This page lists publications known to us which used MicrobeTracker (in some it is mentioned under the old name CellTracker). Please, let us know about your works where you used this program suite so that we can include them as well.


  • Gabriel Billings, Nikolay Ouzounov, Tristan Ursell, Samantha M. Desmarais, Joshua Shaevitz, Zamer Gitai, and Krewyn Casey Huang. "De novo morphogenesis in L-forms via geometric control of cell growth", Molecular Microbiology 2014 (journal)

  • Brandon Williams, Nowsheen Bhat, Peter Chien, and Lucy Shapiro "ClpXP and ClpAP proteolytic activity on divisome substrates is differentially regulated following the Caulobacter asymmetric cell division", Molecular Microbiology 2014 (journal)

  • Hoong Chuin Lim, Ivan Vladimirovich Surovtsev, Bruno Gabriel Beltran, Fang Huang, Jorg Bewersdorf, Christine Jacobs-Wagner "Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation", eLife 2014 (journal)

  • Emilien Nicolas, Amy L. Upton, Stephan Uphoff, Olivia Henry, Anjana Badrinarayanan, David Sherratt "The SMC Complex MukBEF Recruits Topoisomerase IV to the Origin of Replication Region in Live Escherichia coli", mBio 2014 (journal)

  • Benoit S. Marteyn, Gouzel Karimova, Andrew K. Fenton, Anastasia D. Gazi, Nicholas West, Lhousseine Touqui, Marie-Christine Prevost, Jean-Michel Betton, Oemer Poyraz, Daniel Ladant, Kenn Gerdes, Philippe J. Sansonetti, Christoph M. Tang "ZapE Is a Novel Cell Division Protein Interacting with FtsZ and Modulating the Z-Ring Dynamics", mBio 2014 (journal)

  • Patrick Seitz, Melanie Blokesch "DNA Transport across the Outer and Inner Membranes of Naturally Transformable Vibrio cholerae Is Spatially but Not Temporally Coupled", mBio 2014 (journal)

  • Solveig Fossum-Raunehaug, Emily Helgesen, Caroline Stokke, Kirsten Skarstad "Escherichia coli SeqA Structures Relocalize Abruptly upon Termination of Origin Sequestration during Multifork DNA Replication", PLoS One 2014 (journal)

  • Valerie Nicolaes, Hayat El Hajjaji, Rebecca M. Davis, Charles Van der Henst, Matthieu Depuydt, Pauline Leverrier, Abram Aertsen, Vincent Haufroid, Sandrine Ollagnier de Choudens, Xavier De Bolle, Natividad Ruiz, Jean-Francois Collet "Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli", J Bacteriol 2014 (journal)

  • Christian Lesterlin, Graeme Ball, Lothar Schermelleh, David J. Sherratt "RecA bundles mediate homology pairing between distant sisters during DNA break repair", Nature 2014 (journal)

  • Jared M. Schrader, Bo Zhou, Gene-Wei Li, Keren Lasker, W. Seth Childers, Brandon Williams, Tao Long, Sean Crosson, Harley H. McAdams, Jonathan S. Weissman, Lucy Shapiro "The Coding and Noncoding Architecture of the Caulobacter crescentus Genome", PLoS Genet 2014 (journal)

  • Timothy K. Lee, Carolina Tropini, Jen Hsin, Samantha M. Desmarais, Tristan S. Ursell, Enhao Gong, Zemer Gitai, Russell D. Monds, Kerwyn Casey Huang "A dynamically assembled cell wall synthesis machinery buffers cell growth", Proc Natl Acad Sci U S A 2014 (journal)

  • Gaelle Demarre, Elisa Galli, Leila Muresan, Evelyne Paly, Ariane David, Christophe Possoz, Francois-Xavier Barre "Differential Management of the Replication Terminus Regions of the Two Vibrio cholerae Chromosomes during Cell Division", PLoS Genet 2014 (journal)

