Peter Swain

Search results

• 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

  File

  • Microbial Genes 100%
  • Gene Expression 78%
  • Time Series Data 74%
  • Yeast 73%
  • raffinose 72%

• 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

  File

  • Nutrients 100%
  • Affine transformation 89%
  • trade-off 82%
  • Trade-offs 81%
  • glucose 73%
• 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 othersGoldenfeld, 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

  File

  • Physiology 100%
  • Environment 46%
  • Sun 41%
  • Time 29%
  • Experiments 14%
• 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

  File

  • Photons 100%
  • photons 96%
  • Photon 90%
  • Diffusion 57%
  • Fluorescence Spectrometry 55%

• 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

  File

  • Photobleaching 100%
  • Molecules 55%
  • Proteins 52%
  • Fluorescence microscopy 41%
  • Yeast 17%
• 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 Sep 2018, In: Processes. 6, 9, 148.

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

  Open Access

  File

  • Design of experiments 100%
  • Synthetic biology 39%
  • Yeast 32%
  • Networks (circuits) 29%
  • Genes 25%

• 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

  File

  • Transcription Factors 100%
  • Saccharomycetales 40%
  • Decision Making 27%
• 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

  File

  • Fluorescence imaging 100%
  • Optical Imaging 67%
  • Labeling 59%
  • Proteins 56%
  • Fluorescence 35%

• 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

  File

  • Metabolic Networks and Pathways 100%
  • Microbiota 98%
  • Metabolic 80%
  • Community Networks 76%
  • Entropy 59%

• Morphologically constrained and data informed cell segmentation of budding yeast

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

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

  Open Access

  File

  • Yeast 100%
  • Saccharomycetales 88%
  • Segmentation 87%
  • Microfluidics 76%
  • Cell 53%

• 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

  File

  • Signal Transduction 100%
  • Environment 52%
  • Saccharomycetales 37%
  • p38 Mitogen-Activated Protein Kinases 31%
• 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

  File

  • optical density 100%
  • readers 98%
  • microbiology 35%
  • antibiotics 30%
  • cells 23%

• 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

  File

  • Error 100%
  • Amyloid Fibril 79%
  • Growth 67%
  • spindles 57%
  • Spindle Pole Bodies 52%
• 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

  File

  • Computer Simulation 100%
  • Space Flight 27%
  • Manuals 24%
  • Genome 14%

• 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

  File

  • Geometric Analysis 100%
  • Gene Expression 96%
  • Gene expression 84%
  • Messenger RNA 71%
  • Time Scales 52%

• 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

  File

  • Gene Expression 100%
  • Growth 84%
  • Ribosomes 57%
  • Synthetic Biology 38%
  • Biotechnology 32%
• 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

  • Information Theory 100%
  • Biochemistry 97%
  • Psychology Transfer 78%
  • Information theory 77%
  • Gene expression 73%

• 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

  File

  • Saccharomycetales 100%
  • Microfluidics 98%
  • Controlled Environment 22%
  • Lab-On-A-Chip Devices 22%
  • Longevity 14%

• 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

  File

  • Fluorescence 100%
  • Gene Expression 73%
  • Green Fluorescent Proteins 65%
  • Population 23%
  • Proteins 22%
• 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

  File

  • Phosphorylation 100%
  • dephosphorylation 73%
  • Substrate 71%
  • phosphorylation 54%
  • Substrates 43%

• 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

  File

  • Fidelity 100%
  • Synthetic Biology 36%
  • Dynamic Environment 35%
  • trajectories 33%
  • Systems Biology 31%
• 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

  • Quantitative Yield 100%
  • Agarose 98%
  • Microscopy 78%
  • Fluorescence 76%
  • Bacteria 63%

• 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

  • Yeasts 100%
  • Noise 56%
  • Research Design 49%

• 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

  • Gene Expression 100%
  • Proteins 61%
  • Saccharomycetales 28%
  • Messenger RNA 27%
  • Bacteria 16%
• 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

  File

  • Sensing 100%
  • information exchange 92%
  • Trade-offs 74%
  • Sensor 68%
  • transcription factors 56%

• 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

  File

  • Energy Transfer 100%
  • Bayes Theorem 93%
  • Fluorescence Microscopy 37%
  • Statistics 29%
  • Proteins 14%
• 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

  File

  • Biochemical Networks 100%
  • Protein 71%
  • Proteins 62%
  • protein 49%
  • Modeling 44%

• 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

  • Pheromones 100%
  • Yeasts 79%
  • Mitogen-Activated Protein Kinases 49%
  • Proteins 36%
  • Haploidy 31%
• 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

  File

  • information exchange 100%
  • Calcium Signaling 93%
  • cell communication 91%
  • Signal Transduction 85%
  • oscillation 80%
• 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

  • Gene Expression 100%
  • Proteins 61%
  • Messenger RNA 40%
  • Saccharomycetales 28%
  • Genes 9%

