Hosna's library 202 articles Export

	Theory of RNA Folding: From Hairpins to Ribozymes [My Copy] Non-Protein Coding RNAs (2009), pp. 27-47. by D. Thirumalai, Changbong Hyeon posted to secondary_structure_prediction rna_folding by Hosna on 2009-11-19 08:36:16 as
	A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics. [My Copy] Journal of molecular biology, Vol. 378, No. 4. (9 May 2008), pp. 943-953. by Glenna J. Smith, Kang Taek T. Lee, Xiaohui Qu, et al.Zheng Xie, Jelena Pesic, Tobin R. Sosnick, Tao Pan, Norbert F. Scherer posted to rna_folding hierarchical_folding fluorescence_resonance_energy_transfer by Hosna on 2009-11-17 11:17:22 as
	The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction [My Copy] BMC Bioinformatics, Vol. 3, No. 1. (2002), 15. by Jamie Cannone, Sankar Subramanian, Murray Schnare, et al.James Collett, Lisa D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi Madabusi, Kirsten Muller, Nupur Pande, Zhidi Shang, Nan Yu, Robin Gutell posted to secondary_structure_prediction rna_folding data co-transcriptional_folding by Hosna on 2009-11-17 10:24:48 as
	The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. [My Copy] BMC bioinformatics, Vol. 3, No. 1. (2002) by Jamie J. Cannone, Sankar Subramanian, Murray N. Schnare, et al.James R. Collett, Lisa M. D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V. Madabusi, Kirsten M. Müller, Nupur Pande, Zhidi Shang, Nan Yu, Robin R. Gutell posted to secondary_structure_prediction data co-transcriptional_folding by Hosna on 2009-11-17 10:21:16 as along with 2 people and 1 group evaf condon beta
	Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein [My Copy] Nature, Vol. 446, No. 7134. (25 February 2007), pp. 458-461. by Michael D. Stone, Mariana Mihalusova, Catherine M. O/'Connor, Ramadevi Prathapam, Kathleen Collins, Xiaowei Zhuang posted to rna_folding hierarchical_folding by Hosna on 2009-11-17 07:35:27 as along with 1 person yusdi
	RNA SHAPE Chemistry Reveals Nonhierarchical Interactions Dominate Equilibrium Structural Transitions in tRNAAsp Transcripts [My Copy] Journal of the American Chemical Society, Vol. 127, No. 13. (1 April 2005), pp. 4659-4667. by Kevin A. Wilkinson, Edward J. Merino, Kevin M. Weeks posted to rna_folding non_hierarchical_folding by Hosna on 2009-11-17 07:31:31 as along with 1 person and 1 group condon beta
	Exploring the folding landscape of a structured RNA [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 1. (8 January 2002), pp. 155-160. by Rick Russell, Xiaowei Zhuang, Hazen P. Babcock, et al.Ian S. Millett, Sebastian Doniach, Steven Chu, Daniel Herschlag posted to rnase_p_rna large_rna_enzyme data catalytic by Hosna on 2009-09-17 22:42:20 as
	Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. [My Copy] Journal of bacteriology, Vol. 177, No. 8. (April 1995), pp. 1919-1928. by N. R. Pace, J. W. Brown posted to rnase_p_rna large_rna_enzyme data catalytic by Hosna on 2009-09-17 22:41:05 as
	The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme [My Copy] Vol. 35, No. 3. (1 December 1983), pp. 849-857. by Cecilia Guerrier-Takada, Katheleen Gardiner, Terry Marsh, Norman Pace, Sidney Altman posted to rnase_p_rna large_rna_enzyme data catalytic by Hosna on 2009-09-17 22:39:04 as
	The hairpin ribozyme: structure, assembly and catalysis [My Copy] Current Opinion in Chemical Biology (February 1998), pp. 24-30. by N. G. Walter, J. M. Burker posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 22:33:31 as
	Focus on function: Single molecule RNA enzymology [My Copy] Biopolymers, Vol. 87, No. 5-6. (2007), pp. 302-316. by Mark A. Ditzler, Elvin A. Alemán, David Rueda, Nils G. Walter posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 22:08:49 as
	Folding and catalysis of the hairpin ribozyme. [My Copy] Biochemical Society transactions, Vol. 33, No. Pt 3. (June 2005), pp. 461-465. by T. J. Wilson, M. Nahas, T. Ha, D. M. Lilley posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 22:07:09 as
