V Gerganova, C Floderer, A Archetti, L Michon, L Carlini, T Reichler, S Manley+ and SG Martin+. “Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size,” eLife, 2019;8:e45983 (2019)

A Goujon, A Colom, K Straková, K, V Mercier, D Mahecic, S Manley, N Sakai, A Roux, S Matile+Mechanosensitive Fluorescent Probes to Image Membrane Tension in Mitochondria, Endoplasmic Reticulum and Lysosome,” J Am Chem Soc 141, 3380-3384 (2019)

A Archetti, E Glushkov*, C Sieben*, A Stroganov A, A Radenovic, S Manley+, “Waveguide-PAINT offers an open platform for large field-of-view super-resolution imaging,” Nat Commun  10(1):1267. doi: 10.1038/s41467-019-09247-1 (2019)

A Callegari*, C Sieben*, A Benke, D Suter, B Fierz, D Mazza and S Manley+, “Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation,” PLoS Genetics (2019)


M Stefko, B Ottino, KM Douglass and S Manley+, “Autonomous illumination control for localization microscopy,” Opt Express (2018)

MC Donaldson*, S Sungalee*, M Zufferey*, D Tavernari*, N Katanayeva, E Battistello, M Mina, K Douglass, T Rey, F Raynaud, S Manley, G Cirielloand E Oricchio+, “EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within topologically associating domains,” Nat Genetics (2018)

C Sieben*, N Banterle*, K Douglass, Pierre Gönczy and S Manley+, “Multicolor single-particle reconstruction of protein complexes,” Nat Methods 10.1038/s41592-018-0140-x (2018)

A Lambert*, A Vanhecke*, A Archetti, S Holden, F Schaber, Z Pincus, M Laub, E Goley and S Manley+, “Constriction rate modulation can drive cell size control and homeostasis in C. crescentus,” iScience (2018) 


M Prouteau, A Desfosses, C Sieben, C Bourgoint, NL Mozaffari, DD, AK Mitra, P Guichard, S Manley and R Loewith+, “TORC1 Organised in Inhibited Domains (TOROIDs) regulate TORC1 activity,” Nature doi:10.1038/nature24021 (2017) 

A Vancevska*, KM Douglass*, V Pfeiffer, S Manley+ and J Lingner+, “The telomeric DNA damage response occurs in the absence of chromatin decompaction,” Genes Dev, 31(6):567-577 (2017) 

T Verdier, J Gunzenhäuser, S Manley and M Castelnovo+, “Single Particle Maximum Likelihood Reconstruction from Superresolution Microscopy Images,” PLoS One, 12(3), e0172943 (2017) 


M Bergé, S Campagne, J Mignolet, SJ Holden, L Théraulaz, S Manley, FHT Allain and PH Viollier+, “Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria,” eLife 5:e20640 (2016) 

J Mignolet, SJ Holden, M Bergé, G Panis, L Théraulaz, S Manley and PH Viollier+, “Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator,” eLife 5:e18647 (2016)

C Deluz, ET Friman, D Strebinger, A Benke, M Raccaud, A Callegari, S Manley and DM Suter+, “A role for mitotic bookmarking of SOX2 in pluripotency and differentiation,” Genes Dev 30(22) 2538-2550 (2016)

K Douglass+, C Sieben, A Archetti, A Lambert, S Manley+, “Super-resolution imaging of multiple cells by optimized flat-field epi-illumination,” Nat Photonics 10.1038 (2016) Featured in Nat Methods Research Highlights

Y Nasu, A Benke, S Arakawa, GJ Yoshida, G Kawamura, S Manley, S Shimizu, T Ozawa+, “In Situ Characterization of Bak Clusters Responsible for Cell Death Using Single Molecule Localization Microscopy,” Sci Rep 6:27505 (2016)


L Carlini*, S Holden*, K Douglass* and S Manley+, “Correction of a depth-dependent lateral distortion in 3D super-resolution imaging,” PLoS One 10(11) e0142949 (2015) pdf

PJ Fabre, A Benke, E Joye, THN Huynh, S Manley and D Duboule+, “Nanoscale spatial organization of the HoxD cluster in distinct transcriptional states,” Proc Natl Acad Sci USA 112(45) 13964-13969 (2015) pdf

D Sage, H Kirschner, T Pengo, N Stuurman, J Min, S Manley and M Unser+, “Quantitative evaluation of software packages for single-molecule localization microscopy.” Nat Methods,12(8) 717-724 (2015) pdf

T Pengo, S Holden and S Manley+, “PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy,” Bioinformatics, 31(5):797-798 (2015) pdf


J Gunzenhäuser, R Wyss and S Manley+, “A quantitative approach to evaluate the impact of fluorescent labeling on HIV-Gag assembly by titration of unlabeled proteins,” PLoS One, 9(12) e115095 (2014) pdf

J Min*, S Holden*, L Carlini, M Unser, S Manley and JC Ye+, “3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction,” Biomed Opt Express, 5(11):3935-3948 (2014) pdf

