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condon's library [161 articles]

Recent papers added to condon's library ordered by importance.
  • RNA loop-loop interactions as dynamic functional motifs
    Biochimie, Vol. 84, No. 9. (September 2002), pp. 925-944.
    by Christine Brunel, Roland Marquet, Pascale Romby, Chantal Ehresmann
    posted to pseudoknots by condon on 2006-04-13 21:55:25 as *** along with 1 person and 1 group austin beta
  • KnotSeeker: Heuristic pseudoknot detection in long RNA sequences
    RNA, Vol. 14, No. 4. (1 April 2008), pp. 630-640.
    by Jana Sperschneider, Amitava Datta
    posted to pseudoknots by condon on 2008-03-26 20:41:57 as ** along with 2 people Hosna physics
  • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
    Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 58-66.
    by J Ruan, GD Stormo, W Zhang
    posted to heuristic preduction by condon on 2007-07-07 15:35:46 as ** along with 3 people and 1 group evaf arcticrasta Hosna beta
  • Gideon, a program for design of structural dna nanotechnology
    (2006)
    by Jeffrey J Birac
    posted to design by condon on 2007-06-28 04:26:29 as ** along with 1 group beta
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Song Cao, Shi J Chen
    posted to energy-model pseudoknot rna by condon on 2007-05-08 14:18:12 as ** along with 1 person and 1 group Kiarostami beta
  • On the computational power of iterative auctions
    (2005), pp. 29-43.
    by Liad Blumrosen, Noam Nisan
    posted to combinatorial-auctions by condon on 2007-05-07 21:17:08 as ** along with 1 group beta
  • Moments of the Boltzmann distribution for RNA secondary structures
    Bulletin of Mathematical Biology, Vol. 67, No. 5. (2005), pp. 1031-1047.
    by István Miklós, Irmtraud M Meyer, Borbála Nagy
    posted to partition-function rna structure by condon on 2007-05-07 21:14:27 as ** along with 1 person and 1 group raylim beta
  • G-ribo: A new structural motif in ribosomal RNA
    RNA, Vol. 13, No. 4. (1 April 2007), pp. 549-554.
    by Sergey V Steinberg, Yury I Boutorine
    posted to rna structure tertiary by condon on 2007-03-23 23:50:17 as ** along with 1 group beta
  • RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts.
    J Am Chem Soc, Vol. 127, No. 13. (6 April 2005), pp. 4659-4667.
    by KA Wilkinson, EJ Merino, KM Weeks
    posted to hierarchical rna structure tertiary by condon on 2007-03-23 23:22:31 as ** along with 1 group beta
  • RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).
    J Am Chem Soc, Vol. 127, No. 12. (30 March 2005), pp. 4223-4231.
    by EJ Merino, KA Wilkinson, JL Coughlan, KM Weeks
    posted to rna structure tertiary by condon on 2007-03-23 23:19:39 as ** along with 1 person and 1 group eckart_bindewald beta
  • A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. 4912-4924.
    by Lu, Zhi John, Turner, H Douglas, Mathews, H David
    posted to rna energy-parameters by condon on 2007-01-29 15:37:09 as ** along with 1 group beta
  • Truth revelation in approximately efficient combinatorial auctions
    J. ACM, Vol. 49, No. 5. (September 2002), pp. 577-602.
    by Daniel Lehmann, Liadan I O&\#263;allaghan, Yoav Shoham
    posted to combinatorial-auctions by condon on 2006-11-20 04:27:28 as ** along with 1 group beta
  • First blueprint, now bricks: DNA as construction material on the nanoscale.
    Chem Soc Rev, Vol. 35, No. 11. (November 2006), pp. 1111-1121.
    by S Pitchiaya, Y Krishnan
    posted to dna nanotechnology review by condon on 2006-11-11 19:29:02 as ** along with 2 people and 1 group stsaft dna beta
  • Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.