	Single Molecule Fluorescence Control for Nanotechnology [My Copy] Journal of Nanoscience and Nanotechnology, Vol. 5, No. 12. (December 2005), pp. 1990-2000. by David Rueda, Nils G. Walter posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 22:03:09 as
	Single-molecule folding [My Copy] Current Opinion in Structural Biology, Vol. 13, No. 1. (February 2003), pp. 88-97. by X. Zhuang, M. Rief posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 21:57:57 as
	RNA folding and the origins of catalytic activity in the hairpin ribozyme. [My Copy] Blood cells, molecules & diseases, Vol. 38, No. 1. (b 2007), pp. 8-14. by Timothy J. Wilson, Michelle Nahas, Lisa Araki, Shinya Harusawa, Taekjip Ha, David M. Lilley posted to small_ribozyme hairpin_ribozyme hairpin_ data by Hosna on 2009-09-17 21:52:56 as
	Single-molecule RNA folding [My Copy] Accounts of chemical research, Vol. 38 (2005), pp. 566-573. by G. Bokinsky, X. Zhuang posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 20:58:24 as
	SINGLE-MOLECULE RNA SCIENCE [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 34, No. 1. (2005), pp. 399-414. by Xiaowei Zhuang posted to small_ribozyme hairpin_ribozyme data by Hosna on 2009-09-17 20:51:02 as
	RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis. [My Copy] Current opinion in structural biology, Vol. 16, No. 3. (June 2006), pp. 319-326. by Mary R. Stahley, Scott A. Strobel posted to tetrahymena_ribozyme large_rna data by Hosna on 2009-09-17 20:40:22 as along with 1 person austin
	Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. [My Copy] Cell, Vol. 31, No. 1. (November 1982), pp. 147-157. by K. Kruger, P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling, T. R. Cech posted to tetrahymena_ribozyme large_rna data by Hosna on 2009-09-17 20:37:48 as
	Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters [My Copy] RNA, Vol. 15, No. 2. (February 2009), pp. 189-199. by Magdalena A. Jonikas, Randall J. Radmer, Alain Laederach, et al.Rhiju Das, Samuel Pearlman, Daniel Herschlag, Russ B. Altman posted to rna_folding 3d_structure by Hosna on 2009-08-28 14:07:46 as along with 1 person balewis
	In silico selection of RNA aptamers [My Copy] Nucl. Acids Res., Vol. 37, No. 12. (1 July 2009), e87. by Yaroslav Chushak, Morley O. Stone posted to aptamer_selection by Hosna on 2009-08-28 14:05:29 as along with 1 person guhjy
	iFoldRNA: three-dimensional RNA structure prediction and folding [My Copy] Bioinformatics, Vol. 24, No. 17. (1 September 2008), pp. 1951-1952. by Shantanu Sharma, Feng Ding, Nikolay V. Dokholyan posted to rna_folding 3d_structure by Hosna on 2009-08-28 14:01:31 as along with 3 people balewis nuin reyez
	Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships [My Copy] The Journal of Virology, Vol. 83 (July 2009), pp. 6326-6334. by Susan J. Schroeder posted to rna_folding hierarchical_folding by Hosna on 2009-08-27 23:06:35 as
	Hierarchical self-assembly of complex polyhedral microcontainers [My Copy] Journal of Micromechanics and Microengineering, Vol. 19, No. 7. (2009), 075012. by David J. Filipiak, Anum Azam, Timothy G. Leong, David H. Gracias posted to nanotechnology by Hosna on 2009-08-27 22:54:25 as
	Single-molecule fluorescence studies of RNA: A decade’s progress [My Copy] Chemical Physics Letters, Vol. 476, No. 1-3. (07 July 2009), pp. 1-10. by Krishanthi S. Karunatilaka, David Rueda posted to rna_folding hierarchical_folding data by Hosna on 2009-08-27 02:13:16 as
	Thermodynamics and Kinetics of RNA Unfolding and Refolding [My Copy] Non-Protein Coding RNAs (2009), pp. 49-72. by Pan T. X. Li, Ignacio Tinoco posted to rna_folding hierarchical_folding by Hosna on 2009-08-27 02:11:00 as along with 1 person balewis
	Exploring RNA folding one molecule at a time [My Copy] Current Opinion in Chemical Biology, Vol. 12, No. 6. (December 2008), pp. 647-654. by E. Aleman, R. Lamichhane, D. Rueda posted to rna_folding hierarchical_folding by Hosna on 2009-08-27 02:08:24 as along with 1 person balewis
	Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 305-314. by V. Chu, D. Herschlag posted to rna_folding hierarchical_folding by Hosna on 2009-08-27 02:04:23 as along with 1 person benlin
	Prediction of hybridization and melting for double-stranded nucleic acids. [My Copy] Biophysical journal, Vol. 87, No. 1. (July 2004), pp. 215-226. by R. A. Dimitrov, M. Zuker posted to partition_function rna-rna by Hosna on 2009-07-22 16:41:56 as along with 2 people dbikard stsaft
	Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers [My Copy] Science, Vol. 319, No. 5863. (1 February 2008), pp. 630-633. by William J. Greenleaf, Kirsten L. Frieda, Daniel A. N. Foster, Michael T. Woodside, Steven M. Block posted to hierarchical_folding by Hosna on 2009-07-02 20:17:04 as along with 4 people hsekiguc austin jvf666 paulschlesinger
	A partition function algorithm for interacting nucleic acid strands [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i365-373. by Hamidreza Chitsaz, Raheleh Salari, Cenk S. Sahinalp, Rolf Backofen posted to rna-rna rnai by Hosna on 2009-06-15 13:51:37 as along with 1 person reyez
	A model of molecular interactions on short oligonucleotide microarrays. [My Copy] Nat Biotechnol, Vol. 21, No. 7. (July 2003), pp. 818-821. by L. Zhang, M. F. Miles, K. D. Aldape posted to microarray rnai by Hosna on 2009-05-28 21:23:53 as along with 4 people caseybrown nicholso bertelsen talponer
	Derivation of nearest-neighbor properties from data on nucleic acid oligomers. II. Thermodynamic parameters of DNA · RNA hybrids and DNA duplexes [My Copy] Biopolymers, Vol. 42, No. 7. (1997), pp. 795-810. by Donald M. Gray posted to parameter parameters_dna_dna parameters_rna_dna by Hosna on 2009-05-27 19:47:01 as
	Predicting sequence-dependent melting stability of short duplex DNA oligomers [My Copy] Biopolymers, Vol. 44, No. 3. (1997), pp. 217-239. by Richard Owczarzy, Peter M. Vallone, Frank J. Gallo, Teodoro M. Paner, Michael J. Lane, Albert S. Benight posted to parameters_dna_dna by Hosna on 2009-05-25 22:01:47 as along with 1 person Vincent_Rouilly
	A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 95, No. 4. (17 February 1998), pp. 1460-1465. by John Santalucia posted to parameters_dna_dna by Hosna on 2009-05-25 21:56:53 as along with 5 people oteri daforerog davidng stsaft talponer
	Base-stacking and base-pairing contributions into thermal stability of the DNA double helix [My Copy] Nucleic Acids Research, Vol. 34, No. 2. (2006), pp. 564-574. by Peter Yakovchuk, Ekaterina Protozanova, Maxim D. Frank-Kamenetskii posted to parameters_dna_dna by Hosna on 2009-05-25 21:51:42 as along with 2 people NicholasErho Vincent_Rouilly
	RNA Structure Prediction [My Copy] Annual Review of Biophysics and Biophysical Chemistry, Vol. 17, No. 1. (1988), pp. 167-192. by D. H. Turner, N. Sugimoto, S. M. Freier posted to parameter by Hosna on 2009-05-25 21:17:20 as along with 1 person gzm55
	Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes [My Copy] Nucl. Acids Res., Vol. 24, No. 22. (15 November 1996), pp. 4501-4505. by N. Sugimoto, S. Nakano, M. Yoneyama, K. Honda posted to parameters_dna_dna by Hosna on 2009-05-24 16:57:16 as along with 1 group beta
	Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes [My Copy] Biochemistry, Vol. 34, No. 35. (1 September 1995), pp. 11211-11216. by Naoki Sugimoto, Shu-Ichi Nakano, Misa Katoh, et al.Akiko Matsumura, Hiroyuki Nakamuta, Tatsuo Ohmichi, Mari Yoneyama, Muneo Sasaki posted to parameters_rna_dna by Hosna on 2009-05-24 16:53:43 as along with 1 group beta
	IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions [My Copy] Bioinformatics (21 October 2008), btn544. by Anke Busch, Andreas S. Richter, Rolf Backofen posted to data rna-rna rnai by Hosna on 2009-03-02 19:51:01 as along with 1 person druvus
