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  1. Ugolini G.S., Wang M., Secchi E., Pioli R., Ackermann M. and Stocker R., 2024, “Microfluidic approaches in microbial ecology”, Lab on a Chip, doi: 10.1039/d3lc00784g
  2. Seymour J.R., Brumley D.R., Stocker R. and Raina J.-B., 2023, “Swimming towards each other: the role of chemotaxis in bacterial interactions”, Trends in Microbiology, doi: 10.1016/j.tim.2023.12.008.


  1. Riva A., Rasoulimehrabani H., Cruz-Rubio J.M., Schnorr S.L., von Baeckmann C., Inan D., Nikolov G., Herbold C.W., Hausmann B., Pjevac P., Schintlmeister A., Splitter A., Palatinsky M., Kadunic A., Hieger N., Del Favero G., von Bergen M., Jehmlich N., Watzka M., Lee K.S., Wiesenbauer J., Khadem S., Viernstein H., Stocker R., Wagner M., Kaiser C., Richter A., Kleitz F. and Berry D., 2023, “Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting”, Nature Communications, 14, 8210.
  2. Clerc E.E., Raina J.-B, Keegstra J.M., Landry Z., Pontrelli S., Alcolombri U., Lambert B.S., Anelli V., Vincent F., Masdeu-Navarro M., Sichert A., De Schaetzen F., Sauer U., Simó R., Hehemann J.H., Vardi A., Seymour J.R. and Stocker R., 2023, “Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP”, Nature Communications, 14, 8080.
  3. D’Souza G., Schwartzman J., Keegstra J., Schreier J.E., Daniels M., Cordero O., Stocker R.and Ackermann M., 2023, “Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities”, PNAS, 120, 44, e2305198120.
  4. Pfreundt U., Slomka J., Schneider G., Sengupta A., Carrara F., Fernandez V., Ackermann M. and Stocker R., 2023, “Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture”, Science, (Supplementary Materials), 380, 6647, 830-835.
  5. de Schaetzen F., Impiö M., Wagner B., Nienaltowski P., Arnold M., Huber M., Meyer M., Raitoharju J., M. Silva L.G and Stocker R., 2023, “The Riverine Organism Drift Imager: A new technology to study organism drift in rivers and streams”, Methods in Ecology and Evolution, doi: 10.1111/2041-210X.14130.
  6. Kurz D.L., Secchi E., Stocker R. and Jimenez-Martinez J., 2023, “Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics”, Environmental Science & Technology, 57, 5666-5677.
  7. D’Souza G., Ebrahimi A., Stubbusch A., Daniels M., Keegstra J., Stocker R., Cordero O. and Ackermann M., 2023, “Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria”, ISME Journal, 17, 703-711.
  8. Ramirez A.C., Lee K.S., Odriozola A., Kaminek M., Stocker R., Zuber B. and Junier P., 2023, “Multiple roads lead to Rome: unique morphology and chemistry of endospores, exospores, myxospores, cysts and akinetes in bacteria”, Microbiology Society, 169, 2.
  9. Raina J.B., Giardina M., Brumley D.R., Clode P.L., Pernice M., Guagliardo P., Bougoure J., Mendis H., Smirga S., Sonnenschein E.C., Ullrich M. S., Stocker R. and Seymour J.R., 2023, “Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria”, Nature Microbiology, 8, 510-521
  10. Slomka J., Alcolombri U., Carrara F., Foffi R., Peaudecerf F.J., Zbinden M. and Stocker R., 2022, “Encounter rates prime interactions between microorganisms”, Interface Focus, 13, 20220059.


