Danny Barash

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 13

Top Topics

Human Behaviour

Structural Motifs

Secondary Structure

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller
Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. RECOMB-CG (2024)
Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash
A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding. Briefings Bioinform. 24 (3) (2023)
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
Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics. PLoS Comput. Biol. 19 (8) (2023)
Alexander Churkin, Yann Ponty, Danny Barash
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. (8) (2022)
Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. 36 (9) (2020)
Sumit Mukherjee, Sukhen Das Mandal, Nikita Gupta, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta
RiboD: a comprehensive database for prokaryotic riboswitches. Bioinform. 35 (18) (2019)
Alexander Churkin, Danny Barash
A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations. ISBRA (2018)
Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. 19 (2) (2018)
Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash
A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics. Frontiers Appl. Math. Stat. 3 (2017)
Danny Barash, Matan Gavish
Optimal Shrinkage of Singular Values Under Random Data Contamination. NIPS (2017)
Danny Barash, Matan Gavish
Optimal Shrinkage of Singular Values Under Random Data Contamination. CoRR (2017)
Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Matan Drory Retwitzer, Maya Polishchuk, Elena Churkin, Ilona Kifer, Zohar Yakhini, Danny Barash
RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Lina Weinbrand, Assaf Avihoo, Danny Barash
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. Bioinform. 29 (22) (2013)
Alexander Churkin, Idan Gabdank, Danny Barash
On topological indices for small RNA graphs. Comput. Biol. Chem. 41 (2012)
Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash
Efficient procedures for the numerical simulation of mid-size RNA kinetics. Algorithms Mol. Biol. 7 (2012)
Danny Barash, Alexander Churkin
Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. Briefings Bioinform. 12 (2) (2011)
Assaf Avihoo, Alexander Churkin, Danny Barash
RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. BMC Bioinform. 12 (2011)
Alexander Churkin, Idan Gabdank, Danny Barash
The RNAmute web server for the mutational analysis of RNA secondary structures. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Alexander Churkin, Moriah Cohen, Yonat Shemer-Avni, Danny Barash
Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements across genotypes reveals Evidence for Direct Evolution of Genetic Robustness in HCV. J. Bioinform. Comput. Biol. 8 (6) (2010)
Idan Gabdank, Danny Barash, Edward N. Trifonov
FineStr: a web server for single-base-resolution nucleosome positioning. Bioinform. 26 (6) (2010)
Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro, Danny Barash
An image processing approach to computing distances between RNA secondary structures dot plots. Algorithms Mol. Biol. 4 (2009)
Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, L. Paul Chew, Klara Kedem
FASH: A web application for nucleotides sequence search. Source Code Biol. Medicine 3 (2008)
Alexander Churkin, Danny Barash
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. BMC Bioinform. 9 (2008)
Adaya N. Cohen, Samuel Bocobza, Isana Veksler, Idan Gabdank, Danny Barash, Asaph Aharoni, Michal Shapira, Klara Kedem
Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis. Silico Biol. 8 (2) (2008)
Shahar Michal, Tor Ivry, Omer Cohen, Moshe Sipper, Danny Barash
Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (4) (2007)
Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem
A Structure-Based Flexible Search Method for Motifs in RNA. J. Comput. Biol. 14 (7) (2007)
Alexander Churkin, Danny Barash
Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute. EURASIP J. Adv. Signal Process. 2006 (2006)
Alexander Churkin, Danny Barash
RNAmute: RNA secondary structure mutation analysis tool. BMC Bioinform. 7 (2006)
Alexander Churkin, Danny Barash
Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin. CVPR Workshops (2005)
Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash
RNAMute: RNA Secondary Structure Mutation Analysis Tool. CSB Workshops (2005)
Adaya N. Cohen, Klara Kedem, Michal Shapira, Danny Barash
Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes. CSB Workshops (2005)
Assaf Avihoo, Danny Barash
Temperature and Mutation Switches in the Secondary Structure of Small RNAs. CSB Workshops (2005)
Danny Barash, Dorin Comaniciu
Meanshift Clustering for DNA Microarray Analysis. CSB (2004)
Oriel Bergig, Danny Barash, Klara Kedem
) Method. CSB (2004)
Danny Barash, Dorin Comaniciu
A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift. Image Vis. Comput. 22 (1) (2004)
Danny Barash
Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation. Bioinform. 20 (12) (2004)
Assaf Avihoo, Nir Dromi, Danny Barash
Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. CSB (2004)
Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem
STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes. Silico Biol. 4 (4) (2004)
Danny Barash
Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. J. Comput. Biol. 11 (6) (2004)
Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. J. Comput. Chem. 24 (1) (2003)
Danny Barash, Tamar Schlick, Moshe Israeli, Ron Kimmel
Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps. J. Math. Imaging Vis. 19 (1) (2003)
Danny Barash, Dorin Comaniciu
A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion. Scale-Space (2003)
Danny Barash
Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Prediction. CSB (2003)
Danny Barash
A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation. IEEE Trans. Pattern Anal. Mach. Intell. 24 (6) (2002)
Danny Barash
Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint. Scale-Space (2001)
Danny Barash, Moshe Israeli, Ron Kimmel
An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering. Scale-Space (2001)