	The impact of target site accessibility on the design of effective siRNAs [My Copy] Nature Biotechnology, Vol. 26, No. 5. (27 April 2008), pp. 578-583. by Hakim Tafer, Stefan L. Ameres, Gregor Obernosterer, et al.Christoph A. Gebeshuber, Renée Schroeder, Javier Martinez, Ivo L. Hofacker posted to design rna-rna rnai by Hosna on 2009-01-08 02:07:00 as along with 1 person guhjy
	Complex Riboswitches [My Copy] Science, Vol. 319, No. 5871. (28 March 2008), pp. 1795-1797. by Ronald R. Breaker posted to riboswitch by Hosna on 2009-01-08 00:42:23 as along with 4 people hrogers biomcgary sunhwan austin
	Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. [My Copy] Nucleic acids research (15 May 2008) by Zhi John J. Lu, David H H. Mathews posted to design rna-rna rnai by Hosna on 2009-01-08 00:34:59 as along with 2 people puranjoy_b guhjy
	Efficient siRNA selection using hybridization thermodynamics. [My Copy] Nucleic Acids Res, Vol. 36, No. 2. (February 2008), pp. 640-647. by Z. J. Lu, D. H. Mathews posted to rna-rna rnai by Hosna on 2008-12-29 02:19:22 as along with 3 people and 1 group puranjoy_b mtagaya guhjy beta
	OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. [My Copy] Nucleic acids research (19 May 2008) by Zhi John J. Lu, David H H. Mathews posted to rna-rna by Hosna on 2008-12-23 00:41:36 as along with 1 person and 1 group guhjy beta
	Predicting transmembrane beta-barrels and interstrand residue interactions from sequence [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 61-74. by J. Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert posted to protein supersecondary_structure by Hosna on 2008-10-22 23:40:17 as along with 1 group beta
	Predicting novel RNA-RNA interactions. [My Copy] Current opinion in structural biology (14 May 2008) by Irmtraud M M. Meyer posted to rna-rna secondary_structure_prediction by Hosna on 2008-10-22 22:48:12 as along with 2 people and 1 group zwang marck beta
	An Interactive Framework for RNA Secondary Structure Prediction with a Dynamical Treatment of Constraints [My Copy] Journal of Molecular Biology, Vol. 254, No. 2. (24 November 1995), pp. 163-174. by Christine Gaspin, Eric Westhof posted to dynamic_constraint rna_folding by Hosna on 2008-06-19 00:16:52 as along with 1 person eckart_bindewald
	Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. [My Copy] RNA (New York, N.Y.), Vol. 14, No. 6. (1 June 2008), pp. 1164-1173. by Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V. Demidov, Natalia E. Broude, Nikolay V. Dokholyan posted to 3d_structure non_hierarchical_folding by Hosna on 2008-06-19 00:13:28 as along with 3 people balewis carmaus physics
	Novel and efficient RNA secondary structure prediction using hierarchical folding. [My Copy] J Comput Biol, Vol. 15, No. 2. (March 2008), pp. 139-163. by H. Jabbari, A. Condon, S. Zhao posted to hfold hierarchical_folding kissing_hairpins mfe pseudoknot_prediction rna_folding secondary_structure_prediction by Hosna on 2008-06-18 23:00:40 as along with 2 people physics eskay

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rnai	41
data	39
wabi	30
rna_folding	25
pseudoknots	20
rna-rna	17
secondary_structure_prediction	17
hierarchical_folding	14
review	14
pseudoknot_prediction	10
hairpin_ribozyme	9
small_ribozyme	9
adp	8
multi_stable_rna	6
kissing_hairpins	5
parameters_dna_dna	5
partition_function	5
bayesian	4
parameter	4
thesis	4
3d_structure	3
ca	3
catalytic	3
co-transcriptional_folding	3
dsd	3
independent_set	3
large_rna_enzyme	3
mfe	3
rnase_p_rna	3
design	2
energy_model	2
heuristic	2
hfold	2
large_rna	2
non_hierarchical_folding	2
parameters_rna_dna	2
pseudoknot	2
rna_folding_path	2
tetrahymena_ribozyme	2
alzheimer	1
aptamer_selection	1
chemical_modification	1
clustering	1
covariation	1
dna	1
dynamic_constraint	1
estimation	1
example	1
fluorescence_resonance_energy_transfer	1
folding_models	1
hairpin_	1
microarray	1
multiple_sclerosis	1
nanotechnology	1
protein	1
pseudoknot-removal	1
riboswitch	1
sampling	1
snrna	1
stochastic_simulation	1
structure-function	1
supersecondary_structure	1

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