  1. Ahmerkamp S., Liu B., Kindler K., Maerz J., Stocker R., Kuypers M.M.M. and Khalili A., 2022, “Settling of highly porous and impermeable particles in linear stratification: implications for marine aggregates”, Journal of Fluid Mechanics, 931, A9.
  2. Ahmerkamp S., Jalaluddin F.M., Cui Y., Brumley D.R., Pacherres C.O., Berg J.S., Stocker R., Kuypers M.M.M., Koren K. and Behrendt L., 2022, “Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems”, Cell Reports Methods, 2, 100216.
  3. Norris N., Alcolombri U., Keegastra J.M., Yawata Y., Menolascina F., Frazzoli E., Levine N.M., Fernandez V.I. and Stocker R., 2022, “Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake”, Biophysical Journal, 121, 2046-2059.
  4. Hallstrøm S., Raina J.-B., Ostrowski M., Parks D.H., Tyson G.W., Hugenholtz P., Stocker R., Seymour J.R and Riemann L., 2022, “Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean”, ISME , 16, 2525-2534.
  5. Kurz D.L., Secchi E., Stocker R. and Jimenez-Martinez J., 2022, “A microfluidic platform to study bioclogging in porous media”, jove, 188, e64689.
  6. Kurz D.L., Secchi E., Carrillo F.J., Bourg I.C., Stocker R. and Jimenez-Martinez J., 2022, “Competition between growth and shear stress drives intermittency in preferential flow paths in porous medium biofilms”, PNAS, 119, 30, e2122202119
  7. Arguedas-Leiva J. A., Slomka J., Lalescu C.C., Stocker R. and Wilczek M., 2022, “Elongation enhances encounter rates between phytoplankton in turbulence”, PNAS, 119, 32, e2203191119
  8. de Schaetzen F., Fan M., Alcolombri U., Peaudecerf F.J., Drissner D., Loessner M.J., Stocker R. and Schuppler M., 2022, “Random encounters and amoeba locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii”, PNAS, 119, 32, e2122659119
  9. Alcolombri U., Pioli R., Stocker R. and Berry D., 2022, “Single-cell stable isotope probing in microbial ecology”, ISME Communications, 2, 55.
  10. Savorana G., Slomka J., Stocker R., Rusconi R. and Secchi E., 2022, “A microfluidic platform for characterizing the structure and rheology of biofilm streamers”, Royal Society of Chemistry, 18, 3878-3890.
  11. Savorana G., Geisel S., Cen T., Ling Y., Stocker R., Rusconi R. and Secchi E., 2022, “Transport of pseudomonas aeruginosa in polymer solutions”, Frontiers in Physics, 10, 910882
  12. Raina J.B., Lambert B.S., Parks D.H., Rinke C., Siboni N., Bramucci A., Ostrowski M., Signal B., Lutz A., Mendis H., Rubino F., Fernandez V.I., Stocker R., Hugenholtz P., Tyson G.W. and Seymour J.R., 2022, “Chemotaxis shapes the microscale organization of the ocean’s microbiome”, Nature, 605, 132-138.
  13. Nguyen T.T.H., Zakem E.J., Ebrahimi A., Schwartzmann J., Caglar T., Amarnath K., Alcolombri U., Peaudecerf F.J., Hwa T., Stocker R., Cordero O.X. and Levine N.M., 2022, “Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates”, Nature Communications, 13, 1657.
  14. Yue Y., Cheng J., Lee K.S., Stocker R., He X., Yao M. and Wang J., 2022, “Effects of relative humidity on heterogeneous reaction of SO2 with CaCO3 particles and formation of CaSO4.2H2O crystal as secondary aerosol”, Atmospheric Environment, 268, 118776.
  15. Fernandez V.I., Stocker R. and Juarez G., 2022, “A tradeoff between physical encounters and consumption determines an optimal droplet size for microbial degradation of dispersed oil”, Scientific Reports, 12, 4734.
  16. Secchi E., Savorana G., Vitale A., Eberl L., Stocker R. and Rusconi R., 2022, “The structural role of bacterial eDNA in the formation of biofilm streamers”, PNAS, 119, 12, e2113723119
  17. Keegstra J.M., Carrara F. and Stocker R., 2022, “The ecological roles of bacterial chemotaxis”, Nature Review Microbiology, 20, 491-504.


