Peter Swain

2025

Quantifying the nuclear localisation of fluorescently tagged proteins

Hurbain, J., ten Wolde, P. R. & Swain, P. S., 12 May 2025, (E-pub ahead of print) In: Bioinformatics Advances. 14 p., vbaf114.

Research output: Contribution to journal › Article › peer-review

Open Access

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The type of carbon source not the growth rate it supports can determine diauxie in Saccharomyces cerevisiae

Huo, Y., Danecka, W., Farquhar, I., Mailliet, K., Moses, T., Wallace, E. W. J. & Swain, P. S., 27 Feb 2025, In: Communications Biology. 8, 1, 11 p., 325.

Research output: Contribution to journal › Article › peer-review

Open Access

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2024

Escherichia coli maintains pH via the membrane potential

Terradot, G., Krasnopeeva, E., Swain, P. S. & Pilizota, T., 27 Nov 2024, In: PRX Life. 2, 12 p., 043015.

Research output: Contribution to journal › Article › peer-review

Open Access

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2023

Nunchaku: Optimally partitioning data into piece-wise contiguous segments

Huo, Y., Li, H., Wang, X., Du, X. & Swain, P. S., 15 Nov 2023, (E-pub ahead of print) In: Bioinformatics. 39, 12, 8 p., btad688.

Research output: Contribution to journal › Article › peer-review

Open Access

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Determining growth rates from bright-field images of budding cells through identifying overlaps

Pietsch, J. M., Munoz, A. F., Adjavon, D.-Y. A., Farquhar, I., Clark, I. B. & Swain, P. S., 26 Jul 2023, In: eLIFE. 12, e79812.

Research output: Contribution to journal › Article › peer-review

Open Access

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2022

Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Montano Gutierrez, L. F., Manzanaro Moreno, N., Farquhar, I., Huo, Y., Bandiera, L. & Swain, P. S., 26 May 2022, In: PLoS Computational Biology. 18, 5, 12 p., e1010138.

Research output: Contribution to journal › Article › peer-review

Open Access

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Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff

Montano Gutierrez, L. F., Correia, K. & Swain, P. S., 25 Apr 2022, In: PLoS Computational Biology. 18, 4, 15 p., e1010060.

Research output: Contribution to journal › Article › peer-review

Open Access

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2021

Roadmap on biology in time varying environments

Murugan, A., Husain, K., Rust, M., Bass, J. T., Hepler, C., Pietsch, J., Swain, P. S., Jena, S. G., Toettcher, J. E., Chakraborty, A. K., Sprenger, K. G., Mora, T., Walczak, A., Rivoire, O., Wang, S., Wood, K., Skanata, A., Kussell, E., Ranganathan, R. & Shih, H.-Y. & 1 others, Goldenfeld, N., 17 May 2021, In: IOP Conference Series: Materials Science and Engineering. 18, 4, p. 1-33 33 p., 041502.

Research output: Contribution to journal › Article › peer-review

Open Access

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2019

Resolving fluorescent species by their brightness and diffusion using correlated photon-counting histograms

Scales, N. B. & Swain, P., 30 Dec 2019, In: PLoS ONE. 14, 12, e0226063.

Research output: Contribution to journal › Article › peer-review

Open Access

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Estimating numbers of intracellular molecules through analysing fluctuations in photobleaching

Bakker, E. & Swain, P., 23 Oct 2019, In: Scientific Reports. 9, 15238.

Research output: Contribution to journal › Article › peer-review

Open Access

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2018

On-line optimal input design increases the efficiency and accuracy of the modelling of an inducible synthetic promoter

Bandiera, L., Hou, Z., Kothamachu, V. B., Balsa-Canto, E., Swain, P. S. & Menolascina, F., 1 Sept 2018, In: Processes. 6, 9, 148.

Research output: Contribution to journal › Article › peer-review

Open Access

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Distributed and dynamic intracellular organization of extracellular information

Granados Castro, A., Pietsch, J. M. J., Cepeda-Humerez, S. A., Farquhar, I., Tkačik, G. & Swain, P., 5 Jun 2018, In: Proceedings of the National Academy of Sciences (PNAS). 115, 23, p. 6088-6093 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2017

A new method for post-translationally labeling proteins in live cells for fluorescence imaging and tracking

Hinrichsen, M., Lenz, M., Edwards, J. M., Miller, O. K., Mochrie, S. G. J., Swain, P. S., Schwarz-Linek, U. & Regan, L., 6 Dec 2017, In: Protein Engineering, Design & Selection (PEDS). 30, 12, p. 771-780 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Predicting metabolic adaptation from networks of mutational paths

Josephides, C. & Swain, P. S., 1 Dec 2017, In: Nature Communications. 8, 1, 15 p., 685.

