Publications

  1. AA Granados*, JMJ Pietsch*, SA Cepeda-Humerez, IL Farquhar, G Tkacik, and PS Swain (pdf, SI, software, data)
    Distributed and dynamic intracellular organization of extracellular information
    Proc Natl Acad Sci USA 115 (2018) 6088

  2. E Bakker, PS Swain, and MM Crane (pdf, SI, software)
    Morphologically constrained and data informed cell segmentation of budding yeast
    Bioinformatics 34 (2018) 88

  3. M Hinrichsen, M Lenz, JM Edwards, OK Miller, SGJ Mochrie, PS Swain, U Schwarz-Linek, and L Regan (pdf, SI)
    A new method for post-translationally labeling proteins in live cells for fluorescence imaging and tracking
    Protein Eng Des Sel 30 (2017) 771

  4. C Josephides and PS Swain (pdf, SI)
    Predicting metabolic adaptation from networks of mutational paths
    Nat Commun 8 (2017) 685

  5. AA Granados*, MM Crane*, LF Montano-Gutierrez, RJ Tanaka, M Voliotis, and PS Swain (pdf, SI, data)
    Distributing tasks via multiple input pathways increases cellular survival in stress
    eLife 6 (2017) e21415

  6. PS Swain, K Stevenson, A Leary, LF Montano-Gutierrez, IBN Clark, J Vogel, and T Pilizota (pdf, software, data)
    Inferring time derivatives including growth rates using Gaussian processes
    Nat Commun 7 (2016) 13766

  7. K Stevenson, AF McVey, IBN Clark, PS Swain, and T Pilizota (pdf)
    General calibration of microbial growth in microplate readers
    Sci Rep 6 (2016) 38828

  8. N Popovic, C Marr, and PS Swain (pdf)
    A geometric analysis of fast-slow models for stochastic gene expression
    J Math Biol 72 (2016) 87

  9. S Feng, JF Ollivier, PS Swain, and OS Soyer (pdf, SI)
    BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling
    Nucleic Acids Res 43 (2015) e123

  10. AY Weisse, DA Oyarzun, V Danos, and PS Swain (pdf, SI, SBML/Matlab)
    Mechanistic links between cellular trade-offs, gene expression, and growth
    Proc Nat Acad Sci USA 112 (2015) E1038

  11. MM Crane, IBN Clark, E Bakker, S Smith, and PS Swain (pdf, SI)
    A microfluidic system for studying ageing and dynamic single-cell responses in budding yeast
    PLoS One 9 (2014) e100042

  12. CG Bowsher and PS Swain (pdf)
    Environmental sensing, information transfer, and cellular decision-making
    Curr Opin Biotechnol 28C (2014) 149

  13. CA Lichten, R White, IBN Clark, and PS Swain (pdf, software)
    Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers
    BMC Biotechnol 14 (2014) 11

  14. BMC Martins and PS Swain (pdf, SI)
    Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate
    PLoS Comput Biol 9 (2013) e1003175

  15. CG Bowsher, M Voliotis, and PS Swain (pdf, SI)
    The fidelity of dynamic signaling by noisy biomolecular networks
    PLoS Comput Biol 9 (2013) e1002965

  16. D Cottrell, PS Swain, and PF Tupper (pdf, SI)
    Stochastic branching-diffusion models for gene expression
    Proc Nat Acad Sci USA 109 (2012) 9699

  17. CG Bowsher and PS Swain (pdf, SI, summary)
    Identifying sources of variation and the flow of information in biochemical networks
    Proc Nat Acad Sci USA 109 (2012) E1320

  18. JW Young, JC Locke, A Altinok, N Rosenfeld, T Bacarian, PS Swain, E Mjolsness, and MB Elowitz (pdf)
    Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
    Nat Protoc 7 (2011) 80

  19. BMC Martins and PS Swain (pdf)
    Trade-offs and constraints in allosteric sensing
    PLoS Comput Biol 7 (2011) e1002261

  20. CA Lichten and PS Swain (pdf, software)
    A Bayesian method for inferring quantitative information from FRET data
    BMC Biophys 4 (2011) 10

  21. JF Ollivier, V Shahrezaei, and PS Swain (pdf, SI, software)
    Scalable rule-based modelling of allosteric proteins and biochemical networks
    PLoS Comput Biol 6 (2010) e1000975

  22. MK Malleshaiah, V Shahrezaei, PS Swain, and SW Michnick (pdf, SI)
    The scaffold protein Ste5 directly controls a switch-like mating decision in yeast
    Nature 465 (2010) 101

  23. TJ Perkins and PS Swain (pdf)
    Strategies for cellular decision-making
    Mol Syst Biol 5 (2009) 326

  24. F Siso-Nadal, JJ Fox, SA Laporte, TE Hebert, and PS Swain (pdf)
    Signaling pathways can generate robust oscillations in calcium and cAMP
    PLoS One 4 (2009) e7189

  25. V Shahrezaei and PS Swain (pdf, SI, software)
    Analytical distributions for stochastic gene expression
    Proc Nat Acad Sci USA 105 (2008) 17256
    Please note that Eqn. 13 should read F(z)= [f(z)]a = (1+b-bz)-a.