  1. Hunter J.E., Fredericks H.F., Behrendt L., Alcolombri U., Bent S.M., Stocker R. and Van Mooy B.A.S. 2021, “Using High-Sensitivity Lipidomics To Assess Microscale Heterogeneity in Oceanic Sinking Particles and Single Phytoplankton Cells”, Environmental Science & Technology, 55 (22), 15456-15465.
  2. Norris N., Levine N.M., Fernandez V.I. and Stocker R., 2021, “Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria”, PLoS Computational Biology, 17, 5.
  3. Lee K.S., Landry Z., Pereira F.C., Wagner M., Berry D., Huang W.E., Taylor G.T., Kneipp J., Popp J., Zhang M., Cheng J. and Stocker R., 2021, “Raman microspectroscopy for microbiology”, Nature Reviews Methods Primers,1, 80.
  4. Pioli R., Stocker R., Isa L. and Secchi E., 2021, “Patterning of microorganisms and microparticles through sequential capillarity-assisted assembly”, jove, 177, e63131, (video-publication).
  5. Wong G.C.L., Antani J.D., Lele P.P., Chen J., Nan B., Kühn M.J., Persat A., Bru J-L., Hoyland-Kroghsbo N.M., Siryaporn A., Conrad J.C., Carrara F., Yawata Y., Stocker R., Brun Y.V., Whitfield G.B., Lee C.K., de Anda J., Schmidt W.C., Golestaninan R., O’Toole G.A., Floyd K.A., Yildiz F.H., Yang S., Jin F., Toyofuku M., Eberl L., Nomura N., Zacharoff L.A., El-Naggar M.Y., Yalcin S.E., Malvankar N.S., Rojas-Andrade M.D., Hochbaum A.I., Yan J., Stone H.A., Wingreen N.S., Bassler B.L., Wu Y., Xu H., Drescher K. and Dunkel J., 2021, “Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation”, Physical Biology, 18, 051501.
  6. Alcolombri U., Peaudecerf F.J., Fernandez V.I., Behrendt L., Lee K.S. and Stocker R., 2021, “Sinking enhances the degradation of organic particles by marine bacteria”, Nature Geoscience, 14, 775-780.
  7. Gao C., Garren M., Penn K., Fernandez V.I., Seymour J.R., Thompson J.R., Raina J.B. and Stocker R., 2021, “Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen”, ISME Journal, 15, 3668–3682.
  8. Nguyen J., Fernandez V.I., Pontrelli S., Sauer W., Ackermann M. and Stocker R., 2021, “A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations”, Nature Communications, 12, 3662.
  9. D’Souza G.G., Povolo V.R, Keegstra J.M., Stocker R. and Ackermann M., 2021, “Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations”, ISME Journal, 15, 2614-2626.
  10. Courcol JD, Invernizzi C.F., Landry Z.C., Minisini M., Baumgartner D.A., Bonhoeffer S., Chabriw B., Clerc E.E., Daniels M., Getta P., Girod M., Kazala K., Markram H., Pasqualini A., Martinez-Pérez C., Peaudecerf F.J., Peaudecerf M.S., Pfreundt U., Roller B.R.K., Slomka J., Vasse M., Wheeler J.D., Metzger C.M.J.A., Stocker R. and Schürmann F., 2021, “ARC: An open web-platform for request/supply matching for a prioritized and controlled COVID-19 response”, Frontiers in Public Health, 9, 607677.
  11. Carrara F., Sengupta A., Behrendt L., Vardi A. and Stocker R., 2021, “Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence”, PNAS, 118, 5, e2005944118 N
  12. Salek M.M., Fernandez V.I., D’souza G., Puigmarti-Luis J., Stocker R. and Secchi E., 2021, “An interdisciplinary and application-oriented approach to teach microfluidics”, Biomicrofluidics, 15, 014104.
  13. Pioli R., Fernandez-Rodriguez M.A., Grillo F., Alvarez L., Stocker R., Isa L. and Secchi E., 2021, “Sequential capillarity-assisted particle assembly in
    a microfluidic channel”, Lab on a Chip, 21, 888–895.
  14. Nguyen J., Lara-Guiterrez J. and Stocker R., 2021, “Environmental fluctuations and their effects on microbial communities, populations, and individuals”, FEMS Microbiology Reviews, fuaa068, 1–16.
  15. Lee K.S., Pereira F.C., Palatinszky M., Behrendt L., Alcolombri U., Berry D., Wagner M. and Stocker R., 2021, “Optofluidic Raman-activated cell sorting for
    targeted genome retrieval or cultivation of microbial cells with specific functions”, Nature Protocols, 16, 634-676.


