Danny Barash

According to our database, Danny Barash authored at least 46 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans.

Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller

Proceedings of the Comparative Genomics - 21st International Conference, 2024

2023

A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding.

Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash

Briefings Bioinform., May, 2023

Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics.

Atesmachew Hailegiorgis, Yuji Ishida, Nicholson T. Collier, Michio Imamura, Zhenzhen Shi, Vladimir Reinharz, Masataka Tsuge, Danny Barash, Nobuhiko Hiraga, Hiroshi Yokomichi, Chise Tateno, Jonathan Ozik, Susan L. Uprichard, Kazuaki Chayama, Harel Dahari

PLoS Comput. Biol., 2023

2022

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.

Alexander Churkin, Yann Ponty, Danny Barash

BMC Bioinform., 2022

2020

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.

Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash

Bioinform., 2020

2019

RiboD: a comprehensive database for prokaryotic riboswitches.

Sumit Mukherjee, Sukhen Das Mandal, Nikita Gupta, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta

Bioinform., 2019

2018

Design of RNAs: comparing programs for inverse RNA folding.

Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash

Briefings Bioinform., 2018

A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations.

Alexander Churkin, Danny Barash

Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

2017

A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics.

Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash

Frontiers Appl. Math. Stat., 2017

Optimal Shrinkage of Singular Values Under Random Data Contamination.

Danny Barash, Matan Gavish

Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017

2016

incaRNAfbinv: a web server for the fragment-based design of RNA sequences.

Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash

Nucleic Acids Res., 2016

2015

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.

Matan Drory Retwitzer, Maya Polishchuk, Elena Churkin, Ilona Kifer, Zohar Yakhini, Danny Barash

Nucleic Acids Res., 2015

2013

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.

Lina Weinbrand, Assaf Avihoo, Danny Barash

Bioinform., 2013

2012

On topological indices for small RNA graphs.

Alexander Churkin, Idan Gabdank, Danny Barash

Comput. Biol. Chem., 2012

Efficient procedures for the numerical simulation of mid-size RNA kinetics.

Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash

Algorithms Mol. Biol., 2012

2011

The RNAmute web server for the mutational analysis of RNA secondary structures.

Alexander Churkin, Idan Gabdank, Danny Barash

Nucleic Acids Res., 2011

RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences.

Assaf Avihoo, Alexander Churkin, Danny Barash

BMC Bioinform., 2011

Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction.

Danny Barash, Alexander Churkin

Briefings Bioinform., 2011

2010

Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements across genotypes reveals Evidence for Direct Evolution of Genetic Robustness in HCV.

Alexander Churkin, Moriah Cohen, Yonat Shemer-Avni, Danny Barash

J. Bioinform. Comput. Biol., 2010

FineStr: a web server for single-base-resolution nucleosome positioning.

Idan Gabdank, Danny Barash, Edward N. Trifonov

Bioinform., 2010

2009

An image processing approach to computing distances between RNA secondary structures dot plots.

Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro, Danny Barash

Algorithms Mol. Biol., 2009

2008

FASH: A web application for nucleotides sequence search.

Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, L. Paul Chew, Klara Kedem

Source Code Biol. Medicine, 2008

Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis.

Adaya N. Cohen, Samuel Bocobza, Isana Veksler, Idan Gabdank, Danny Barash, Asaph Aharoni, Michal Shapira, Klara Kedem

Silico Biol., 2008

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

Alexander Churkin, Danny Barash

BMC Bioinform., 2008

2007

Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System.

Shahar Michal, Tor Ivry, Omer Cohen, Moshe Sipper, Danny Barash

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

A Structure-Based Flexible Search Method for Motifs in RNA.

Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem

J. Comput. Biol., 2007

2006

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute.

Alexander Churkin, Danny Barash

EURASIP J. Adv. Signal Process., 2006

RNAmute: RNA secondary structure mutation analysis tool.

Alexander Churkin, Danny Barash

BMC Bioinform., 2006

2005

Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin.

Alexander Churkin, Danny Barash

Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2005

Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes.

Adaya N. Cohen, Klara Kedem, Michal Shapira, Danny Barash

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

RNAMute: RNA Secondary Structure Mutation Analysis Tool.

Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

Temperature and Mutation Switches in the Secondary Structure of Small RNAs.

Assaf Avihoo, Danny Barash

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

2004

Spectral Decomposition for the Search and Analysis of RNA Secondary Structure.

Danny Barash

J. Comput. Biol., 2004

A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift.

Danny Barash, Dorin Comaniciu

Image Vis. Comput., 2004

STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes.

Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem

Silico Biol., 2004

Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation.

Danny Barash

Bioinform., 2004

RNA Motif Search Using the Structure to String (STR²) Method.

Oriel Bergig, Danny Barash, Klara Kedem

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

Meanshift Clustering for DNA Microarray Analysis.

Danny Barash, Dorin Comaniciu

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs.

Assaf Avihoo, Nir Dromi, Danny Barash

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps.

Danny Barash, Tamar Schlick, Moshe Israeli, Ron Kimmel

J. Math. Imaging Vis., 2003

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.

Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick

J. Comput. Chem., 2003

A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion.

Danny Barash, Dorin Comaniciu

Proceedings of the Scale Space Methods in Computer Vision, 4th International Conference, 2003

Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Prediction.

Danny Barash

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation.

Danny Barash

IEEE Trans. Pattern Anal. Mach. Intell., 2002

2001

An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering.

Danny Barash, Moshe Israeli, Ron Kimmel

Proceedings of the Scale-Space and Morphology in Computer Vision, 2001

Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint.

Danny Barash

Proceedings of the Scale-Space and Morphology in Computer Vision, 2001