1. Moor K., Diard M., Sellin M.E., Felmy B., Wotzka S.Y., Toska A., Bakkeren E., Arnoldini M., Bansept F., Dal Co A., Völler T., Minola A., Fernandez-Rodriguez B., Agatic G., Barbieri S., Piccoli L., Casiraghi C., Corti D., Lanzavecchia A., Regoes R.R., Loverdo C., Stocker R., Brumley D.R., Hardt W.D. and Slack E., 2017, “High-avidity IgA protects the intestine by enchaining growing bacteria”, Nature, doi:10.1038/nature22058.
  2. Beyersmann P.G., Tomasch J., Son K., Stocker R., Göker M., Wagner-Döbler I., Simon M. and Brinkhoff T. 2017, “Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens”, Scientific Reports, DOI:10.1038/s41598-017-00784-7.
  3. Sengupta A., Carrara F. and Stocker R., 2017, “Phytoplankton can actively diversify their migation strategy in response to turbulent cues”, Nature, doi:10.1038/nature21415.
  4. Miño L. Gastón., Koehl M.A.R., King Nicole and Stocker R., 2017, “Finding patches in a heterogeneous aquatic environment: pH-taxis by the dispersal stage of choanoflagellates”, Limnology and Oceanography Letters, 2, 37-46.
  5. Cordero Otto X. and Stocker R., 2017, “A particularly useful system to study the ecology of microbes”, Environmental Microbiology Reports, 9, 16-17.
  6. Jang H., Rusconi R., and Stocker R., 2017, “Biofilm disruption by an air bubble reveals heterogeneous age-dependent detachment patterns dictated by initial extracellular matrix distribution”, npj Biofilms and Microbiomes, doi:10.1038/s41522-017-0014-5.
  7. Menolascina F., Rusconi R., Fernandez V.I., Smriga S., Aminzare Z., Sontag E.D., and Stocker R., 2017, “Logarithmic sensing in Bacillus subtilis aerotaxis”, npj Systems Biology and Applications, 3, 16036.
  8. Fernandez V. I. and Stocker R., 2016, “Modus vivendi”, Nature Physics, doi:10.1038/nphys4004.
  9. Son K., Menolascina F. and Stocker R., 2016, “Speed-dependent chemotactic precision in marine bacteria”, PNAS, 113, 8624-8629.
  10. Nelson M., Chase A., Martiny J., Stocker R., Nguyen J., Lloyd K., Oshiro R., Kearns D., Schneider J., Ringel P., Basler M., Olson C., Vuong H., Hsiao E., Roller B., Ackermann M., Smillie C., Chien D., Alm E. and Jermy A., 2016, “The Microbial Olympics 2016”, Nature Microbiology, 1, 16122.
  11. Hein A., Carrara F., Brumley D., Stocker R. and Levin S., 2016, “Natural search algorithms as a bridge between organisms, evolution, and ecology”, PNAS, 113, 9413-9420.
  12. Emge P., Moeler J., Jang H., Rusconi R., Yawata Y., Stocker R. and Vogel V. 2016, “Resilience of bacterial quorum sensing against fluid flow”, Scientific Reports, 6, 33115.
  13. Yawata Y., Nguyen J., Stocker R., Rusconi R. 2016, “Microfluidics Studies of Biofilm Formation in Dynamic Environments”, Journal of Bacteriology, doi:10.1128/JB.00118-16.
  14. Nadeau J., Lindensmith C., Deming J.W., Fernandez V.I. and Stocker R. 2016, “Microbial Morphology and Motility as Biosignatures for Outer Planet Missions”, Astrobiology, 16, 755-774.
  15. Secchi E., Rusconi R., Buzzaccaro S., Salek M.M., Smriga S., Piazza R., Stocker R. 2016, “Intermittent turbulence in flowing bacterial suspensions”, Journal of the Royal Society Interface , 13, 20160175.
  16. Shapiro O.H., Kramarsky-Winter E., Gavish A.R., Stocker R. and Vardi A., 2016, “A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals”, Nature Communications, 7, 10860.
