, I. Hopkinson, S. Imbeaud, H. Inoko, A. Kanapin, Y. Kaneko, T. Kasukawa, J. Kelso, P. Kersey, R. Kikuno, K. Kimura, B. Korn, V. Kuryshev, I. Makalowska, T. Makino, S. Mano, R. Mariage-Samson, J. Mashima, H. Matsuda, H. W. Mewes, S. Minoshima, K. Nagai, H. Nagasaki, N. Nagata, R. Nigam, O. Ogasawara, O. Ohara, M. Ohtsubo, N. Okada, T. Okido, S. Oota, M. Ota, T. Ota, T. Otsuki, D. Piatier-Tonneau, A. Poustka, S. X. Ren, N. Saitou, K. Sakai, S. Sakamoto, R. Sakate, I. Schupp, F. Servant, S. Sherry, R. Shiba, N. Shimizu, M. Shimoyama, A. J. Simpson, B. Soares, C. Steward, M. Suwa, M. Suzuki, A. Takahashi, G. Tamiya, H. Tanaka, T. Taylor, J. D. Terwilliger, P. Unneberg, V. Veeramachaneni, S. Watanabe, L. Wilming, N. Yasuda, H. S. Yoo, M. Stodolsky, W. Makalowski, M. Go, K. Nakai, T. Takagi, M. Kanehisa, Y. Sakaki, J. Quackenbush, Y. Okazaki, Y. Hayashizaki, W. Hide, R. Chakraborty, K. Nishikawa, H. Sugawara, Y. Tateno, Z. Chen, M. Oishi, P. Tonellato, R. Apweiler, K. Okubo, L. Wagner, S. Wiemann, R. L. Strausberg, T. Isogai, C. Auffray, N. Nomura, T. Gojobori, S. Sugano posted to annotation cdna_library genome-wide validation by raylim on 2008-03-08 23:18:16 as along with 3 people and 1 group balicea Cortel kaspermunch Bioinformatics
	Fast and reliable prediction of noncoding RNAs. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 7. (15 February 2005), pp. 2454-2459. by S. Washietl, I. L. Hofacker, P. F. Stadler posted to ncrna prediction by raylim on 2008-03-08 23:11:04 as along with 14 people and 3 groups rb_india NicholasErho antonkratz balaji heliopais gangli evaf dayjm marcius eckart_bindewald tardigrade dquest Eonwe ilh tulip BioinfoCIPF SGU-CIPF
	Identification and Classification of Conserved RNA Secondary Structures in the Human Genome [My Copy] PLoS Comput Biol, Vol. 2, No. 4. (21 April 2006), e33. by Jakob S. Pedersen, Gill Bejerano, Adam Siepel, et al.Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler posted to genome-wide rna rna_folding secondary_structure by raylim on 2008-03-08 23:09:43 as along with 14 people and 2 groups rb_india guhjy NicholasErho marcius eckart_bindewald tardigrade arcticrasta tabu mtagaya Eonwe ilh djkt tale hpaces BioinfoCIPF SGU-CIPF
	Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome [My Copy] 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 ncrna rna_folding by raylim on 2008-03-08 23:07:33 as along with 7 people and 3 groups marcius eckart_bindewald tardigrade tabu cdawson ilh rb_india BioinfoCIPF SGU-CIPF GIG
	Local RNA base pairing probabilities in large sequences [My Copy] Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 614-615. by Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler posted to genome-wide rna_folding by raylim on 2008-03-08 23:03:02 as along with 1 person ilh
	Prediction of locally stable RNA secondary structures for genome-wide surveys. [My Copy] Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 186-190. by I. L. Hofacker, B. Priwitzer, P. F. Stadler posted to genome-wide rna_folding by raylim on 2008-03-08 23:00:33 as along with 6 people and 1 group NicholasErho thegoose2 tharris evaf ilh reyez C. elegans / WormBase
	RNA sequence analysis using covariance models [My Copy] Nucl. Acids Res., Vol. 22, No. 11. (11 June 1994), pp. 2079-2088. by Sean R. Eddy, Richard Durbin posted to covariance_models ncrna rna rna_folding by raylim on 2008-03-08 22:52:52 as along with 6 people and 1 group jengeldk danatcaret evaf arcticrasta vwchan elfar beta
	Stochastic context-free grammars for modeling RNA [My Copy] System Sciences, 1994. Vol.V: Biotechnology Computing, Proceedings of the Twenty-Seventh Hawaii International Conference on In System Sciences, 1994. Vol.V: Biotechnology Computing, Proceedings of the Twenty-Seventh Hawaii International Conference on, Vol. 5 (1994), pp. 284-293. by Y. Sakakibara, M. Brown, R. C. Underwood, I. S. Mian, D. Haussler posted to rna rna_folding scfgs by raylim on 2008-03-08 22:51:41 as
