W. Kasprzak

发表

B. Shapiro, E. Bindewald, P. Zakrevsky, 2016, ACS combinatorial science.

Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling.

B. Shapiro, C. O’Connell, D. Atha, 2001, Nucleic acids research.

RNA folding pathway functional intermediates: their prediction and analysis.

J. C. Wu, B. Shapiro, W. Kasprzak, 2001, Journal of molecular biology.

Computational and Experimental RNA Nanoparticle Design

Cody W. Geary, L. Jaeger, B. Shapiro, 2009 .

Multifunctional RNA Nanoparticles

Wade W Grabow, Wade W. Grabow, W. Chiu, 2014, Nano letters.

In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles

B. Shapiro, E. Bindewald, M. Kashlev, 2014, Accounts of chemical research.

Computational and experimental characterization of RNA cubic nanoscaffolds.

A. R. Diehl, Praneet S. Puppala, R. Jernigan, 2014, Methods.

Dynamic Behavior of RNA Nanoparticles Analyzed by AFM on a Mica/Air Interface.

B. Shapiro, M. Dobrovolskaia, K. Afonin, 2018, Langmuir : the ACS journal of surfaces and colloids.

Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates.

L. Jaeger, B. Shapiro, E. Bindewald, 2020, Nanoscale.

Functionally-interdependent shape-switching nanoparticles with controllable properties

Emil F. Khisamutdinov, Jacob S. Lu, B. Shapiro, 2017, Nucleic acids research.

Triggering RNAi with multifunctional RNA nanoparticles and their delivery

B. Shapiro, K. Afonin, Mathias Viard, 2015, DNA and RNA nanotechnology.

Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles

B. Shapiro, M. Dobrovolskaia, K. Afonin, 2014, ACS nano.

RNA Structure Analysis: A Multifaceted Approach

Jin Chu Wu, Bruce A. Shapiro, Wojciech Kasprzak, 1999, Pattern Discovery in Biomolecular Data.

The role of cytokine mRNA stability in the pathogenesis of autoimmune disease.

B. Shapiro, S. Cole, W. Kasprzak, 2006, Autoimmunity reviews.

Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities

B. Shapiro, E. Bindewald, M. Kashlev, 2013, Nucleic acids research.

Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch

F. Gao, B. Shapiro, W. Kasprzak, 2017, eLife.

Role of Dynamics in RNA Nanostructure Design

B. Shapiro, W. Kasprzak, 2013 .

Conformational dynamics of the hepatitis B virus pre-genomic RNA on multiple time scales: implications for viral replication.

B. Shapiro, Christina Bergonzo, W. Kasprzak, 2022, Journal of molecular biology.

Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires

Yun-Xing Wang, B. Shapiro, Shuo Gu, 2019, Cell reports.

Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.

A. Wlodawer, B. Shapiro, M. Swain, 2021, Nucleic Acids Research.

RNA–Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics

B. Shapiro, Shuo Gu, W. Kasprzak, 2018, Molecules.

An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells

Octavio A. Quiñones, W. Alvord, R. Leighty, 2009, PloS one.

Identification of Cis-Acting Elements in the 3′-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication*

B. Shapiro, W. Kasprzak, B. Falgout, 2011, The Journal of Biological Chemistry.

Computational Generation of RNA Nanorings.

B. Shapiro, W. Kasprzak, Eckart Bindewald, 2017, Methods in molecular biology.

Modeling ligand docking to RNA in the design of RNA-based nanostructures.

B. Shapiro, W. Kasprzak, N. Ahmed, 2019, Current opinion in biotechnology.

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires

Yun-Xing Wang, B. Shapiro, Shuo Gu, 2018, bioRxiv.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

Taejin Kim, Bruce A Shapiro, Wojciech K Kasprzak, 2017, Methods in molecular biology.

Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target

B. Shapiro, W. Kasprzak, T. K. Dayie, 2023, Molecules.

Structural insights of the conserved “priming loop” of hepatitis B virus pre-genomic RNA

B. Shapiro, J. Ivanic, S. L. Le Grice, 2021, Journal of biomolecular structure & dynamics.

RiboSketch: versatile visualization of multi‐stranded RNA and DNA secondary structure

Eckart Bindewald, Bruce A. Shapiro, Wojciech Kasprzak, 2018, Bioinform..

Genomic Analyses Reveal Broad Impact of miR-137 on Genes Associated with Malignant Transformation and Neuronal Differentiation in Glioblastoma Cells

S. Kuersten, L. Penalva, H. Nakaya, 2014, PloS one.

The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers

F. Gao, B. Shapiro, W. Kasprzak, 2014, Journal of Virology.

Distinct frequency patterns of LILRB3 and LILRA6 allelic variants in Europeans

W. Kasprzak, A. Bashirova, M. Carrington, 2022, Immunogenetics.

Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.