  17. Ricardo G.F, Jones R.J., Negri A.P. and Stocker R., 2016, “That sinking feeling: Suspended sediments can prevent the ascent of coral egg bundles”, Scientific Reports, 6, 21567.
  18. Smriga S., Fernandez V.I., Mitchel J.G. and Stocker R., 2016, “Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria”, Proceedings of the National Academy of Sciences, 113, 1576-1851.
  19. Hein A.W., Brumley D.R., Carrara F., Stocker R., and Levin S.A., 2016, “Physical limits on bacterial navigation in dynamic environments”, Journal of the Royal Society Interface, 13, 20150844
  20. Garren M., Son K., Tout J., Seymour J.R. and Stocker R., 2015, “Temperature-induced behavioral switches in a bacterial coral pathogen”, ISME Journal, 1-10
  21. Dörgens A.L., Ahmerkamp S., Müssig J., Stocker R., Kuypers M.M.M., Khalili A., and Kindler K., 2015, “A laboratory model of marine snow: Preparation and characterization of porous fiber particles”, Limnology and Oceanography: Methods, 13, 664-671.
  22. Stocker R., 2015, “The 100 µm length scale in the microbial ocean”, Aquatic Microbial Ecology, 76, 189-194.
  23. Brumley D.R., Rusconi R., Son K., and Stocker R., 2015, “Flagella, flexibility and flow: Physical processes in microbial ecology”, The European Physical Journal, 224, 3119-3140.
  24. Watteaux R., Stocker R., and Taylor J.R., 2015, “Sensitivity of the rate of nutrient uptake by chemotactic bacteria to physical and biological parameters in a turbulent environment”, Journal of Theoretical Biology, 387, 120-135.
  25. Barry M.T., Rusconi R., Guasto J.S., and Stocker R., 2015, “Shear-induced orientational dynamics and spatial heterogeneity in suspensions of motile phytoplankton”, The Royal Society Publishing, 12, 20150791.
  26. Son K., Brumley D.R., and Stocker R., 2015, “Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics”, Nature Reviews Microbiology, Vol. 13, 761-775.
  27. Rusconi R. and Stocker R., 2015, “Microbes in flow”, Current Opinion in Microbiology, 25:1-8.
  28. Giometto A., Altermatt F., Maritan A., Stocker R., and Rinaldo A., 2015, “Generalized receptor law governs phototaxis in the phytoplankton Euglena gracilis“, PNAS, 112, 7045-7050.
  29. Tout J., Siboni N., Messer L.F., Garren M., Stocker R., Webster N.S., Ralph P.J., and Seymour J.R., 2015, “Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis”, Frontiers in Microbiology, 6, 432, 1-12.
  30. Tout J., Jeffries T.C., Petrou K., Tyson G.W., Webster N.S., Garren M., Stocker R., Ralph P.J., and Seymour J.R., 2015, “Chemotaxis by natural populations of coral reef bacteria”, ISME Journal, 9, 1764-1777.
  31. Lecuyer S., Stocker R., and Rusconi R., 2015, “Focus on the physics of biofilms”, New Journal of Physics, 17, 030401.
  32. Pollock F.J., Krediet C.J., G. Melissa, Stocker R., Winn K., Wilson B., Huete-Stauffer C., Willis B.L., and Bourne D.G., 2015, “Visualization of coral host-pathogen interactions using a stable GFP-labeled Vibrio coralliilyticus strain”, Coral Reefs, 34, 655-662.
  33. Shapiro O.H., Fernandez V.I., Garren M.S., Guasto J.S., Debaillon-Vesque F.P., Kramarski-Winter E., Vardi A. & Stocker R., 2014, “Vortical ciliary flows actively enhance mass transport in reef corals”, Proceedings of the National Academy of Sciences, 111, 13391-13396.