Research output: Contribution to journal › Article › peer-review

Open Access

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Morphologically constrained and data informed cell segmentation of budding yeast

Bakker, E., Swain, P. S. & Crane, M. M., 4 Sept 2017, In: Bioinformatics. 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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Distributing tasks via multiple input pathways increases cellular survival in stress

Granados, A. A., Crane, M., Montaño-gutierrez, L., Tanaka, R. J., Voliotis, M. & Swain, P., 17 May 2017, In: eLIFE. 6, p. 1-21 21 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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2016

General calibration of microbial growth in microplate readers

Stevenson, K., McVey, A., Clark, I. B. N., Swain, P. & Pilizota, T., 13 Dec 2016, In: Scientific Reports. 6, 7 p., 38828.

Research output: Contribution to journal › Article › peer-review

Open Access

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Inferring time-derivatives including cell growth rates using Gaussian processes

Swain, P., Stevenson, K., Leary, A., Montano-Gutierrez, L. F., Clark, I. B. N., Vogel, J. & Pilizota, T., 12 Dec 2016, In: Nature Communications. 7, 8 p., 13766.

Research output: Contribution to journal › Article › peer-review

Open Access

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2015

BioJazz: In silico evolution of cellular networks with unbounded complexity using rule-based modeling

Feng, S., Ollivier, J. F., Swain, P. S. & Soyer, O. S., 22 Jun 2015, (E-pub ahead of print) In: Nucleic Acids Research. 43, 19, e123.

Research output: Contribution to journal › Article › peer-review

Open Access

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A geometric analysis of fast-slow models for stochastic gene expression

Popovic, N., Carsten, M. & Swain, P., 2 Apr 2015, In: Journal of Mathematical Biology.

Research output: Contribution to journal › Article › peer-review

Open Access

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Mechanistic links between cellular trade-offs, gene expression, and growth

Weisse, A., Oyarzun, D. A., Danos, V. & Swain, P., 3 Mar 2015, In: Proceedings of the National Academy of Sciences (PNAS). 112, 9, p. E1038-E1047 10 p.

Research output: Contribution to journal › Article › peer-review

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2014

Environmental sensing, information transfer, and cellular decision-making

Bowsher, C. G. & Swain, P. S., Aug 2014, In: Current opinion in biotechnology. 28, p. 149-155 7 p.

Research output: Contribution to journal › Article › peer-review

A microfluidic system for studying ageing and dynamic single-cell responses in budding yeast

Crane, M. M., Clark, I. B. N., Bakker, E., Smith, S. & Swain, P. S., 20 Jun 2014, In: PLoS ONE. 9, 6, 10 p., e100042.

Research output: Contribution to journal › Article › peer-review

Open Access

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Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers

Lichten, C. A., White, R., Clark, I. B. & Swain, P. S., 3 Feb 2014, In: BMC Biotechnology. 14, 1, 11.

Research output: Contribution to journal › Article › peer-review

Open Access

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2013

Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate

Martins, B. M. C. & Swain, P. S., Aug 2013, In: PLoS Computational Biology. 9, 8, e1003175.

Research output: Contribution to journal › Article › peer-review

Open Access

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The fidelity of dynamic signaling by noisy biomolecular networks

Bowsher, C. G., Voliotis, M. & Swain, P. S., Mar 2013, In: PLoS Computational Biology. 9, 3, 9 p., e1002965.

Research output: Contribution to journal › Article › peer-review

Open Access

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2012

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

Young, J. W., Locke, J. C. W., Altinok, A., Rosenfeld, N., Bacarian, T., Swain, P. S., Mjolsness, E. & Elowitz, M. B., Jan 2012, In: Nature Protocols. 7, 1, p. 80-88 9 p.

Research output: Contribution to journal › Article › peer-review

Identifying sources of variation and the flow of information in biochemical networks

Bowsher, C. G. & Swain, P. S., 2012, In: Proceedings of the National Academy of Sciences (PNAS). 109, 20, p. E1320–E1328

Research output: Contribution to journal › Article › peer-review

Stochastic branching-diffusion models for gene expression

Cottrell, D., Swain, P. S. & Tupper, P. F., 2012, In: Proceedings of the National Academy of Sciences (PNAS). 109, 25, p. 9699-9704 6 p.

Research output: Contribution to journal › Article › peer-review

2011

Trade-Offs and Constraints in Allosteric Sensing

Martins, B. M. C. & Swain, P. S., Nov 2011, In: PLoS Computational Biology. 7, 11, p. - 13 p., e1002261.