	Rfam: annotating non-coding RNAs in complete genomes. [My Copy] Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005) by S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R. Eddy, A. Bateman posted to database ncrna by raylim on 2008-03-08 22:49:13 as along with 7 people natstreet ppgardne mtagaya Hosna dandaman austin eskay
	Coexpression Analysis of Human Genes Across Many Microarray Data Sets [My Copy] Genome Research, Vol. 14, No. 6. (June 2004), pp. 1085-1094. by Homin K. Lee, Amy K. Hsu, Jon Sajdak, Jie Qin, Paul Pavlidis posted to gene_coexpression by raylim on 2008-03-08 22:35:42 as along with 17 people and 2 groups sficklin cabbagezs cswinburne pengchy jiny maryee gpalidwor giovanni jeremymiller hawkeyehammer grahamc macavity1g sgoetz wilbur jo_davies nedwards dragonrez GeschwindLab Indigene
	A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules [My Copy] Science, Vol. 302, No. 5643. (10 October 2003), pp. 249-255. by Joshua M. Stuart, Eran Segal, Daphne Koller, Stuart K. Kim posted to gene_coexpression by raylim on 2008-03-08 07:20:32 as along with 24 people and 7 groups sficklin roys thegoose2 cswinburne carlk saket pengchy nolodie jeremymiller tharris dragonrez textoris lfriedl balajis nuke2005 maryee tardigrade opheliav wnpx neveaire macle lp2 karfunkel vertikalist C. elegans / WormBase kdl Biostatistics Computational-Genomics Bioinformatics Neuroscience BTS-PT-AS-CS
	Non-coding RNAs: hope or hype? [My Copy] Trends in Genetics, Vol. 21, No. 5. (May 2005), pp. 289-297. by Alexander Hüttenhofer, Peter Schattner, Norbert Polacek posted to ncrna by raylim on 2008-03-08 05:12:55 as along with 7 people YukaH antonkratz myrtilus setar eckart_bindewald arcticrasta eskay
	The Transcriptional Landscape of the Mammalian Genome [My Copy] Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563. by The FANTOM Consortium, P. Carninci, T. Kasukawa, et al.S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, Madan M. Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schonbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, RIKEN Genome Exploration Research Group and Genome Science Group Genome Network Project Core Group, C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, Y. Hayashizaki posted to mouse transcriptome by raylim on 2008-03-08 04:57:43 as along with 19 people and 1 group hagechouchin443 daforerog guhjy myrtilus setar miguel Cortel jwortman jfr tuck lyongu eckart_bindewald troels_marstrand kaspermunch balicea forbiddenfaith99 mtagaya olympos gjuggler Bioinformatics
	Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. [My Copy] Genome Res, Vol. 16, No. 1. (January 2006), pp. 11-19. by T. Ravasi, H. Suzuki, K. C. Pang, et al.S. Katayama, M. Furuno, R. Okunishi, S. Fukuda, K. Ru, M. C. Frith, M. M. Gongora, S. M. Grimmond, D. A. Hume, Y. Hayashizaki, J. S. Mattick posted to experimental_validation mouse ncrna by raylim on 2008-03-08 04:50:31 as along with 3 people galka8_diploma alexg mtagaya
	SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework [My Copy] PLoS Comput Biol, Vol. 3, No. 8. (10 August 2007), e149. by Irmtraud M. Meyer, István Miklós posted to pseudoknots rna secondary_structure by raylim on 2007-09-20 19:53:04 as along with 4 people jmallos zwang cabbagezs bertelsen
	Pure multiple RNA secondary structure alignments: a progressive profile approach. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 1, No. 1. (r 2004), pp. 53-62. by M. Höchsmann, B. Voss, R. Giegerich posted to alignments rna_forester secondary_structure by raylim on 2007-09-11 05:59:50 as along with 1 person emidio_capriotti
	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2688-2690. by A. Stamatakis posted to no-tag by raylim on 2007-04-30 07:06:46 as
	Unexpected point mutations activate cryptic 3' splice sites by perturbing a natural secondary structure within a yeast intron. [My Copy] Genes Dev., Vol. 5, No. 7. (1 July 1991), pp. 1252-1263. by J. O. Deshler, J. J. Rossi posted to 3ss intron secondary_structure splice_site by raylim on 2007-04-30 05:52:28 as