    In the news: This research was also featured on the cover of Science, Feb 2014 (Image by V. Fernandez, O. Shapiro, M. Garren, A. Vardi & R. Stocker); WIRED.CO.UK; MIT News

  34. Mayola A., Irazoki O., Martinez I.A., Petrov D., Menolascina F., Stocker R., Reyes-Darias J.A., Krell T., Barbe J. & Campoy S., 2014, “RecA protein plays a role in the chemotactic response and chemoreceptor clustering of Salmonella enterica”, PLOS ONE, 9, e105578.
  35. Molaei M., Barry M., Stocker R. & Sheng J., 2014, “Failed escape: Solid surfaces prevent tumbling of Escherichia coli“, Physical Review Letters, 113, 068103.
  36. Kashtan N., Roggensack S.E., Rodrigue S., Thompson J.W., Biller S.J., Coe A., Ding H., Marttinen P., Malmstrom R.R., Stocker R., Follows M.J., Stepanauskas R. & Chisholm S.W., 2014, “Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus“, Science, 344, 416-420.
  37. Rusconi R., Garren M.S. & Stocker R., 2014, “Microfluidics expanding the frontiers of microbial ecology”, Annual Review of Biophysics, 43:2.1-2.27.
  38. Yawata Y., Cordero O.X., Menolascina F., Hehemann J.H., Polz M.F. & Stocker R., 2014, “Competition-dispersal trade-off ecologically differentiates recently speciated marine bacterioplankton populations”, Proceedings of the National Academy of Sciences, 111, 5622-5627.

    In the news: The Scientist

  39. Rusconi R., Guasto J.S. and Stocker R., 2014, “Bacterial transport suppressed by fluid shear”, Nature Physics, 10, 212-217.
  40. Lillo F.D., Cencini M., Durham V.M., Barry M., Stocker R., Climent E. & Boffetta G., 2014, “Turbulent fluid acceleration generates clusters of gyrotactic microorganisms”, Physical Review Letters, 112, 044502.
  41. Tout J., Jeffries T.C., Webster N.S., Stocker R., Ralph P.J. & Seymour J.R., 2014, “Variability in microbial community composition and function between different niches within a coral reef”, Microbial Ecology, 67, 3, 540-552.
  42. Yang R., Jang H., Stocker R. & Gleason K., 2013, “Synergistic prevention of biofouling in seawater desalination by zwitterionic surfaces and low-level chlorination”, Advanced Materials, DOI: 10.1002/adma.201304386.
  43. Norris Noele., Menolascina F., Frazzoli E. and Stocker R., 2014, “The Effect of Reversals for a Stochastic Source-Seeking Process Inspired by Bacterial Chemotaxis”, American Control Conference, Portland, Oregon.
  44. Crouzier T., Jang H., Ahn J., Stocker R. & Ribbeck K., 2013, “Cell patterning with mucin biopolymers”, Biomacromolecules, 14, 3010-3016.
  45. Billings N., Millan M.R., Caldara M., Rusconi R., Tarasova Y., Stocker R. & Ribbeck K., 2013, “The extracellular matrix component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biolfilms”, PLOS Pathogens, 9, e1003526.
  46. Durham W.M., Climent E., Barry M., De Lillo F., Boffetta G., Cencini M. & Stocker R., 2013, “Turbulence drives microscale patches of motile phytoplankton”, Nature Communications, 4, 2148.

    In the news: MIT News; Nature World News; Science Newsline

  47. Son K., Guasto J.S. & Stocker R., 2013, “Bacteria can exploit a flagellar buckling instability to change direction”, Nature Physics, 9, 494-498.