  1. Pereira F.C., Wasmund K., Cobankovic I., Jehmlich N., Herbold C.W., Lee K.S., Sziranyi B., Vesley C., Decker T., Stocker R., Warth B., von Bergen M., Wagner M. and Berry D., 2020, “Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization”, Nature Communications, 11, 5104.
  2. Gralka M., Szabo R., Stocker R. and Cordero O.X., 2020, “Trophic Interactions and the Drivers of Microbial Community Assembly”, Current Biology, 30, 19, R1176-R1188.
  3. Yawata Y., Carrara F., Menolascina F. and Stocker R., 2020, “Constrained optimal foraging by marine bacterioplankton on particulate organic matter”, PNAS, 117, 25571-25579.
  4. Clerc E.E., Raina J.B., Lambert B.S., Seymour J. and Stocker R., 2020, “In situ chemotaxis assay to examine microbial behavior in aquatic ecosystems”, Journal of Visualized Experiments , 159, e61062.
  5. De Anna P., Pahlavan A.A., Yawata Y., Stocker R. and Juanes R., 2020, “Chemotaxis under flow disorder shapes microbial dispersion in porous media”, Nature Physics, 17, 68–73.
  6. Guasto J.S., Estrada J.B., Menolascina F., Burton L.J., Patel M., Franck C., Hosoi A.E., Zimmer R.K. and Stocker R., 2020, “Flagellar kinematics reveals the role of environment in shaping sperm motility”, Journal of the Royal Society Interface, 17, 20200525.
  7. Behrendt L., Salek M.M., Trampe E.L., Fernandez V.I., Lee K.S., Kühl M. and Stocker R., 2020, “PhenoChip: A single-cell phenomic platform for highthroughput photophysiological analyses of microalgae”, Science Advances, 6, 2754.
  8. Brumley D.R., Carrara F., Hein A.M., Hagstrom G.I., Levin S.A. and Stocker R., 2020, “Cutting through the noise: bacterial chemotaxis in marine microenvironments”, Frontiers in Marine Science, 7, 527.
  9. Slomka J. and Stocker R., 2020, “Bursts characterize coagulation of rods in a quiescent fluid”, Physical Review Letters, 124, 25-26.
  10. Secchi E., Vitale A., Miño G.L., Kantsler V., Eberl L., Rusconi R. and Stocker R., 2020, “The effect of flow on swimming bacteria controls the initial colonisation of curved surfaces”, Nature Communications, 11, 2851.
  11. Borer B., Jimenez-Martinez J., Stocker R. and Or D., 2020, “Reduced gravity promotes bacterially mediated anoxic hotspots in unsaturated porous media”, Scientific Reports, 10, 8614.
  12. Gao C., Fernandez V.I., Lee K.S., Fenizia S., Pohnert G., Seymour J.R., Raina J.B. and Stocker R., 2020, “Single-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling”, Nature Communications, 11, 1942.
  13. Slomka J., Alcolombri U., Secchi E., Stocker R. and Fernandez V.I., 2020, “Encounter rates between bacteria and small sinking particles”, New Journal of Physics, 22, 043016.
  14. Sekar K., Linker S.M., Nguyen J., Grünhagen A., Stocker R. and Sauer U., 2020, “Bacterial glycogen provides short-term benefits in changing environments”, Applied and Environmental Microbiology, 86, e00049-20.
  15. Lee K.S., Wagner M. and Stocker R., 2020, “Raman-based sorting of microbial cells to link functions to their genes”, Microbial Cell, 7, 62-65.
  16. Carrara F., Brumley D.R., Hein A.H., Yawata Y., Salek M.M., Lee K.S., Sliwerska E., Levin S.A. and Stocker R., 2020, “Generating controlled, dynamic chemical landscapes to study microbial behavior”, jove, Journal of Visualized Experiments, 155, e60589.
  17. Slomka J. and Stocker R., 2020, “On the collision of rods in a quiescent fluid”, PNAS, 117, 3372-3374.


  1. Lovecchio S., Climent E., Stocker R. and Durham W.M., 2019, “Chain formation can enhance the vertical migration of phytoplankton through turbulence”, Science Advances, 5, eaaw7879.
  2. Wheeler J.D., Secchi E., Rusconi R. and Stocker R., 2019, “Not just going with the flow: the effects of fluid flow on bacteria and plankton”, Annual Review of Cell and Developmental Biology, 35, 213-237.
  3. Salek M.M., Carrara F., Fernandez V.I. and Stocker R., 2019, “Bacterial maze runners reveal hidden diversity in chemotactic performance”, Microbial Cell, 6, 370-372.
  4. Zaoli S., Giometto A., Maranon E., Escrig S., Meibom A., Ahluwalia A., Stocker R., Maritan A. and Rinaldo A., 2019, “Generalized size scaling of metabolic rates basded on single-cell measurements with freshwater phytoplankton”, PNAS, 116, 17323-17329.
  5. Lambert B.S., Fernandez V.I. and Stocker R., 2019, “Motility drives bacterial encounter with particles responsible for carbon export throughout the ocean”, Limnology and Oceanography Letters, 4, 113-118.
  6. Brumley D.R., Carrara F., Hein A.M., Yawata Y., Levin S.A. and Stocker R., 2019, “Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients”, PNAS, 116 (22), 10792-10797.
  7. Salek M.M., Carrara F., Fernandez V.I., Guasto J.S. and Stocker R., 2019, “Bacterial chemotaxis in a microfluidic T-maze reveals strong phenotypic heterogeneity in chemotactic sensitivity”, Nature Communications, 10, 1877.
    In the news: ETH News; Science Daily; PhysOrg,
  8. Raina J.B., Fernandez V.I., Lambert B., Stocker R. and Seymour J.R., 2019, “The role of microbial motility and chemotaxis in symbiosis”, Nature Reviews Microbiology, 17, 284-294.
  9. Lee K.S., Palatinszky M., Pereira F.C., Nguyen J., Fernandez V.I., Mueller A.J., Menolascina F., Daims H., Berry D., Wagner M. and Stocker R., 2019 “An automated Raman-based platform for the sorting of live cells by functional properties”, Nature Microbiology, 4, 1035-1048.
  10. Fernandez V.I., Yawata Y. and Stocker R., 2019, “A foraging mandala for aquatic microorganisms”, ISME Journal, 13, 563-575.


