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Items: 30

1.

Computational design and interpretation of single-RNA translation experiments.

Aguilera LU, Raymond W, Fox ZR, May M, Djokic E, Morisaki T, Stasevich TJ, Munsky B.

PLoS Comput Biol. 2019 Oct 16;15(10):e1007425. doi: 10.1371/journal.pcbi.1007425. [Epub ahead of print]

2.

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition.

Thompson J, Johansen R, Dunbar J, Munsky B.

PLoS One. 2019 Jul 1;14(7):e0215502. doi: 10.1371/journal.pone.0215502. eCollection 2019.

3.

Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation.

Tanhaemami M, Alizadeh E, Sanders CK, Marrone BL, Munsky B.

Phys Biol. 2019 Jul 22;16(5):055001. doi: 10.1088/1478-3975/ab2c60.

PMID:
31234155
4.

Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting.

Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ.

Mol Cell. 2019 Jul 11;75(1):172-183.e9. doi: 10.1016/j.molcel.2019.05.002. Epub 2019 Jun 6.

PMID:
31178355
5.

Bayesian Estimation for Stochastic Gene Expression Using Multifidelity Models.

Vo HD, Fox Z, Baetica A, Munsky B.

J Phys Chem B. 2019 Mar 14;123(10):2217-2234. doi: 10.1021/acs.jpcb.8b10946. Epub 2019 Mar 5.

PMID:
30777763
6.

The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments.

Fox ZR, Munsky B.

PLoS Comput Biol. 2019 Jan 15;15(1):e1006365. doi: 10.1371/journal.pcbi.1006365. eCollection 2019 Jan.

7.

Distribution shapes govern the discovery of predictive models for gene regulation.

Munsky B, Li G, Fox ZR, Shepherd DP, Neuert G.

Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):7533-7538. doi: 10.1073/pnas.1804060115. Epub 2018 Jun 29.

8.

Identification of gene regulation models from single-cell data.

Weber L, Raymond W, Munsky B.

Phys Biol. 2018 May 18;15(5):055001. doi: 10.1088/1478-3975/aabc31.

9.

Adsorption-Coupled Diffusion of Gold Nanoclusters within a Large-Pore Protein Crystal Scaffold.

Hartje LF, Munsky B, Ni TW, Ackerson CJ, Snow CD.

J Phys Chem B. 2017 Aug 17;121(32):7652-7659. doi: 10.1021/acs.jpcb.7b03999. Epub 2017 Aug 7.

PMID:
28714685
10.

The finite state projection approach to analyze dynamics of heterogeneous populations.

Johnson R, Munsky B.

Phys Biol. 2017 May 11;14(3):035002. doi: 10.1088/1478-3975/aa6e5a.

11.

Finite state projection based bounds to compare chemical master equation models using single-cell data.

Fox Z, Neuert G, Munsky B.

J Chem Phys. 2016 Aug 21;145(7):074101. doi: 10.1063/1.4960505.

12.

The eighth q-bio conference: meeting report and special issue preface.

Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O.

Phys Biol. 2015 Dec 30;12(6):060401. doi: 10.1088/1478-3975/12/6/060401. No abstract available.

PMID:
26716953
13.

From analog to digital models of gene regulation.

Munsky B, Neuert G.

Phys Biol. 2015 Jun 18;12(4):045004. doi: 10.1088/1478-3975/12/4/045004. Review.

14.

Using noise to control heterogeneity of isogenic populations in homogenous environments.

Szymańska P, Gritti N, Keegstra JM, Soltani M, Munsky B.

Phys Biol. 2015 Jun 18;12(4):045003. doi: 10.1088/1478-3975/12/4/045003.

15.

Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics.

Munsky B, Fox Z, Neuert G.

Methods. 2015 Sep 1;85:12-21. doi: 10.1016/j.ymeth.2015.06.009. Epub 2015 Jun 12. Review.

16.

The Seventh q-bio Conference: meeting report and preface.

Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y.

Phys Biol. 2014 Aug;11(4):040301. doi: 10.1088/1478-3975/11/4/040301. Epub 2014 Jul 30. No abstract available.

17.

Transcription factors modulate c-Fos transcriptional bursts.

Senecal A, Munsky B, Proux F, Ly N, Braye FE, Zimmer C, Mueller F, Darzacq X.

Cell Rep. 2014 Jul 10;8(1):75-83. doi: 10.1016/j.celrep.2014.05.053. Epub 2014 Jun 26.

18.

Perspective on the q-bio Summer School and Conference: 2007 - 2014 and beyond.

Resnekov O, Munsky B, Hlavacek WS.

Quant Biol. 2014 Mar 1;2(1):54-58. No abstract available.

19.

Special section dedicated to The Sixth q-bio Conference: meeting report and preface.

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR.

Phys Biol. 2013 Jun;10(3):030301. doi: 10.1088/1478-3975/10/3/030301. Epub 2013 Jun 4. No abstract available.

PMID:
23735417
20.

Counting small RNA in pathogenic bacteria.

Shepherd DP, Li N, Micheva-Viteva SN, Munsky B, Hong-Geller E, Werner JH.

Anal Chem. 2013 May 21;85(10):4938-43. doi: 10.1021/ac303792p. Epub 2013 Apr 25.

PMID:
23577771
21.

Systematic identification of signal-activated stochastic gene regulation.

Neuert G, Munsky B, Tan RZ, Teytelman L, Khammash M, van Oudenaarden A.

Science. 2013 Feb 1;339(6119):584-7. doi: 10.1126/science.1231456.

22.

Ribozyme-based insulator parts buffer synthetic circuits from genetic context.

Lou C, Stanton B, Chen YJ, Munsky B, Voigt CA.

Nat Biotechnol. 2012 Nov;30(11):1137-42. doi: 10.1038/nbt.2401. Epub 2012 Oct 3.

23.

Using gene expression noise to understand gene regulation.

Munsky B, Neuert G, van Oudenaarden A.

Science. 2012 Apr 13;336(6078):183-7. doi: 10.1126/science.1216379. Review.

24.

Identification from stochastic cell-to-cell variation: a genetic switch case study.

Munsky B, Khammash M.

IET Syst Biol. 2010 Nov;4(6):356-66. doi: 10.1049/iet-syb.2010.0013.

PMID:
21073235
25.

The simplicity of completion time distributions for common complex biochemical processes.

Bel G, Munsky B, Nemenman I.

Phys Biol. 2009 Dec 21;7(1):016003. doi: 10.1088/1478-3975/7/1/016003.

PMID:
20026876
26.

Specificity and completion time distributions of biochemical processes.

Munsky B, Nemenman I, Bel G.

J Chem Phys. 2009 Dec 21;131(23):235103. doi: 10.1063/1.3274803. Erratum in: J Chem Phys. 2012 May 28;136(20):209902.

PMID:
20025351
27.

Listening to the noise: random fluctuations reveal gene network parameters.

Munsky B, Trinh B, Khammash M.

Mol Syst Biol. 2009;5:318. doi: 10.1038/msb.2009.75. Epub 2009 Oct 13.

28.

Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks.

Munsky B, Khammash M.

IET Syst Biol. 2008 Sep;2(5):323-33. doi: 10.1049/iet-syb:20070082.

PMID:
19045827
29.

Reduction and solution of the chemical master equation using time scale separation and finite state projection.

Peles S, Munsky B, Khammash M.

J Chem Phys. 2006 Nov 28;125(20):204104.

PMID:
17144687
30.

The finite state projection algorithm for the solution of the chemical master equation.

Munsky B, Khammash M.

J Chem Phys. 2006 Jan 28;124(4):044104.

PMID:
16460146

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