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eckart_bindewald's rna [130 articles]

Recent papers added to eckart_bindewald's library classified by the tag rna. You can also see everyone's rna.
  • 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
  • How RNA folds.
    J Mol Biol, Vol. 293, No. 2. (22 October 1999), pp. 271-281.
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
  • Candidates for Novel RNA Topologies
    Journal of Molecular Biology, Vol. 341, No. 5. (27 August 2004), pp. 1129-1144.
    by Namhee Kim, Nahum Shiffeldrim, Hin H Gan, Tamar Schlick
  • Deoxyribozymes that recode sequence information.
    Nucleic Acids Res, Vol. 34, No. 8. (2006), pp. 2166-2172.
    by JJ Tabor, M Levy, AD Ellington
    posted to design dna rna by eckart_bindewald on 2007-11-06 16:24:08 as *** along with 1 person JKelly555
  • Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA
    RNA, Vol. 9, No. 4. (1 April 2003), pp. 377-383.
    by Scott K Silverman
    posted to riboswitch ribozyme rna sensor switch by eckart_bindewald on 2007-11-06 16:23:06 as ***
  • A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes
    Nucl. Acids Res., Vol. 30, No. 8. (15 April 2002), pp. 1735-1742.
    by Dennis Y Wang, Beatrice H Lai, Anat R Feldman, Dipankar Sen
  • A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
    Science, Vol. 306, No. 5694. (8 October 2004), pp. 275-279.
    by Maumita Mandal, Mark Lee, Jeffrey E Barrick, Zasha Weinberg, Gail M Emilsson, Walter L Ruzzo, Ronald R Breaker
  • Cooperative binding of effectors by an allosteric ribozyme
    Nucl. Acids Res., Vol. 29, No. 7. (1 April 2001), pp. 1631-1637.
    by Antony M Jose, Garrett A Soukup, Ronald R Breaker
    posted to aptamer cooperative design effector ribozyme rna by eckart_bindewald on 2007-11-06 15:51:26 as ****
  • A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC)
    Nucl. Acids Res., Vol. 27, No. 4. (15 February 1999), pp. 949-955.
    by Y Tanaka, S Fujii, H Hiroaki, T Sakata, T Tanaka, S Uesugi, K Tomita, Y Kyogoku
    posted to a-form groove helix rna by eckart_bindewald on 2007-11-01 18:48:54 as ***
  • 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
  • Topological constraints in nucleic acid hybridization kinetics
    Nucleic Acids Research, Vol. 33, No. 13. (2005), pp. 4090-4095.
    by Justin S Bois, Suvir Venkataraman, Harry M Choi, Andrew J Spakowitz, Zhen-Gang Wang, Niles A Pierce
  • Fast-Find: a novel computational approach to analyzing combinatorial motifs.
    BMC Bioinformatics, Vol. 7 (2006)
    by M Hamady, E Peden, R Knight, R Singh
    posted to database motif prediction rna search by eckart_bindewald on 2007-10-26 13:30:28 as ***
  • Evolutionary rates vary among rRNA structural elements
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3339-3354.
    by S Smit, J Widmann, R Knight
  • Modeling RNA tertiary structure motifs by graph-grammars.
    Nucleic Acids Res, Vol. 35, No. 5. (2007), pp. 1726-1736.
    by K St-Onge, P Thibault, S Hamel, F Major
    posted to graph motif rna structure by eckart_bindewald on 2007-10-23 14:25:06 as *** along with 1 person debatebob
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
  • Stem kernels for RNA sequence analyses.
    J Bioinform Comput Biol, Vol. 5, No. 5. (October 2007), pp. 1103-1122.
    posted to alignment noncoding prediction rna sequence by eckart_bindewald on 2007-10-17 18:33:48 as **
  • Prediction of small, noncoding RNAs in bacteria using heterogeneous data.
    J Math Biol (13 March 2007)
    by Brian Tjaden
    posted to ecoli hmm markov noncoding prediction rna secondary_structure by eckart_bindewald on 2007-03-15 19:26:37 as ****
  • Multiple structural alignment and clustering of RNA sequences.
    Bioinformatics (25 February 2007)
    by Elfar Torarinsson, Jakob H H Havgaard, Jan Gorodkin
  • RNA tectonics: towards RNA design.
    Fold Des, Vol. 1, No. 4. (1996)
    posted to tectoshapes rna nanotechnology design by eckart_bindewald on 2007-02-09 12:05:21 as *****
  • Computational RNA secondary structure design: empirical complexity and improved methods
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Rosalia A Hernandez, Holger Hoos, Anne Condon
  • Considerations in the identification of functional RNA structural elements in genomic alignments
    BMC Bioinformatics, Vol. 8 (30 January 2007), 33.
    by Tomas Babak, Benjamin J Blencowe, Timothy R Hughes
  • The architectonics of programmable RNA and DNA nanostructures
    Current Opinion in Structural Biology, Vol. 16, No. 4. (August 2006), pp. 531-543.
    by Luc Jaeger, Arkadiusz Chworos
  • Direct evolution of genetic robustness in microRNA
    PNAS, Vol. 103, No. 17. (25 April 2006), pp. 6593-6598.
    by Elhanan Borenstein, Eytan Ruppin
  • Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, Vol. 49, No. 2. (February 1999), pp. 145-165.
  • Modelling 'evo-devo' with RNA.
