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Publications

2016
  • JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.     
    Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
    Nucl. Acids Res. 2016 May 27. pii: gkw453.
  • The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.
    Parlea LG, Sweeney BA, Hosseini-Asanjan M, Zirbel CL, Leontis NB.
    Methods. 2016 Apr 25. pii: S1046-2023(16)30104-9. doi: 10.1016/j.ymeth.2016.04.025. PDF
2015
  • RNA 3D modules in genome-wide predictions of RNA 2D structure     
    Corinna Theis, Craig Zirbel, Christian Hoener zu Siederdissen, Christian Anthon, Ivo L. Hofacker, Henrik Nielsen, Jan Gorodkin.
    PLOS ONE. DOI:10.1371/journal.pone.0139900. 10(10): e0139900; Oct 28, 2015. PDF
  • Identifying novel sequence variants of RNA 3D motifs
    Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung and Neocles B. Leontis.
    Nucl. Acids Res. 3;43(15):7504-20; Sep, 2015.
  • R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server     
    Jamie J. Cannone, Blake A. Sweeney, Anton I. Petrov, Robin R. Gutell, Craig L. Zirbel and Neocles B. Leontis.
    Nucl. Acids Res. 43(W1):W15-23; Jul 01, 2015. 
  • An introduction to recurrent nucleotide interactions in RNA.     
    Sweeney BA, Roy P, Leontis NB.
    Wiley Interdiscip Rev RNA. 2015 Jan-Feb;6(1):17-45. Review.
2014
  • Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence
    Evgeny E. Akkuratov, Lorraine Walters, Arnab Saha-Mandal, Sushant Khandekar, Erin Crawford, Craig L. Zirbel, Scott Leisner, Ashwin Prakash, Larisa Fedorova, Alexei Fedorov.
    Gene. Volume 548, Issue 1, 10 September 2014, Pages 81–90
  • Chemistry. Self-assembled RNA nanostructures.
    Leontis NB, Westhof E.
    Science. 2014 Aug 15;345(6198):732-3. doi: 10.1126/science.1257989.
  • The Nucleic Acid Database: new features and capabilities
    Buvaneswari Coimbatore Narayanan, John Westbrook, Saheli Ghosh, Anton I. Petrov, Blake A. Sweeney, Craig L. Zirbel, Neocles B. Leontis and Helen M. Berman
    Nucl. Acids Res. 42(Database issue):D114-22; Jan, 2014.
2013
  • Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop
    Havrila M, Réblov á  K, Zirbel CL, Leontis B, Šponer J.
    J. Phys. Chem B117(46):14302-19; Nov 21, 2013.  
  • Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
    Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis.
    RNA. 1327-1340; Oct 19, 2013.
  • RNA nanotechnology for computer design and in vivo computation
    Qiu M, Khisamutdinov E, Zhao Z, Pan C, Choi JW, Leontis NB, Guo P.
    Philos Trans A Math Phys Eng Sci. 2013 Sep 2;371(2000):20120310. doi: 10.1098/rsta.2012.0310. Print 2013 Oct 13.
  • Conference Scene: Advances in RNA nanotechnology promise to transform medicine.
    Leontis N, Sweeney B, Haque F, Guo P
    Nanomedicine (Lond). 2013 Jul;8(7):1051-4. doi: 10.2217/nnm.13.105.
  • 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 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417. 
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; 2012 Apr 7.
  • RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.
    NCruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E.
    RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23.
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
    Nucl. Acids Res. DOI: 10.1093/nar/gkr810. Publication Date: November 03, 2011.
  • 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. 2011;6(1) 53-89.
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.