  • Ariane David, Gaelle Demarre, Leila Muresan, Evelyne Paly, Francois-Xavier Barre, Christophe Possoz "The Two Cis-Acting Sites, parS1 and oriC1, Contribute to the Longitudinal Organisation of Vibrio cholerae Chromosome I", PLoS Genet 2014 (journal)

  • Seamus J. Holden, Thomas Pengo, Karin L. Meibom, Carmen Fernandez Fernandez, Justine Collier, Suliana Manley "High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization", Proc Natl Acad Sci U S A 2014 (journal)

  • Bradley R. Parry, Ivan V. Surovtsev, Matthew T. Cabeen, Corey S. OHern, Eric R. Dufresne, Christine Jacobs-Wagner "The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity", Cell 2014 (journal)


  • Diego l. Cattoni,Jean-Bernard Fiche, Alessandro Valeri, Tam Mignot, Marcelo Nollmann,"Super-Resolution Imaging of Bacteria in a Microfluidics Device", PLoS One. 2013 (journal)

  • Jonathan T. Henry and Sean Crosson,"Chromosome replication and segregation govern the biogenesis and inheritance of inorganic polyphosphate granules", Mol Biol Cell. 2013 (journal)

  • Matthieu J. Berge, Alain Kamgoue, Bernard Martin, Patrice Polard, Nathalie Campo, Jean-Pierre Claverys ,"Midcell Recruitment of the DNA Uptake and Virulence Nuclease, EndA, for Pneumococcal Transformation", PLoS One. 2013 (journal)

  • Soren Abel, Tabitha Bucher, Miael Nicollier, Isabelle Hug, Volkhard Kaever, Pia Abel zur Wiesch, and Urs Jenal ,"Bi-modal Distribution of the Second Messenger c-di-GMP Controls Cell Fate and Asymmetry during the Caulobacter Cell Cycle", PLoS Genet. 2013 (journal)

  • Marie H. Foss, Ye-Jin Eun, Charles I. Grove, Daniel A. Pauw, Nohemy A. Sorto, Jarred W. Rensvold, David J. Pagliarini, Jared T. Shaw, Douglas B. Weibel,"Inhibitors of bacterial tubulin target bacterial membranes in vivo", Med. Chem. Commun., 2013 (journal)

  • Jae-hyeong Ko, Paula Montero Llopis, Jennifer Heinritz, Christine Jacobs-Wagner, Dieter Soll,"Suppression of Amber Codons in Caulobacter crescentus by the Orthogonal Escherichia coli Histidyl-tRNA Synthetase/tRNAHis Pair", PLoS One. 2013 (journal)

  • Desmarais, S. M., De Pedro, M. A., Cava, F. and Huang, K. C.,"Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly", Mol Microbiol. 2013 (journal)

  • Gaurav M,Enrique R. R,Ajay G,Kerwyn C.H.,"Mechanical Consequences of Cell-Wall Turnover in the Elongation of a Gram-Positive Bacterium coli", Biophys J. 2013 (journal)

  • Fenton A, Gerdes K.,"Direct interaction of FtsZ and MreB is required for septum synthesis and cell division in Escherichia coli", EMBO J. 2013 (journal)

  • Laloux G, Jacobs-Wagner C.,"Spatiotemporal control of PopZ localization through cell cycle-coupled multimerization", J Cell Biol. 2013 (PubMed, journal)

  • Barns KJ, Weisshaar JC.,"Real-time attack of LL-37 on single Bacillus subtilis cells ", Biochim Biophys Acta. 2013 (PubMed, journal)

  • Liu, H., Bouillaut, L., Sonenshein, A. L. and Melville, S. B., "Use of a mariner-based transposon mutagenesis system to isolate Clostridium perfringens mutants deficient in gliding motility", J. Bacteriol., 2013 (PubMed, journal)