Research output: Contribution to journal › Article › peer-review

Open Access

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A Bayesian method for inferring quantitative information from FRET data

Lichten, C. A. & Swain, P. S., 2011, In: BMC Biophysics. 4, p. 10

Research output: Contribution to journal › Article › peer-review

Open Access

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2010

Scalable rule-based modelling of allosteric proteins and biochemical networks

Ollivier, J. F., Shahrezaei, V. & Swain, P. S., Nov 2010, In: PLoS Computational Biology. 6, 11, 12 p., e1000975.

Research output: Contribution to journal › Article › peer-review

Open Access

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The scaffold protein Ste5 directly controls a switch-like mating decision in yeast

Malleshaiah, M. K., Shahrezaei, V., Swain, P. S. & Michnick, S. W., 2010, In: Nature. 465, 7294, p. 101-105 5 p.

Research output: Contribution to journal › Article › peer-review

2009

Cross-talk between signaling pathways can generate robust oscillations in calcium and cAMP

Siso-Nadal, F., Fox, J. J., Laporte, S. A., Hébert, T. E. & Swain, P. S., 2009, In: PLoS ONE. 4, 10, 10 p., e7189.

Research output: Contribution to journal › Article › peer-review

Open Access

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2008

Analytical distributions for stochastic gene expression

Shahrezaei, V. & Swain, P. S., Nov 2008, In: Proceedings of the National Academy of Sciences (PNAS). 105, 45, p. 17256–17261 6 p.

Research output: Contribution to journal › Article › peer-review

Colored extrinsic fluctuations and stochastic gene expression

Shahrezaei, V., Ollivier, J. F. & Swain, P. S., 2008, In: Molecular Systems Biology. 4, p. 1-9 9 p., 196.

Research output: Contribution to journal › Article › peer-review

Open Access

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Inferring the lifetime of endosomal protein complexes by fluorescence recovery after photobleaching

Gousseva, V., Simaan, M., Laporte, S. A. & Swain, P. S., 2008, In: Biophysical Journal. 94, 2, p. 679-87 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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The stochastic nature of biochemical networks

Shahrezaei, V. & Swain, P. S., 2008, In: Current opinion in biotechnology. 19, 4, p. 369-74 6 p.

Research output: Contribution to journal › Article › peer-review

2007

Accurate prediction of gene feedback circuit behavior from component properties

Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B., 2007, In: Molecular Systems Biology. 3, p. 1-4 4 p., 143.

Research output: Contribution to journal › Article › peer-review

Open Access

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Facile: a command-line network compiler for systems biology

Siso-Nadal, F., Ollivier, J. F. & Swain, P. S., 2007, In: BMC Systems Biology. 1, 6 p., 36.

Research output: Contribution to journal › Article › peer-review

Open Access

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Noisy information processing through transcriptional regulation

Libby, E., Perkins, T. J. & Swain, P. S., 2007, In: Proceedings of the National Academy of Sciences (PNAS). 104, 17, p. 7151-6 6 p.

Research output: Contribution to journal › Article › peer-review

2006

A fluctuation method to quantify in vivo fluorescence data

Rosenfeld, N., Perkins, T. J., Alon, U., Elowitz, M. B. & Swain, P. S., 2006, In: Biophysical Journal. 91, 2, p. 759-66 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

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An entropic mechanism to generate highly cooperative and specific binding from protein phosphorylations

Lenz, P. & Swain, P. S., 2006, In: Current biology : CB. 16, 21, p. 2150-5 6 p.

Research output: Contribution to journal › Article › peer-review

Noise in genetic and neural networks

Swain, P. S. & Longtin, A., 2006, In: Chaos: An Interdisciplinary Journal of Nonlinear Science. 16, 2, p. 026101

Research output: Contribution to journal › Article › peer-review

2005

Gene regulation at the single-cell level

Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B., 2005, In: Science. 307, 5717, p. 1962-5 4 p.

Research output: Contribution to journal › Article › peer-review

Tracing the sources of cellular variation

Ramanathan, S. & Swain, P. S., 2005, In: Developmental Cell. 9, 5, p. 576-8 3 p.

Research output: Contribution to journal › Article › peer-review

2004

Efficient attenuation of stochasticity in gene expression through post-transcriptional control

Swain, P. S., 2004, In: Journal of Molecular Biology. 344, 4, p. 965-76 12 p.

Research output: Contribution to journal › Article › peer-review

2002

Open Access

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Peter Swain

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