Publications

Table of Contents

2013

  • 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

2012

  • 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

2011

      • 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.

2010

    • 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.