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Hosna's library [155 articles]

Recent papers added to Hosna's library ordered by importance.
  • From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
    RNA, Vol. 14, No. 3. (1 March 2008), pp. 410-416.
    by Sandra Smit, Kristian Rother, Jaap Heringa, Rob Knight
    posted to independent_set pseudoknot-removal by Hosna on 2008-04-18 20:17:41 as *****
  • New clique and independent set algorithms for circle graphs
    Discrete Applied Mathematics, Vol. 36, No. 1. (30 March 1992), pp. 1-24.
    by Alberto Apostolico, Mikhail J Atallah, Susanne E Hambrusch
    posted to independent_set by Hosna on 2008-04-18 20:05:17 as *****
  • Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA
    RNA (24 October 2007), rna.676707.
    by Gang Chen, Jin-Der Wen, Ignacio Tinoco
    posted to rna_folding_path by Hosna on 2007-11-15 22:40:04 as *****
  • Antisense RNAs everywhere?
    Trends in Genetics, Vol. 18, No. 5. (1 May 2002), pp. 223-226.
    by Wagner, Klas Flardh
    posted to rnai by Hosna on 2007-10-26 20:54:40 as *****
  • The role of site accessibility in microRNA target recognition
    Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1278-1284.
    by Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran Segal
    posted to rnai by Hosna on 2007-10-24 00:10:41 as ***** along with 13 people and 1 group mtagaya rdiaz djkt Garamonfok physics bootsy epigenetics lp2 cabbagezs heliopais uwe yavanna maralena microRNA
  • Fast and effective prediction of microRNA/target duplexes.
    RNA, Vol. 10, No. 10. (October 2004), pp. 1507-1517.
    by M Rehmsmeier, P Steffen, M Hochsmann, R Giegerich
    posted to rnai by Hosna on 2007-10-21 22:39:33 as ***** along with 4 people and 1 group eckart_bindewald mortenlindow mtagaya maralena microRNA
  • Thermodynamic Analysis of Interacting Nucleic Acid Strands
    SIAM Review, Vol. 49, No. 1. (2007), pp. 65-88.
    by Robert M Dirks, Justin S Bois, Joseph M Schaeffer, Erik Winfree, Niles A Pierce
    posted to rnai rna-rna by Hosna on 2007-10-16 00:33:15 as ***** along with 1 person stsaft
  • Space and Time Efficient Algorithms to Discover Endogenous RNAi Patterns in Complete Genome Data
    Bioinformatics Research and Applications (2007), pp. 260-269.
    by Sudha Balla, Sanguthevar Rajasekaran
    posted to rnai by Hosna on 2007-10-09 19:34:05 as *****
  • Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
    BMC Bioinformatics, Vol. 7 (27 November 2006), 516.
    by Wuming Gong, Yongliang Ren, Qiqi Xu, Yejun Wang, Dong Lin, Haiyan Zhou, Tongbin Li
    posted to rnai by Hosna on 2007-10-09 19:32:27 as ***** along with 2 people puranjoy_b tardigrade
  • OptiRNAi, an RNAi design tool
    Computer Methods and Programs in Biomedicine, Vol. 75, No. 1. (July 2004), pp. 67-73.
    by Wenwu Cui, Jianchang Ning, Ulhas P Naik, Melinda K Duncan
    posted to rnai by Hosna on 2007-10-09 19:27:34 as *****
  • A DNA vector-based RNAi technology to suppress gene expression in mammalian cells
    Proceedings of the National Academy of Sciences, Vol. 99, No. 8. (16 April 2002), pp. 5515-5520.
    by Guangchao Sui, Christina Soohoo, El B Affar, Frederique Gay, Yujiang Shi, William C Forrester, Yang Shi
    posted to rnai by Hosna on 2007-10-09 19:23:57 as ***** along with 1 person clearbluespring
  • Killing the messenger: short RNAs that silence gene expression.