  1. Sekar K., Rusconi R., Sauls J.T., Fuhrer T., Noor E., Nguyen J., Fernandez V.I., Buffing M.F., Berney M., Jun S., Stocker R. and Sauer U., 2018, “Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria”, Molecular Systems Biology, 14, e8623.
  2. Roggo C., Clerc E.E., Hadadi N., Carraro N., Stocker R. and van der Meer J.R., 2018, “Heterologous expression of Pseudomonas putida methyl-accepting chemotaxis proteins yields Escherichia coli cells chemotactic to aromatic compounds”, Applied and Environmental Microbiology, 84, e01362-18.


  1. Di Giacomo R., Krödel S., Maresca B., Benzoni P., Rusconi R., Stocker R. and Daraio C., 2017, “Deployable micro-traps to
    sequester motile bacteria”, Scientific Reports, 7, 45897.
  2. Tout J., Astudillo-Garcia C., Taylor M.W., Tyson G.W, Stocker R., Ralph P.J., Seymour J.R. and Webster N.S., 2017, “Redefining the sponge-symbiont acquisition paradigm: Sponge microbes exhibit chemotaxis towards host-derived compounds”, Environmental Microbiology Reports (2017), 9, 750-755.
  3. Lambert B.S., Raina J.B., Fernandez V.I., Rinke C., Siboni N., Rubino F., Hugenholtz P., Tyson G.W., Seymour J.R. and Stocker R., 2017, “A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities”, Nature Microbiology, 2, 1344-1349.
  4. Seymour J.R., Amin S.A., Raina J.B. and Stocker R., 2017, “Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships”, Nature Microbiology, 2, 17065.
  5. 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, 544, 498-502.
  6. 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, 7, 730.
  7. Sengupta A., Carrara F. and Stocker R., 2017, “Phytoplankton can actively diversify their migration strategy in response to turbulent cues”, Nature, 543, 555-558.
  8. Miño G.L., Koehl M.A.R., King N. 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.
  9. Cordero O.X. and Stocker R., 2017, “A particularly useful system to study the ecology of microbes”, Environmental Microbiology Reports, 9, 16-17.
  10. 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, 3, 6.
  11. 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.


  1. Hussain Y.H., Guasto J.S., Zimmer R.K., Stocker R. and Riffell J.A., 2016, “Sperm chemotaxis promotes individual fertilization success in sea urchins”, Journal of Experimental Biology, 219, 1458-1466.
  2. Rinke C., Low S., Woodcroft B.J., Raina J.-B., Skarshewski A., Le X.H., Butler M.K., Stocker R., Seymour J., Tyson G.W. and Hugenholtz P., 2016, “Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics”, PeerJ, 4:e2486.
  3. Fernandez V.I. and Stocker R., 2016, “Modus vivendi”, Nature Physics, 13, 326-327.
  4. Son K., Menolascina F. and Stocker R., 2016, “Speed-dependent chemotactic precision in marine bacteria”, PNAS, 113, 8624-8629.
  5. Nelson M.B., Chase A.B., Martiny J.B.H., Stocker R., Nguyen J., Lloyd K., Oshiro R.T., Kearns D.B., Schneider J.P., Ringel P.D., Basler M., Olson C.A., Vuong H.E., Hsiao E.Y., Roller B.R.K., Ackermann M., Smillie C., Chien D., Alm E. and Jermy A.J., 2016, “The Microbial Olympics 2016”, Nature Microbiology, 1, 16122.
  6. Hein A.M., Carrara F., Brumley D.R., Stocker R. and Levin S.A., 2016, “Natural search algorithms as a bridge between organisms, evolution, and ecology”, PNAS, 113, 9413-9420.
  7. Emge P., Moeller 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.
  8. Yawata Y., Nguyen J., Stocker R. and Rusconi R., 2016, “Microfluidic studies of biofilm formation in dynamic environments”, Journal of Bacteriology, 198(19), 2589-2595.
  9. 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.
  10. Secchi E., Rusconi R., Buzzaccaro S., Salek M.M., Smriga S., Piazza R. and Stocker R., 2016, “Intermittent turbulence in flowing bacterial suspensions”, Journal of the Royal Society Interface , 13, 20160175.
  11. 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.
  12. 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.
  13. Smriga S., Fernandez V.I., Mitchell J.G. and Stocker R., 2016, “Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria”, Proceedings of the National Academy of Sciences, 113, 1576-1581.
  14. Hein A.M., 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.
  15. Garren M., Son K., Tout J., Seymour J.R. and Stocker R., 2016, “Temperature-induced behavioral switches in a bacterial coral pathogen”, The ISME Journal, 10, 1363-1372.


