Selected Publications
Z. Fox, G. Neuert and B. Munsky, Finite state projection based bounds to compare chemical master equation models using single-cell data, Journal of Chemical Physics, 145:7, 074101 (2016), online here
P. Szymanska, N. Gritti, J. M. Keegstra, M. Soltani and B. Munsky, Using noise to control heterogeneity of isogenic populations in homogenous environments, Physical Biology, 12:4, 045003 (2015), online here
B. Munsky, Z. Fox, G. Neuert, Integrating Single-Molecule Experiments and Discrete Stochastic Models to Understand Heterogeneous Gene Transcription, Methods, 85, 12-21, (2015), online here
A Senecal, B Munsky, F Proux, N Ly, FE Braye, C Zimmer, F Mueller, X Darzacq, Transcription Factors Modulate c-Fos Transcriptional Bursts, Cell Reports, 8:1, 75-83 (2014), online here
D Shepherd, N Li, S N Micheva-Viteva, B Munsky, E Hong-Geller, J H Werner, Counting Small RNA in Pathogenic Bacteria, Analytical Chemistry, 85:10, 4938-4943 (2013) (Cover Article), reprint (.pdf)
G Neuert, B Munsky, R-Z Tan, L Teytelman, M Khammash, A van Oudenaarden, Systematic Identification of Signal-Activated Stochastic Gene Regulation, Science, 339:6119, 584-587 (2013). reprint (.pdf)
Munsky, B., Neuert, G., van Oudenaarden, A., Using Gene Expression Noise to Understand Gene Regulation, Science, 336:6078, 183-187, (2012). reprint (.pdf)
Lou, C., Stanton, B., Chen, Y-C., Munsky, B., Voigt, C. A., Ribozyme-based "insulator parts" buffer synthetic circuits from genetic context, Nature Biotechnology, 30:11, 1137-1142 (2012). reprint (.pdf)
Munsky, B., Modeling Cellular Variability, in Quantitative Biology From Molecular to Cellular Systems, pp. 234-266, M. Wall, Ed. (Taylor & Francis Group, New York, 2012). preprint (.pdf)
Bel, G., Munsky, B., Nemenman, I., Simplicity of Completion Time Distributions for Common Complex Biochemical Processes, Physical Biology, 7:016003 (2010). reprint (.pdf)
Munsky, B., Trinh, B., Khammash, M., Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters, Molecular Systems Biology, 5:318 (2009). reprint (.pdf) [Journal Site]
Munsky, B., Khammash, M., The FSP Approach for the Analysis of Stochastic Noise in Gene Networks, IEEE Transactions on Automatic Control, 53, 201-214 (2008). reprint (.pdf)
Munsky, B., Khammash, M., The Finite State Projection Algorithm for the Solution of the Chemical Master Equation, Journal of Chemical Physics, 124 :044104 (2006). reprint (.pdf)
Publications by Year
2017
R. Johnson and B. Munsky, The finite state projection approach to analyze dynamics of heterogeneous populations, Physical Biology, 14:3, 035002 (2017), online here
L.F. Hartje, B. Munsky, T.W. Ni, CJ Ackerson, C.D. Snow, Adsorption-Coupled Diffusion of Gold Nanoclusters Within a Large-Pore Protein Crystal Scaffold, J Physical Chemistry B, XX:X, (2017), PubMed Entry
2016
Z. Fox, G. Neuert and B. Munsky, Finite state projection based bounds to compare chemical master equation models using single-cell data, Journal of Chemical Physics, 145:7, 074101 (2016), online here
2015
P. Szymanska, N. Gritti, J. M. Keegstra, M. Soltani and B. Munsky, Using noise to control heterogeneity of isogenic populations in homogenous environments, Physical Biology, 12:4, 045003 (2015), online here
B. Munsky, Z. Fox, G. Neuert, Integrating Single-Molecule Experiments and Discrete Stochastic Models to Understand Heterogeneous Gene Transcription, Methods, 85, 12-21, (2015), online here
B. Munsky, G. Neuert, From analog to digital models of gene regulation, Physical Biology, 12:4, 045004, (2015), online here
2014
A Senecal, B Munsky, F Proux, N Ly, FE Braye, C Zimmer, F Mueller, X Darzacq, Transcription Factors Modulate c-Fos Transcriptional Bursts, Cell Reports, 8:1, 75-83 (2014), online here
O Resnekov, B Munsky, WS Hlavacek, Perspective on the q-bio Summer School and Conference: 2007-2014 and beyond, Quantitative Biology, 2:1, 54-58, online here
2013
D Shepherd, N Li, S N Micheva-Viteva, B Munsky, E Hong-Geller, J H Werner, Counting Small RNA in Pathogenic Bacteria, Analytical Chemistry, 85:10, 4938-4943 (2013) (Cover Article), reprint (.pdf)
G Neuert, B Munsky, R-Z Tan, L Teytelman, M Khammash, A van Oudenaarden, Systematic Identification of Signal-Activated Stochastic Gene Regulation, Science, 339:6119, 584-587 (2013). reprint (.pdf)
Nemenman, I., Gnanakaran, S.,Munsky, B., Wall, M.E., Jiang, Y., Hlavacek, W.S., Faeder. J. The Fifth Annual q-bio Conference on Cellular Information Processing, Physical Biology, 9:050201, 2012. reprint (.pdf)