    Nat Rev Mol Cell Biol, Vol. 4, No. 6. (June 2003), pp. 457-467.
    by DM Dykxhoorn, CD Novina, PA Sharp
    posted to rnai rna-rna by Hosna on 2007-10-09 19:16:30 as *****
  • RNA-RNA interaction prediction and antisense RNA target search.
    J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 267-282.
    by C Alkan, E Karakoç, JH Nadeau, SC Sahinalp, K Zhang
    posted to rnai rna-rna by Hosna on 2007-10-09 19:06:25 as *****
  • Predicting oligonucleotide affinity to nucleic acid targets.
    RNA, Vol. 5, No. 11. (November 1999), pp. 1458-1469.
    by DH Mathews, ME Burkard, SM Freier, JR Wyatt, DH Turner
    posted to rnai rna-rna by Hosna on 2007-10-09 18:57:58 as ***** along with 1 person stsaft
  • From RNAi to Epigenomes: How RNA Rules The World
    ChemBioChem, Vol. 6, No. 2. (2005), pp. 441-443.
    by Eric Westhof, Witold Filipowicz
    posted to rnai rna-rna by Hosna on 2007-10-08 20:22:18 as ***** along with 1 person Scis0000002
  • A dynamic programming algorithm for RNA structure prediction including pseudoknots.
    J Mol Biol, Vol. 285, No. 5. (5 February 1999), pp. 2053-2068.
    by E Rivas, SR Eddy
    posted to energy_model pseudoknot_prediction by Hosna on 2007-04-03 21:41:39 as ***** along with 9 people and 1 group evaf balajis eckart_bindewald arcticrasta dquest condon jarasch physics guxiyou beta
  • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
    RNA, 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 2 people carmaus physics
  • A New Simple Algorithm for the Maximum-Weight Independent Set Problem on Circle Graphs
    Algorithms and Computation (2003), pp. 129-137.
    by Gabriel Valiente
    posted to independent_set by Hosna on 2008-04-11 22:27:36 as **** along with 1 person ima
  • 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 heuristic pseudoknot_prediction by Hosna on 2008-03-26 22:26:08 as **** along with 2 people condon physics
  • Variations on RNA folding and alignment: lessons from Benasque
    Journal of Mathematical Biology, Vol. 56, No. 1. (24 January 2008), pp. 129-144.
    by Athanasius Bompfünewerer, Rolf Backofen, Stephan Bernhart, Jana Hertel, Ivo Hofacker, Peter Stadler, Sebastian Will
    posted to rna-rna by Hosna on 2007-12-13 23:27:53 as ****
  • The computer simulation of RNA folding pathways using a genetic algorithm.
    J Mol Biol, Vol. 250, No. 1. (30 June 1995), pp. 37-51.
    by AP Gultyaev, FH van Batenburg, CW Pleij
    posted to parameter secondary_structure_prediction by Hosna on 2007-11-21 21:04:49 as **** along with 2 people and 1 group condon guxiyou beta
  • Impact of RNA interference on gene networks.
    Metab Eng (4 August 2006)
    by Laetitia Malphettes, Martin Fussenegger
    posted to rnai by Hosna on 2007-10-16 01:34:29 as **** along with 3 people and 2 groups bala tardigrade andersbj microRNA DictyosteliumGroup
  • Genomic approaches to drug discovery
    Current Opinion in Chemical Biology, Vol. 10, No. 4. (August 2006), pp. 303-308.
    by Darrell O Ricke, Shaowen Wang, Richard Cai, Dalia Cohen
    posted to rnai by Hosna on 2007-10-16 01:31:32 as **** along with 1 person tardigrade
  • Beyond Mfold: Recent advances in RNA bioinformatics.
    J Biotechnol (9 March 2006)
    by Jens Reeder, Matthias Höchsmann, Marc Rehmsmeier, Björn Voss, Robert Giegerich
    posted to rnai by Hosna on 2007-10-16 01:26:03 as **** along with 12 people and 4 groups marcius eckart_bindewald tardigrade andersbj arcticrasta mtagaya condon Eonwe cthachuk stajich physics reyez microRNA beta BioinfoCIPF SGU-CIPF
  • RNAi and microRNAs: from animal models to disease therapy.
