Rob Phillips

Summary

Affiliation: California Institute of Technology
Country: USA

Publications

  1. pmc Tuning promoter strength through RNA polymerase binding site design in Escherichia coli
    Robert C Brewster
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS Comput Biol 8:e1002811. 2012
  2. pmc Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping
    Stephanie Johnson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 8:e75799. 2013
  3. pmc Concentration and length dependence of DNA looping in transcriptional regulation
    Lin Han
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS ONE 4:e5621. 2009
  4. pmc Sequence dependence of transcription factor-mediated DNA looping
    Stephanie Johnson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
    Nucleic Acids Res 40:7728-38. 2012
  5. pmc Entropic tension in crowded membranes
    Martin Lindén
    Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
    PLoS Comput Biol 8:e1002431. 2012
  6. pmc Single-cell census of mechanosensitive channels in living bacteria
    Maja Bialecka-Fornal
    Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California, United States of America
    PLoS ONE 7:e33077. 2012
  7. pmc Emerging roles for lipids in shaping membrane-protein function
    Rob Phillips
    Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
    Nature 459:379-85. 2009
  8. pmc Membrane-protein interactions in mechanosensitive channels
    Paul Wiggins
    Department of Physics, California Institute of Technology, Pasadena, California 91106, USA
    Biophys J 88:880-902. 2005
  9. pmc Operator sequence alters gene expression independently of transcription factor occupancy in bacteria
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Cell Rep 2:150-61. 2012
  10. pmc Cooperative gating and spatial organization of membrane proteins through elastic interactions
    Tristan Ursell
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS Comput Biol 3:e81. 2007

