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ORCIDDanny Barash
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2020 – today
- 2024
[c14]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: 248-270- 2023
- [j32]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) - [j31]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) - 2022
- [j30]Alexander Churkin, Yann Ponty, Danny Barash:
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. 23-S(8): 424 (2022) - 2020
- [j29]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): 2920-2922 (2020)
2010 – 2019
- 2019
- [j28]Sumit Mukherjee, Sukhen Das Mandal, Nikita Gupta, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta:
RiboD: a comprehensive database for prokaryotic riboswitches. Bioinform. 35(18): 3541-3543 (2019) - 2018
- [j27]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): 350-358 (2018) - [c13]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: 174-178 - 2017
- [j26]Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash:
A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics. Frontiers Appl. Math. Stat. 3: 20 (2017) - [c12]Danny Barash, Matan Gavish:
Optimal Shrinkage of Singular Values Under Random Data Contamination. NIPS 2017: 6160-6170 - [i1]Danny Barash, Matan Gavish:
Optimal Shrinkage of Singular Values Under Random Data Contamination. CoRR abs/1710.09787 (2017) - 2016
- [j25]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): W308-W314 (2016) - 2015
- [j24]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): W507-W512 (2015) - 2013
- [j23]Lina Weinbrand, Assaf Avihoo, Danny Barash:
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. Bioinform. 29(22): 2938-2940 (2013) - 2012
- [j22]Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash:
Efficient procedures for the numerical simulation of mid-size RNA kinetics. Algorithms Mol. Biol. 7: 24 (2012) - [j21]Alexander Churkin, Idan Gabdank, Danny Barash:
On topological indices for small RNA graphs. Comput. Biol. Chem. 41: 35-40 (2012) - 2011
- [j20]Danny Barash, Alexander Churkin:
Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. Briefings Bioinform. 12(2): 104-114 (2011) - [j19]Assaf Avihoo, Alexander Churkin, Danny Barash:
RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. BMC Bioinform. 12: 319 (2011) - [j18]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): 92-99 (2011) - 2010
- [j17]Idan Gabdank, Danny Barash, Edward N. Trifonov:
FineStr: a web server for single-base-resolution nucleosome positioning. Bioinform. 26(6): 845-846 (2010) - [j16]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): 1013-1026 (2010)
2000 – 2009
- 2009
- [j15]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) - 2008
- [j14]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) - [j13]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): 105-120 (2008) - [j12]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) - 2007
- [j11]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): 908-926 (2007) - [j10]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): 596-610 (2007) - 2006
- [j9]Alexander Churkin, Danny Barash:
RNAmute: RNA secondary structure mutation analysis tool. BMC Bioinform. 7: 221 (2006) - [j8]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) - 2005
- [c11]Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash:
RNAMute: RNA Secondary Structure Mutation Analysis Tool. CSB Workshops 2005: 139-141 - [c10]Adaya N. Cohen, Klara Kedem, Michal Shapira, Danny Barash:
Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes. CSB Workshops 2005: 193-195 - [c9]Assaf Avihoo, Danny Barash:
Temperature and Mutation Switches in the Secondary Structure of Small RNAs. CSB Workshops 2005: 235-238 - [c8]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: 139 - 2004
- [j7]Danny Barash:
Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation. Bioinform. 20(12): 1861-1869 (2004) - [j6]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): 593-604 (2004) - [j5]Danny Barash, Dorin Comaniciu:
A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift. Image Vis. Comput. 22(1): 73-81 (2004) - [j4]Danny Barash:
Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. J. Comput. Biol. 11(6): 1169-1174 (2004) - [c7]Danny Barash, Dorin Comaniciu:
Meanshift Clustering for DNA Microarray Analysis. CSB 2004: 578-579 - [c6]Oriel Bergig, Danny Barash, Klara Kedem:
RNA Motif Search Using the Structure to String (STR2) Method. CSB 2004: 660-661 - [c5]Assaf Avihoo, Nir Dromi, Danny Barash:
Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. CSB 2004: 724-725 - 2003
- [j3]Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick:
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. J. Comput. Chem. 24(1): 77-88 (2003) - [j2]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): 33-48 (2003) - [c4]Danny Barash:
Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Prediction. CSB 2003: 602-603 - [c3]Danny Barash, Dorin Comaniciu:
A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion. Scale-Space 2003: 683-698 - 2002
- [j1]Danny Barash:
A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation. IEEE Trans. Pattern Anal. Mach. Intell. 24(6): 844-847 (2002) - 2001
- [c2]Danny Barash:
Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint. Scale-Space 2001: 273-280 - [c1]Danny Barash, Moshe Israeli, Ron Kimmel:
An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering. Scale-Space 2001: 281-289
Coauthor Index
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