    Birth Defects Res C Embryo Today, Vol. 78, No. 2. (June 2006), pp. 150-171.
    by A Fjose, O Drivenes
    posted to rnai by Hosna on 2007-10-16 01:14:57 as **** along with 1 person tardigrade
  • Running Interference: Prospects and Obstacles to Using Small Interfering RNAs as Small Molecule Drugs.
    Annu Rev Biomed Eng (29 June 2005)
    by Derek M M Dykxhoorn, Judy Lieberman
    posted to rnai by Hosna on 2007-10-16 01:11:18 as **** along with 2 people eckart_bindewald tardigrade
  • RNA interference as a gene-specific approach for molecular medicine.
    Curr Med Chem, Vol. 12, No. 26. (2005), pp. 3143-3161.
    by A Grünweller, RK Hartmann
    posted to rnai by Hosna on 2007-10-16 01:08:40 as **** along with 2 people tardigrade tabu
  • Cell microarrays and RNA interference chip away at gene function.
    Nat Genet, Vol. 37 Suppl (June 2005)
    by DB Wheeler, AE Carpenter, DM Sabatini
    posted to rnai by Hosna on 2007-10-16 01:03:19 as **** along with 2 people jyuh textoris
  • A brief history of RNAi: the silence of the genes.
    FASEB J, Vol. 20, No. 9. (July 2006), pp. 1293-1299.
    by GL Sen, HM Blau
    posted to rnai by Hosna on 2007-10-16 01:02:15 as **** along with 8 people and 2 groups bala tkershaw tardigrade mgantier Fritz adalb_decode srfairclough epigenetics neurolit DictyosteliumGroup
  • Perspective: machines for RNAi
    Genes Dev., Vol. 19, No. 5. (1 March 2005), pp. 517-529.
    by Yukihide Tomari, Phillip D Zamore
    posted to rnai by Hosna on 2007-10-16 01:00:04 as **** along with 2 people ttjoseph shuzhens
  • Enhancing and confirming the specificity of RNAi experiments
    Nature Methods, Vol. 3, No. 9. (23 August 2006), pp. 677-681.
    by Bryan R Cullen
    posted to rnai by Hosna on 2007-10-16 00:57:46 as **** along with 7 people and 3 groups jyuh ecattell tardigrade dchughes Fritz Verena isera G4ID neurolit Genetics-of-Gambling
  • Unlocking the potential of the human genome with RNA interference
    Nature, Vol. 431, No. 7006. (2004), pp. 371-378.
    by Gregory J Hannon, John J Rossi
    posted to rnai by Hosna on 2007-10-16 00:55:51 as **** along with 2 people and 1 group xtizon Fritz neurolit
  • RNA interference: its use as antiviral therapy.
    Handb Exp Pharmacol, No. 173. (2006), pp. 117-150.
    by J Haasnoot, B Berkhout
    posted to rnai by Hosna on 2007-10-16 00:53:45 as **** along with 2 people tardigrade zyb301214
  • Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosak virus RNA
    Nucl. Acids Res., Vol. 13, No. 21. (11 November 1985), pp. 7673-7686.
    by Alex Belkum, Jan P Abrahams, Cornelis W Pleij, Leendert Bosch
    posted to pseudoknots data by Hosna on 2007-01-22 20:50:45 as ****
  • 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 pseudoknots data by Hosna on 2007-01-22 20:44:21 as **** along with 1 person and 1 group condon beta
  • Secondary Structure of Vertebrate Telomerase RNA
    Cell, Vol. 100, No. 5. (3 March 2000), pp. 503-514.