Collaborators

Detail Information

Publications40

  1. pmc Tuning promoter strength through RNA polymerase binding site design in Escherichia coli
    Robert C Brewster
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS Comput Biol 8:e1002811. 2012
    ....
  2. pmc Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping
    Stephanie Johnson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 8:e75799. 2013
    ....
  3. pmc Concentration and length dependence of DNA looping in transcriptional regulation
    Lin Han
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS ONE 4:e5621. 2009
    ..The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping...
  4. pmc Sequence dependence of transcription factor-mediated DNA looping
    Stephanie Johnson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
    Nucleic Acids Res 40:7728-38. 2012
    ....
  5. pmc Entropic tension in crowded membranes
    Martin Lindén
    Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
    PLoS Comput Biol 8:e1002431. 2012
    ....
  6. pmc Single-cell census of mechanosensitive channels in living bacteria
    Maja Bialecka-Fornal
    Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California, United States of America
    PLoS ONE 7:e33077. 2012
    ..As shown by numerous biophysical models, both the number of such channels and their variability can impact many physiological processes including osmoprotection, channel gating probability, and channel clustering...
  7. pmc Emerging roles for lipids in shaping membrane-protein function
    Rob Phillips
    Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
    Nature 459:379-85. 2009
    ..The free-energy cost of such perturbations can be estimated quantitatively, and measurements of channel gating in model systems of membrane proteins with their lipid partners are now confirming predictions of simple models...
  8. pmc Membrane-protein interactions in mechanosensitive channels
    Paul Wiggins
    Department of Physics, California Institute of Technology, Pasadena, California 91106, USA
    Biophys J 88:880-902. 2005
    ..Finally, we compare the predictions of our model to experimental results from the recent investigations of the MscL channel by a variety of investigators and suggest a suite of new experiments...
  9. pmc Operator sequence alters gene expression independently of transcription factor occupancy in bacteria
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Cell Rep 2:150-61. 2012
    ....
  10. pmc Cooperative gating and spatial organization of membrane proteins through elastic interactions
    Tristan Ursell
    Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America
    PLoS Comput Biol 3:e81. 2007
    ..This has important implications for how conformational changes organize membrane proteins into functional groups within membranes...
  11. pmc Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Biopolymers 85:115-30. 2007
    ..The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques...
  12. pmc The transcription factor titration effect dictates level of gene expression
    Robert C Brewster
    Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Cell 156:1312-23. 2014
    ..Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle...
  13. pmc Real-time observations of single bacteriophage lambda DNA ejections in vitro
    Paul Grayson
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 104:14652-7. 2007
    ..The details of ejection revealed in this study are probably generic features of DNA translocation in bacteriophages and have implications for the dynamics of DNA in other biological systems...
  14. pmc Membrane shape as a reporter for applied forces
    Heun Jin Lee
    Department of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:19253-7. 2008
    ..To illustrate the potential power of this technique, we apply an axial force with optical tweezers to vesicles and explicitly demonstrate that the applied force is equal to the force computed from the membrane conformation...
  15. pmc Connection between oligomeric state and gating characteristics of mechanosensitive ion channels
    Christoph A Haselwandter
    Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
    PLoS Comput Biol 9:e1003055. 2013
    ....
  16. pmc Dynamics of DNA ejection from bacteriophage
    Mandar M Inamdar
    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
    Biophys J 91:411-20. 2006
    ....
  17. pmc Thermodynamics of biological processes
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, California, USA
    Methods Enzymol 492:27-59. 2011
    ..These case studies should provide a template for tailoring equilibrium ideas to other problems of biological interest...
  18. pmc A single-molecule Hershey-Chase experiment
    David Van Valen
    Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
    Curr Biol 22:1339-43. 2012
    ..This provides a picture of the early stages of phage infection and sheds light on the problem of polymer translocation...
  19. pmc Theoretical and experimental dissection of DNA loop-mediated repression
    James Q Boedicker
    Department of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA
    Phys Rev Lett 110:018101. 2013
    ..Our results help clarify the short-length mechanical properties of DNA...
  20. pmc Lipid bilayer mechanics in a pipette with glass-bilayer adhesion
    Tristan Ursell
    Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
    Biophys J 101:1913-20. 2011
    ..Third, we show that reversible adhesion leads to a predictable change in the population response of gating channels in a bilayer patch...
  21. pmc Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes
    David Wu
    California Institute of Technology, Pasadena, California, USA
    Phys Rev Lett 103:050603. 2009
    ..The covariances are the dynamical equivalents of Maxwell-like equilibrium reciprocal relations and Onsager-like dynamical relations...
  22. pmc The effect of genome length on ejection forces in bacteriophage lambda
    Paul Grayson
    Department of Physics, California Institute of Technology, Pasadena, 91125, USA
    Virology 348:430-6. 2006
    ....
  23. pmc Exact theory of kinkable elastic polymers
    Paul A Wiggins
    Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 71:021909. 2005
    ....
  24. pmc Measuring flux distributions for diffusion in the small-numbers limit