    In the news: MIT News; ScienceNews

  48. News and views: Nature Physics


  49. Peruzzo P., Defina A., Nepf H.M. & Stocker R., 2013, “Capillary interception of floating particles by surface-piercing vegetation”, Physical Review Letters, 111, 164501.
  50. Garren M., Son K., Raina J.B., Rusconi R., Menolascina F., Shapiro O.H., Tout J., Bourne D.G., Seymour J.R. & Stocker R., 2013, “A bacteria pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals”, The ISME Journal, 8, 999-1007.
  51. Stocker R., 2012, “Marine microbes see a sea of gradients”, Science, 338, 628-633.
  52. Taylor J.R. & Stocker R., 2012, “Trade-offs of chemotactic foraging in turbulent water”, Science, 338, 675-679.
  53. Durham W.M., Tranzier O., Leombruni A. & Stocker R., 2012, “Division by fluid incision: Biofilm patch development in porous media”, Physics of Fluids, 24, 091107.
  54. Stocker R. & Seymour J.R., 2012, “Ecology and physics of bacterial chemotaxis in the ocean”, Microbiology and Molecular Biology Reviews, 76, 792-812 (Featured on the cover).
  55. Hyon Y., Marcos, Powers T.R., Stocker R. & Fu H.C., 2012, “The wiggling trajectories of bacteria”, Journal of Fluid Mechanics, 705, 58-76.
  56. Marcos, Fu H.C., Powers T.R. & Stocker R., 2012, “Bacterial rheotaxis”, Proceedings of the National Academy of Sciences, 109, 4780-4785.
  57. Doostmohammadi A., Stocker R. & Ardekani A.M., 2012, “Low Reynolds number swimming at pycnoclines”, Proceedings of the National Academy of Sciences, 109, 3586-3861.
  58. Durham W.M. & Stocker R., 2012, “Thin phytoplankton layers: Characteristics, mechanisms and consequences”, Annual Review of Marine Sciences, 4, 177–207.
  59. Guasto J.S., Rusconi R. & Stocker R., 2012, “Fluid mechanics of planktonic microorganisms”, Annual Review of Fluid Mechanics, 44, 373-400.
  60. Lewpiriyawong N., Kandaswamy K., Yang C., Ivanov V. & Stocker R., 2011, “Microfluidic characterization and continuous separation of cells and particles using conducting poly(dimethyl siloxane) electrode induced alternating current-dielectrophoresis”, Analytical Chemistry, 83, 9579-9585.
  61. Steger D., Berry D., Haider S., Horn M., Wagner M., Stocker R. & Loy A., 2011, “Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion”, PLoS ONE, 6, e23727.
  62. Lazova M.D., Ahmed T., Bellomo D., Stocker R. & Shimizu T.S., 2011, “Response rescaling in bacterial chemotaxis”, Proceedings of the National Academy of Sciences, 108, 13870-13875.
  63. Durham W.M., Climent E. & Stocker R., 2011, “Gyrotaxis in a steady vortical flow”, Physical Review Letters, 106, 238102.
  64. Marcos, Seymour J.R., Luhar M., Durham W.M., Mitchell J.G., Macke A. & Stocker R., 2011, “Microbial alignment in flow changes ocean light climate”, Proceedings of the National Academy of Sciences, 108, 3860-3864.
  65. Giuffré C., Hinow P., Vogel R., Ahmed T., Stocker R., Consi T.R. & Strickler J.R., 2011, “The ciliate Paramecium shows higher motility in non-uniform chemical landscapes”, PLoS ONE, 6, e15274.
  66. Aristoff J.M., Stocker R., Reis P.M. & Jung S., 2011, “On the water lapping of felines and the water running of lizards: A unifying physical perspective”, Communicative and Integrative Biology, 4, 1-3.
  67. Stocker R., 2011, “Reverse and flick: Hybrid locomotion in bacteria”, Proceedings of the National Academy of Sciences, 108. 2635-2636.
  68. Stocker R., Aristoff J.M., Jung S. & Reis P.M., 2010, “Response to comment on how cats lap: Water uptake by Felis catus”, Science, 334, 311.
  69. Reis P.M., Jung S., Aristoff J.M. & Stocker R., 2010, “How cats lap: Water uptake by Felis catus”, Science, 330, 1231-1234. (All authors equal in status)
    (Featured on the cover).