    Nucleic Acids Res, Vol. 8, No. 10. (24 May 1980), pp. 2275-2293.
    by CR Woese, LJ Magrum, R Gupta, RB Siegel, DA Stahl, J Kop, N Crawford, J Brosius, R Gutell, JJ Hogan, HF Noller
    posted to classic comparative rna by condon on 2006-11-11 18:19:54 as ** along with 2 people and 1 group mcox eckart_bindewald beta
  • Predicting RNA pseudoknot folding thermodynamics
    Nucleic Acids Research, Vol. 34, No. 9. (2006), pp. 2634-2652.
    by Song Cao, Shi-Jie Chen
    posted to energy-model pseudoknot rna by condon on 2006-10-31 21:49:48 as ** along with 4 people and 1 group Hosna apop physics Kiarostami beta
  • RNA Structure Prediction Including Pseudoknots Based on Stochastic Multiple Context-Free Grammar
    Workshop on Probabilistic Modeling and Machine Learning in Structural and Systems Biology (2006)
    by Yuki Kato, Hiroyuki Seki, Tadao Kasami
    posted to rna tags by condon on 2006-10-27 17:46:08 as ** along with 1 group beta
  • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE (2004), pp. 290-299.
    by H Matsui, K Sato, Y Sakakibara
    posted to rna tags by condon on 2006-10-27 17:31:00 as ** along with 1 group beta
  • Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.
    Antisense Nucleic Acid Drug Dev, Vol. 13, No. 2. (April 2003), pp. 83-105.
    by J Harborth, SM Elbashir, K Vandenburgh, H Manninga, SA Scaringe, K Weber, T Tuschl
    posted to review rna structure by condon on 2006-10-27 17:19:36 as ** along with 1 group beta
  • The equilibrium partition function and base pair binding probabilities for RNA secondary structure.
    Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119.
    by JS McCaskill
    posted to rna by condon on 2006-10-17 21:26:04 as ** along with 5 people and 3 groups evaf marcius arcticrasta Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
  • Versatile and declarative dynamic programming using pair algebras.
    BMC Bioinformatics, Vol. 6, No. 1. (12 September 2005)
    by Peter Steffen, Robert Giegerich
    posted to dynamic-programming by condon on 2006-10-10 03:45:18 as ** along with 3 people and 1 group BragilMassoud Hosna Kiarostami beta
  • INFO-RNA--a fast approach to inverse RNA folding.
    Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1823-1831.
    by A Busch, R Backofen
    posted to design by condon on 2006-10-10 03:11:23 as ** along with 1 group beta
  • The importance of thermodynamic equilibrium for high throughput gene expression arrays.
    Biophys J, Vol. 84, No. 1. (January 2003), pp. 124-135.
    by G Bhanot, Y Louzoun, J Zhu, C Delisi
    posted to dna by condon on 2006-10-09 05:17:32 as ** along with 1 person and 1 group stsaft beta
  • A thermodynamic approach to designing structure-free combinatorial DNA word sets
    Nucleic Acids Research, Vol. 33, No. 15. (2005), pp. 4965-4977.
    by Michael R Shortreed, Seo B Chang, Donggee Hong, Maggie Phillips, Bridget Campion, Dan C Tulpan, Mirela Andronescu, Anne Condon, Holger H Hoos, Lloyd M Smith
    posted to design by condon on 2006-10-05 00:54:41 as ** along with 1 group beta
  • Thermodynamically based DNA strand design
    Nucleic Acids Research, Vol. 33, No. 15. (2005), pp. 4951-4964.
    by Dan Tulpan, Mirela Andronescu, Seo B Chang, Michael R Shortreed, Anne Condon, Holger H Hoos, Lloyd M Smith
    posted to design by condon on 2006-10-05 00:52:21 as ** along with 1 person and 1 group stsaft beta
  • Gene2Oligo: oligonucleotide design for in vitro gene synthesis.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by JM Rouillard, W Lee, G Truan, X Gao, X Zhou, E Gulari
    posted to oligo-design by condon on 2006-09-01 16:09:19 as ** along with 1 person and 1 group cthachuk beta
  • A bayesian statistical algorithm for RNA secondary structure prediction.
