Eckart Bindewald

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Predicting RNA SHAPE scores with deep learning

B. Shapiro, Noah Bliss, Eckart Bindewald, 2020, RNA biology.

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

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

Computational Generation of RNA Nanorings.

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

Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities.

B. Shapiro, E. Bindewald, K. Afonin, 2015, Methods in enzymology.

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

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

In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles

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

Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference

N. Sonenberg, N. Colburn, B. Shapiro, 2009, PloS one.

Cellular Delivery of RNA Nanoparticles.

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

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

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

The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus–induced microRNAs

M. Carrington, C. Hagedorn, B. Shapiro, 2013, Nature Immunology.

IFNL 3 ( IL 28 B ) favorable genotype escapes hepatitis C virus-induced microRNAs and mRNA decay

M. Carrington, C. Hagedorn, B. Shapiro, 2013 .

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.

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

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

Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine

Wade W Grabow, Wade W. Grabow, L. Jaeger, 2011, Nature Protocols.

CyloFold: secondary structure prediction including pseudoknots

Eckart Bindewald, Bruce A. Shapiro, Tanner Kluth, 2010, Nucleic Acids Res..

Computational detection of abundant long-range nucleotide covariation in Drosophila genomes

B. Shapiro, E. Bindewald, Eckart Bindewald, 2013, 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.

RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers.

B. Shapiro, E. Bindewald, Eckart Bindewald, 2006, RNA.

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments

Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro, 2006, Nucleic Acids Res..

A divide and conquer approach to fast loop modeling.

Eckart Bindewald, Silvio C. E. Tosatto, Reinhard Männer, 2002, Protein engineering.

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

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

RNA Nanostructures

B. Shapiro, Eckart Bindewald, 2017, Methods in Molecular Biology.

Implementing Genetic Algorithms with Sterical Constraints for Protein Structure Prediction

Eckart Bindewald, Reinhard Männer, Jürgen Hesser, 1998, PPSN.

The SSEA server for protein secondary structure alignment

Silvio C. E. Tosatto, P. Fontana, S. Toppo, 2005, Bioinform..

Functionally-interdependent shape-switching nanoparticles with controllable properties

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

Computational and experimental characterization of RNA cubic nanoscaffolds.

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

In vitro Assembly of Cubic RNA-Based Scaffolds Designed in silico

L. Jaeger, B. Shapiro, E. Bindewald, 2010, Nature nanotechnology.

Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.

L. Jaeger, B. Shapiro, E. Bindewald, 2011, ACS nano.

Ring Catalog: A resource for designing self-assembling RNA nanostructures.

Nathan Bartlett, Bruce A Shapiro, Eckart Bindewald, 2016, Methods.

Preparation of a Conditional RNA Switch.

B. Shapiro, P. Zakrevsky, K. Afonin, 2017, Methods in molecular biology.

Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.

Bruce A. Shapiro, Taejin Kim, Eckart Bindewald, 2016, Nano letters.

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

Bruce A Shapiro, Eckart Bindewald, Calvin Grunewald, 2008, Journal of molecular graphics & modelling.

Achieving Multiple Goals via Voluntary Efforts and Motivation Asymmetry pdf

Eckart Bindewald, Eckart Bindewald, 2015, ArXiv.

The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities.

E. Freed, B. Shapiro, E. Bindewald, 2016, Nano letters.

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..

Restore: an R of sustainability that can tame the\conundrum"

Eckart Bindewald, Eckart Bindewald, 2018 .

A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides

B. Shapiro, E. Bindewald, P. Zakrevsky, 2019, Nanomaterials.

Ab Initio Loop Modeling with Precalculated Synthetic Loops and Sidechain Placement

Silvio C. E. Tosatto, Reinhard Männer, Jürgen Hesser, 2001 .

Computational and Experimental RNA Nanoparticle Design

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

A survey suggests individual priorities are virtually unique: Implications for group dynamics, goal achievement and ecology

E. Bindewald, Eckart Bindewald, 2017 .

Correlating SHAPE signatures with three-dimensional RNA structures.

B. Shapiro, E. Bindewald, M. Wendeler, 2011, RNA.

A scoring function for docking ligands to low‐resolution protein structures

Eckart Bindewald, Jeffrey Skolnick, J. Skolnick, 2005, J. Comput. Chem..

RNA Toehold Interactions Initiate Conditional Gene Silencing

B. Shapiro, P. Zakrevsky, Eckart Bindewald, 2016, DNA and RNA nanotechnology.

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.

IFNL3 (IL28B) favorable genotype escapes hepatitis C virus-induced microRNAs and mRNA decay

M. Carrington, C. Hagedorn, B. Shapiro, 2013, Nature Immunology.

MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification.

Silvio C. E. Tosatto, Jürgen Hesser, Matthias Heiler, 2003, Protein engineering.

Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.

L. Jaeger, B. Shapiro, K. Afonin, 2011, ACS nano.

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

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