  • Nan B, Bandaria JN, Moghtaderi A, Sun IH, Yildiz A, Zusman DR., "Flagella stator homologs function as motors for myxobacterial gliding motility by moving in helical trajectories", PLoS Comput Biol. 2013 (PubMed, journal)

  • Lu J, Carter DA, Turnbull L, Rosendale D, Hedderley D, Stephens J, Gannabathula S, Steinhorn G, Schlothauer RC, Whitchurch CB, Harry EJ., "The effect of New Zealand kanuka, manuka and clover honeys on bacterial growth dynamics and cellular morphology varies according to the species.", PLoS One., 2013 (PubMed, journal)

  • Takacs CN, Hocking J, Cabeen MT, Bui NK, Poggio S, Vollmer W, Jacobs-Wagner C., "Growth medium-dependent glycine incorporation into the peptidoglycan of Caulobacter crescentus", PLoS One., 2013 (PubMed, journal)

  • Vallet-Gely I, Boccard F.,"Chromosomal organization and segregation in Pseudomonas aeruginosa", PLoS Genet., 2013 (PubMed, journal)

  • Ullman G, Wallden M, Marklund EG, Mahmutovic A, Razinkov I, Elf J., "High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking", Philos Trans R Soc Lond B Biol Sci. 2013 (PubMed, journal)

  • Fiche JB, Cattoni DI, Diekmann N, Langerak JM, Clerte C, Royer CA, Margeat E, Doan T, Nollmann M., "Recruitment, assembly, and molecular architecture of the SpoIIIE DNA pump revealed by superresolution microscopy", PLoS Biol., 2013 (PubMed, journal)


  • LeRoux M, De Leon JA, Kuwada NJ, Russell AB, Pinto-Santini D, Hood RD, Agnello DM, Robertson SM, Wiggins PA, Mougous JD.,"Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword", Proc Natl Acad Sci U S A. 2012 (PubMed, journal)

  • Montero Llopis P, Sliusarenko O, Heinritz J, Jacobs-Wagner C, "In vivo biochemistry in bacterial cells using FRAP: insight into the translation cycle", Biophys J. 2012 (PubMed, journal)

  • Chen AH, Afonso B, Silver PA, Savage DF. "Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942.", Biophys J. 2012 (PubMed, journal)

  • Massoni SC, Leeson MC, Long JE, Gemme K, Mui A, Sandler SJ., "Factors Limiting SOS Expression in Log-Phase Cells of Escherichia coli", J Bacteriol. 2012 (PubMed, journal)

  • Tuson HH, Auer GK, Renner LD, Hasebe M, Tropini C, Salick M, Crone WC, Gopinathan A, Huang KC, Weibel DB., "Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity ", Mol Microbiol. 2012 (PubMed, journal)

  • Beilharz K, Nováková L, Fadda D, Branny P, Massidda O, Veening JW., "Control of cell division in Streptococcus pneumoniae by the conserved Ser/Thr protein kinase StkP", Proc Natl Acad Sci U S A. 2012 (PubMed, journal)

  • Lo Scrudato M, Blokesch M.,"The regulatory network of natural competence and transformation of Vibrio cholerae", PLoS Genet. 2012 (PubMed, journal)

  • van Teeffelen S, Shaevitz JW, Gitai Z, "Image analysis in fluorescence microscopy: Bacterial dynamics as a case study", Bioessays, 2012; 34(5): 427-436 (PubMed, journal) (review mentioning the suite).

  • Shikuma NJ, Fong JC, and Yildiz FH, "Cellular levels and binding of c-di-GMP control subcellular localization and activity of the Vibrio cholerae transcriptional regulator VpsT", PLoS Pathog., 2012; online ahead of print (PubMed, journal).

  • Hocking J, Priyadarshini R, Takacs CN, Costa T, Dye NA, Shapiro L, Vollmer W, and Jacobs-Wagner C, "Osmolality-dependent relocation of penicillin-binding protein PBP2 to the division site in Caulobacter crescentus", J Bacteriol., 2012; online ahead of print (PubMed, journal).

