Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint. - Danny Barash (Scale-Space, 2001)

An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering. - Danny Barash; Moshe Israeli; Ron Kimmel (Scale-Space, 2001)

A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation. - Danny Barash (IEEE Trans. Pattern Anal. Mach. Intell., 2002)

Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Prediction. - Danny Barash (CSB, 2003)

A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion. - Danny Barash; Dorin Comaniciu (Scale-Space, 2003)

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. - Danny Barash; Linjing Yang; Xiaoliang Qian; Tamar Schlick (J. Comput. Chem., 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)

Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. - Assaf Avihoo; Nir Dromi; Danny Barash (CSB, 2004)

Meanshift Clustering for DNA Microarray Analysis. - Danny Barash; Dorin Comaniciu (CSB, 2004)

RNA Motif Search Using the Structure to String (STR2) Method. - Oriel Bergig; Danny Barash; Klara Kedem (CSB, 2004)

Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation. - Danny Barash (Bioinform., 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)

A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift. - Danny Barash; Dorin Comaniciu (Image Vis. Comput., 2004)

Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. - Danny Barash (J. Comput. Biol., 2004)

Temperature and Mutation Switches in the Secondary Structure of Small RNAs. - Assaf Avihoo; Danny Barash (CSB Workshops, 2005)

RNAMute: RNA Secondary Structure Mutation Analysis Tool. - Alexander Churkin; Ornit Elgad; Oshrat Petgho; Danny Barash (CSB Workshops, 2005)

Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes. - Adaya N. Cohen; Klara Kedem; Michal Shapira; Danny Barash (CSB Workshops, 2005)

Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin. - Alexander Churkin; Danny Barash (CVPR Workshops, 2005)

RNAmute: RNA secondary structure mutation analysis tool. - Alexander Churkin; Danny Barash (BMC Bioinform., 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)

A Structure-Based Flexible Search Method for Motifs in RNA. - Isana Veksler-Lublinsky; Michal Ziv-Ukelson; Danny Barash; Klara Kedem (J. Comput. Biol., 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)

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)

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)

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)

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)

FineStr: a web server for single-base-resolution nucleosome positioning. - Idan Gabdank; Danny Barash; Edward N. Trifonov (Bioinform., 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)

Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. - Danny Barash; Alexander Churkin (Briefings Bioinform., 2011)

RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. - Assaf Avihoo; Alexander Churkin; Danny Barash (BMC Bioinform., 2011)

The RNAmute web server for the mutational analysis of RNA secondary structures. - Alexander Churkin; Idan Gabdank; Danny Barash (Nucleic Acids Res., 2011)

Efficient procedures for the numerical simulation of mid-size RNA kinetics. - Iddo Aviram; Ilia Veltman; Alexander Churkin; Danny Barash (Algorithms Mol. Biol., 2012)

On topological indices for small RNA graphs. - Alexander Churkin; Idan Gabdank; Danny Barash (Comput. Biol. Chem., 2012)

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. - Lina Weinbrand; Assaf Avihoo; Danny Barash (Bioinform., 2013)

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)

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)

Optimal Shrinkage of Singular Values Under Random Data Contamination. - Danny Barash; Matan Gavish (NIPS, 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)

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 (ISBRA, 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)

RiboD: a comprehensive database for prokaryotic riboswitches. - Sumit Mukherjee; Sukhen Das Mandal; Nikita Gupta; Matan Drory Retwitzer; Danny Barash; Supratim Sengupta (Bioinform., 2019)

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)

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. - Alexander Churkin; Yann Ponty; Danny Barash (BMC Bioinform., 2022)

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; et al. (PLoS Comput. Biol., 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., 2023)

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 (RECOMB-CG, 2024)

Leveraging Computational Pathology AI for Noninvasive Optical Imaging Analysis Without Retraining. - Danny Barash; Emilie Manning; Aidan Van Vleck; Omri Hirsch; Kyi Lei Aye; Jingxi Li; Philip O. Scumpia; Aydogan Ozcan; Sumaira Aasi; Kerri E. Rieger; Kavita Y. Sarin; Oren Freifeld; et al. (CoRR, 2024)