Prof. Danny Barash

dbarash foto Professor

Consultation by e-mail appointment

Contacts

Email:
Homepage:
Office: 105 in 37 building
Phone number: 08-6472714
Fax number: 08-6477650
Box number: 42
Office hours: Sun 12:00-14:00

Teaching

Fall 2017-2018 20213011 Introduction to Numerical Analysis
Fall 2016-2017 20214801 Topics in Bioinformatic
Fall 2016-2017 20213011 Introduction to Numerical Analysis
Spring 2017 20225341 Application of Scientific Computing
Spring 2017 20221541 Advanced Seminar D
Spring 2017 20221521 Advanced Seminar B
Spring 2016 20214191 Mini Project in Scientific Computing
Spring 2016 20225341 Application of Scientific Computing
Fall 2014-2015 20213011 Introduction to Numerical Analysis
Fall 2014-2015 20214801 Topics in Bioinformatic
Spring 2015 20225341 Application of Scientific Computing
Fall 2013-2014 20213011 Introduction to Numerical Analysis
Spring 2014 20225341 Application of Scientific Computing
Spring 2014 20225351 Selected Topics In Applied Scientific Computing
Spring 2014 20214811 Topics in Bioinformatics 2
Fall 2012-2013 20213011 Introduction to Numerical Analysis
Fall 2012-2013 20214801 Topics in Bioinformatic
Spring 2013 20225351 Selected Topics In Applied Scientific Computing
Spring 2013 20225581 Research Seminar on RNA Computational Modeling
Spring 2013 20225341 Application of Scientific Computing
Spring 2012 20225351 Selected Topics In Applied Scientific Computing
Spring 2012 20225341 Application of Scientific Computing
Spring 2012 20214191 Mini Project in Scientific Computing
Fall 2010-2011 20225671 Research Seminar on RNA Folding Prediction
Fall 2010-2011 20213011 Introduction to Numerical Analysis
Fall 2009-2010 20228161 Seminar on Computational Biology of RNA Structure
Fall 2009-2010 20213011 Introduction to Numerical Analysis
Spring 2010 20225341 Application of Scientific Computing
Spring 2010 20225351 Selected Topics In Applied Scientific Computing
Spring 2010 20214811 Topics in Bioinformatics 2
Fall 2008-2009 20213011 Introduction to Numerical Analysis
Fall 2008-2009 20225611 Research Seminar on computational methods for the prediction of RNA structures
Spring 2009 20225341 Application of Scientific Computing
Spring 2009 20214021 Project in Bioinformatics
Spring 2009 20214191 Mini Project in Scientific Computing
Spring 2009 20225351 Selected Topics In Applied Scientific Computing
Fall 2007-2008 20013011 Introduction to Numerical Analysis for IAF
Fall 2007-2008 20228151 Research Seminar on Nucleic Acid Folding Prediction
Fall 2007-2008 20225351 Selected Topics In Applied Scientific Computing
Fall 2006-2007 20225591 Research Seminar on Bioinformatics of RNA
Fall 2006-2007 20213011 Introduction to Numerical Analysis
Spring 2007 20214811 Topics in Bioinformatics 2
Spring 2007 20225411 Scientific Computation with Applications
Fall 2005-2006 20214021 Project in Bioinformatics
Fall 2005-2006 20225351 Selected Topics In Applied Scientific Computing
Fall 2005-2006 20213011 Introduction to Numerical Analysis
Fall 2005-2006 20225341 Application of Scientific Computing
Spring 2006 20215461 Topics in the Frontiers of Computer Science for Honor Students
Spring 2006 20225581 Research Seminar on RNA Computational Modeling
Fall 2004-2005 20213011 Introduction to Numerical Analysis
Fall 2004-2005 20225351 Selected Topics In Applied Scientific Computing
Fall 2004-2005 20214021 Project in Bioinformatics
Spring 2005 20214811 Topics in Bioinformatics 2

Research groups

Bioinformatics
Scientific Computing and Numerical Analysis

Education

1996  -  M.Sc  University of California, Davis (LLNL), Applied Science
1999  -  Ph.D  University of California, Davis (LLNL), Applied Science