  26. V Shahrezaei and PS Swain (pdf)
    The stochastic nature of biochemical networks
    Curr Opin Biotechnol 19 (2008) 369

  27. V Shahrezaei, JF Ollivier, and PS Swain (pdf, SI, software)
    Colored extrinsic fluctuations and stochastic gene expression
    Mol Syst Biol 4 (2008) 196

  28. V Gousseva, M Simaan, SA Laporte, and PS Swain (pdf)
    Inferring the lifetime of endosomal protein complexes by fluorescence recovery after photobleaching
    Biophys J 94 (2008) 679

  29. N Rosenfeld, JW Young, U Alon, PS Swain, and MB Elowitz (pdf)
    Accurate prediction of gene feedback circuit behavior from component properties
    Mol Syst Biol 3 (2007) 143

  30. F Siso-Nadal, JF Ollivier, and PS Swain (pdf, software)
    Facile: a command-line network compiler for systems biology
    BMC Syst Biol 1 (2007) 36

  31. E Libby, TJ Perkins, and PS Swain (pdf, SI, press)
    Noisy information processing through transcriptional regulation
    Proc Nat Acad Sci USA 104 (2007) 7151

  32. P Lenz and PS Swain (pdf, SI)
    An entropic mechanism to generate highly cooperative and specific binding from protein phosphorylations
    Curr Biol 16 (2006) 2150

  33. PS Swain and A Longtin (pdf)
    Noise in genetic and neural networks
    Chaos 16 (2006) 26101
    A special Chaos issue of tutorial articles highlighting and contrasting stochastic modelling in genetic and neural systems.

  34. N Rosenfeld, TJ Perkins, U Alon, MB Elowitz, and PS Swain (pdf, software)
    A fluctuation method to quantify in vivo fluorescence data
    Biophys J 91 (2006) 759

  35. S Ramanathan and PS Swain (pdf)
    Tracing the sources of cellular variation
    Dev Cell 9 (2005) 576

  36. N Rosenfeld, JW Young, U Alon, PS Swain, and MB Elowitz (pdf, SI)
    Gene regulation at the single-cell level
    Science 307 (2005) 1962

  37. PS Swain (pdf)
    Efficient attenuation of stochasticity in gene expression through post-transcriptional control
    J Mol Biol 344 (2004) 965

  38. PS Swain, MB Elowitz, and ED Siggia (pdf, SI)
    Intrinsic and extrinsic contributions to stochasticity in gene expression
    Proc Nat Acad Sci USA 99 (2002) 12795

  39. MB Elowitz, AJ Levine, ED Siggia, and PS Swain (pdf, SI)
    Stochastic gene expression in a single cell
    Science 297 (2002) 1183

  40. PS Swain and ED Siggia (pdf)
    The role of proof-reading in signal transduction specificity
    Biophys J 82 (2002) 2928

  41. PS Swain and D Andelman (pdf)
    Supported membranes on chemically structured and rough surfaces
    Phys Rev E 63 (2001) 051911

  42. R Lipowsky, P Lenz, and PS Swain (pdf)
    Wetting and dewetting of structured and imprinted surfaces
    Colloid Surface A 161 (2000) 3

  43. PS Swain and R Lipowsky (pdf)
    Wetting between structured surfaces: liquid bridges and induced forces
    Europhys Lett 49 (2000) 203

  44. PS Swain and D Andelman (pdf)
    The influence of surface structure on membrane adhesion
    Langmuir 15 (1999) 8902

  45. PS Swain and R Lipowsky (pdf)
    Contact angles on heterogeneous surfaces: a new look at Cassie's and Wenzel's laws
    Langmuir 14 (1998) 6772

  46. PS Swain and AO Parry (pdf)
    Corrugation induced first-order wetting: an effective Hamiltonian study
    Eur Phys J B 4 (1998) 459

  47. AO Parry and PS Swain (pdf)
    Coupled Hamiltonians and three dimensional short-range wetting transitions
    Physica A 250 (1998) 167

  48. AO Parry and PS Swain (pdf)
    Multi-field effective Hamiltonian theory
    Fluid Phase Equilibr 150 (1998) 573

  49. PS Swain and AO Parry (pdf)
    Two parameters for three dimensional wetting transitions
    Europhys Lett 37 (1997) 207

  50. AO Parry and PS Swain (pdf)
    Correlation function algebra for inhomogeneous fluids
    J Phys: Condens Matter 9 (1997) 2351

  51. PS Swain and AO Parry (pdf)
    An exact solution for two dimensional wetting with a corrugated wall
    J Phys A 30 (1997) 4597

  52. AO Parry, PS Swain, and JA Fox (pdf)
    Fluid adsorption at a non-planar wall: roughness induced first-order wetting
    J Phys: Condens Matter 8 (1996) L659

  53. AO Parry, CJ Boulter, and PS Swain (pdf)
    Coupled fluctuations near critical wetting
    Phys Rev E 52 (1995) R5768


Book chapters

  1. TJ Perkins, AY Weisse, and PS Swain (pdf)
    Chance and memory
    Quantitative biology: from molecular to cellular systems (2012) edited by ME Wall (CRC Press, Boca Raton, Florida).


Lecture notes

  1. PS Swain (pdf)
    Lecture notes on stochastic models in systems biology
    arXiv (last updated 2010).