arcticrasta's library 136 articles Export

	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. S. Lander, Jim Kent, Webb Miller, David Haussler posted to bioinformatics gene rna search by arcticrasta on 2006-06-22 18:40:38 as along with 14 people and 2 groups rb_india guhjy NicholasErho marcius eckart_bindewald tardigrade tabu mtagaya Eonwe ilh djkt raylim tale hpaces BioinfoCIPF SGU-CIPF
	Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. [My Copy] J Mol Biol, Vol. 342, No. 1. (3 September 2004), pp. 19-30. by S. Washietl, I. L. Hofacker posted to bioinformatics gene rna search by arcticrasta on 2006-06-22 17:48:15 as along with 4 people dayjm Eonwe ilh elfar
	HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns [My Copy] Nucl. Acids Res., Vol. 29, No. 1. (1 January 2001), pp. 196-198. by Stefan Graf, Dirk Strothmann, Stefan Kurtz, Gerhard Steger posted to bioinformatics pattern rna search by arcticrasta on 2006-06-22 10:11:16 as along with 1 person Eonwe
	GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. [My Copy] Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 762-764. by W. Gerlach, R. Giegerich posted to bioinformatics motif rna search by arcticrasta on 2006-06-21 16:57:29 as along with 1 person and 1 group andersbj microRNA
	Human MicroRNA targets. [My Copy] PLoS Biol, Vol. 2, No. 11. (November 2004) by B. John, A. J. Enright, A. Aravin, T. Tuschl, C. Sander, D. S. Marks posted to bioinformatics mirna rna targets by arcticrasta on 2006-06-21 16:26:23 as along with 12 people and 2 groups daforerog jfr eckart_bindewald tardigrade mortenlindow dsm mtagaya ealloza wulanw heliopais jdiezperezj Alexander_Kanitz microRNA BioinfoCIPF
	A method for aligning RNA secondary structures and its application to RNA motif detection. [My Copy] BMC bioinformatics, Vol. 6 (2005) by J. Liu, J. T. Wang, J. Hu, B. Tian posted to bioinformatics homology rna search by arcticrasta on 2006-06-20 19:25:59 as along with 2 people and 1 group vwchan emidio_capriotti beta
	Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. [My Copy] J Mol Biol, Vol. 313, No. 5. (9 November 2001), pp. 1003-1011. by D. Gautheret, A. Lambert posted to bioinformatics homology rna search by arcticrasta on 2006-06-20 18:40:37 as along with 1 person evaf
	Pair hidden Markov models on tree structures. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by Y. Sakakibara posted to bioinformatics homology rna search by arcticrasta on 2006-06-20 17:49:45 as
	Sequence-based heuristics for faster annotation of non-coding RNA families. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 1. (1 January 2006), pp. 35-39. by Zasha Weinberg, Walter L. L. Ruzzo posted to bioinformatics homology rna search by arcticrasta on 2006-06-20 17:32:57 as along with 2 people ppgardne jwortman
	Rapid and sensitive sequence comparison with FASTP and FASTA. [My Copy] Methods in enzymology, Vol. 183 (1990), pp. 63-98. by W. R. Pearson posted to bioinformatics homology search by arcticrasta on 2006-06-17 12:20:05 as along with 4 people jmeppley treangen jlh64 granujilla
	Improved tools for biological sequence comparison. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 8. (April 1988), pp. 2444-2448. by W. R. Pearson, D. J. Lipman posted to bioinformatics homology search by arcticrasta on 2006-06-17 10:31:06 as along with 15 people and 2 groups rshe maria_hauser pachorip parnell carlosviana cawelsh9 ffranca gurkanbebek bsmagic CitoJam lusk cjeans sujaikumar Ema bozdagd Bioinformatics bioinplant
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to bioinformatics homology search by arcticrasta on 2006-06-17 09:07:50 as along with 77 people and 6 groups VGreiff richter80 krapnik azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog mcbla coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	An algorithm for detecting homologues of known structured RNAs in genomes. [My Copy] Proc IEEE Comput Syst Bioinform Conf (2004), pp. 300-310. by S. Y. Le, J. V. Maizel, K. Zhang posted to bioinformatics homology rna search by arcticrasta on 2006-06-16 16:33:03 as along with 2 people and 4 groups marcius bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