  1. Dörgens A.L., Ahmerkamp S., M¸ssig 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.
  2. Stocker R., 2015, “The 100 µm length scale in the microbial ocean”, Aquatic Microbial Ecology, 76, 189-194.
  3. Brumley D.R., Rusconi R., Son K. and Stocker R., 2015, “Flagella, flexibility and flow: Physical processes in microbial ecology”, The European Physical Journal Special Topics, 224, 3119-3140.
  4. 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.
  5. Barry M.T., Rusconi R., Guasto J.S. and Stocker R., 2015, “Shear-induced orientational dynamics and spatial heterogeneity in suspensions of motile phytoplankton”, Journal of the Royal Society Interface, 12, 20150791.
  6. 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, 13, 761-775.
  7. Rusconi R. and Stocker R., 2015, “Microbes in flow”, Current Opinion in Microbiology, 25:1-8.
  8. 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.
  9. 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.
  10. 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”, The ISME Journal, 9, 1764-1777.
  11. Lecuyer S., Stocker R. and Rusconi R., 2015, “Focus on the physics of biofilms”, New Journal of Physics, 17, 030401.
  12. Pollock F.J., Krediet C.J., Garren M., 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.


  1. Shapiro O.H., Fernandez V.I., Garren M., Guasto J.S., Debaillon-Vesque F.P., Kramarsky-Winter E., Vardi A. and 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, 7 Feb 2014 (Image by V. Fernandez, O. Shapiro, M. Garren, A. Vardi and R. Stocker); WIRED.CO.UK; MIT News
  2. Mayola A., Irazoki O., Martinez I.A., Petrov D., Menolascina F., Stocker R., Reyes-Darias J.A., Krell T., Barbé J. and Campoy S., 2014, “RecA protein plays a role in the chemotactic response and chemoreceptor clustering of Salmonella enterica“, PLoS ONE, 9, e105578.
  3. Molaei M., Barry M., Stocker R. and Sheng J., 2014, “Failed escape: Solid surfaces prevent tumbling of Escherichia coli“, Physical Review Letters, 113, 068103.
  4. 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. and Chisholm S.W., 2014, “Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus“, Science, 344, 416-420.
  5. Rusconi R., Garren M. and Stocker R., 2014, “Microfluidics expanding the frontiers of microbial ecology”, Annual Review of Biophysics, 43, 65-91.
  6. Yawata Y., Cordero O.X., Menolascina F., Hehemann J.H., Polz M.F. and Stocker R., 2014, “Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations”, Proceedings of the National Academy of Sciences, 111, 5622-5627.
    In the news: The Scientist
  7. Rusconi R., Guasto J.S. and Stocker R., 2014, “Bacterial transport suppressed by fluid shear”, Nature Physics, 10, 212-217.
  8. De Lillo F., Cencini M., Durham W.M., Barry M., Stocker R., Climent E. and Boffetta G., 2014, “Turbulent fluid acceleration generates clusters of gyrotactic microorganisms”, Physical Review Letters, 112, 044502.
  9. Tout J., Jeffries T.C., Webster N.S., Stocker R., Ralph P.J. and Seymour J.R., 2014, “Variability in microbial community composition and function between different niches within a coral reef”, Microbial Ecology, 67, 540-552.
  10. Yang R., Jang H., Stocker R. and Gleason K.K., 2014, “Synergistic prevention of biofouling in seawater desalination by zwitterionic surfaces and low-level chlorination”, Advanced Materials, 26, 1711-1718.
  11. Norris N., Menolascina F., Frazzoli E. and Stocker R., 2014, “The effect of reversals for a stochastic source-seeking process inspired by bacterial chemotaxis”, 2014 American Control Conference, 3411-3416.
  12. Garren M., Son K., Raina J.-B., Rusconi R., Menolascina F., Shapiro O.H., Tout J., Bourne D.G., Seymour J.R. and Stocker R., 2014, “A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals”, The ISME Journal, 8, 999-1007.


  1. Crouzier T., Jang H., Ahn J., Stocker R. and Ribbeck K., 2013, “Cell patterning with mucin biopolymers”, Biomacromolecules, 14, 3010-3016.
  2. Billings N., Millan M.R., Caldara M., Rusconi R., Tarasova Y., Stocker R. and Ribbeck K., 2013, “The extracellular matrix component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biofilms”, PLoS Pathogens, 9, e1003526.
  3. Durham W.M., Climent E., Barry M., De Lillo F., Boffetta G., Cencini M. and Stocker R., 2013, “Turbulence drives microscale patches of motile phytoplankton”, Nature Communications, 4, 2148.
    In the news: MIT News; Nature World News; Science Newsline
  4. Son K., Guasto J.S. and Stocker R., 2013, “Bacteria can exploit a flagellar buckling instability to change direction”, Nature Physics, 9, 494-498.
    In the news: MIT News; ScienceNews News and views: Nature Physics
  5. Peruzzo P., Defina A., Nepf H.M. and Stocker R., 2013, “Capillary interception of floating particles by surface-piercing vegetation”, Physical Review Letters, 111, 164501.


