Publication list at scholar.google.com
RNA Bioinformatics and Probabilistic Modeling
(2019) A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana, by Jian Wu, Neocles B. Leontis, Craig L. Zirbel, David M. Bisaro, Biao Ding.
Published October 23, 2019 in PLoS Pathogens.
(2018) How to fold and protect mitochondrial ribosomal RNA with fewer guanines,
by Maryam Hosseini, Poorna Roy, Marie Sissler, Craig L. Zirbel, Eric Westhof and Neocles Leontis.
Published September 12, 2018 in Nucleic Acids Research.
(2018) Allelic RNA Motifs in Regulating Systemic Trafficking of Potato Spindle Tuber Viroid,
by R. Takeda, Craig L. Zirbel, Neocles B. Leontis, Ying Wang, and Biao Ding.
Viruses 30, E160-171 (2018). PMC 5923454
(2018) RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution,
by Ying Wang, Craig L. Zirbel, Neocles B. Leontis, Biao Ding.
PLOS Pathogens Pearl series, February 22, 2018.
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs,
by James Roll, Craig L. Zirbel, Blake Sweeney, Anton I. Petrov and Neocles Leontis. Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw453
The RNA 3D Motif Atlas: Computational Methods for Extraction,
Organization and Evaluation of RNA Motifs, by Lorena G Parlea, Blake
S Sweeney, Maryam Hosseini Asanjan, Craig L Zirbel, Neocles B.
Leontis. Methods, April 2016.
Detecting conformational differences between RNA 3D Structures,
by Ryan R. Rahrig and Craig L. Zirbel. JP Journal of Biostatistics,
Volume 12, Issue 2 (December 2015)
Identifying novel sequence variants of RNA 3D motifs, by
Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis.
Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv651
RNA 3D modules in genome-wide predictions of RNA 2D structure,
by Corinna Theis, Craig Zirbel, Christian Hoener zu Siederdissen,
Christian Anthon, Ivo L. Hofacker, Henrik Nielsen, Jan Gorodkin.
PLoS ONE 10(10): e0139900. doi:10.1371/journal.pone.0139900.
Published October 28, 2015.
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server, by
Jamie J. Cannone, Blake A. Sweeney, Anton I. Petrov, Robin R. Gutell, Craig L. Zirbel and Neocles Leontis.
Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv543
Bioinformatics analysis of plant orthologous introns:
identification of an intronic tRNA-like sequence, by Evgeny
E. Akkuratov, Lorraine Walters, Arnab Saha-Mandal, Sushant
Khandekar, Erin Crawford, Craig L. Zirbel, Scott Leisner,
Ashwin Prakash, Larisa Fedorova, Alexei Fedorov. Gene (2014)
Volume 548, Issue 1, 10 September 2014, Pages 81–90.
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. (1 January 2014) 42 (D1): D114-D122. doi:
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. (2013) 117 (46), pp
14302–14319. DOI: 10.1021/jp408530w
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.
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, Nucl. Acids Res. (1 July 2013) 41 (W1): W15-W21.
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.
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
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,
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)
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)
WebFR3D - a server for finding, aligning and analyzing recurrent RNA 3D motifs,
by Anton I. Petrov, Craig L. Zirbel, Neocles B. Leontis. Nucleic Acids Research, 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
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.
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.
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.
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.
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.
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.
Discrete velocity fields with explicitly computable Lagrangian law, with Curtis D. Bennett. Journal of Statistical Physics 111 (2003) 681--701.
Lagrangian observations of homogeneous random environments, Advances in Applied Probability 33 (2001) 810--835.
Markov velocity fields and the generalized Lagrangian velocity
Random velocity fields with known Lagrangian law (Poster from Courant Nonlinear Analysis 2000 conference)
Random velocity fields with known Lagrangian law (Slides from talk at TIES-SPRUCE 2000 conference)
Nonlinear Schrödinger Equation
A mean-field statistical theory for the nonlinear Schrödinger equation, with Richard Jordan and Bruce Turkington. Physica D 137, (2000), 353--378.
Rotation of particles in polarized Brownian flows, with Wojbor A. Woyczynski. Stochastics and Dynamics 2 (2002) 109--129.
Translation and dispersion of mass by isotropic Brownian flows
Stochastic Processes and their Applications, Volume 70, Issue 1, 1 October 1997, Pages 1-29.
Mass transport by Brownian flows, with Erhan Çinlar.
In Stochastic Models in Geosystems, 1997, pp 459-492.
Mean occupation times of continuous one-dimensional Markov processes.
Stochastic Processes and their Applications 69, (1997), 161-178.
Dispersion of particle systems by Brownian flows, with Erhan Çinlar.
Advances in Applied Probability 28, (1996), 53-74.
Random measures carried by Brownian flows on R^d
Stochastic Flows: Dispersion of a mass distribution and Lagrangian observations of a random field