J Min, C Vonesch*, H Kirschner*, L Carlini*, N Olivier, S Holden, S Manley, JC Ye and M Unser+, “FALCON: Fast and unbiased reconstruction of high-density super-resolution microscopy data,” Sci Rep 4:4577 (2014) pdf

SJ Holden, T Pengo, K Meibom, C Fernandez-Fernandez, J Collier and S Manley+In vivo quantitative analysis of Caulobacter crescentus z-ring organization by high throughput 3D PALM,” Proc Natl Acad Sci USA 111(12):4566-4571 (2014) Featured in Nat Methods Research Highlights  pdf

L Carlini, A Benke, L Reymond, G Lukinavicius and S Manley+, “Reduced dyes enhance single molecule localization density for live superresolution imaging,” ChemPhysChem 15(4):750-755 (2014) pdf 

D Keller, M Orpinell, L Reymond, N Olivier, M Wachsmuth, R Mahen, R Wyss, V Hachet, J Ellenberg, S Manley, and P Gönczy+Mechanisms of HsSAS-6 assembly promoting centriole formation in human cells,” J Cell Biol 204(5):697-712 (2014) pdf 


L Carlini and S Manley+, “Live intracellular super-resolution imaging using site-specific stains,” ACS Chem Biol 8(12):2643-2648 (2013) pdf

N Olivier+, D Keller, P Gönczy and S Manley+, “Resolution doubling in 3D STORM imaging through improved buffers,” PLoS One 8(7):e69004 (2013) pdf

N Olivier+, D Keller, VS Rajan, P Gönczy and S Manley+, “Simple buffers for 3D STORM microscopy,” Biomed Opt Express 4(6):885-899 (2013) pdf

J Min, C Vonesch, N Olivier, H Kirshner, S Manley, JC Ye and M Unser+, “Continuous localization using sparsity constraints for high-density super-resolution microscopy,” ISBI (2013) pdf

G Lukinavicius, K Umezawa, N Olivier, A Honigmann, G Yang, T Plass, V Mueller, L Reymond, IR Correa Jr., Z-G Luo, C Schultz, EA Lemke, P Heppenstall, C Eggeling, S Manley and K Johnsson+, “A near-infrared fluorophore for live-cell superresolution microscopy of cellular proteins,” Nat Chem 5(2):132-139 (2013) pdf


N Hoze, D Nair, E Hosy, C Sieben, S Manley, A Herrmann, J-B Sibarita, D Choquet and D Holcman+“Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging,” Proc Natl Acad Sci USA, 109(42):17052-17057 (2012) pdf

J Gunzenhäuser, N Olivier, T Pengo and S Manley+“Quantitative super-resolution imaging reveals protein stoichiometry and nanoscale morphology of assembling HIV-Gag virions,” Nano Lett 12(9):4705-10 (2012) pdf

H Kirschner, T Pengo, N Olivier, D Sage, S Manley, and M Unser+ “A PSF-based approach to Biplane calibration in 3D super-resolution microscopy,” ISBI (2012) pdf

A Benke*, N Olivier*, J Gunzenhäuser and S Manley+“Multicolor single molecule tracking of stochastically active synthetic dyes,” Nano Lett 12(5):2619-2624 (2012) pdf

A Benke and S Manley+, “Live-cell dSTORM of cellular DNA based on direct DNA labeling,” ChemBioChem, 13(2):298-301 (2012) “Very Important Paper” and cover, Featured in Nat Methods Research Highlights pdf

S Banala, D Maurel, S Manley and K Johnsson+ “A caged, localizable rhodamine derivative for superresolution microscopy,” ACS Chem Biol, 7(2) (2012) pdf


E Sherman, V Barr, S Manley, G Patterson, L Balagopalan, I Akpan, C Regan, R Merrill, C Sommers, J Lippincott-Schwartz and L Samelson “Functional nanoscale organization of signaling molecules downstream of the T cell antigen receptor,” Immunity, 35(5):705-720 (2011) pdf

DT Burnette, S Manley, P Sengupta, R Sougrat, MW Davidson, B Kachar and J Lippincott-Schwartz “A role for actin arcs in the leading edge advance of migrating cells,” Nat Cell Biol, 13(4):371-382 (2011) pdf

FV Subach*, GH Patterson*, S Manley, JM Gillette, J Lippincott-Schwartz and VV Verkhusha “Photoactivatable mCherry for high-resolution two-color fluorescence microscopy,” Nat Methods 6(2):153-159 (2009) pdf

G Shtengel, JA Galbraith, CG Galbraith, J Lippincott-Schwartz, JM Gillette, S Manley, R Sougrat, CM Waterman, P Kanchanawong, M Davidson, R Fetter and HF Hess “Interferometric fluorescent super-resolution microscopy resolves 3D cellular nano-architecture,” Proc Natl Acad Sci USA, 106:3125-3130 (2009) pdf

