Publication list at scholar.google.com
(2013) The nucleic acid database: new features and
capabilities, by Buvaneswari Coimbatore Narayanan, John
Westbrook, Saheli Ghosh, Anton I. Petrov, Blake Sweeney,
Craig L. Zirbel, Neocles B. Leontis and Helen M. Berman.
Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt980. Published
October 31, 2013.
(2013) Isosteric and Non-Isosteric Base Pairs in RNA Motifs:
Molecular Dynamics and Bioinformatics Study of the
Sarcin-Ricin Internal Loop, by Marek Havrila, Kamila Reblova,
Craig L. Zirbel, Neocles B. Leontis, and Jiri Sponer.
Journal of Physical Chemistry B. Published online October
(2013) Automated classification of RNA 3D motifs and the RNA
3D Motif Atlas, by Anton I. Petrov, Craig L. Zirbel, and
Neocles B. Leontis. RNA. Published online August 22, 2013.
(2013) R3D Align web server for global nucleotide to
nucleotide alignments of RNA 3D structures, by Ryan R.
Rahrig, Anton I. Petrov, Neocles B. Leontis, and Craig L.
Zirbel, Nucleic Acids Research Advance Access published May
(2012) Nonredundant 3D Structure Datasets for RNA Knowledge
Extraction and Benchmarking, by Neocles Leontis and Craig L.
Zirbel, in RNA 3D Structure Analysis and
Prediction, edited by Neocles Leontis and Eric Westhof.
pdf of the entire book, see Chapter 13.
(2011) Comprehensive survey and geometric classification of
base triples in RNA structures, by
Amal S. Abu Almakarem, Anton I. Petrov, Jesse Stombaugh,
Craig L. Zirbel, Neocles B. Leontis. Nucleic Acids
(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, by 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) Sharing and archiving
nucleic acid structure mapping
data, by 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)
(2011) Meeting report of the RNA Ontology Consortium January
8-9, 2011, by
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)
(2011) 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.
(2011) The RNA Ontology (RNAO): An Ontology for
Integrating RNA Sequence and Structure Data, by 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
(2010) R3D Align: Global pairwise alignment of RNA 3D
structures using local superpositions, by Ryan R. Rahrig,
Neocles B. Leontis, Craig L. Zirbel. Bioinformatics (2010) 26 (21): 2689-2697.
(2009) The RNA Ontology (RNAO): An Ontology for Integrating
RNA Sequence and Structure Data, by 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.
(2009) Understanding sequence variability of RNA motifs using
geometric search and isodiscrepancy matrices, by Anton I. Petrov, Jesse Stombaugh, Craig L. Zirbel, Neocles B. Leontis.
Proceedings of the 2009 OCCBIO Conference on Bioinformatics.
(2009) Classification and energetics of the base-phosphate
interactions in RNA, by Craig L. Zirbel, Judit E. Sponer,
Jiri Sponer, Jesse Stombaugh, Neocles B. Leontis, Nucleic
Acids Research (2009) 37, No.
15, pages 4898-4918.
Frequency and isostericity of RNA base pairs, by Jesse Stombaugh,
Craig L. Zirbel, Eric Westhof, Neocles B. Leontis.
Nucleic Acids Research
(2009) 37, No. 7, pages
RNA 3D Structural Motifs: Definition, Identification, Annotation, and
Database Searching, by 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, by Michael Sarver, Craig L. Zirbel, Jesse Stombaugh, Ali
Mokdad, Neocles B. Leontis. Journal of Mathematical Biology. 56, Nos. 1-2, January 2008.
(2013) On the correlation of the supremum
and the infimum and of maximum gain and maximum loss of Brownian
motion with drift, with Ceren Vardar-Acar and Gábor J. Székely.
Journal of Computational and Applied Mathematics 248,
15 August 2013, Pages 61–75.
(2003) Discrete velocity fields with explicitly computable Lagrangian law, with Curtis D. Bennett. Journal of Statistical Physics 111 (2003) 681--701.
(2001) Lagrangian observations of homogeneous random environments, Advances in Applied Probability 33 (2001) 810--835. ps pdf
(2000) Markov velocity fields and the generalized Lagrangian velocity ps pdf
(2000) Random velocity fields with known Lagrangian law (Poster from Courant Nonlinear Analysis 2000 conference) ps pdf
(2000) Random velocity fields with known Lagrangian law (Slides from talk at TIES-SPRUCE 2000 conference) ps pdf
(2000) A mean-field statistical theory for the nonlinear Schrödinger equation, with Richard Jordan and Bruce Turkington. Physica D 137, (2000), 353--378. Preprint
(2002) Rotation of particles in polarized Brownian flows, with Wojbor A. Woyczynski. Stochastics and Dynamics 2 (2002) 109--129.
(1997) Translation and dispersion of mass by isotropic Brownian flows ps pdf
(1997) Mass transport by Brownian flows, with Erhan
Çinlar ps pdf
(1997) Mean occupation times of continuous one-dimensional Markov processes ps pdf
(1996) Dispersion of particle systems by Brownian flows, with Erhan
Çinlar ps pdf
(1995) Random measures carried by Brownian flows on R^d ps pdf
(1993) Stochastic Flows: Dispersion of a mass distribution and Lagrangian observations of a random field pdf format