    Bioessays, Vol. 24, No. 12. (December 2002), pp. 1164-1177.
    by W Fontana
  • Viral RNA and evolved mutational robustness.
    J Exp Zool, Vol. 285, No. 2. (15 August 1999), pp. 119-127.
    by A Wagner, PF Stadler
  • The robustness of naturally and artificially selected nucleic acid secondary structures.
    J Mol Evol, Vol. 58, No. 6. (June 2004), pp. 681-691.
    posted to structure secondary robustness rna mutation by eckart_bindewald on 2007-01-23 16:27:10 as *****
  • Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
    Comput Appl Biosci, Vol. 13, No. 1. (February 1997), pp. 1-12.
    by KM Currey, BA Shapiro
  • Non-coding RNAs: hope or hype?
    Trends in Genetics, Vol. 21, No. 5. (May 2005), pp. 289-297.
    by Alexander Huttenhofer, Peter Schattner, Norbert Polacek
  • The transcriptional landscape of the mammalian genome.
    Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563.
    by P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, AR Forrest, M Zavolan, MJ Davis, LG Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK 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, SP Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan 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, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schönbach, K Sekiguchi, CA 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, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, V Brusic, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, 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, ,
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
    Nature, Vol. 420, No. 6915. (5 December 2002), pp. 563-573.
  • 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
  • RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences.
    Nucleic Acids Res, Vol. 32, No. 10. (2004), pp. 3258-3269.
    by G Pavesi, G Mauri, M Stefani, G Pesole
  • Noncoding RNA gene detection using comparative sequence analysis.
    BMC Bioinformatics, Vol. 2, No. 1. (2001)
    by E Rivas, SR Eddy
  • MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
    PNAS, Vol. 101, No. 33. (17 August 2004), pp. 12102-12107.
    by Alex Coventry, Daniel J Kleitman, Bonnie Berger
    posted to noncoding prediction rna secondary_structure by eckart_bindewald on 2007-01-05 19:54:57 as read
  • No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution.
    Nucleic Acids Res, Vol. 27, No. 24. (15 December 1999), pp. 4816-4822.
    by C Workman, A Krogh
    posted to mrna rna secondary_structure by eckart_bindewald on 2006-12-29 12:09:08 as **** along with 1 person mtagaya
  • Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway.
    Proc Natl Acad Sci U S A, Vol. 103, No. 11. (14 March 2006), pp. 4192-4197.
    by MP Samanta, W Tongprasit, H Sethi, CS Chin, V Stolc
    posted to genome noncoding rna tiling by eckart_bindewald on 2006-12-28 20:05:08 as **** along with 1 person alexg
  • A high-resolution map of transcription in the yeast genome
    PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325.
    by Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J Palm, Lee Bofkin, Ted Jones, Ronald W Davis, Lars M Steinmetz
  • A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge.
    Bioinformatics (12 October 2006)
    by Jiang Du, Joel S S Rozowsky, Jan O O Korbel, Zhengdong D D Zhang, Thomas E E Royce, Martin H H Schultz, Michael Snyder, Mark Gerstein
  • The transcriptome of the sea urchin embryo.
    Science, Vol. 314, No. 5801. (10 November 2006), pp. 960-962.
    by MP Samanta, W Tongprasit, S Istrail, RA Cameron, Q Tu, EH Davidson, V Stolc
    posted to genome noncoding rna tiling by eckart_bindewald on 2006-12-28 19:45:36 as ***
  • Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
    Genome Res (21 November 2006)
    by Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, Joel S S Rozowsky, Alexander E E Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark Gerstein
    posted to genome noncoding rna tiling by eckart_bindewald on 2006-12-28 19:39:39 as ***
  • Predicting non-coding RNA genes in <it>Escherichia coli</it> with boosted genetic programming
    Nucleic Acids Research, Vol. 33, No. 10. (2005), pp. 3263-3270.
    by Pal Saetrom, Ragnhild Sneve, Knut I Kristiansen, Ola Snove, Thomas Grunfeld, Torbjorn Rognes, Erling Seeberg
    posted to genetic_programming noncoding prediction rna by eckart_bindewald on 2006-12-28 16:07:01 as read
  • PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2590-2596.
    posted to ecoli noncoding rna by eckart_bindewald on 2006-12-28 16:03:36 as read
  • RNAs everywhere: genome-wide annotation of structured RNAs.
    J Exp Zoolog B Mol Dev Evol (14 December 2006)
    by Rolf Backofen, Stephan H H Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L L Hofacker, Kristin Missal, Axel Mosig, Sonja J J Prohaska, Dominic Rose, Peter F F Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
  • Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.
    Genome Res (2 June 2006)
    by Elfar Torarinsson, Milena Sawera, Jakob H H Havgaard, Merete Fredholm, Jan Gorodkin
  • ddbRNA: detection of conserved secondary structures in multiple alignments.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1606-1611.
  • Identification of a large noncoding RNA in extremophilic eubacteria.
    Proc Natl Acad Sci U S A (12 December 2006)
    by Elena Puerta-Fernandez, Jeffrey E E Barrick, Adam Roth, Ronald R R Breaker
    posted to noncoding rna by eckart_bindewald on 2006-12-15 11:41:30 as ** along with 1 person stajich
  • Further biochemical and kinetic characterization of human eukaryotic initiation factor 4H.
    J Biol Chem, Vol. 274, No. 50. (10 December 1999), pp. 35415-35424.
    by NJ Richter, GW Rogers, JO Hensold, WC Merrick