  1. Stocker R., 2012, “Marine microbes see a sea of gradients”, Science, 338, 628-633.
  2. Taylor J.R. and Stocker R., 2012, “Trade-offs of chemotactic foraging in turbulent water”, Science, 338, 675-679.
  3. Durham W.M., Tranzier O., Leombruni A. and Stocker R., 2012, “Division by fluid incision: Biofilm patch development in porous media”, Physics of Fluids, 24, 091107.
  4. Stocker R. and 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).
  5. Hyon Y., Marcos, Powers T.R., Stocker R. and Fu H.C., 2012, “The wiggling trajectories of bacteria”, Journal of Fluid Mechanics, 705, 58-76.
  6. Marcos, Fu H.C., Powers T.R. and Stocker R., 2012, “Bacterial rheotaxis”, Proceedings of the National Academy of Sciences, 109, 4780-4785.
  7. Doostmohammadi A., Stocker R. and Ardekani A.M., 2012, “Low-Reynolds-number swimming at pycnoclines”, Proceedings of the National Academy of Sciences, 109, 3856-3861.
  8. Durham W.M. and Stocker R., 2012, “Thin phytoplankton layers: Characteristics, mechanisms and consequences”, Annual Review of Marine Science, 4, 177-207.
  9. Guasto J.S., Rusconi R. and Stocker R., 2012, “Fluid mechanics of planktonic microorganisms”, Annual Review of Fluid Mechanics, 44, 373-400.


  1. Lewpiriyawong N., Kandaswamy K., Yang C., Ivanov V. and 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.
  2. Steger D., Berry D., Haider S., Horn M., Wagner M., Stocker R. and 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.
  3. Lazova M.D., Ahmed T., Bellomo D., Stocker R. and Shimizu T.S., 2011, “Response rescaling in bacterial chemotaxis”, Proceedings of the National Academy of Sciences, 108, 13870-13875.
  4. Durham W.M., Climent E. and Stocker R., 2011, “Gyrotaxis in a steady vortical flow”, Physical Review Letters, 106, 238102.
  5. Marcos, Seymour J.R., Luhar M., Durham W.M., Mitchell J.G., Macke A. and Stocker R., 2011, “Microbial alignment in flow changes ocean light climate”, Proceedings of the National Academy of Sciences, 108, 3860-3864.
  6. Giuffre C., Hinow P., Vogel R., Ahmed T., Stocker R., Consi T.R. and Strickler J.R., 2011, “The ciliate Paramecium shows higher motility in non-uniform chemical landscapes”, PLoS ONE, 6, e15274.
  7. Aristoff J.M., Stocker R., Reis P.M. and Jung S., 2011, “On the water lapping of felines and the water running of lizards: A unifying physical perspective”, Communicative and Integrative Biology, 4, 213-215.
  8. Stocker R., 2011, “Reverse and flick: Hybrid locomotion in bacteria”, Proceedings of the National Academy of Sciences, 108. 2635-2636.
  9. Stocker R., Aristoff J.M., Jung S. and Reis P.M., 2011, “Response to comment on “How cats lap: Water uptake by Felis catus“”, Science, 334, 311.


  1. Reis P.M., Jung S., Aristoff J.M. and 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:  Quirks’N’Quarks
    (Canadian Broadcasting Company Radio) –
    Tonight Show with Jay Leno – World 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);; 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.
  2. Kindler K., Khalili A. and Stocker R., 2010, “Diffusion-limited retention of porous particles at density interfaces”, Proceedings of the National Academy of Sciences, 107, 22163-22168.
  3. Ahmed T., Shimizu T.S. and Stocker R., 2010, “Microfluidics for bacterial chemotaxis”, Integrative Biology, 2, 604-629.
  4. Ardekani A.M. and Stocker R., 2010, “Stratlets: Low Reynolds number point-force solutions in a stratified fluid”, Physical Review Letters, 105, 084502.
  5. Sutherland K.R., Madin L.P. and Stocker R., 2010, “Filtration of submicrometer particles by pelagic tunicates”, Proceedings of the National Academy of Sciences, 107, 15129-15134.
  6. Seymour J.R., Simó R., Ahmed T. and Stocker R., 2010, “Chemoattraction to dimethylsulfoniopropionate 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.
  7. Ahmed T., Shimizu T.S. and Stocker R., 2010, “Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients”, Nano Letters, 10, 3379-3385.
  8. Seymour J.R., Ahmed T., Durham W.M. and Stocker R., 2010, “Chemotactic response of marine bacteria to the extracellular products of Synechococcus and Prochlorococcus“, Aquatic Microbial Ecology, 59, 161-168.


