Craig Zirbel

Professor Emeritus

Email: zirbel@bgsu.edu
Address:
Department of Mathematics and Statistics
Bowling Green State University
Bowling Green, OH 43403-0206

Research Interests

• Probability theory; Applied probability
• RNA 3D structure and sequence variability
• Stochastic models of complex fluid flows
• Brownian flows, random measures, mass transport

Education

• Ph.D. Princeton University, 1993, Applied and Computational Mathematics. Advisor: Erhan Çinlar
• B.A. Illinois Wesleyan University, 1989, Mathematics and Physics.

Professional Experience

• Bowling Green State University, Department of Mathematics and Statistics, Assistant Professor, 1996-2001, Associate Professor 2001-2012, Professor 2012-2024, Professor Emeritus 2024-present
  
• University of Massachusetts, Department of Mathematics and Statistics, Visiting Assistant Professor, 1994-1996
• University of Minnesota, Institute for Mathematics and its Applications, Research Associate, 1993-1994.

Publications

RNA Bioinformatics and Probabilistic Modeling

(2024) R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species, by Sri Devan Appasamy, Craig L. Zirbel.  Published November 15, 2024 in Bioinformatics.

(2024) RNA three-dimensional structure drives the sequence organization of potato spindle tuber viroid quasispecies, by Jian Wu, Yuhong Zhang,Yuxin Nie, Fei Yan, Craig L. Zirbel, David M. Bisaro. Published April 4, 2024 in PLoS Pathogens.

(2023) The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids, by Catherine Lawson, Helen Berman, Li Chen, Brinda Vallat, Craig L. Zirbel.  Published November 11, 2023 in Nucleic Acids Research.

(2023) Anionic G•U pairs in bacterial ribosomal rRNAs, by Eric Westhof, Zoe Watson, Craig L. Zirbel, and Jamie Cate.  RNA. 2023 Jul;29(7):1069-1076.

(2023) Predicting the 3D Structure of RNA from Sequence, by James Roll and Craig L. Zirbel.  Published February 8, 2023 in Handbook of Chemical Biology of Nucleic Acids.  Springer.

(2022) Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey, by Craig L. Zirbel and Pascal Auffinger.  Published July 7, 2022 in Molecules.

(2022) Seriation Using Tree-Penalized Path Length, by Denis Aliyev and Craig L. Zirbel.  Published June 17, 2022 in the European Journal of Operational Research.

(2020) Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA, by Jian Wu, Cuiji Zhou, James Li, Chun Li, Xiaorong Tao, Neocles B Leontis, Craig L Zirbel, David M Bisaro, Biao Ding.  Published February 21, 2020 in Nucleic Acids Research.

(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.

(2016) 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

(2016) 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. 

(2015) 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) 

(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

(2015) 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.

(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

(2014) 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.

(2014) 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: 10.1093/nar/gkt980.

(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. (2013) 117 (46), pp 14302–14319.  DOI: 10.1021/jp408530w

(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, Nucl. Acids Res. (1 July 2013) 41 (W1): W15-W21. doi: 10.1093/nar/gkt417.

(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. 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 Research (2011).

(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.

(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) 17:1204-1212. 

(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) 4:252-256.

(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.

(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 6(1) 53-89.

(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.

(2009) 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 2294–2312.

(2009) 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.

(2008) 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.

Stochastic processes

(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.

Lagrangian Observations and random flows

(2021) Using symbolic expressions to get the Taylor expansion of the Lagrangian auto-covariance function, by Eduardo Schneider and Craig L. Zirbel.  Proceeding Series of the Brazilian Society of Computational and Applied Mathematics Volume 8, Number 1 (2021).

(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.

(2000) Markov velocity fields and the generalized Lagrangian velocity

(2000) Random velocity fields with known Lagrangian law (Poster from Courant Nonlinear Analysis 2000 conference)

(2000) Random velocity fields with known Lagrangian law (Slides from talk at TIES-SPRUCE 2000 conference)

Nonlinear Schrödinger Equation

(2000) A mean-field statistical theory for the nonlinear Schrödinger equation, with Richard Jordan and Bruce Turkington. Physica D 137, (2000), 353--378.

Brownian Flows

(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 Stochastic Processes and their Applications, Volume 70, Issue 1, 1 October 1997, Pages 1-29.

(1997) Mass transport by Brownian flows, with Erhan Çinlar. In Stochastic Models in Geosystems, 1997, pp 459-492.

(1997) Mean occupation times of continuous one-dimensional Markov processes. Stochastic Processes and their Applications 69, (1997), 161-178.

(1996) Dispersion of particle systems by Brownian flows, with Erhan Çinlar. Advances in Applied Probability 28, (1996), 53-74.

(1995) Random measures carried by Brownian flows on R^d

Ph.D. Dissertation

(1993) Stochastic Flows: Dispersion of a mass distribution and Lagrangian observations of a random field