  • Beilharz K, Nováková L, Faddac D, Branny P, Massiddac O, and Veening JW, "Control of cell division in Streptococcus pneumoniae by the conserved Ser/Thr protein kinase StkP", PNAS, 2012; 109(15): E905-E913 (PubMed, journal).

  • Badrinarayanan A, Lesterlin C, Reyes-Lamothe R, Sherratt D., "The Escherichia coli SMC complex, MukBEF, shapes nucleoid organization independently of DNA replication.", J Bacteriol. 2012 (PubMed, journal).

  • Tropini C, Huang KC.,"Interplay between the localization and kinetics of phosphorylation in flagellar pole development of the bacterium Caulobacter crescentus.", PLoS Comput Biol. 2012 (PubMed, journal).

  • Kwak IH, Son M, Hagen SJ.,"Analysis of gene expression levels in individual bacterial cells without image segmentation.", Biochem Biophys Res Commun. 2012 (PubMed, journal).


  • Wesolowski D, Tae HS, Gandotra N, Llopis P, Shen N, Altman S.,"Basic peptide-morpholino oligomer conjugate that is very effective in killing bacteria by gene-specific and nonspecific modes", Proc Natl Acad Sci U S A. 2011 (PubMed, journal)

  • Garner EC, Bernard R, Wang W, Zhuang X, Rudner DZ, Mitchison T.,"Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis.", Science. 2011 (PubMed, journal)

  • Sliusarenko O, Heinritz J, Emonet T, and Jacobs-Wagner C, "High- throughput, subpixel-precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics", Mol. Micro, 2011; 80(3): 612:627 (PubMed, journal) (suggested citation for the suite).


  • Schofield WB, Lim HC, Jacobs-Wagner C, "Cell cycle coordination and regulation of bacterial chromosome segregation dynamics by polarly localized proteins", EMBO J, 2010; 29(18): 3068-3081 (PubMed, journal).

  • Poggio S, Takacs CN, Vollmer W, Jacobs-Wagner C, "A protein critical for cell constriction in the Gram-negative bacterium Caulobacter crescentus localizes at the division site through its peptidoglycan-binding LysM domains", Mol. Micro, 2010; 77(1): 74:89 (PubMed, journal).

  • Montero Llopis P, Jackson AF, Sliusarenko O, Suvorovtsev I, Heinritz J, Emonet T, and Jacobs-Wagner C, "Spatial organization of the flow of genetic information in bacteria", Nature, 2010; 466: 77-81 (PubMed, journal).

  • Sliusarenko O, Cabeen MT, Wolgemuth C, Jacobs-Wagner C, Emonet T, "Processivity of peptidoglycan synthesis provides a built-in mechanism for the robustness of straight-rod cell morphology", PNAS, 2010; 107(22): 10086-10091 (PubMed, journal).

  • Cabeen MT, Murolo MA, Briegel A, Bui NK, Vollmer W, Ausmees N, Jensen GJ, Jacobs-Wagner C, "Mutations in the lipopolysaccharide biosynthesis pathway interfere with crescentin-mediated cell curvature in Caulobacter crescentus", J Bacteriol., 2010; 192(13): 3368-3378 (PubMed, journal).

  • Angelastro PS, Sliusarenko O, Jacobs-Wagner C. "Polar localization of the CckA histidine kinase and cell cycle periodicity of the essential master regulator CtrA in Caulobacter crescentus" J Bacteriol. 2010; 192(2):539-52 (PubMed, journal).


  • Cabeen MT, Charbon G, Vollmer W, Born P, Ausmees N, Weibel DB, Jacobs-Wagner C. "Bacterial cell curvature through mechanical control of cell growth" EMBO J. 2009; 28(9):1208-19 (PubMed, journal).