Quantification of biofilm structures by the novel computer program comstat

Adams, 1999, Impact of rpoS deletion on Escherichia coli biofilms, Appl Environ Microbiol, 65, 4285, 10.1128/AEM.65.9.4285-4287.1999

Andersen, 1998, New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria, Appl Environ Microbiol, 64, 2240, 10.1128/AEM.64.6.2240-2246.1998

Anwar, 1992, Establishment of aging biofilms: possible mechanism of bacterial resistance to antimicrobial therapy, Antimicrob Agents Chemother, 36, 1347, 10.1128/AAC.36.7.1347

Brooun, 2000, A dose–response study of antibiotic resistance in Pseudomonas aeruginosa biofilms, Antimicrob Agents Chemother, 44, 640, 10.1128/AAC.44.3.640-646.2000

Caldwell, 1992, Confocal laser microscopy and digital image analysis in microbial ecology, Advances in Microbial Ecology, 1, 10.1007/978-1-4684-7609-5_1

Christensen, 1999, Molecular tools for study of biofilm physiology, Methods Enzymol, 310, 20, 10.1016/S0076-6879(99)10004-1

Costerton, 1999, Bacterial biofilms: a common cause of persistent infections, Science, 284, 1318, 10.1126/science.284.5418.1318

Dalton, 1994, Substratum-induced morphological changes in a marine bacterium and their relevance to biofilm structure, J Bacteriol, 176, 6900, 10.1128/jb.176.22.6900-6906.1994

Davies, 1995, Regulation of the alginate biosynthesis gene algC in Pseudomonas aeruginosa during biofilm development in continuous culture., Appl Environ Microbiol, 61, 860, 10.1128/AEM.61.3.860-867.1995

Davies, 1993, Exopolysaccharide production in biofilms: substratum activation of alginate gene expression by Pseudomonas aeruginosa, Appl Environ Microbiol, 59, 1181, 10.1128/AEM.59.4.1181-1186.1993

Davies, 1998, The involvement of cell-to-cell signals in the development of a bacterial biofilm, Science, 280, 295, 10.1126/science.280.5361.295

Fukunaga, 1972, Introduction to Statistical Pattern Recognition

Hermanowicz, 1995, Fractal structure of biofilms: new tools for investigation of morphology., Water Sci Technol, 32, 99, 10.2166/wst.1995.0273

Heydorn, 2000, Experimental reproducibility in flow-chamber biofilms:, Microbiology, 146, 2409, 10.1099/00221287-146-10-2409

Holloway, 1955, Genetic recombination in Pseudomonas aeruginosa, J Gen Microbiol, 13, 572

Hughs, 1968, On the mean accuracy of statistical pattern recognizers, IEEE Trans Inf Theory, 14, 55, 10.1109/TIT.1968.1054102

Kharazmi, 1999, Robbins device in biofilm research, Methods Enzymol, 310, 207, 10.1016/S0076-6879(99)10018-1

Korber, 1992, Programs for determining statistically representative areas of microbial biofilms., Binary, 4, 204

Korber, 1993, Analysis of spatial variability within Mot+ and Mot− Pseudomonas fluorescens biofilms using representative elements, Biofouling, 7, 339, 10.1080/08927019309386264

Korber, 1994, Effect of motility on surface colonization and reproductive success of Pseudomonas fluorescens in dual-dilution continuous culture and batch culture systems, Appl Environ Microbiol, 60, 1421, 10.1128/AEM.60.5.1421-1429.1994

Kuehn, 1998, Automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms., Appl Environ Microbiol, 64, 4115, 10.1128/AEM.64.11.4115-4127.1998

Lanzer, 1988, Promoters largely determine the efficiency of repressor action, Proc Natl Acad Sci U S A, 85, 8973, 10.1073/pnas.85.23.8973

Lewandowski, 1999, Quantifying biofilm structure, Water Sci Technol, 39, 71, 10.2166/wst.1999.0331

de Lorenzo, 1990, Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria, J Bacteriol, 172, 6568, 10.1128/jb.172.11.6568-6572.1990

de Lorenzo, 1993, Analysis of Pseudomonas gene-products using lacIQ Ptrp-Lac plasmids and transposons that confer conditional phenotypes., Gene, 123, 17, 10.1016/0378-1119(93)90533-9

Mavrodi, 1998, A seven-gene locus for synthesis of phenazine-1-carboxylic acid by Pseudomonas fluorescens 2-79, J Bacteriol, 180, 2541, 10.1128/JB.180.9.2541-2548.1998

Mazzola, 1995, Variation in sensitivity of Gaeumannomyces graminis to antibiotics produced by fluorescent Pseudomonas spp and effect on biological control of take-all of wheat, Appl Environ Microbiol, 61, 2554, 10.1128/AEM.61.7.2554-2559.1995

Molina, 1998, Construction of an efficient biologically contained Pseudomonas putida strain and its survival in outdoor assays, Appl Environ Microbiol, 64, 2072, 10.1128/AEM.64.6.2072-2078.1998

Møller, 1996, Activity and three-dimensional distribution of toluene-degrading Pseudomonas putida in a multispecies biofilm assessed by quantitative in situ hybridization and scanning confocal laser microscopy, Appl Environ Microbiol, 62, 4632, 10.1128/AEM.62.12.4632-4640.1996

