BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

179 related articles for article (PubMed ID: 33002005)

  • 1. RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis.
    Gumna J; Zok T; Figurski K; Pachulska-Wieczorek K; Szachniuk M
    PLoS One; 2020; 15(10):e0239287. PubMed ID: 33002005
    [TBL] [Abstract][Full Text] [Related]  

  • 2. RNAProbe: a web server for normalization and analysis of RNA structure probing data.
    Wirecki TK; Merdas K; Bernat A; Boniecki MJ; Bujnicki JM; Stefaniak F
    Nucleic Acids Res; 2020 Jul; 48(W1):W292-W299. PubMed ID: 32504492
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.
    Lee S; Kim H; Tian S; Lee T; Yoon S; Das R
    Bioinformatics; 2015 Sep; 31(17):2808-15. PubMed ID: 25943472
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Automated RNA 3D Structure Prediction with RNAComposer.
    Biesiada M; Purzycka KJ; Szachniuk M; Blazewicz J; Adamiak RW
    Methods Mol Biol; 2016; 1490():199-215. PubMed ID: 27665601
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Computational analysis of RNA structures with chemical probing data.
    Ge P; Zhang S
    Methods; 2015 Jun; 79-80():60-6. PubMed ID: 25687190
    [TBL] [Abstract][Full Text] [Related]  

  • 6. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.
    Li Y; Shi X; Liang Y; Xie J; Zhang Y; Ma Q
    BMC Bioinformatics; 2017 Jan; 18(1):51. PubMed ID: 28109252
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
    Wu Y; Shi B; Ding X; Liu T; Hu X; Yip KY; Yang ZR; Mathews DH; Lu ZJ
    Nucleic Acids Res; 2015 Sep; 43(15):7247-59. PubMed ID: 26170232
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.
    von Löhneysen S; Spicher T; Varenyk Y; Yao HT; Lorenz R; Hofacker I; Stadler PF
    J Comput Biol; 2024 Jun; 31(6):549-563. PubMed ID: 38935442
    [TBL] [Abstract][Full Text] [Related]  

  • 9. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.
    Piatkowski P; Kasprzak JM; Kumar D; Magnus M; Chojnowski G; Bujnicki JM
    Methods Mol Biol; 2016; 1490():217-35. PubMed ID: 27665602
    [TBL] [Abstract][Full Text] [Related]  

  • 10. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.
    Reeder J; Steffen P; Giegerich R
    Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W320-4. PubMed ID: 17478505
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools.
    Kielpinski LJ; Sidiropoulos N; Vinther J
    Methods Enzymol; 2015; 558():153-180. PubMed ID: 26068741
    [TBL] [Abstract][Full Text] [Related]  

  • 12. INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.
    Busch A; Backofen R
    Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W310-3. PubMed ID: 17452349
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Computational approaches for RNA energy parameter estimation.
    Andronescu M; Condon A; Hoos HH; Mathews DH; Murphy KP
    RNA; 2010 Dec; 16(12):2304-18. PubMed ID: 20940338
    [TBL] [Abstract][Full Text] [Related]  

  • 14. StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.
    Tack DC; Tang Y; Ritchey LE; Assmann SM; Bevilacqua PC
    Methods; 2018 Jul; 143():12-15. PubMed ID: 29410279
    [TBL] [Abstract][Full Text] [Related]  

  • 15. iFoldRNA v2: folding RNA with constraints.
    Krokhotin A; Houlihan K; Dokholyan NV
    Bioinformatics; 2015 Sep; 31(17):2891-3. PubMed ID: 25910700
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Crumple: An Efficient Tool to Explore Thoroughly the RNA Folding Landscape.
    Guerra I; Schroeder SJ
    Methods Mol Biol; 2016; 1490():1-14. PubMed ID: 27665589
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Modeling RNA secondary structure folding ensembles using SHAPE mapping data.
    Spasic A; Assmann SM; Bevilacqua PC; Mathews DH
    Nucleic Acids Res; 2018 Jan; 46(1):314-323. PubMed ID: 29177466
    [TBL] [Abstract][Full Text] [Related]  

  • 18. StructRNAfinder: an automated pipeline and web server for RNA families prediction.
    Arias-Carrasco R; Vásquez-Morán Y; Nakaya HI; Maracaja-Coutinho V
    BMC Bioinformatics; 2018 Feb; 19(1):55. PubMed ID: 29454313
    [TBL] [Abstract][Full Text] [Related]  

  • 19. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.
    Washietl S; Hofacker IL; Stadler PF; Kellis M
    Nucleic Acids Res; 2012 May; 40(10):4261-72. PubMed ID: 22287623
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.
    Washietl S; Bernhart SH; Kellis M
    Methods Mol Biol; 2014; 1097():125-41. PubMed ID: 24639158
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.