	Revolutions in RNA Secondary Structure Prediction [My Copy] Journal of Molecular Biology, Vol. 359, No. 3. (9 June 2006), pp. 526-532. by David H. Mathews posted to bioinformatics prediction rna secondary structure by arcticrasta on 2006-06-15 19:13:09 as along with 12 people and 2 groups rb_india bmduggan heliopais marcius penka Eonwe cthachuk emidio_capriotti physics maralena winterschlaefer austin BioinfoCIPF SGU-CIPF
	Vienna RNA secondary structure server [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3429-3431. by I. L. Hofacker posted to bioinformatics prediction rna secondary structure by arcticrasta on 2006-06-15 16:06:11 as along with 13 people stharward ellarond heliopais evaf dayjm eckart_bindewald balicea mtagaya dquest ilh onufriev maralena reyez
	Prediction of RNA secondary structure based on helical regions distribution [My Copy] Bioinformatics, Vol. 14, No. 8. (1 September 1998), pp. 700-706. by L. Wuju, W. Jiajin posted to bioinformatics rna secondary statistical structure by arcticrasta on 2006-06-15 14:26:35 as
	CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. [My Copy] Nucleic acids research, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. by J. D. Thompson, D. G. Higgins, T. J. Gibson posted to alignment sequence by arcticrasta on 2006-06-12 19:02:01 as along with 34 people and 1 group biomcgary vprieto tomjad oceanwind Blackbeard db344 udivi daforerog Md_2007 sebk cen4ik usagi-kirin jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg dullhunk caporaso ahanora Haggan BioNica timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
	RAGA: RNA sequence alignment by genetic algorithm [My Copy] Nucl. Acids Res., Vol. 25, No. 22. (15 November 1997), pp. 4570-4580. by C. Notredame, Ea O'Brien, Dg Higgins posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-07 15:31:15 as
	Edit distance between two RNA structures [My Copy] In RECOMB (2001), pp. 211-220. by Guo H. Lin, Bin Ma, Kaizhong Zhang posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-07 15:10:55 as
	MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. [My Copy] Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3352-3359. by S. Siebert, R. Backofen posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-07 14:54:26 as along with 2 people and 2 groups marcius ilh BioinfoCIPF SGU-CIPF
	Local similarity in RNA secondary structures. [My Copy] Proc IEEE Comput Soc Bioinform Conf, Vol. 2 (2003), pp. 159-168. by M. Höchsmann, T. Töller, R. Giegerich, S. Kurtz posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-07 14:39:30 as
	A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. [My Copy] Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1591-1602. by Y. Ji, X. Xu, G. D. Stormo posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 20:10:10 as
	Discovering common stem-loop motifs in unaligned RNA sequences. [My Copy] Nucleic Acids Res, Vol. 29, No. 10. (15 May 2001), pp. 2135-2144. by J. Gorodkin, S. L. Stricklin, G. D. Stormo posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 19:57:58 as along with 1 person evaf
	The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W650-653. by J. H. Havgaard, R. B. Lyngsø, J. Gorodkin posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 19:00:59 as along with 3 people and 1 group rb_india reyez condon beta
	Finding the most significant common sequence and structure motifs in a set of RNA sequences. [My Copy] Nucleic acids research, Vol. 25, No. 18. (15 September 1997), pp. 3724-3732. by J. Gorodkin, L. J. Heyer, G. D. Stormo posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 18:55:32 as along with 1 person evaf
	Predicting a set of minimal free energy RNA secondary structures common to two sequences. [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2246-2253. by D. H. Mathews posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 16:10:58 as along with 4 people and 2 groups rb_india marcius eckart_bindewald austin BioinfoCIPF SGU-CIPF
	Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. [My Copy] J Mol Biol, Vol. 317, No. 2. (22 March 2002), pp. 191-203. by D. H. Mathews, D. H. Turner posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 16:08:13 as along with 1 person evaf