Møller, 1997, Impact of nutrient composition on a degradative biofilm community, Appl Environ Microbiol, 63, 2432, 10.1128/AEM.63.6.2432-2438.1997

Møller, 1998, In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members, Appl Environ Microbiol, 64, 721, 10.1128/AEM.64.2.721-732.1998

Morrison, 1990, Multivariate Statistical Methods

Murga, 1995, Quantitative analysis of biofilm thickness variability, Biotechnol Bioeng, 45, 503, 10.1002/bit.260450607

Nielsen, 2000, Role of commensal relationships on the spatial structure of a surface-attached microbial consortium, Environ Microbiol, 2, 59, 10.1046/j.1462-2920.2000.00084.x

O’Toole, 1998, Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development, Mol Microbiol, 30, 295, 10.1046/j.1365-2958.1998.01062.x

O’Toole, 2000, The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa., J Bacteriol, 182, 425, 10.1128/JB.182.2.425-431.2000

Palmer, 1999, Microscopy flowcells: perfusion chambers for real-time study of biofilms., Methods Enzymol, 310, 160, 10.1016/S0076-6879(99)10014-4

Park, 1998, Biofilm properties under different substrate loading rates in a rotating biological contactor, Biotechnol Tech, 12, 587

Peyton, 1996, Effects of shear stress and substrate loading rate on Pseudomonas aeruginosa biofilm thickness and density, Water Res, 30, 29, 10.1016/0043-1354(95)00110-7

Picioreanu, 1998a, A new combined differential-discrete cellular automaton approach for biofilm modeling: application for growth in gel beads, Biotechnol Bioeng, 57, 718, 10.1002/(SICI)1097-0290(19980320)57:6<718::AID-BIT9>3.0.CO;2-O

Picioreanu, 1998b, Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach, Biotechnol Bioeng, 58, 101, 10.1002/(SICI)1097-0290(19980405)58:1<101::AID-BIT11>3.0.CO;2-M

Pratt, 1998, Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili, Mol Microbiol, 30, 285, 10.1046/j.1365-2958.1998.01061.x

Prigent-Combaret, 1999, Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli., J Bacteriol, 181, 5993, 10.1128/JB.181.19.5993-6002.1999

Rainey, 1999, Adaptation of Pseudomonas fluorescens to the plant rhizosphere, Environ Microbiol, 1, 243, 10.1046/j.1462-2920.1999.00040.x

Ramos, 1991, Survival in soils of an herbicide-resistant Pseudomonas putida strain bearing a recombinant TOL plasmid, Appl Environ Microbiol, 57, 260, 10.1128/AEM.57.1.260-266.1991

Ramos, 1994, The behavior of bacteria designed for biodegradation, Biotechnology, 12, 1349

Ramos-Diaz, 1998, Combined physical and genetic map of the Pseudomonas putida KT2440 chromosome, J Bacteriol, 180, 6352, 10.1128/JB.180.23.6352-6363.1998

Russ, 1994, The Image Processing Handbook

Saitou, 1987, The neighbor-joining method: a new method for reconstruction of phylogenetic trees, Mol Biol Evol, 4, 406

Sieracki, 1989, Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis, Appl Environ Microbiol, 55, 2762, 10.1128/AEM.55.11.2762-2772.1989

Stewart, 1993, Quantitative observations of heterogeneities in Pseudomonas aeruginosa biofilms., Appl Environ Microbiol, 59, 327, 10.1128/AEM.59.1.327-329.1993

Thompson, 1995, Survival, colonization and dispersal of genetically modified Pseudomonas fluorescens SBW25 in the phytosphere of field-grown sugar-beet., Biotechnology, 13, 1493

Tümmler, 1999, Cystic fibrosis: an inherited susceptibility to bacterial respiratory infections, Mol Med Today, 5, 351, 10.1016/S1357-4310(99)01506-3

Van Loosdrecht, 1995, Biofilm structures., Water Sci Technol, 32, 35, 10.2166/wst.1995.0258

Vroom, 1999, Depth penetration and detection of pH gradients in biofilms by two-photon excitation microscopy., Appl Environ Microbiol, 65, 3502, 10.1128/AEM.65.8.3502-3511.1999

Wimpenny, 1997, A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models, FEMS Microbiology Ecology, 22, 1, 10.1111/j.1574-6941.1997.tb00351.x

Wolfaardt, 1994, Multicellular organization in a degradative biofilm community, Appl Environ Microbiol, 60, 434, 10.1128/AEM.60.2.434-446.1994

Wood, 1997, N-Acyl-homoserine lactone-mediated regulation of phenazine gene expression by Pseudomonas aureofaciens 30-84 in the wheat rhizosphere, J Bacteriol, 179, 7663, 10.1128/jb.179.24.7663-7670.1997

Xu, 1998, Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability, Appl Environ Microbiol, 64, 4035, 10.1128/AEM.64.10.4035-4039.1998

Yang, 2000, Quantifying biofilm structure using image analysis, J Microbiol Methods, 39, 109, 10.1016/S0167-7012(99)00097-4

Zhang, 1994, Density, porosity, and pore structure of biofilms, Water Res, 28, 2267, 10.1016/0043-1354(94)90042-6