Danny Barash - RankMe

49 papers Journal 35Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3. Briefings Bioinform. Rami Zakh, Alexander Churkin, Marina Parr, Tamir Tuller, Ohad Etzion, Harel Dahari, Danny Barash
2024	—	`conf`	Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans. RECOMB-CG Alma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller
2024	J	`jnl`	Leveraging Computational Pathology AI for Noninvasive Optical Imaging Analysis Without Retraining. CoRR 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, Yonatan Winetraub
2023	J	`jnl`	A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding. Briefings Bioinform. Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash
2023	J	`jnl`	Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics. PLoS Comput. Biol. 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
2022	J	`jnl`	IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. Alexander Churkin, Yann Ponty, Danny Barash
2020	J	`jnl`	incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash
2019	J	`jnl`	RiboD: a comprehensive database for prokaryotic riboswitches. Bioinform. Sumit Mukherjee, Sukhen Das Mandal, Nikita Gupta, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta
2018	—	`conf`	A Biologically Meaningful Extension of the Efficient Method for Deleterious Mutations Prediction in RNAs: Insertions and Deletions in Addition to Substitution Mutations. ISBRA Alexander Churkin, Danny Barash
2018	J	`jnl`	Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2017	J	`jnl`	A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics. Frontiers Appl. Math. Stat. Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash
2017	—	`conf`	Optimal Shrinkage of Singular Values Under Random Data Contamination. NIPS Danny Barash, Matan Gavish
2017	J	`jnl`	Optimal Shrinkage of Singular Values Under Random Data Contamination. CoRR Danny Barash, Matan Gavish
2016	J	`jnl`	incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2015	J	`jnl`	RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. Nucleic Acids Res. Matan Drory Retwitzer, Maya Polishchuk, Elena Churkin, Ilona Kifer, Zohar Yakhini, Danny Barash
2013	J	`jnl`	RNAfbinv: an interactive Java application for fragment-based design of RNA sequences. Bioinform. Lina Weinbrand, Assaf Avihoo, Danny Barash
2012	J	`jnl`	Efficient procedures for the numerical simulation of mid-size RNA kinetics. Algorithms Mol. Biol. Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash
2012	J	`jnl`	On topological indices for small RNA graphs. Comput. Biol. Chem. Alexander Churkin, Idan Gabdank, Danny Barash
2011	J	`jnl`	Mutational analysis in RNAs: comparing programs for RNA deleterious mutation prediction. Briefings Bioinform. Danny Barash, Alexander Churkin
2011	J	`jnl`	RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. BMC Bioinform. Assaf Avihoo, Alexander Churkin, Danny Barash
2011	J	`jnl`	The RNAmute web server for the mutational analysis of RNA secondary structures. Nucleic Acids Res. Alexander Churkin, Idan Gabdank, Danny Barash
2010	J	`jnl`	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. Alexander Churkin, Moriah Cohen, Yonat Shemer-Avni, Danny Barash
2010	J	`jnl`	FineStr: a web server for single-base-resolution nucleosome positioning. Bioinform. Idan Gabdank, Danny Barash, Edward N. Trifonov
2009	J	`jnl`	An image processing approach to computing distances between RNA secondary structures dot plots. Algorithms Mol. Biol. Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro, Danny Barash
2008	J	`jnl`	An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. BMC Bioinform. Alexander Churkin, Danny Barash
2008	J	`jnl`	Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis. Silico Biol. Adaya N. Cohen, Samuel Bocobza, Isana Veksler, Idan Gabdank, Danny Barash, Asaph Aharoni, Michal Shapira, Klara Kedem
2008	J	`jnl`	FASH: A web application for nucleotides sequence search. Source Code Biol. Medicine Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, L. Paul Chew, Klara Kedem
2007	J	`jnl`	A Structure-Based Flexible Search Method for Motifs in RNA. J. Comput. Biol. Isana Veksler-Lublinsky, Michal Ziv-Ukelson, Danny Barash, Klara Kedem
2007	J	`jnl`	Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System. IEEE ACM Trans. Comput. Biol. Bioinform. Shahar Michal, Tor Ivry, Omer Cohen, Moshe Sipper, Danny Barash
2006	J	`jnl`	RNAmute: RNA secondary structure mutation analysis tool. BMC Bioinform. Alexander Churkin, Danny Barash
2006	J	`jnl`	Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute. EURASIP J. Adv. Signal Process. Alexander Churkin, Danny Barash
2005	—	`conf`	Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes. CSB Workshops Adaya N. Cohen, Klara Kedem, Michal Shapira, Danny Barash
2005	—	`conf`	Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin. CVPR Workshops Alexander Churkin, Danny Barash
2005	—	`conf`	RNAMute: RNA Secondary Structure Mutation Analysis Tool. CSB Workshops Alexander Churkin, Ornit Elgad, Oshrat Petgho, Danny Barash
2005	—	`conf`	Temperature and Mutation Switches in the Secondary Structure of Small RNAs. CSB Workshops Assaf Avihoo, Danny Barash
2004	J	`jnl`	A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift. Image Vis. Comput. Danny Barash, Dorin Comaniciu
2004	—	`conf`	Fine-Grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs. CSB Assaf Avihoo, Nir Dromi, Danny Barash
2004	—	`conf`	Meanshift Clustering for DNA Microarray Analysis. CSB Danny Barash, Dorin Comaniciu
2004	—	`conf`	RNA Motif Search Using the Structure to String (STR CSB Oriel Bergig, Danny Barash, Klara Kedem
2004	J	`jnl`	STR2: A structure to string approach for locating G-box riboswitch shapes in pre-selected genes. Silico Biol. Oriel Bergig, Danny Barash, Evgeny Nudler, Klara Kedem
2004	J	`jnl`	Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation. Bioinform. Danny Barash
2004	J	`jnl`	Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. J. Comput. Biol. Danny Barash
2003	—	`conf`	A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion. Scale-Space Danny Barash, Dorin Comaniciu
2003	J	`jnl`	Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. J. Comput. Chem. Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick
2003	J	`jnl`	Multiplicative Operator Splittings in Nonlinear Diffusion: From Spatial Splitting to Multiple Timesteps. J. Math. Imaging Vis. Danny Barash, Tamar Schlick, Moshe Israeli, Ron Kimmel
2003	—	`conf`	Spectral Decomposition of the Laplacian Matrix Applied to RNA Folding Prediction. CSB Danny Barash
2002	J	`jnl`	A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing, and the Nonlinear Diffusion Equation. IEEE Trans. Pattern Anal. Mach. Intell. Danny Barash
2001	—	`conf`	An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering. Scale-Space Danny Barash, Moshe Israeli, Ron Kimmel
2001	—	`conf`	Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint. Scale-Space Danny Barash