Patents

A Low Complexity Method for Enhancing Compressibility and Visual-Quality of Scanned Document Images
Authors: R.P. Maurer, D. Barash. Assigned to Hewlett-Packard Co.
Filed with the US Patent and Trademark Office, Application serial number 09/675,270. Sept 29, 2000.
A Method for Compression of Scanned Document Images
Authors: R.P. Maurer, D. Barash, R.A. Burgin. Assigned to Hewlett-Packard Co.
Filed with the US Patent and Trademark Office, Application serial number 09/676,867. Sept 29, 2000.
Filtering in a Demosaicing Process
Authors: R. Keshet, D. Barash, D. Shaked, M. Elad, R. Kimmel. Assigned to Hewlett-Packard Co.
Filed with the US Patent and Trademark Office, Application serial number 09/843,834. April 30, 2001.
Method and Apparatus for Processing Sensor Images
Authors: R. Keshet, R.P. Maurer, Y. Hel-Or, D. Shaked, D. Barash. Assigned to Hewlett-Packard Co.
Filed with the US Patent and Trademark Office, Application serial number 10/096,025. March 11, 2002.

Selected publications all BibTex

 
Articles
A. Churkin, M. Drory-Retwitzer, V. Reinharz, Y. Ponty, J. Waldispuhl, D. Barash. Design of RNAs: Comparing Programs for Inverse RNA Folding. Briefings in Bioinformatics, In Press, 2016.
M. Drory-Retwitzer, V. Reinharz, Y. Ponty, J. Waldispuhl, D. Barash. IncaRNAfbinv: A Webserver for the Fragment-Based Design of RNA Sequences. Nucleic Acids Research, 44(W1):W308-W314, July 2016.
M. Drory-Retwitzer, I. Kifer, S. Sengupta, Z. Yakhini, D. Barash. An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PLOS One, 10(7):e0134262:1-18, July 2015.
M. Drory-Retwitzer , M. Polishchuk, E. Churkin , I. Kifer , Z. Yakhini , D. Barash. RNAPattMatch: A Webserver for RNA Sequence/Structure Motif Detection Based on Pattern Matching with Flexible Gaps. Nucleic Acids Research, 43(W1):W507-W512, July 2015.
A. Churkin, L. Weinbrand, D. Barash. Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design. Methods in Molecular Biology, 1269:3-16, 2015.
A. Churkin, D. Barash, M. Schechter. Acoustic Interactions between Inversion Symmetric and Asymmetric Two-Level Systems. Journal of Physics: Condensed Matter, 26:325401:1-6, 2014.
A. Churkin, D. Barash, M. Schechter. Non-Homogeneity of the Density of States of Tunneling Two-Level Systems at Low Energies. Physical Review B, 89:104202:1-5, 2014.
A. Churkin, A. Avihoo, M. Shapira, D. Barash. RNAthermsw: Direct Temperature Simulations for Predicting the Location of RNA Thermometers. PLOS One, 9(4):e94340:1-7, 2014.
A. Churkin, D. Barash. RNA Dot Plots: An Image Representation for RNA Secondary Structure Analysis and Manipulations. Wiley Interdisciplinary Reviews: RNA, 4:205-216, 2013. Advanced Review.
L. Weinbrand, A. Avihoo, D. Barash. RNAfbinv: An Interactive Java Application for Fragment-Based Design of RNA Sequences. Bioinformatics, 29(22):2938-2940, 2013.
A. Churkin, I. Gabdank, D. Barash. On Topological Indices for Small RNA Graphs. Computational Biology and Chemistry, 41:35-40, October 2012.
I. Aviram, I. Veltman, A. Churkin, D. Barash. Efficient Procedures for the Numerical Simulation of Mid-Size RNA Kinetics. Algorithms for Molecular Biology, 7:24, 2012.
A. Avihoo, A. Churkin, D. Barash. RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. BMC Bioinformatics, 12(319):24, August 2011.
A. Churkin, I. Gabdank, D. Barash. The RNAmute Web Server for the Mutational Analysis of RNA Secondary Structures. Nucleic Acids Research, 39(2):W92-W99, July 2011. Web Server Issue.