    Comput Chem, Vol. 23, No. 3-4. (15 June 1999), pp. 387-400.
    by Y Ding, CE Lawrence
    posted to prediction rna structure by condon on 2006-08-17 20:37:30 as ** along with 3 people and 3 groups marcius eckart_bindewald arcticrasta beta BioinfoCIPF SGU-CIPF
  • Statistical and Bayesian approaches to RNA secondary structure prediction.
    RNA, Vol. 12, No. 3. (March 2006), pp. 323-331.
    by Y Ding
    posted to review rna structure by condon on 2006-08-17 20:35:41 as ** along with 6 people and 3 groups marcius arcticrasta penka Hosna physics Kiarostami beta BioinfoCIPF SGU-CIPF
  • Extracting stacking interaction parameters for RNA from the data set of native structures.
    J Mol Biol, Vol. 347, No. 1. (18 March 2005), pp. 53-69.
    by RI Dima, C Hyeon, D Thirumalai
    posted to energy-model rna structure by condon on 2006-08-17 20:33:41 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • CONTRAfold: RNA secondary structure prediction without physics-based models.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by CB Do, DA Woods, S Batzoglou
    posted to rna scfgs structure by condon on 2006-08-17 19:46:39 as ** along with 6 people and 3 groups austin balajis marcius tardigrade penka acarbo beta BioinfoCIPF SGU-CIPF
  • Efficient Algorithm for RNA Pseudoknotted Secondary Structure Prediction Given a Pseudoknot Free Structure
    (2005)
    by YS Zhao
    posted to hierarchical rna structure by condon on 2006-07-14 23:43:50 as ** along with 1 group beta
  • New insight into RNase P RNA structure from comparative analysis of the archaeal RNA.
    RNA, Vol. 7, No. 2. (February 2001), pp. 220-232.
    by JK Harris, ES Haas, D Williams, DN Frank, JW Brown
    posted to rna structure by condon on 2006-07-13 21:03:31 as ** along with 1 group beta
  • Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot
    Journal of Molecular Biology, Vol. 270, No. 3. (18 July 1997), pp. 451-463.
    by Thomas C Gluick, Resi B Gerstner, David E Draper
    posted to experimental folding-pathways rna structure by condon on 2006-07-13 19:54:21 as ** along with 1 group beta
  • Crystal structure of a hepatitis delta virus ribozyme.
    Nature, Vol. 395, No. 6702. (8 October 1998), pp. 567-574.
    by AR Ferré-D'Amaré, K Zhou, JA Doudna
    posted to experimental rna structure by condon on 2006-07-13 19:32:24 as ** along with 1 person and 1 group Hosna beta
  • Structural genomics of RNA.
    Nat Struct Biol, Vol. 7 Suppl (November 2000), pp. 954-956.
    by JA Doudna
    posted to review rna structure by condon on 2006-07-13 19:16:24 as ** along with 3 people and 5 groups marcius dchughes arcticrasta G4ID beta BioinfoCIPF SGU-CIPF Genetics-of-Gambling
  • An introduction to the mechanics of DNA.
    Philos Transact A Math Phys Eng Sci, Vol. 362, No. 1820. (15 July 2004), pp. 1265-1279.
    by AA Travers, JM Thompson
    posted to dna mechanics by condon on 2006-07-13 00:52:37 as ** along with 1 person and 1 group hirokiS beta
  • Probing the Mechanical Folding Kinetics of TAR RNA by Hopping, Force-Jump, and Force-Ramp Methods
    Biophys. J., Vol. 90, No. 1. (1 January 2006), pp. 250-260.
    by Pan T Li, Delphine Collin, Steven B Smith, Carlos Bustamante, Ignacio Tinoco
    posted to folding-pathways rna structure by condon on 2006-07-09 18:27:51 as ** along with 1 person and 1 group ruudvanleeuwen beta
  • Strategies for RNA folding and assembly.
    Nat Rev Mol Cell Biol, Vol. 5, No. 11. (November 2004), pp. 908-919.
    by R Schroeder, A Barta, K Semrad
    posted to folding-pathways review rna structure by condon on 2006-07-09 18:26:24 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • Native secondary structure formation in RNA may be a slave to tertiary folding
    PNAS, Vol. 95, No. 20. (29 September 1998), pp. 11506-11508.
    by D Thirumalai
    posted to review rna structure tertiary by condon on 2006-07-09 18:21:21 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • Co-transcriptional folding is encoded within RNA genes.
