Danny Barash's Journal Publications in Chronological Order (November 2016)

  • A. Churkin, M. Drory-Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash. Design of RNAs: Comparing Programs for Inverse RNA Folding. Briefings in Bioinformatics, In Press, 2016. [PDF File 468K]
  • M. Drory-Retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, D. Barash. IncaRNAfbinv: A Webserver for the Fragment-Based Design of RNA Sequences. Nucleic Acids Research, 44(W1), W308-W314 (2016). Web Server Issue. [PDF File 1652K]
  • 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 (2015). [PDF File 3396K]
  • 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 (2015). Web Server Issue. [PDF File 2052K]
  • 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). [HTML Page]
  • A. Churkin, D. Barash, M. Schechter. Acoustic Interactions between Inversion Symmetric and Asymmetric Two-Level Systems. Journal of Physics: Condensed Matter, 26(32):325401 (2014). [PDF File 788K]
  • A. Churkin, A. Avihoo, M. Shapira, D. Barash. RNAthermsw: Direct Temperature Simulations for Predicting the Location of RNA Thermometers. PLOS One, 9(4):e94340 (2014). [PDF File 590K]
  • 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 (2014). [PDF File 761K]
  • 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. [PDF File 490K]
  • L. Weinbrand, A. Avihoo, D. Barash. RNAfbinv: An Interactive Java Application for Fragment-Based Design of RNA Sequences. Bioinformatics, 29(22), 2938-2940 (2013). [PDF File 180K]
  • A. Churkin, I. Gabdank, D. Barash. On Topological Indices for Small RNA Graphs. Computational Biology and Chemistry, 41, 35-40 (2012). [PDF File 664K]
  • 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). [PDF File 1351K]
  • A. Avihoo, A. Churkin, D. Barash. RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. BMC Bioinformatics, 12:319 (2011). [PDF File 634K]
  • 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 (2011). Web Server Issue. [PDF File 715K]
  • 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. [PDF File 775K]
  • D. Barash, I. Gabdank. Energy Minimization Methods Applied to Riboswitches: A Perspective and Challenges. RNA Biology, 7(1), 90-97 (2010). Special Focus Review. [PDF File 640K]
  • I. Gabdank, D. Barash, E.N. Trifonov. FineStr: A Web server for Single-Base-Resolution Nucleosome Positioning. Bioinformatics, 26(6), 845-846 (2010). [PDF File 155K]
  • 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). [PDF File 1049K]
  • M. David, I. Gabdank, M. 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), 364-274 (2010). [PDF File 868K]
  • I. Gabdank, D. Barash, E.N. Trifonov. Single-Base Resolution Nucleosome Mapping of DNA Sequences. Journal of Biomolecular Structure and Dynamics, 28(1), 107-122 (2010). [PDF File 6070K]
  • 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 (2009). [PDF File 918K]
  • I. Gabdank, D. Barash, E.N. Trifonov. Nucleosome DNA Bendability Matrix (C. elegans) . Journal of Biomolecular Structure and Dynamics, 26(4), 403-412 (2009). [PDF File 1086K]
  • 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 (2008). [PDF File 1151K]
  • 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 (2008). [PDF File 2374K]
  • I. Veksler-Lublinsky, 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). [PDF File 613K]
  • 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). [PDF File 164K]
  • S. Michal, T. Ivry, O. Shalit, 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 (2007). [PDF File 4140K]
  • 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). [PDF File 486K]
  • A. Avihoo, I. Gabdank, M. Shapira, D. Barash. In Silico Design of Small RNA Switches. IEEE Transactions on Nanobiosciences, Special issue on Computational Nanobioscience, 6(1), 4-11 (2007). [PDF File 933K]
  • A. Aouacheria, V. Navratil, R. Lopez-Perez, N.C. Gutierrez, A. Churkin, D. Barash, D. Mouchiroud, C. Gautier. In Silico Whole-Genome Screening for Cancer Related Single-Nucleotide Polymorphisms Located in Human mRNA Untranslated Regions. BMC Genomics, 8:2 (2007). [PDF File 387K]
  • 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 the International Conference on New Horizons in Evolutionary Biology, 52(3-4), 263-279 (2007). [PDF File 954K]
  • A. Churkin, D. Barash. RNAMute: RNA Secondary Structure Mutation Analysis Tool. BMC Bioinformatics, 7:221 (2006). [PDF File 1252K]
  • A. Avihoo, D. Barash. Shape Similarity for the Design of Small RNA Switches. Journal of Biomolecular Structure and Dynamics, 24(1), 17-24 (2006). [PDF File 553K]
  • I. Gabdank, D. Barash, E.N. Trifonov. Tracing Ancient mRNA Hairpins. Journal of Biomolecular Structure and Dynamics, 24(2), 163-170 (2006). [PDF File 697K]
  • A. Churkin, D. Barash. Structure Analysis of Single Point Mutations Given an RNA Sequence: A Case Study with RNAMute. EURASIP Journal of Applied Signal Processing, Special Issue on Bioinformatics Methods, 2006:56246, 1-7 (2006). [PDF File 1394K]
  • E.N. Trifonov, I. Gabdank, D. Barash, Y. Sobolevsky. Primordia Vita. Deconvolution from Modern Sequences. Origins of Life and Evolution of Biospheres, 36(5), 559-565 (2006). [PDF File 1864K]
  • D. Barash. Nonlinear Diffusion Filtering on Extended Neighborhood. Applied Numerical Mathematics, 52(1), 1-11 (2005). [PDF File 461K]
  • 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). [HTML Page]
  • D. Barash. Spectral Decomposition for the Search and Analysis of RNA Secondary Structure. Journal of Computational Biology, 11(6), 1169-1174 (2004). [PDF File 77K]
  • D. Barash. Second Eigenvalue of the Laplacian Matrix for Predicting RNA Conformational Switch by Mutation. Bioinformatics, 20(12), 1861-1869 (2004). [PDF File 209K]
  • 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). [PDF File 309K]
  • D. Barash. Deleterious Mutation Prediction in the Secondary Structure of RNAs. Nucleic Acids Research, 31(22), 6578-6584 (2003). [PDF File 186K]
  • 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). [PDF File 716K]
  • D. Barash, L. Yang, X. Qian, T. Schlick. Inherent Speedup Limitations in Multiple Timestep/Particle Mesh Ewald . Journal of Computational Chemistry, 14(7), 908-926 (2003). [PDF File 507K]
  • D. Strahs, D. Barash, X. Qian, T. Schlick. Sequence-Dependent Solution Structure and Motions of 13 TATA/TBP Complexes. Biopolymers, 69, 216-243 (2003). [PDF File 5412K]
  • 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). [PDF File 417K]
  • 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). [PDF File 62K]
  • 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). [PDF File 57K]
  • 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). [PDF File 202K]

 

Copyright Danny Barash. (Updated November 2016)