Publications

All publications via Google Scholar

• Google scholar publication listing for Craig L. Zirbel
  

2018

• How to fold and protect mitochondrial ribosomal RNA with fewer guanines.     
  Hosseini M,  Roy P,  Sissler M,  Zirbel C. L,  Westhof E, Leontis N.
  Nucl. Acids Res. 2018 Sep 12. pii: gky762.

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 B. 117(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 Biology. 56, Nos. 1-2, January 2008. pdf.