	An Intronic Splicing Enhancer Element in Survival Motor Neuron (SMN) Pre-mRNA [My Copy] J. Biol. Chem., Vol. 278, No. 18. (25 April 2003), pp. 15825-15831. by Hidenobu Miyaso, Masayo Okumura, Shinichi Kondo, Satoshi Higashide, Hiroshi Miyajima, Kazunori Imaizumi posted to intronic_splicing_enhancer pre_mrna smn by raylim on 2007-04-30 05:26:10 as
	Genetic basis of variable exon 9 skipping in cystic fibrosis transmembrane conductance regulator mRNA [My Copy] Nat Genet, Vol. 3, No. 2. (February 1993), pp. 151-156. by Chin-Shyan Chu, Bruce C. Trapnell, Sheila Curristin, Garry R. Cutting, Ronald G. Crystal posted to cftr exon_skipping by raylim on 2007-04-30 03:55:00 as
	Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17 [My Copy] PNAS, Vol. 96, No. 14. (6 July 1999), pp. 8229-8234. by Luca Varani, Masato Hasegawa, Maria G. Spillantini, et al.Michael J. Smith, Jill R. Murrell, Bernardino Ghetti, Aaron Klug, Michel Goedert, Gabriele Varani posted to exon rna secondary_structure splicing_regulatory_element by raylim on 2007-04-30 03:16:59 as
	The iStem, a Long-Range RNA Secondary Structure Element Required for Efficient Exon Inclusion in the Drosophila Dscam Pre-mRNA [My Copy] Mol. Cell. Biol., Vol. 25, No. 23. (1 December 2005), pp. 10251-10260. by Jenny M. Kreahling, Brenton R. Graveley posted to dscam exon_inclusion intron pre_mrna secondary_structure by raylim on 2007-04-30 02:57:08 as
	Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. [My Copy] Nucleic acids research, Vol. 30, No. 1. (1 January 2002), pp. 52-55. by Ada Hamosh, Alan F. Scott, Joanna Amberger, Carol Bocchini, David Valle, Victor A. McKusick posted to database genetic_disorders omim by raylim on 2007-04-29 22:49:09 as
	The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch [My Copy] Molecular Cell, Vol. 18, No. 1. (1 April 2005), pp. 49-60. by Kenneth J. Wickiser, Wade C. Winkler, Ronald R. Breaker, Donald M. Crothers posted to riboswitch transcription_speed by raylim on 2007-04-28 09:36:05 as
	hnRNP proteins and the biogenesis of mRNA. [My Copy] Annu Rev Biochem, Vol. 62 (1993), pp. 289-321. by G. Dreyfuss, M. J. Matunis, S. Piñol-Roma, C. G. Burd posted to hnrnp premrna_binding_elements by raylim on 2007-04-28 08:45:37 as
	Secondary Structure of the Ribosome Binding Site Determines Translational Efficiency: A Quantitative Analysis [My Copy] PNAS, Vol. 87, No. 19. (1 October 1990), pp. 7668-7672. by Mh de Smit, J. van Duin posted to rbs secondary_structure translational_efficiency by raylim on 2007-04-28 07:46:37 as

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secondary_structure	24
rna	19
alternative_splicing	7
enhancers	7
rna_folding	7
splicing	7
genome-wide	6
ncrna	6
prediction	5
annotation	4
microarray	4
mouse	4
cdna	3
cftr	3
database	3
exon	3
histone_methylations	3
motifs	3
transcriptome	3
affy	2
gene_coexpression	2
genetic_disease	2
histone_modifications	2
illumina	2
intron	2
mechanism	2
mrna	2
p300	2
pre_mrna	2
r	2
regulation	2
scfgs	2
splice_site	2
splice_sites	2
translation_initiation_control	2
virus	2
3ss	1
additional_info	1
alignments	1
alternative	1
boltzmann_dist	1
cdna_library	1
c_elegans	1
clustal	1
code	1
co-transcriptional	1
covariance_models	1
dhs	1
dna_background_model	1
dscam	1
enhancer_display	1
ensembl	1
ese	1
ests	1
evolution	1
exon_flanks	1
exonic_mutations	1
exon_inclusion	1
exon_skipping	1
experimental_validation	1
folding	1
foxa	1
gene_ontology	1
gene_scoring	1
genetic	1
genetic_disorders	1
genome_database	1
hnrnp	1
intronic_splicing_enhancer	1
intron_loss	1
leukemia	1
mcmc	1
mfe	1
motif_discovery	1
multiple_sequence_alignment	1
murine	1
omim	1
periodic_pattern	1
pfold	1
premrna_binding_elements	1
protein_coding	1
protein_recruitment	1
pseudoknots	1
pseudoviewer	1
rbs	1
ribosome-mediated	1
riboswitch	1
rnaalifold	1
rna_forester	1
rnai	1
roc	1
selection	1
smn	1
spliceosome	1
splicing_efficiency	1
splicing_regulatory_element	1
split_genes	1
synonymous_mutations	1
synonymous_substitution	1
transcription_factors	1
transcription_speed	1
translational_efficiency	1
translational_pause	1
translation_regulation	1
validation	1

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