D. Barash, A. Churkin. Mutational Analysis in RNAs: Comparing Programs for RNA Deleterious Mutation Prediction. Briefings in Bioinformatics, 12(2):104-114, 2011. Software Review.
D. Barash, I. Gabdank. Energy Minimization Methods Applied to Riboswitches: A Perspective and Challenges. RNA Biology, 7(1):90-97, January 2010. Special Focus Review.
I. Gabdank, D. Barash, E.N. Trifonov. FineStr: A Web Server for Single-Base-Resolution Nucleosome Positioning. Bioinformatics, 26(6):845-846, March 2010.
I. Gabdank, D. Barash, E.N. Trifonov. Single-Base Resolution Nucleosome Mapping on DNA Sequences. Journal of Biomolecular Structure and Dynamics, 28(1):107-122, 2010.
A. Churkin, M. Cohen, Y. Shemer-Avni, D. Barash. Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements Across Genotypes Reveals Evidence for Direct Evolution of Genetic Robustness in HCV. Journal of Bioinformatics and Computational Biology, 8(6):1013-1026, 2010.
M. David, I. Gabdank, A. Ben David, A. Zilka, I. Orr, D. Barash, M. Shapira. Preferential Translation of Hsp83 in Leishmania Requires a Thermosensitive Polypyrimidine-Rich Element in the 3' UTR and Involves Scanning of the 5' UTR. RNA, 16(2):364-374, 2010.
T. Ivry, S. Michal, A. Avihoo, G. Sapiro, D. Barash. An Image Processing Approach to Computing Distances Between RNA Secondary Structures Dot Plots. Algorithms for Molecular Biology, 4(4), Feb 2009.
I. Gabdank, D. Barash, E.N. Trifonov. Nucleosome DNA Bendability Matrix (C. elegans). Journal of Biomolecular Structure and Dynamics, 26(4):403-412, 2009.
A. Churkin, D. Barash. An Efficient Method for the Prediction of Deleterious Multiple-Point Mutations in the Secondary Structure of RNAs Using Suboptimal Folding Solutions. BMC Bioinformatics, 9(222), April 2008.
N. Dromi, A. Avihoo, D. Barash. Reconstruction of Natural RNA Sequences from RNA Shape, Thermodynamic Stability, Mutational Robustness, and Linguistic Complexity by Evolutionary Computation. Journal of Biomolecular Structure and Dynamics, 26(1):147-162, August 2008.
I. Veksler-Lublinksy, D. Barash, C. Avisar, E. Troim, P. Chew, K. Kedem. FASH: A Web Application for Nucleotides Sequence Search. Source Code for Biology and Medicine, 3(9), 2008.
A. Cohen, S. Bocobza, I. Veksler-Lublinsky, I. Gabdank, D. Barash, A. Aharoni, M. Shapira, K. Kedem. Computational Identification of Three-Way Junctions in Folded RNAs: A Case Study in Arabidopsis. In Silico Biology, 8(2):105-120, 2008.
S. Michal, T. Ivry, O.S. Cohen, M. Sipper, D. Barash. Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(4):596-610, October 2007.
I. Veksler-Lublinsky, M. Ziv-Ukelson, D. Barash, K. Kedem. A Structure Based Flexible Search Method for Motifs in RNA. Journal of Computational Biology, 14(7):908-926, 2007.
D. Barash, J. Sikorski, L. Perry, E. Nevo, E. Nudler. Adaptive Mutations in RNA-based Regulatory Mechanisms: Computational and Experimental Investigations. Israel Journal of Ecology and Evolution, Special Issue with a Compendium on New Horizons in Evolutionary Biology, 52(3-4):263-279, 2007.
A. Avihoo, I. Gabdank, M. Shapira, D. Barash. In Silico Design of Small RNA Switches. IEEE Transactions on Nanobioscience, Special Issue on Computational Nanobioscience, 6(1):4-11, 2007.
A. Aouacheria, V. Navratil, R. Lopez-Perez, N.C. Gutierrez, A. Churkin, D. Barash, D. Mouchiroud, C. Gautier. In Silico Whole-Genome Screening for Caner-Related Single-Nucleotide Polymorphisms Located in Human mRNA Untranslated Regions. BMC Genomics, 8(2), 2007.
A. Churkin, D. Barash. RNAMute: RNA Secondary Structure Mutation Analysis Tool. BMC Bioinformatics, 7(221), April 2006.