    BMC Mol Biol, Vol. 5, No. 1. (6 August 2004)
    by IM Meyer, I Miklós
    posted to co-transcriptional-folding rna structure by condon on 2006-07-09 18:17:04 as ** along with 4 people and 3 groups evaf marcius Hosna raylim beta BioinfoCIPF SGU-CIPF
  • Overlaps between RNA secondary structures.
    PHYSICAL REVIEW LETTERS, Vol. 76, No. 4. (22 January 1996), pp. 704-707.
    by PG Higgs
    posted to energy-landscapes rna structure by condon on 2006-07-09 18:11:55 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • Comparative sequence analysis of tmRNA.
    Nucleic Acids Res, Vol. 27, No. 10. (15 May 1999), pp. 2063-2071.
    by C Zwieb, I Wower, J Wower
    posted to rna structure by condon on 2006-07-09 18:00:17 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods
    Genetics, Vol. 157, No. 1. (1 January 2001), pp. 399-411.
    by Nicholas J Savill, David C Hoyle, Paul G Higgs
    posted to phylogeny-model rna by condon on 2006-07-09 17:57:20 as ** along with 3 people and 4 groups marcius penka i000 beta BioinfoCIPF SGU-CIPF YY1
  • RNA backbone is rotameric.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 13904-13909.
    by LJ Murray, WB Arendall, DC Richardson, JS Richardson
    posted to computational-experimental rna structure tertiary by condon on 2006-07-09 17:38:25 as ** along with 1 person and 3 groups marcius beta BioinfoCIPF SGU-CIPF
  • Methods for refining interactively established models of ribosomal RNA towards a physico-chemically plausible structure
    Journal of Computational Chemistry, Vol. 22, No. 4. (2001), pp. 407-417.
    by Ingolf Sommer, Richard Brimacombe
    posted to computational-experimental rna structure tertiary by condon on 2006-07-09 16:47:28 as ** along with 1 group beta
  • The language of RNA: a formal grammar that includes pseudoknots.
    Bioinformatics, Vol. 16, No. 4. (April 2000), pp. 334-340.
    by E Rivas, SR Eddy
    posted to pseudoknots rna structure by condon on 2006-07-05 22:17:02 as ** along with 3 people and 1 group evaf Hosna cthachuk beta
  • Threshold circuits of bounded depth
    J. Comput. Syst. Sci., Vol. 46, No. 2. (April 1993), pp. 129-154.
    by Andr&\#225;s Hajnal, Wolfgang Maass, Pavel Pudl&\#225;k, Gy&\#246;rgy Tur&\#225;n, M&\#225;ri&\#243; Szegedy
    posted to dnf by condon on 2006-07-03 21:02:52 as ** along with 1 group beta
  • SCOR: Structural Classification of RNA, version 2.0.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by M Tamura, DK Hendrix, PS Klosterman, NR Schimmelman, SE Brenner, SR Holbrook
    posted to database rna tertiary by condon on 2006-07-02 19:21:50 as ** along with 3 people and 3 groups reyez marcius debatebob beta BioinfoCIPF SGU-CIPF
  • Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting.
    J Mol Biol, Vol. 298, No. 2. (28 April 2000), pp. 167-185.
    by DP Giedroc, CA Theimer, PL Nixon
    posted to pseudoknots rna tertiary by condon on 2006-07-02 04:35:17 as ** along with 2 people and 1 group Hosna physics beta
  • Algorithms for the prediction of 3D RNA molecules
    (1998)
    by Alexander Renner
    posted to precition rna tertiary by condon on 2006-07-02 04:32:39 as ** along with 1 group beta
  • Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs.
    Nucleic Acids Res, Vol. 33, No. 4. (2005), pp. 1384-1398.
    by S Pasquali, HH Gan, T Schlick
    posted to design rna tertiary by condon on 2006-07-02 04:24:17 as ** along with 1 person and 1 group debatebob beta
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