2012
Munsky, B., Neuert, G., van Oudenaarden, A., Using Gene Expression Noise to Understand Gene Regulation, Science, 336:6078, 183-187, (2012). reprint (.pdf)
Lou, C., Stanton, B., Chen, Y-C., Munsky, B., Voigt, C. A., Ribozyme-based "insulator parts" buffer synthetic circuits from genetic context, Nature Biotechnology, 30:11, 1137-1142 (2012). reprint (.pdf)
Munsky, B., Modeling Cellular Variability, in Quantitative Biology From Molecular to Cellular Systems, pp. 234-266, M. Wall, Ed. (Taylor & Francis Group, New York, 2012). preprint (.pdf)
DP Shepherd, N Li, E Hong-Geller, B Munsky, JH Werner, New tools for discovering the role sRNA plays in cellular regulation, Proc. SPIE, 8228:822808, (2012). preprint (.pdf)
Tapia, J., Faeder, J., Munsky, B., Adaptive Coarse-Graining for Transient and Quasi-Equilibrium Analyses of Stochastic Gene Regulation, Proc. of the 51st IEEE Conference on Decision and Control, 5361-5366, Maui, HI, Dec. 2012. reprint (.pdf)
Nemenman, I., Gnanakaran, S., Hlavacek, W., Jiang, Y., Munsky, B., Wall, M., Faeder. J. The Fifth Annual q-bio Conference on Cellular Information Processing, Physical Biology, 9:050201, 2012. reprint (.pdf)
2010
Bel, G., Munsky, B., Nemenman, I., Simplicity of Completion Time Distributions for Common Complex Biochemical Processes, Physical Biology, 7:016003 (2010). reprint (.pdf)
Munsky, B., Khammash, M., Identification from stochastic cell-to-cell variation: A genetic switch case study, IET Systems Biology, 4:6, 356-366 (2010). reprint (.pdf)
Khammash, M. Munsky, B., Stochastic Gene Expression: Modeling, Analysis, and Identification, in The Control Handbook, B. Levine, Ed. (Taylor & Francis Group, New York, NY, Second Edition, 2010). preprint (.pdf)
2009
Munsky, B., Trinh, B., Khammash, M., Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters, Molecular Systems Biology, 5:318 (2009). reprint (.pdf) [Journal Site]
Munsky, B., Nemenman, I. Bel, G., Specificity and Completion Time Distributions of Biochemical Processes, Journal of Chemical Physics, 131, No. 235104 (2009). reprint (.pdf)
2008
Munsky, B., Khammash, M., The FSP Approach for the Analysis of Stochastic Noise in Gene Networks, IEEE Transactions on Automatic Control, 53, 201-214 (2008). reprint (.pdf)
Munsky, B., Khammash, M., Transient Analysis of Stochastic Switches and Trajectories with Applications to Gene Regulatory Networks, IET Systems Biology, 2, No. 2, 323-333 (2008).[.pdf] [IEEE Site]
Munsky, B., Khammash, M., Using Noise Transmission Properties to Identify Stochastic Gene Regulatory Networks, Proc. 46th IEEE Conference on Decision and Control, Cancun, Mexico (2008).[.pdf]
Munsky, B., Khammash, M., Computation of Switch Time Distributions in Stochastic Gene Regulatory Networks, Proc. 2008 American Control Conference, THB10.2, Seattle, WA.[.pdf]
2007
Inglesias, P., Khammash, M., Munsky, B., Sontag, E., Del Vecchio, D., Systems Biology and Control - A Tutorial, Proc. 45th IEEE Conference on Decision and Control, New Orleans, LA (2007).[.pdf]
Munsky, B., Khammash, M., A Multiple Time Interval Finite State Projection Algorithm for the Solution to the Chemical Master Equation, Journal of Computational Physics, 226, 818-835 (2007).[.pdf]
Munsky, B., Khammash, M., Analysis of Noise Induced Stochastic Fluctuations in Gene Regulatory Networks , J. SICE, 5, 405-411 (2007).[.pdf]
Peles, S., Munsky, B., Khammash, M., Reduction and Solution of the Chemical Master Equation Using Time Scale Separation and Finite State Projection, Journal of Chemical Physics, 125, 204104 (2007).[.pdf]
2006
Munsky, B., Khammash, M., The Finite State Projection Algorithm for the Solution of the Chemical Master Equation, Journal of Chemical Physics, 124 :044104 (2006). reprint (.pdf)
Munsky, B., Khammash, M., A Reduced Model Solution for the Chemical Master Equation Arising in Stochastic Analyses of Biological Networks, Proc. 45th IEEE Conference on Decision and Control, San Diego, CA (2006).[.pdf]
Munsky, B., Khammash, M., The Finite State Projection Algorithm for the Solution of the Chemical Master Equation, Journal of Chemical Physics, 124 , 044104 (2006).[.pdf]
Khammash, M., Munsky, B., Systems Theory Applications in Biology: From Stochastic Chemical Kinetics to Deterministic Model Invalidation, Invited paper-European Control Conference, Kos, Greece (2007).[.pdf]