    Effrosyni Seitaridou
    Division of Engineering and Applied Science and Kavli Nanoscience Institute, California Institute of Technology, Pasadena, California 91125, USA
    J Phys Chem B 111:2288-92. 2007
    ..Here, we introduce a new fluctuation theorem, for the fluxes, and we find that it is confirmed quantitatively by our experiments...
  25. pmc Ion-dependent dynamics of DNA ejections for bacteriophage lambda
    David Wu
    Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California, USA
    Biophys J 99:1101-9. 2010
    ..We also present evidence that phage DNA forms loops during ejection, and confirm that this effect occurs using optical tweezers...
  26. pmc Quantitative dissection of the simple repression input-output function
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 108:12173-8. 2011
    ....
  27. pmc Forces during bacteriophage DNA packaging and ejection
    Prashant K Purohit
    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
    Biophys J 88:851-66. 2005
    ..The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure...
  28. pmc Analytic models for mechanotransduction: gating a mechanosensitive channel
    Paul Wiggins
    Division of Physics, Mathematics, and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 9500, USA
    Proc Natl Acad Sci U S A 101:4071-6. 2004
    ....
  29. pmc Comparison and calibration of different reporters for quantitative analysis of gene expression
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, California, USA
    Biophys J 101:535-44. 2011
    ..These qualities make the reporters complementary and necessary when trying to experimentally verify the predictions from the theoretical models...
  30. pmc Elastic energy of polyhedral bilayer vesicles
    Christoph A Haselwandter
    Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 83:061901. 2011
    ..Instead, we find that, for large polyhedron sizes, the snub dodecahedron and the snub cube both have lower total bending energies than the icosahedron...
  31. pmc Building enhancers from the ground up: a synthetic biology approach
    Roee Amit
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Cell 146:105-18. 2011
    ..Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers...
  32. pmc Transcription by the numbers redux: experiments and calculations that surprise
    Hernan G Garcia
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Trends Cell Biol 20:723-33. 2010
    ..We consider several appealing case studies to illustrate how quantitative models have been used to dissect transcriptional regulation...
  33. pmc Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins
    David Van Valen
    Department of Applied Physics, California Institute of Technology, Pasadena, California, USA
    Biophys J 96:1275-92. 2009
    ..More generally, tethered ligands competing with those free in solution are common phenomena in biology, making this an important specific example of a widespread biological idea...
  34. pmc DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation
    James Q Boedicker
    Departments of Applied Physics and Biology, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA
    Phys Biol 10:066005. 2013
    ..Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. ..
  35. pmc Minimal bending energies of bilayer polyhedra
    Christoph A Haselwandter
    Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA
    Phys Rev Lett 105:228101. 2010
    ..However, our analysis also implies that, contrary to what has been suggested on the basis of experiments, the snub dodecahedron, rather than the icosahedron, generally represents the energetically favorable shape of bilayer polyhedra...
  36. pmc Probing individual environmental bacteria for viruses by using microfluidic digital PCR
    Arbel D Tadmor
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
    Science 333:58-62. 2011
    ..Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments...
  37. pmc Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
    Eric L Peterson
    Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 25:1356-62. 2009
    ..Given the structural similarity exhibited by many apparently dissimilar sequences, we undertook this study looking for improvements in fold recognition by comparing protein sequences written in a reduced alphabet...
  38. pmc Volume-exclusion effects in tethered-particle experiments: bead size matters
    Darren E Segall
    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, USA
    Phys Rev Lett 96:088306. 2006
    ..Finally, our results give a precise, experimentally testable prediction for the probability distribution of the bead center measured from the polymer attachment point...
  39. pmc Morphology and interaction between lipid domains
    Tristan S Ursell
    Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 106:13301-6. 2009
    ..We demonstrate that lipid domains can adopt a flat or dimpled morphology, where the latter facilitates a repulsive interaction that slows coalescence and helps regulate domain size and tends to laterally organize domains in the membrane...
  40. pmc Mechanics of DNA packaging in viruses
    Prashant K Purohit
    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 100:3173-8. 2003
    ..Because the packing of DNA in viral capsids occurs under circumstances of high internal pressure, we also compute how much pressure a capsid can sustain without rupture...

Research Grants3

  1. Single-Molecule and Single-Cell Analysis of Transcription Factor-DNA Complexes
    Rob Phillips; Fiscal Year: 2010
    ..The work proposed here aims to strengthen our understanding of transcription in microbes in a way that will have applications from synthetic biology to the study of pathogens. ..
  2. Single-Molecule and Single-Cell Analysis of Transcription Factor-DNA Complexes
    Rob Phillips; Fiscal Year: 2009
    ..The work proposed here aims to strengthen our understanding of transcription in microbes in a way that will have applications from synthetic biology to the study of pathogens. ..
  3. Single-Molecule and Single-Cell Analysis of Transcription Factor-DNA Complexes
    Rob Phillips; Fiscal Year: 2009
    ..The work proposed here aims to strengthen our understanding of transcription in microbes in a way that will have applications from synthetic biology to the study of pathogens. ..