	Accelerated probabilistic inference of RNA structure evolution. [My Copy] BMC bioinformatics, Vol. 6, No. 1. (2005) by I. Holmes posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 16:04:20 as
	Alignment of RNA base pairing probability matrices. [My Copy] Bioinformatics, Vol. 20, No. 14. (22 September 2004), pp. 2222-2227. by I. L. Hofacker, S. H. Bernhart, P. F. Stadler posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 15:59:22 as along with 3 people ereehuis ilh reyez
	CARNAC: folding families of related RNAs. [My Copy] Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004) by H. Touzet, O. Perriquet posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 15:55:41 as
	CMfinder--a covariance model based RNA motif finding algorithm. [My Copy] Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 445-452. by Z. Yao, Z. Weinberg, W. L. Ruzzo posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-06 15:51:42 as along with 1 person and 2 groups bsmagic Bioinformatics bioinplant
	An RNA folding method capable of identifying pseudoknots and base triples [My Copy] Bioinformatics, Vol. 14, No. 8. (1 September 1998), pp. 691-699. by Je Tabaska, Rb Cary, Hn Gabow, Gd Stormo posted to bioinformatics comparative prediction pseudoknots rna secondary structure by arcticrasta on 2006-06-06 09:33:51 as along with 2 people gzm55 guxiyou
	Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2611-2617. by H. Matsui, K. Sato, Y. Sakakibara posted to bioinformatics comparative prediction pseudoknot rna secondary structure by arcticrasta on 2006-06-05 19:21:10 as
	Predicting RNA structure using mutual information. [My Copy] Appl Bioinformatics, Vol. 4, No. 1. (2005), pp. 53-59. by E. Freyhult, V. Moulton, P. Gardner posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-05 19:16:34 as along with 4 people and 2 groups evaf marcius eckart_bindewald eweaver BioinfoCIPF SGU-CIPF
	BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. [My Copy] RNA, Vol. 10, No. 9. (September 2004), pp. 1323-1336. by R. Knight, A. Birmingham, M. Yarus posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-05 18:06:35 as
	RNA secondary structure prediction based on free energy and phylogenetic analysis. [My Copy] J Mol Biol, Vol. 289, No. 4. (18 June 1999), pp. 935-947. by V. Juan, C. Wilson posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-05 18:04:09 as along with 1 person eckart_bindewald
	Prediction of common secondary structures of RNAs: a genetic algorithm approach [My Copy] Nucl. Acids Res., Vol. 28, No. 4. (15 February 2000), pp. 991-999. by Jih-H Chen, Shu-Yun Le, Jacob V. Maizel posted to bioinformatics comparative genetic_algorithm prediction rna secondary structure by arcticrasta on 2006-06-05 15:12:47 as
	ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. [My Copy] Nucleic Acids Res, Vol. 27, No. 21. (1 November 1999), pp. 4208-4217. by R. Lück, S. Gräf, G. Steger posted to bioinformatics comparative prediction rna secondary structure by arcticrasta on 2006-06-05 14:17:37 as
	A comparative method for finding and folding RNA secondary structures within protein-coding regions. [My Copy] Nucleic Acids Res, Vol. 32, No. 16. (2004), pp. 4925-4936. by J. S. Pedersen, I. M. Meyer, R. Forsberg, P. Simmonds, J. Hein posted to comparative prediction rna secondary structure by arcticrasta on 2006-06-05 14:02:55 as along with 1 person eckart_bindewald
	Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. [My Copy] BMC Bioinformatics, Vol. 5 (5 August 2004) by K. J. Doshi, J. J. Cannone, C. W. Cobaugh, R. R. Gutell posted to bioinformatics evaluation mfold rna secondary structure by arcticrasta on 2006-05-18 13:06:43 as along with 3 people heliopais ellarond eckart_bindewald
	RNA secondary structure: physical and computational aspects. [My Copy] Q Rev Biophys, Vol. 33, No. 3. (August 2000), pp. 199-253. by P. G. Higgs posted to bioinformatics rna secondary structure by arcticrasta on 2006-05-15 15:05:17 as along with 2 people and 2 groups marcius penka BioinfoCIPF SGU-CIPF
