Journal_Papers

Danny Barash's Journal Publications in Chronological Order (November 2023)

S. Mukherjee, D. Barash. Designing RNA Switches for Synthetic Biology using Inverse RNA Folding. Trends in Biotechnology, In Press (2023).
A. Hailegiorgis, Y. Ishida, N. Collier, M. Imamura, U. Kumar, V. Reinharz, M. Tsuge, D. Barash, N, Hiraga, H. Yokomichi, C. Tateno, J. Ozik, S.L. Uprichard, K. Chayama, H. Dahari.Understanding Multiphasic Hepatitis B Virus Kinetic Patterns in Humanized Chimeric Mice Via Quantized Viral Production Mathematical Modeling Approach. PLOS Computational Biology, 19(8),e1011309 (2023). [PDF File 2939K]
S. Mukherjee, M. Drory-Retwitzer, S.M. Hubbell, M.M. Meyer, D. Barash. A Computational Approach for the Identification of Distant Homologs of Bacterial Riboswitches based on Inverse RNA Folding. Briefings in Bioinformatics, 24(3),bbad110:1-12 (2023). [PDF File 2559K]
A. Churkin, D. Barash. Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels. Mathematics Journal, Special Issue on Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels, 10(23),4446 (2022). [PDF File 1049K]
A. Mhlanga, R. Zakh, A. Churkin, V. Reinharz, J.S. Glenn, O. Etzion, S.J. Cotler, C. Yudaydin, D. Barash, H. Dahari. Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients. Mathematics Journal, Special Issue on Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels, 10(20),3917 (2022). [PDF File 6579K]
A. Churkin, Y. Ponty, D. Barash. IndelsRNAmute: An Application for Predicting RNA Deleterious Multiple Point Substitutions and Indels Mutations. BMC Bioinformatics, 23:424 (2022). [PDF File 2556K]
V. Reinharz, A. Churkin, H. Dahari, D. Barash. Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics. Mathematics Journal, Special Issue on Selected Papers from the 19th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2021), 10,2136 (2022). [PDF File 1717K]
A. Goyal, A. Churkin, D. Barash, S.J. Cotler, A. Shlomai, O. Etzion, H. Dahari. Modeling-Based Response-Guided DAA Therapy for Chronic Hepatitis C to Identify Individuals for Shortening Treatment Duration. Open Forum Infections Diseases, 9(5):1-4 (2022). [PDF File 393K]
S. Mukherjee, Z. Kuang, S. Ghosh, R. Detroja, G. Carmi, S. Tripathy, D. Barash, M. Frenkel-Morgenstern, E. Nevo, K. Li. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-coding RNAs Analysis. Biology Journal, 11(8),110 (2022). [PDF File 3372K]
A. Churkin, S. Kriss, A. Uziel, A. Goyal, R. Zakh, S.J. Cotler, O. Etzion, A. Shlomai, H.G. Rotstein, H. Dahari, D. Barash. Machine Learning for Mathematical Models of HCV Kinetics During Antiviral Therapy. Mathematical Biosciences, 343,108756 (2022). [PDF File 1549K]
R. Zakh, A. Churkin, W. Bietsch, M. Lachiany, S.J. Cotler, A. Ploss, H. Dahari, D. Barash. A Mathematical Model for Early HBV and -HDV Kinetics during Anti-HDV Treatment. Mathematics Journal, Special Issue on Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels, 9(24),3323 (2021). [PDF File 691K]
R. Zakh, A. Churkin, F. Totzeck, M. Parr, T. Tuller, O. Etzion, H. Dahari, M. Roggendorf, D. Frishman, D. Barash. A Mathematical Analysis of HDV Genotypes: From Molecules to Cells. Mathematics Journal, Special Issue on Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels, 9(17),2063 (2021). [PDF File 785K]
A. Churkin, F. Totzeck, R. Zakh, M. Parr, T. Tuller, D. Frishman, D. Barash. A Mathematical Analysis of RNA Structural Motifs in Viruses. Mathematics Journal, Special Issue on Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels, 9(6),585 (2021). [PDF File 2659K]
A. Churkin, S. Lewkiewicz, V. Reinharz, H. Dahari, D. Barash. Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics. Mathematics Journal, Special Issue on Mathematical Modelling in Biomedicine, 8(9),1483 (2020). [PDF File 4195K]
E. Gorstein, M. Martinello, A. Churkin, S. Dasgupta, K. Walsh, T.L. Applegate, D. Yardeni, O. Etzion, S.L. Uprichard, D. Barash, S.J. Cotler, G.V. Matthews, H. Dahari. Modeling Based Response Guided Therapy in Subjects with Recent Hepatitis C Infection. Antiviral Research, 180:104862 (2020). [PDF File 691K]
S. Dasgupta, M. Imamura, E. Gorstein, T. Nakahara, M. Tsuge, A. Churkin, D. Yardeni, O. Etzion, S.L. Uprichard, D. Barash, S.J. Cotler, H. Dahari, K. Chayama. Modeling-Based Response-Guided Glecaprevir-Pibrentasvir Therapy for Chronic Hepatitis C to Identify Patients for Ultrashort Treatment Duration. Journal of Infectious Diseases, 222(7):1165-1169 (2020). [PDF File 1333K]
M. Drory-Retwitzer, V. Reinharz, A. Churkin, Y. Ponty, J. Waldispühl, D. Barash. IncaRNAfbinv 2.0: A Webserver and Software with Motif Control for Fragment-Based Design of RNAs. Bioinformatics, 36(9):2920-2922 (2020). [PDF File 354K]
V. Reinharz, A. Churkin, S. Lewkiewicz, H. Dahari, D. Barash. A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics. Bulletin of Mathematical Biology, 81(10):3675-3721 (2019). [PDF File 2098K]
S. Mukherjee, S.D. Mandal, N. Gupta, M. Drory-Retwitzer, D. Barash, S. Sengupta. RiboD: A Comprehensive Database for Prokaryotic Riboswitches. Bioinformatics, 35(18):3541-3543 (2019). [PDF File 170K]
R. Ben-Hamo, A. Zilberberg, H. Cohen, K. Bahar-Shany, C. Wachtel, J. Korach, S. Aviel-Ronen, I. Barshack, D. Barash, K. Levanon, S. Efroni. Resistance to Paclitaxel is Associated with a Variant of the Gene BCL2 in Multiple Tumor Types. NPJ Precision Oncology, 3:12 (2019). [PDF File 1835K]
V. Reinharz, H. Dahari, D. Barash. Numerical Schemes for Solving and Optimizing Multiscale Models with Age of Hepatitis C Virus Dynamics. Mathematical Biosciences, 300: 1-13 (2018). [PDF File 552K]
S. Mukherjee, M. Drory-Retwitzer, D. Barash, S. Sengupta. Phylogenomic and Comparative Analysis of the Distribution and Regulatory Patterns of TPP Riboswitches in Fungi. Scientific Reports, 8(1):5563 (2018). [PDF File 4080K]
V. Reinharz, A. Churkin, H. Dahari, D. Barash. A Robust and Efficient Numerical Method for RNA-mediated Viral Dynamics . Frontiers in Applied Mathematics and Statistics, section on Mathematics of Biomolecules, 3(20) (2017). [PDF File 3004K]
S. Mukherjee, D. Barash, S. Sengupta. Comparative Genomics and Phylogenomic Analyses of Lysine Riboswitch Distributions in Bacteria . PLOS One, 12(9):e0184314 (2017). [PDF File 8607K]
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, bbw120, 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). [PDF File 185K]
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]