• 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

  File

  • Calculation Algorithm 100%
  • Biochemistry 99%
  • Gene Expression 85%
  • Stochastic systems 81%
  • Gene expression 74%

• 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

  File

  • Fluorescence Recovery After Photobleaching 100%
  • Proteins 25%
  • Bradykinin B2 Receptors 17%
  • Photobleaching 16%
  • beta-Arrestins 16%

• 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

  • Messenger RNA 100%
  • Biotechnology 91%
  • Viruses 83%
  • Bacteria 79%
  • Gene expression 77%
• 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

  File

  • Synthetic Biology 100%
  • synthetic biology 92%
  • gene regulatory networks 80%
  • Gene Regulatory Networks 78%
  • Fluorescence Microscopy 72%

• 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

  File

  • Compiler 100%
  • Systems Biology 98%
  • Biochemical Networks 55%
  • Line 50%
  • Bifurcation Analysis 39%

• 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

  • Electronic Data Processing 100%
  • Nutrients 83%
  • Lac Operon 61%
  • Gene Regulatory Networks 53%
  • Decision Making 40%
• 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

  File

  • Fluorescence 100%
  • Systems Biology 36%
  • Calibration 31%
  • Datasets 24%
  • Proteins 22%

• 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

  • protein phosphorylation 100%
  • cooperatives 90%
  • Carrier Proteins 76%
  • Phosphorylation 62%
  • Protein 37%

• 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

  • Genetic Network 100%
  • Genes 63%
  • Neural Networks 61%
  • Neurons 60%
  • Neural networks 39%
• 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

  • Noise 100%
  • Genes 87%
  • Proteins 80%
  • Bacteriophage lambda 79%
  • Gene Fusion 61%

• 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

  • Pheromones 100%
  • Pheromone 93%
  • Saccharomycetales 90%
  • Cell Cycle 58%
  • Genome 50%
• 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

  • Noise 100%
  • Gene Expression 97%
  • Messenger RNA 93%
  • Macromolecular Substances 76%
  • Ribosomal Proteins 68%
• 2002

  Intrinsic and extrinsic contributions to stochasticity in gene expression

  Swain, P. S., Elowitz, M. B. & Siggia, E. D., 2002, In: Proceedings of the National Academy of Sciences (PNAS). 99, 20, p. 12795-800 6 p.

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

  • Noise 100%
  • Gene Expression 65%
  • Genes 31%
  • Repressor Proteins 22%
  • Biochemical Phenomena 20%

• Stochastic gene expression in a single cell

  Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S., 2002, In: Science. 297, 5584, p. 1183-6 4 p.

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

  • Noise 100%
  • Gene Expression 65%
  • Biochemical Phenomena 23%
  • Population Biological Variation 22%
  • Biological Phenomena 17%

• The role of proofreading in signal transduction specificity

  Swain, P. S. & Siggia, E. D., 2002, In: Biophysical Journal. 82, 6, p. 2928-33 6 p.

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

  Open Access

  File

  • Signal Transduction 100%
  • Phosphotransferases 99%
  • Intracellular Signaling Peptides and Proteins 40%
  • Phosphoric Monoester Hydrolases 25%
  • Transcription Factors 19%
• 2001

  Supported membranes on chemically structured and rough surfaces

  Swain, P. S. & Andelman, D., 2001, In: Physical Review E. 63, 5 Pt 1, 12 p., 051911.

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

  Open Access

  File

  • Rough Surface 100%
  • Adhesion 77%
  • Membrane 75%
  • membranes 55%
  • adhesion 51%
• 2000

  Wetting and dewetting of structured and imprinted surfaces

  Lipowsky, R., Lenz, P. & Swain, P. S., 15 Jan 2000, In: Colloids and Surfaces A: Physicochemical and Engineering Aspects. 161, 1, p. 3-22 20 p.

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

  • Wetting 100%
  • drying 98%
  • wetting 93%
  • Surface 31%
  • Tension 23%

• Wetting between structured surfaces: Liquid bridges and induced forces

  Swain, P. S. & Lipowsky, R., Jan 2000, In: European Physical Society Letters (EPL). 49, 2, p. 203-209 7 p.

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

  Open Access

  File

  • liquid bridges 100%
  • wetting 68%
  • slabs 15%
  • geometry 10%
  • interactions 7%
• 1999

  The influence of substrate structure on membrane adhesion

  Swain, P. S. & Andelman, D., 21 Dec 1999, In: Langmuir. 15, 26, p. 8902-8914 13 p.

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

  • Adhesion 100%
  • adhesion 91%
  • Membranes 91%
  • membranes 79%
  • Substrates 76%
• 1998

  Contact angles on heterogeneous surfaces: A new look at Cassie's and Wenzel's laws

  Swain, P. S. & Lipowsky, R., 10 Nov 1998, In: Langmuir. 14, 23, p. 6772-6780 9 p.

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

  • Free energy 100%
  • Gravity 95%
  • Contact angle 91%
  • Tension 80%
  • Gravitation 74%