    by Jiunn-Liang Chen, Maria A Blasco, Carol W Greider
    posted to pseudoknots data by Hosna on 2007-01-22 20:42:02 as **** along with 1 person aredash
  • The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase
    J. Virol., Vol. 71, No. 8. (1 August 1997), pp. 5990-5996.
    by Ba Deiman, Rm Kortlever, Cw Pleij
    posted to pseudoknots data by Hosna on 2007-01-22 20:38:30 as ****
  • 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 data by Hosna on 2007-01-22 20:34:05 as **** along with 2 people and 1 group condon physics beta
  • PseudoBase: a database with RNA pseudoknots
    Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 201-204.
    by FHD van Batenburg, AP Gultyaev, CWA Pleij, J Ng, J Oliehoek
    posted to pseudoknots data by Hosna on 2007-01-20 02:14:50 as **** along with 3 people and 3 groups marcius arcticrasta condon beta BioinfoCIPF SGU-CIPF
  • The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
    RNA (New York, N.Y.) (27 March 2008)
    by Zasha Weinberg, Elizabeth E E Regulski, Ming C C Hammond, Jeffrey E E Barrick, Zizhen Yao, Walter L L Ruzzo, Ronald R R Breaker
    posted to pseudoknots by Hosna on 2008-04-22 22:19:40 as ***
  • Efficient parameter estimation for RNA secondary structure prediction.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by Mirela Andronescu, Anne Condon, Holger H H Hoos, David H H Mathews, Kevin P P Murphy
    posted to estimation parameter by Hosna on 2007-12-19 19:44:23 as *** along with 2 groups Bioinformatics beta
  • The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases
    RNA, Vol. 12, No. 7. (1 July 2006), pp. 1149-1153.
    by Norma M Wills, John F Atkins
    posted to alzheimer pseudoknot by Hosna on 2007-05-08 01:14:12 as ***
  • PseudoBase: structural information on RNA pseudoknots.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 194-195.
    by FH van Batenburg, AP Gultyaev, CW Pleij
    posted to data pseudoknots wabi by Hosna on 2007-01-22 19:48:26 as *** along with 1 person and 1 group condon beta
  • The Ribonuclease P Database
    Nucl. Acids Res., Vol. 27, No. 1. (1 January 1999), 314.
    by Jw Brown
    posted to pseudoknots data by Hosna on 2007-01-22 19:32:58 as *** along with 2 people and 1 group arcticrasta condon beta
  • Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res, Vol. 26, No. 1. (1 January 1998), pp. 148-153.
    by M Sprinzl, C Horn, M Brown, A Ioudovitch, S Steinberg
    posted to data pseudoknots wabi by Hosna on 2007-01-22 19:27:06 as *** along with 2 people and 1 group evaf condon beta
  • Equilibrium Unfolding Pathway of an H-type RNA Pseudoknot which Promotes Programmed 1 Ribosomal Frameshifting
    pp. 1283-1299.
    by CA Theimer
    posted to pseudoknots data by Hosna on 2007-01-22 00:02:06 as ***
  • Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function.
    Mol Cell, Vol. 17, No. 5. (4 March 2005), pp. 671-682.
    by CA Theimer, CA Blois, J Feigon
    posted to pseudoknots data by Hosna on 2007-01-21 23:55:39 as *** along with 2 people bpagano physics
  • Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA
    PNAS, Vol. 100, No. 2. (21 January 2003), pp. 449-454.
    by Carla A Theimer, David L Finger, Lukas Trantirek, Juli Feigon
    posted to pseudoknots data by Hosna on 2007-01-21 23:49:49 as ***
  • Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot
    pp. 545-564.
    by CA Theimer
    posted to pseudoknots data by Hosna on 2007-01-21 23:28:28 as ***
  • Thermodynamics of Folding of the RNA Pseudoknot of the T4 Gene 32 Autoregulatory Messenger RNA
    Biochemistry, Vol. 35, No. 13. (2 April 1996), pp. 4176-4186.
    by H Qiu, K Kaluarachchi, Z Du, DW Hoffman, DP Giedroc
    posted to pseudoknots data by Hosna on 2007-01-21 23:23:04 as ***
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