	A complex adaptive systems approach to the kinetic folding of RNA. [My Copy] Biosystems, Vol. 82, No. 3. (December 2005), pp. 257-265. by W. Ndifon posted to bioinformatics kinetics rna secondary structure by arcticrasta on 2006-05-10 14:43:47 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	The equilibrium partition function and base pair binding probabilities for RNA secondary structure. [My Copy] Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119. by J. S. Mccaskill posted to bioinformatics function partition rna secondary structure by arcticrasta on 2006-05-10 10:08:47 as along with 9 people and 3 groups NicholasErho saunders rb_india ellarond evaf marcius condon Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
	RNA folding at elementary step resolution. [My Copy] RNA, Vol. 6, No. 3. (March 2000), pp. 325-338. by C. Flamm, W. Fontana, I. L. Hofacker, P. Schuster posted to bioinformatics folding kinetic rna secondary structure by arcticrasta on 2006-05-10 09:56:54 as along with 4 people austin ilh mtw Kiarostami
	RDfolder: a web server for prediction of RNA secondary structure. [My Copy] Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004) by X. Ying, H. Luo, J. Luo, W. Li posted to bioinformatics rna secondary structure by arcticrasta on 2006-05-09 18:45:13 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	A bayesian statistical algorithm for RNA secondary structure prediction. [My Copy] Comput Chem, Vol. 23, No. 3-4. (15 June 1999), pp. 387-400. by Y. Ding, C. E. Lawrence posted to bayesian bioinformatics function partition rna secondary structure by arcticrasta on 2006-05-06 19:28:21 as along with 3 people and 3 groups marcius eckart_bindewald condon beta BioinfoCIPF SGU-CIPF
	An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. [My Copy] J Comput Chem, Vol. 25, No. 10. (30 July 2004), pp. 1295-1304. by R. M. Dirks, N. A. Pierce posted to bioinformatics function partition rna secondary structure by arcticrasta on 2006-05-06 19:17:04 as along with 2 people evaf miyake
	Kinetics of an RNA conformational switch. [My Copy] Proc Natl Acad Sci U S A, Vol. 91, No. 8. (12 April 1994), pp. 3373-3377. by K. A. Lecuyer, D. M. Crothers posted to conformational kinetics rna secondary structure switch by arcticrasta on 2006-05-05 18:49:57 as along with 1 person physics
	RNALOSS: a web server for RNA locally optimal secondary structures. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by P. Clote posted to bioinformatics prediction rna secondary structure webserver by arcticrasta on 2006-05-04 20:34:40 as along with 3 people and 3 groups rb_india marcius condon beta BioinfoCIPF SGU-CIPF
	RNAshapes: an integrated RNA analysis package based on abstract shapes. [My Copy] Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 500-503. by P. Steffen, B. Voss, M. Rehmsmeier, J. Reeder, R. Giegerich posted to bioinformatics rna secondary structure by arcticrasta on 2006-05-04 20:03:04 as

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rna	112
bioinformatics	90
structure	67
secondary	65
prediction	33
comparative	25
search	18
non-coding	10
motifs	9
homology	8
noncoding	7
dna	6
function	6
mfe	6
partition	6
folding	5
genome	5
pseudoknots	5
sequence	5
bayesian	4
database	4
energy	4
kinetics	4
evolution	3
free	3
gene	3
alignment	2
complete	2
genetic	2
mirna	2
motif	2
pattern	2
pseudoknot	2
antisense	1
benchmark	1
citron	1
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complexity	1
computational	1
computer	1
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covariance	1
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genomic	1
genomics	1
identification	1
inactivation	1
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introns	1
kinetic	1
lab	1
mammalian	1
mfold	1
microrna	1
minimization	1
minimum	1
models	1
ncrna	1
np	1
prion	1
prions	1
programming	1
protein	1
ribozyme	1
rnaanalyzer	1
rnai	1
rnamot	1
rna_world	1
rnaz	1
scfg	1
screen	1
snorna	1
statistical	1
structural	1
suboptimal	1
switch	1
targets	1
tertiary	1
thermodynamics	1
transcript	1
transcription	1
webserver	1
wet	1
x-chromosome	1
yeast	1

arcticrasta's library 136 articles Export

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