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Publications

  • Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
    Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis
    RNA October 2013 19: 1327-1340; Published in Advance August 22, 2013.
  • R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures
    Ryan Rahrig, Anton I. Petrov, Neocles Leontis, Craig L. Zirbel
    Nucl. Acids Res. (2013), Web Server Issue
  • Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking
    Neocles Leontis and Craig L. Zirbel
    In N. Leontis & E. Westhof (Eds.), (Vol. 27, pp. 281–298). Springer Berlin Heidelberg. doi:10.1007/978-3-642-25740-7_13
  • Comprehensive survey and geometric classification of base triples in RNA structures
    Amal S. Abu Almakarem · Anton I. Petrov · Jesse Stombaugh · Craig L. Zirbel · Neocles B. Leontis
    Nucleic Acids Research
  • Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base – phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations
    M. Zgarbova · P. Jurecka · P. Banas · M. Otyepka · J.E. Sponer · N.B. Leontis · C.L. Zirbel · J. Sponer
    J. Phys. Chem. A. DOI: 10.1021/jp204820b. Publication Date (Web): September 12, 2011. pdf.
  • Sharing and archiving nucleic acid structure mapping data
    Philippe Rocca-Serra · Stanislav Bellaousov · Amanda Birmingham · Chunxia Chen · Pablo Cordero · Rhiju Das · Lauren Davis-Neulander · Caia Duncan · Matthew Halvorsen · Rob Knight · Neocles Leontis · David H. Mathews · Justin Ritz · Jesse Stombaugh · Kevin Weeks · Craig Zirbel · Alain Laederach
    RNA (2011) 17:1204-1212. pdf.
  • Meeting report of the RNA Ontology Consortium January 8-9, 2011
    Amanda Birmingham · Jose C. Clemente · Narayan Desai · Jack Gilbert · Antonio Gonzalez · Nikos Kyrpides · Folker Meyer · Eric Nawrocki · Peter Sterk · Jesse Stombaugh · Zasha Weinberg · Doug Wendel · Neocles B. Leontis · Craig Zirbel · Rob Knight · Alain Laederach
    Standards in Genomic Sciences (2011) 4:252-256. pdf.
  • WebFR3D – a server for finding, aligning and analyzing recurrent RNA 3D motifs
    Anton I. Petrov · Craig L. Zirbel · Neocles B. Leontis
    Nucleic Acids Research, 2011. pdf.
  • The RNA Ontology (RNAO):  An Ontology for Integrating RNA Sequence and Structure Data
    Robert Hoehndorf · Colin Batchelor · Thomas Bittner · Michel Dumontier · Karen Eilbeck · Rob Knight · Chris J. Mungall · Jane S. Richardson · Jesse Stombaugh · Eric Westhof · Craig L. Zirbel  · Neocles B. Leontis
    Applied Ontology 6(1) 53-89. pdf.
  • R3D Align: Global pairwise alignment of RNA 3D structures using local superpositions
    Ryan R. Rahrig · Neocles B. Leontis · Craig L. Zirbel
    Bioinformatics (2010) 26 (21): 2689-2697.
  • The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data
    Colin Batchelor · Thomas Bittner · Karen Eilbeck · Chris Mungall · Jane Richardson · Rob Knight · Jesse Stombaugh · Craig Zirbel · Eric Westhof · Neocles Leontis
    Proceedings of the International Conference on Biomedical Ontology, August 2009, pages 7-10.  pdf.
  • Understanding sequence variability of RNA motifs using geometric search and isodiscrepancy matrices
    Anton I. Petrov · Jesse Stombaugh · Craig L. Zirbel · Neocles B. Leontis
    Proceedings of the 2009 OCCBIO Conference on Bioinformatics.  pdf.
  • Classification and energetics of the base-phosphate interactions in RNA
    Craig L. Zirbel · Judit E. Sponer · Jiri Sponer · Jesse Stombaugh · Neocles B. Leontis
    Nucleic Acids Research (2009) 37, No. 15, pages 4898-4918.  pdf.
  • Frequency and isostericity of RNA base pairs
    Jesse Stombaugh · Craig L. Zirbel · Eric Westhof · Neocles B. Leontis
    Nucleic Acids Research (2009) 37, No. 7, pages 2294–2312. pdf.
  • RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching
    Lorena Nasalean · Jesse Stombaugh · Craig L. Zirbel · Neocles B. Leontis
    In Non-Protein Coding RNAs, Springer Series in Biophysics , Vol. 13, pp. 1-26. Walter, Nils G.; Woodson, Sarah A.; Batey, Robert T. (Eds.) 2009. google books preview
  • FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures
    Michael Sarver · Craig L. Zirbel · Jesse Stombaugh · Ali Mokdad · Neocles B. Leontis
    Journal of Mathematical Biology56, Nos. 1-2, January 2008. pdf.