    Media: Video 1Video 2Video 3Quirks’N’Quarks
    (Canadian Broadcasting Company Radio) –
    Tonight Show with Jay LenoWorld Today (BBC World Service).

    In the news: ABC (Spain); All Things Considered (National Public Radio); BBC News; Boston Globe (Front Page); CBS News; Ciencia Hoje (Brazil); Ciencia Hoje (Portugal); CNN; Der Spiegel (Germany); Discover Magazine; Discovery News; Duetschlandfunk Radio; El Mundo (Spain); Encyclopedia Britannica; Focus (Germany); Geekmom; iG (Brazil); La Republica (Italy); Le Figaro (France); Los Angeles Times; MIT Homepage Spotlight; MIT News; MSNBC; New York Times (Front Page); New York Times Learning Blog; NU (Netherlands); Philadelphia Inquirer (Front Page); Physicsworld.com; Reuters; Sabado (Portugal); Science & Vie (France); Science News; Science Now; Science News For Kids; Scientific American; Sydney Morning News (Australia); The Guardian (UK); The Telegraph (UK); Time; Toronto Star (Canada); Veja (Brazil); Washington Post (Front Page); Wired.

  71. Kindler K., Khalili A. & Stocker R., 2010, “Diffusion-limited retention of porous particles at density interfaces”, Proceedings of the National Academy of Sciences, 107, 22163-22168.
  72. Ahmed T., Shimizu T.S. & Stocker R., 2010, “Microfluidics for bacterial chemotaxis”, Integrative Biology, 2, 604-629. (Among the top ten articles accessed from the online version in March 2011.)
  73. Ardekani A.M. & Stocker R., 2010, “Stratlets: Low Reynolds number point-force solutions in a stratified fluid”, Physical Review Letters, 105, 084502.
  74. Sutherland K.R., Madin L.P. & Stocker R., 2010, “Filtration of submicrometer particles by pelagic tunicates”, Proceedings of the National Academy of Sciences, 107, 15129-15134.
  75. Seymour J.R., Simó R., Ahmed T. & Stocker R., 2010, “Chemoattraction to dimethyl-sulfoniopropionate throughout the marine microbial food web”, Science, 329, 342-345.

    In the news: Compound Crucial in Sea and Air; Culturing Science; MIT Media Relations; SINC News.

  76. Ahmed T., Shimizu T.S. & Stocker R., 2010, “Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients”, Nano Letters, 10, 3379-3385.
  77. Seymour J.R., Ahmed T., Durham W.M. & Stocker R., 2010, “Chemotactic response of marine bacteria to the extracellular products of Synechococcus and Prochlorococcus”, Aquatic Microbial Ecology, 59, 161-168.
  78. Seymour J.R., Ahmed T. & Stocker R., 2009, “Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo”, Journal of Plankton Research, 31, 1557-1561.
  79. Stocker R. & Durham W.M., 2009, “Tumbling for stealth?”, Science, 325, 400-402.
  80. Yick K.Y., Torres C., Peacock T. & Stocker R., 2009, “Enhanced drag of a sphere settling in a stratified fluid at small Reynolds numbers”, Journal of Fluid Mechanics, 632, 49-68.
  81. Marcos, Fu H., Powers T.R. & Stocker R., 2009, “Separation of microscale objects by flow”, Physical Review Letters, 102, 158103.

    In the news: NSF News; CEE News; Eurekalert; Medgadget; Virtual Journal of Nanoscale Science & Technology (April 27, 2009 issue); Virtual Journal of Biological Physics Research (April 15, 2009 issue).

  82. Durham W.M., Kessler J.O. & Stocker R., 2009, “Disruption of vertical motility by shear triggers formation of thin phytoplankton layers”, Science, 323, 1067-1070.

    In the news: New York Times; Boston Globe; Discovery Channel; BBC Wildlife’s July Discoveries; Science Daily News; Science News; Faculty of 1000 Biology.