Javed M. Aman, Bruce A Shapiro, Wojciech Kasprzak, 2006, Journal of molecular graphics & modelling.

The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels.

Bruce A Shapiro, Wojciech K Kasprzak, B. Shapiro, 2009, RNA.

The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing.

Bruce A Shapiro, Wojciech K Kasprzak, B. Shapiro, 2006, RNA.

Protocols for the in silico design of RNA nanostructures.

Wojciech Kasprzak, Bruce A Shapiro, Eckart Bindewald, 2008, Methods in molecular biology.

Bridging the gap in RNA structure prediction.

Wojciech Kasprzak, Bruce A Shapiro, Yaroslava G Yingling, 2007, Current opinion in structural biology.

Inhibition of vemurafenib-resistant melanoma by interference with pre-mRNA splicing

T. Misteli, B. Shapiro, T. Voss, 2015, Nature Communications.

Structural Differentiation of the HIV-1 Poly(A) Signals

Wojciech Kasprzak, Bruce A Shapiro, A. H. Gee, 2006, Journal of biomolecular structure & dynamics.

Structural polymorphism of the HIV-1 leader region explored by computational methods

Bruce A. Shapiro, Wojciech Kasprzak, Eckart Bindewald, 2005, Nucleic acids research.

Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus

Wojciech Kasprzak, Charles D Schwieters, Bruce A Shapiro, 2010, Proceedings of the National Academy of Sciences.

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

Bruce A. Shapiro, Wojciech Kasprzak, Yaroslava G. Yingling, 2008, Journal of Virology.

Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer

B. Shapiro, W. Kasprzak, A. Simon, 2022, Nucleic acids research.

The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin

Suna P. Gulay, F. Gao, B. Shapiro, 2013, Journal of Virology.

The kl-TSS translational enhancer of PEMV can bind simultaneously to

Suna P. Gulay, F. Gao, B. Shapiro, 2013 .

RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences

Bruce A Shapiro, Wojciech K Kasprzak, Anne E Simon, 2019, RNA biology.

Vascular plants of Łempis nature reserve in the Augustów forest (NE Poland)

W. Kasprzak, P. Pawlikowski, I. Dembicz, 2018 .

Stem Trace: an interactive visual tool for comparative RNA structure analysis

Bruce A. Shapiro, Wojciech Kasprzak, B. Shapiro, 1999, Bioinform..

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

Eckart Bindewald, Robert Hayes, Bruce A. Shapiro, 2007, Nucleic Acids Res..

HLA class I signal peptide polymorphism determines the level of CD94/NKG2–HLA-E-mediated regulation of effector cell responses

A. McMichael, V. Naranbhai, Mathias Viard, 2023, Nature Immunology.

Bolaamphiphiles as carriers for siRNA delivery: From chemical syntheses to practical applications.

B. Shapiro, R. Blumenthal, K. Afonin, 2015, Journal of controlled release : official journal of the Controlled Release Society.

STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis.

B A Shapiro, W Kasprzak, B. Shapiro, 1996, Journal of molecular graphics.

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

Bruce A. Shapiro, Wojciech K. Kasprzak, Jonathan D. Dinman, 2014, Nature.

Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction

Bruce A. Shapiro, Jih-Hsiang Chen, Jacob V. Maizel, 1995, Int. J. High Perform. Comput. Appl..

A Ribosome-Binding, 3′ Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction

F. Gao, B. Shapiro, W. Kasprzak, 2012, Journal of Virology.

Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch

B. Shapiro, W. Kasprzak, A. Simon, 2017, RNA biology.

Triggerable RNA nanodevices

B. Shapiro, P. Zakrevsky, K. Afonin, 2016, RNA & disease.

Use of RNA structure flexibility data in nanostructure modeling.

Tae-Jin Kim, Luc Jaeger, Wojciech Kasprzak, 2011, Methods.

MPGAfold in dengue secondary structure prediction.

Bruce A Shapiro, Wojciech K Kasprzak, B. Shapiro, 2014, Methods in molecular biology.

The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin

Suna P. Gulay, F. Gao, B. Shapiro, 2013, Journal of Virology.

Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus

Bruce A. Shapiro, Wojciech K. Kasprzak, B. Shapiro, 2012 .

Visual Data Mining of RNA Secondary Structure and Folding Pathways as Determined by the Massively Parallel Genetic Algorithm

B. Shapiro, W. Kasprzak, 2007 .

RNA–Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics

B. Shapiro, Shuo Gu, W. Kasprzak, 2018, Molecules.