  1. Seymour J.R., Ahmed T. and Stocker R., 2009, “Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo“, Journal of Plankton Research, 31, 1557-1561.
  2. Stocker R. and Durham W.M., 2009, “Tumbling for stealth?”, Science, 325, 400-402.
  3. Yick K.Y., Torres C.R., Peacock T. and Stocker R., 2009, “Enhanced drag of a sphere settling in a stratified fluid at small Reynolds numbers”, Journal of Fluid Mechanics, 632, 49-68.
  4. Marcos, Fu H.C., Powers T.R. and Stocker R., 2009, “Separation of microscale chriral objects by shear 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).
  5. Durham W.M., Kessler J.O. and 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.
  6. Seymour J.R., Marcos and Stocker R., 2009, “Resource patch formation and exploitation throughout the marine microbial food web”, American Naturalist, 173, E15-E29.


  1. Ahmed T. and Stocker R., 2008, “Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics”, Biophysical Journal, 95, 4481-4493.
  2. Seymour J.R., Ahmed T., Marcos and Stocker R., 2008, “A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches”, Limnology and Oceanography: Methods, 6, 477-488.
  3. Stocker R., Seymour J.R., Samadani A., Hunt D.E. and 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.


  1. Seymour J.R., Marcos and Stocker R., 2007, “Chemotactic response of marine micro-organisms to micro-scale nutrient layers”, Journal of Visualized Experiments, 4, e203 (video-publication:
  2. Stocker R. and 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
  3. Yick K.-Y., Stocker R. and Peacock T., 2007, “Microscale Synthetic Schlieren”, Experiments in Fluids, 42, 41-48.


  1. Marcos and Stocker R., 2006, “Microorganisms in vortices: A microfluidic setup”, Limnology and Oceanography: Methods, 4, 392-398.


  1. Heitz R., Peacock T. and Stocker R., 2005, “Optimizing diffusion-driven flow in a fissure”, Physics of Fluids, 17, 128104.
  2. Stocker R. and Hosoi A.E., 2005, “Lubrication in a corner”, Journal of Fluid Mechanics, 544, 353-377.


  1. Stocker R. and Hosoi A.E., 2004, “Corner flow in free liquid films”, Journal of Engineering Mathematics, 50, 267-288.
  2. Peacock T., Stocker R. and Aristoff J.M., 2004, “An experimental investigation of the angular dependence of diffusion-driven flow”, Physics of Fluids, 16, 3503-3505.
  3. Wake G.W., Ivey G.N., Imberger J., McDonald N.R. and Stocker R., 2004, “Baroclinic geostrophic adjustment in a rotating
    circular basin”, Journal of Fluid Mechanics, 515, 63-86.


  1. Laval B., Imberger J., Hodges B.R. and Stocker R., 2003, “Modeling circulation in lakes: Spatial and temporal variations”, Limnology and Oceanography, 48, 983-994.
  2. Stocker R. and Imberger J., 2003, “Energy partitioning and horizontal dispersion in a stratified rotating lake”, Journal of Physical Oceanography, 33, 512-529.
  3. Johnson D., Stocker R., Head R., Imberger J. and 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.
  4. Stocker R. and Imberger J., 2003, “Horizontal transport and dispersion in the surface layer of a medium-sized lake”, Limnology and Oceanography, 48, 971-982.

Book Chapters

  • J.R. and Stocker R., “The ocean’s microscale: A microbe’s view of the sea”, in Microbial Ecology of the Oceans, 3rd Edition, J. M. Gasol and K. L. Kirchmann eds, Wiley, 2018, Chapter 8, 289-332.
  • Fernandez V.I., Stocker R. and Juarez G., „Modeling the impact of dilution on the microbial degradation of dispersed oil in marine environments”, in Oilfield Microbiology, 1st Edition, Skovhus T.B., Whitby C., 2019, Chapter 13, 215-232.
  • Clerc E.E., Raina J.B., Peaudecerf F.J., Seymour J.R. and Stocker R., “Survival in a sea of gradients: Bacterial and archaeal foraging in a heterogeneous ocean”, in The Marine Microbes, 2nd Edition, Stal L.J, Cretoiu M.S., 2022, Chapter 2, 47-102.