  83. Seymour J.R., Marcos & Stocker R., 2009, “Resource patch formation and exploitation throughout the marine microbial food web”, American Naturalist, 173, E15-E29.
  84. Ahmed T. & Stocker R., 2008, “Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics”, Biophysical Journal, 95, 4481-4493.
  85. Seymour J.R., Ahmed T., Marcos & Stocker R., 2008, “A microfluidic chemotaxis assay to study microbial behaviour in diffusing nutrient patches”, Limnology and Oceanography: Methods, 6, 477-488.
  86. Stocker R., Seymour J.R., Samadani A., Hunt D.E. & Polz M.F., 2008, “Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches”, Proceedings of the National Academy of Sciences, 105, 4209-4214.

    In the news: Science Daily News; PhysOrg; On Balance; CEE News; Tech Talk.

  87. Seymour J.R., Marcos & Stocker R., 2007, “Chemotactic response of marine microorganisms to microscale nutrient layers”, Journal of Visualized Experiments, 4, 052807 (video-publication: www.jove.com/index/details.stp?ID=203).
  88. Stocker R. & Bush J.W.M., 2007, “Spontaneous oscillations of a sessile lens”, Journal of Fluid Mechanics, 583, 465-475.

    In the news: New York Times; Cosmos Magazine; MIT News; PhysOrg; Science Daily; Science Daily News; Science et vie; Softpedia

  89. Yick K.Y., Stocker R. & Peacock T., 2007, “Microscale Synthetic Schlieren”, Experiments in Fluids, 42, 41-48.
  90. Marcos & Stocker R., 2006, “Microorganisms in vortices: A microfluidic setup”, Limnology and Oceanography: Methods, 4, 392-398.
  91. Heitz R., Peacock T. & Stocker R., 2005, “Optimizing diffusion-driven flow in a fissure”, Physics of Fluids, 17, 128104, 1-3.
  92. Stocker R. & Hosoi A.E., 2005, “Lubrication in a corner”, Journal of Fluid Mechanics, 544, 353-377.
  93. Stocker R. & Hosoi A.E., 2004, “Corner flow in free liquid films”, Journal of Engineering Mathematics, 50, 267-288.
  94. Peacock T., Stocker R. & Aristoff J.M., 2004, “An experimental investigation of the angular dependence of diffusion-driven flow”, Physics of Fluids, 16, 3503-3505.
  95. Wake G., Ivey G.N., Imberger J., MacDonald R. & Stocker R., 2004, “Baroclinic geostrophic adjustment in a rotating circular basin”, Journal of Fluid Mechanics, 515, 63-86.
  96. Laval B., Imberger J., Hodges B.R. & Stocker R., 2003, “Modelling circulation in lakes: Spatial and temporal variations”, Limnology and Oceanography, 48, 983-994.
  97. Stocker R. & Imberger J., 2003, “Energy partitioning and horizontal dispersion in a stratified rotating lake”, Journal of Physical Oceanography, 33, 512-529.
  98. Johnson D., Stocker R., Head R., Imberger J. & Pattiaratchi C., 2003, “A compact, low-cost GPS drifter for use in the Oceanic nearshore zone, lakes and estuaries”, Journal of Atmospheric and Oceanic Technology, 20, 1880-1884.
  99. Stocker R. & Imberger J., 2003, “Horizontal transport and dispersion in the surface layer of a medium-sized lake”, Limnology and Oceanography, 48, 971-982.

  100. Book Chapters

    Khalili A., Liu B., Morad R., Javadi K., Morad M.R., Matyka M., Kindler K., Stocker R. & Koza Z. “Application of porous media in marine biological modeling”, in “Application of porous media in biology and biotechnology”, K. Vafai ed., Dekker, 2010.


    1. Interview @ JOVE
      Studies of Bacterial Chemotaxis Using Microfluidics
    2. Making Microchannels
      for Microbial Ecology Studies
      JOVE video article
    3. Interview for NECN @ Museum of Sciences
      SciTech Today (February 7, 2007)