S Manley, JM Gillette, H Shroff, H Hess, E Betzig and J Lippincott-Schwartz “High-density mapping of single-molecule trajectories with photoactivated localization microscopy,” Nat Methods 5(2):155-157 (2008) Featured in Nat Methods News and Views; F1000: ‘Must Read’ pdf


S Manley, MR Horton, S Leszczynski and AP Gast, “Sorting of protein crystals on phase-separating membranes,” Biophys J 95:2301-2307 (2008) pdf

MR Horton, S Manley, S Arevalo, AE Lobkovsky and AP Gast, “Crystalline protein domains and lipid bilayer vesicle shape transformations,” J Phys Chem B 111:880-885 (2007) pdf

G Popescu, T Ikeda, K Goda, CA Best, M Laposata, S Manley, RR Dasari, K Badizadegan and M Feld, “Optical measurement of red blood cell membrane tension,” Phys Rev Lett 97:218101 (2006) pdf


J Conrad, HM Wyss, V Trappe, S Manley, K Miyazaki, LJ Kaufman, A Schofield, DR Reichman and DA Weitz “Colloidal gels formed by arrested phase separation: structure, dynamics and rheology,” J Rheology, 54(2):421-438 (2010) pdf

AE Bailey, WCK Poon, RJ Christianson, AB Schofield, U Gasser, V Prasad, S Manley, PN Segre, L Cipelletti, WV Meyer, MP Doherty, S Sankaran, AL Jankovsky, WL Shiley, JP Bowen, JC Eggers, C Kurta, T Lorik, PN Pusey, and DA Weitz, “Spinodal decomposition in a model colloid-polymer mixture in microgravity,” Phys Rev Lett 99:205701 (2007) pdf

S Manley, HM Wyss, K Miyazaki, J Conrad, V Trappe, LJ Kaufman, DR Reichman and DA Weitz, “Glasslike arrest in spinodal decomposition as a route to gelation,” Phys Rev Lett 95:238302 (2005) Featured in Research Highlights, Nature pdf

S Manley, B Davidovitch, NR Davies, L Cipelletti, AE Bailey, RJ Christianson, U Gasser, V Prasad, PN Segre, MP Doherty, S Sankaran, AL Jankovsky, WL Shiley, J Bowen, J Eggers, C Kurta, T Lorik and DA Weitz, “Time-dependent strength of colloidal gels,” Phys Rev Lett 95:048302 (2005) pdf

S Manley, JM Skotheim, L Mahadevan and DA Weitz, “Gravitational collapse of colloidal gels,” Phys Rev Lett 94:218302 (2005) pdf

S Manley, L Cipelletti, V Trappe, AE Bailey, RJ Christianson, U Gasser, V Prasad, PN Segre, MP Doherty, S Sankaran, AL Jankovsky, WL Shiley, J Bowen, J Eggers, C Kurta, T Lorik and DA Weitz, “Limits to gelation in colloidal aggregation,” Phys Rev Lett 93:108302 (2004) pdf

L Cipelletti, L Ramos, S Manley, E Pitard, DA Weitz, EE Pashkovski and M Johansson, “Universal non-diffusive slow dynamics in aging soft matter,” Faraday Disc 123:237-251 (2003) pdf

S-Y Tee, PJ Mucha, L Cipelletti, S Manley, MP Brenner, PN Segre and DA Weitz, “Nonuniversal velocity fluctuations of sedimenting particles,” Phys Rev Lett 89:054501 (2002) pdf

L Cipelletti, S Manley, RC Ball and DA Weitz, “Universal aging features in restructuring of fractal colloidal gels,” Phys Rev Lett 84:2275 (2000) pdf


JAJ Fitzpatrick, Y Inouye, S Manley and WE Moerner, “From “there’s plenty of room at the bottom” to seeing what is actually there,” ChemPhysChem 15(4):547-549 (2014)

P Achurra, S Holden, T Pengo and S Manley, “Photoactivated localization microscopy for cellular imaging,” Neuromethods 86:87-111 (2014)

S Manley, J Gunzenhaeuser and N Olivier, “A starter kit for point-localization super-resolution imaging,” Curr Opin Chem Biol 15(6):813-821 (2011) pdf

GH Patterson, M Davidson, S Manley, HF Hess and J Lippincott-Schwartz, “Superresolution imaging using single-molecule localization,” Annu Rev Phys Chem 61:345-367 (2010) pdf

S Manley, JM Gillette and J Lippincott-Schwartz, “Single particle tracking photoactivated localization microscopy (sptPALM) for mapping single molecule dynamics,” Methods Enzymol 475 (C): 109-120 (2010) pdf

J Lippincott-Schwartz and S Manley, “Putting super-resolution fluorescence microscopy to work,” Nat Methods 6:21 – 23 (2009) pdf

S Manley and VD Gordon, “Making giant unilamellar vesicles via hydration of a lipid film,” Curr Protocols Cell Biol Unit 24.3 (2008) pdf