Publications

Selected Publications

  • Z. Fox, G. Neuert and B. MunskyFinite 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. MunskyUsing 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. MunskyThe 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. MunskyFinite 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. MunskyUsing 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]