Craig L. Zirbel

发表

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

Ryan R. Rahrig, Anton I. Petrov, Neocles Leontis, 2013, Nucleic Acids Res..

Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking

Craig L. Zirbel, Neocles B. Leontis, N. Leontis, 2012 .

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

Jamie J. Cannone, Robin Ray Gutell, Anton I. Petrov, 2015, Nucleic Acids Res..

On the correlation of the supremum and the infimum and of maximum gain and maximum loss of Brownian motion with drift

Gábor J. Székely, Craig L. Zirbel, Ceren Vardar-Acar, 2013, J. Comput. Appl. Math..

The Nucleic Acid Database: new features and capabilities

John D. Westbrook, Helen M. Berman, Anton I. Petrov, 2013, Nucleic Acids Res..

WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs

Anton I. Petrov, Neocles Leontis, Craig L. Zirbel, 2011, Nucleic Acids Res..

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs

Anton I. Petrov, Neocles Leontis, Craig L. Zirbel, 2016, Nucleic Acids Res..

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Karen Eilbeck, Michel Dumontier, Robert Hoehndorf, 2009, Appl. Ontology.

R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

Ryan R. Rahrig, Neocles Leontis, Craig L. Zirbel, 2010, Bioinform..

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Rob Knight, Thomas Bittner, Karen Eilbeck, 2009 .

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Anton I. Petrov, Craig L. Zirbel, N. Leontis, 2013, RNA.

Identifying novel sequence variants of RNA 3D motifs

Anton I. Petrov, Craig L. Zirbel, N. Leontis, 2015, Nucleic acids research.

Classification and energetics of the base-phosphate interactions in RNA

Craig L. Zirbel, N. Leontis, J. Stombaugh, 2009, Nucleic acids research.

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

Craig L. Zirbel, N. Leontis, J. Stombaugh, 2007, Journal of mathematical biology.

Sharing and archiving nucleic acid structure mapping data.

Craig L. Zirbel, R. Knight, D. Mathews, 2011, RNA.

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.

Craig L. Zirbel, N. Leontis, B. Sweeney, 2016, Methods.

RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

Jesse Stombaugh, Craig L. Zirbel, Neocles B. Leontis, 2009 .

Comprehensive survey and geometric classification of base triples in RNA structures

Jesse Stombaugh, Anton I. Petrov, Craig L. Zirbel, 2011, Nucleic acids research.

Frequency and isostericity of RNA base pairs

Eric Westhof, Jesse Stombaugh, Craig L. Zirbel, 2009, Nucleic acids research.

Dispersion of particle systems in Brownian flows

Erhan Çinlar, Craig L. Zirbel, 1996 .

Lagrangian observations of homogeneous random environments

Craig L. Zirbel, 2001, Advances in Applied Probability.

How to fold and protect mitochondrial ribosomal RNA with fewer guanines

Craig L. Zirbel, E. Westhof, N. Leontis, 2018, Nucleic acids research.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Craig L. Zirbel, Christian Höner zu Siederdissen, I. Hofacker, 2015, PloS one.

R 3 D Align web server for global nucleotide to nucleotide alignments of RNA 3 D structures

Ryan R. Rahrig, Anton I. Petrov, Craig L. Zirbel, 2013 .

Meeting report of the RNA Ontology Consortium January 8-9, 2011

Eric P. Nawrocki, Craig L. Zirbel, J. Clemente, 2011, Standards in genomic sciences.

Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.

Craig L. Zirbel, L. Fedorova, E. Crawford, 2014, Gene.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Craig L. Zirbel, Christian Höner zu Siederdissen, I. Hofacker, 2015, PloS one.

Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

Craig L. Zirbel, P. Auffinger, 2022, Molecules.

Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.

Craig L. Zirbel, K. Réblová, J. Šponer, 2013, The journal of physical chemistry. B.

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA

Craig L. Zirbel, N. Leontis, Chun Xing Li, 2020, Nucleic acids research.

A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana

Craig L. Zirbel, N. Leontis, B. Ding, 2019, PLoS pathogens.

Seriation using tree-penalized path length

Craig L. Zirbel, D. A. Aliyev, 2022, Eur. J. Oper. Res..

Preprint C a Class of Velocity Elds with Known Lagrangian Law

Craig L. Zirbel, B. Zirbel, 1999 .

Dispersion of particle systems in Brownian flows

Craig L. Zirbel, E. Çinlar, 1996, Advances in Applied Probability.

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.

Craig L. Zirbel, J. Šponer, N. Leontis, 2011, The journal of physical chemistry. A.

JAR 3 D Webserver : Scoring and aligning RNA loop sequences to known 3 D motifs

Anton I. Petrov, Craig L. Zirbel, N. Leontis, 2016 .

A mean-field statistical theory for the nonlinear Schrödinger equation

Craig L. Zirbel, Richard Jordan, Bruce Turkington, 1999, chao-dyn/9904030.

Understanding Sequence Variability of RNA Motifs Using Geometric Search and IsoDiscrepancy Matrices

Anton I. Petrov, Craig L. Zirbel, N. Leontis, 2009, 2009 Ohio Collaborative Conference on Bioinformatics.

RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution

Craig L. Zirbel, N. Leontis, B. Ding, 2018, PLoS pathogens.

Allelic RNA Motifs in Regulating Systemic Trafficking of Potato Spindle Tuber Viroid

Craig L. Zirbel, N. Leontis, B. Ding, 2018, Viruses.

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA

Craig L. Zirbel, N. Leontis, Chun Xing Li, 2020, Nucleic acids research.

The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.

Craig L. Zirbel, Brinda K. Vallat, Catherine L Lawson, 2023, Nucleic acids research.

ROTATION OF PARTICLES IN POLARIZED BROWNIAN FLOWS

Craig L. Zirbel, W. Woyczynski, 2002 .

Translation and dispersion of mass by isotropic Brownian flows

Craig L. Zirbel, 1997 .

Mean occupation times of continuous one-dimensional Markov processes

Craig L. Zirbel, 1997 .

Stochastic flows : dispersion of a mass distribution and Lagrangian observations of a random field

Craig L. Zirbel, 1993 .

Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.

Craig L. Zirbel, K. Réblová, J. Šponer, 2013, The journal of physical chemistry. B.

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.

Craig L. Zirbel, N. Leontis, M. Otyepka, 2011, The journal of physical chemistry. A.