I. Gabdank, D. Barash, E.N. Trifonov. Tracing Ancient mRNA Hairpins. Journal of Biomolecular Structure and Dynamics, 24(2):163-170, 2006.
E.N. Trifonov, I. Gabdank, D. Barash, Y. Sobolevsky. Primordia Vita. Deconvolution from Modern Sequences. Origins of Life and Evolution of Biospheres, 36(5-6):559-565, 2006.
A. Churkin, D. Barash. Structural Analysis of Single-Point Mutations Given an RNA Sequence. EURASIP Journal on Applied Signal Processing, Special Issue on Bioinformatics, 56246:1-7, 2006.
A. Avihoo, D. Barash. Shape Similarity Measures for the Design of Small RNA Switches. Journal of Biomolecular Structure and Dynamics, 24(1):17-24, 2006.
D. Barash. Nonlinear Diffusion Filtering on Extended Neighborhood. Applied Numerical Mathematics, 52(1):1-11, 2005.
D. Barash. Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. Journal of Computational Biology, 11(6):1169-1174, 2004.
O.Bergig, D.Barash, E.Nudler, K.Kedem. STR2: A Structure to String Approach for Locating G-box Riboswitches in Pre-Selected Genes. In Silico Biology, 4(4):593-604, 2004.
D. Barash. Second Eigenvalue of the Laplacian Matrix for Predicting RNA Conformational Switch by Mutation. Bioinformatics, 20(12):1861-1869, 2004.
D. Barash, D. Comaniciu. A Common Framework for Nonlinear Diffusion, Adaptive Smoothing, Bilateral Filtering and Mean Shift. Journal of Image and Vision Computing, 22(1):73-81, 2004.
D.Strahs, D.Barash, X.Qian, T.Schlick. Sequence-Dependent Solution Structure and Motions of 13 TATA/TBP Complexes. Biopolymers, 69:216-243, 2003.
D.Barash, L.Yang, X.Qian, T.Schlick. Inherent Speedup Limitations in Multiple Timestep/Particle Mesh Ewald Algorithms. Journal of Computational Chemistry, 24(1):77-88, 2003.
D. Barash. Deleterious Mutation Prediction in the Secondary Structure of RNAs. Nucleic Acids Research, 31(22):6578-6584, 2003.
D.Barash, T.Schlick, M.Israeli, R.Kimmel. Multiplicative Operator Splitting in Nonlinear Diffusion: from Spatial Splitting to Multiple Timesteps. Journal of Mathematical Imaging and Vision, 19(1):33-48, 2003.
D.Barash. A Fundamental Relationship between Bilateral Filtering, Adaptive Smoothing and the Nonlinear Diffusion Equation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 24(6):844-847, 2002.
D.Barash, A.E.Orel, R.Baer. Laser Induced Resonance States as Dynamic Suppressors of Ionization in High Frequency Short Pulses. Physical Review A, 61:013402, 2000.
D.Barash, A.E.Orel, R.V.Vemuri. A Genetic Search in Frequency Space to Stabilize Atoms by High-Intensity Laser Fields. Journal of Computing and Information Technology, 8(2):103-113, 2000.
D.Barash, A.E.Orel, R.Baer. A comment on the Stabilization of a One-Dimensional Short-Range Model Atom in Intense Laser Fields. Journal of Physics B: Atomic, Molecular and Optical Physics, 33:1279-1282, 2000.
 
Articles In Collection
D. Barash, D. Comaniciu. A Common Viewpoint on Broad Kernel Filtering and Nonlinear Diffusion. In Proceedings of the 4th International Conference on Scale-Space Theories in Computer Vision, LNCS Series, pages 683-698, Springer-Verlag, 2003.
D. Barash. Bilateral Filtering and Anisotropic Diffusion: Towards a Unified Viewpoint. In Proceedings of the 3rd International Conference on ScaleSpace and Morphology, LNCS Series, pages 273-280, Springer-Verlag, 2001.
D. Barash, M. Israeli, R. Kimmel. An Accurate Operator Splitting Scheme for Nonlinear Diffusion Filtering. In Proceedings of the 3rd International Conference on ScaleSpace and Morphology, LNCS Series, pages 281-289, Springer-Verlag, 2001.