Experimental methods and modeling techniques for description of cell population heterogeneity.

[1]  Mogens Henze,et al.  Activated sludge models ASM1, ASM2, ASM2d and ASM3 , 2015 .

[2]  T. Egli,et al.  Physiological Stress Responses in Bioprocesses , 2010 .

[3]  D. Pang,et al.  Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon. , 2010, Biosensors & bioelectronics.

[4]  S. Mukherjee,et al.  Biofunctionalised quantum dots for sensing and identification of waterborne bacterial pathogens , 2010 .

[5]  Nicolas Jaccard,et al.  Microfluidic approaches for systems and synthetic biology. , 2010, Current opinion in biotechnology.

[6]  Gürkan Sin,et al.  Application of mechanistic models to fermentation and biocatalysis for next-generation processes. , 2010, Trends in biotechnology.

[7]  P. Bae,et al.  Simple route for the detection of Escherichia coli using quantum dots , 2010 .

[8]  Bertram Manz,et al.  Advanced imaging techniques for assessment of structure, composition and function in biofilm systems. , 2010, FEMS microbiology ecology.

[9]  Frederik Hammes,et al.  Cytometric methods for measuring bacteria in water: advantages, pitfalls and applications , 2010, Analytical and bioanalytical chemistry.

[10]  S. Ishii,et al.  Single-cell analysis and isolation for microbiology and biotechnology: methods and applications , 2010, Applied Microbiology and Biotechnology.

[11]  Duu-Jong Lee,et al.  Stereological assessment of extracellular polymeric substances, exo-enzymes, and specific bacterial strains in bioaggregates using fluorescence experiments. , 2010, Biotechnology advances.

[12]  Luis A. García,et al.  Application of flow cytometry to industrial microbial bioprocesses , 2010 .

[13]  Andreas Schmid,et al.  Chemical and biological single cell analysis. , 2010, Current opinion in biotechnology.

[14]  Thomas Bley,et al.  Origin and analysis of microbial population heterogeneity in bioprocesses. , 2010, Current opinion in biotechnology.

[15]  E. Papoutsakis,et al.  Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. , 2010, Current opinion in biotechnology.

[16]  Ke‐long Huang,et al.  A rapid and universal bacteria-counting approach using CdSe/ZnS/SiO2 composite nanoparticles as fluorescence probe , 2010, Analytical and bioanalytical chemistry.

[17]  Michail Stamatakis,et al.  Cell population balance, ensemble and continuum modeling frameworks: Conditional equivalence and hybrid approaches , 2010 .

[18]  I. Matic,et al.  Reliable Detection of Dead Microbial Cells by Using Fluorescent Hydrazides , 2009, Applied and Environmental Microbiology.

[19]  Hilal Taymaz-Nikerel,et al.  Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses , 2009, Biotechnology and bioengineering.

[20]  Ali Bashashati,et al.  A Survey of Flow Cytometry Data Analysis Methods , 2009, Adv. Bioinformatics.

[21]  Kai Zhang,et al.  CFD simulation coupled with population balance equations for aerated stirred bioreactors , 2009 .

[22]  H. J. Beaumont,et al.  Experimental evolution of bet hedging , 2009, Nature.

[23]  K. Gernaey,et al.  Application of near‐infrared spectroscopy for monitoring and control of cell culture and fermentation , 2009, Biotechnology progress.

[24]  Andreas G. Boudouvis,et al.  A novel free boundary algorithm for the solution of cell population balance models , 2009 .

[25]  R. Vogel,et al.  Metabolic impact and potential exploitation of the stress reactions in lactobacilli. , 2009, Food microbiology.

[26]  B. B. Johnson,et al.  Measuring 'hydrophobicity' of filamentous bacteria found in wastewater treatment plants. , 2009, Colloids and surfaces. B, Biointerfaces.

[27]  Krist V Gernaey,et al.  Application of microbioreactors in fermentation process development: a review , 2009, Analytical and bioanalytical chemistry.

[28]  Yali Cao,et al.  Experimental evaluation of decrease in bacterial activity due to cell death and activity decay in activated sludge. , 2009, Water research.

[29]  P. Joyce,et al.  Evolution of Diversity in Spatially Structured Escherichia coli Populations , 2009, Applied and Environmental Microbiology.

[30]  L. Balan,et al.  The exposure of bacteria to CdTe-core quantum dots: the importance of surface chemistry on cytotoxicity , 2009, Nanotechnology.

[31]  P. Lasch,et al.  Phenotypic heterogeneity within microbial populations at the single-cell level investigated by confocal Raman microspectroscopy. , 2009, The Analyst.

[32]  B. Dietzek,et al.  Raman and CARS microspectroscopy of cells and tissues. , 2009, The Analyst.

[33]  J. Mesirov,et al.  Automated high-dimensional flow cytometric data analysis , 2009, Proceedings of the National Academy of Sciences.

[34]  M. Bouix,et al.  Fermentation pH Influences the Physiological-State Dynamics of Lactobacillus bulgaricus CFL1 during pH-Controlled Culture , 2009, Applied and Environmental Microbiology.

[35]  Isabel Rocha,et al.  Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis , 2009, Biotechnology progress.

[36]  Belinda C. Ferrari,et al.  Applications of flow cytometry in environmental microbiology and biotechnology , 2009, Extremophiles.

[37]  J. Sørensen,et al.  Multiple physiological states of a Pseudomonas fluorescens DR54 biocontrol inoculant monitored by a new flow cytometry protocol. , 2009, FEMS microbiology ecology.

[38]  M. Boxus,et al.  Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli , 2009, Microbial cell factories.

[39]  T. Zotta,et al.  Viability staining and detection of metabolic activity of sourdough lactic acid bacteria under stress conditions , 2009 .

[40]  G. Nebe-von-Caron Standardization in microbial cytometry , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[41]  Maureen A Walling,et al.  Quantum Dots for Live Cell and In Vivo Imaging , 2009, International journal of molecular sciences.

[42]  Damià Barceló,et al.  Sensors and biosensors in support of EU Directives , 2009 .

[43]  Lilia Alberghina,et al.  Analysis and modeling of growing budding yeast populations at the single cell level , 2009, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[44]  Qikai Xu,et al.  Global Protein Stability Profiling in Mammalian Cells , 2008, Science.

[45]  E. Papoutsakis,et al.  Development and Application of Flow-Cytometric Techniques for Analyzing and Sorting Endospore-Forming Clostridia , 2008, Applied and Environmental Microbiology.

[46]  B. Pozzetto,et al.  Use of Flow Cytometry To Monitor Legionella Viability , 2008, Applied and Environmental Microbiology.

[47]  James C S Wood,et al.  MIFlowCyt: The minimum information about a flow cytometry experiment , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[48]  U. Cronin,et al.  Monitoring growth phase-related changes in phosphatidylcholine-specific phospholipase C production, adhesion properties and physiology of Bacillus cereus vegetative cells , 2008, Journal of Industrial Microbiology & Biotechnology.

[49]  L. Rossetti,et al.  Quantification of Enterococcus italicus in traditional Italian cheeses by fluorescence whole-cell hybridization. , 2008, Systematic and applied microbiology.

[50]  J. R. van der Meer,et al.  Use of flow cytometric methods for single-cell analysis in environmental microbiology. , 2008, Current opinion in microbiology.

[51]  Jizhong Zhou,et al.  Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico , 2008, Applied and Environmental Microbiology.

[52]  J. Nielsen,et al.  Quantification of lipids and protein in thin biofilms by fluorescence staining , 2008, Biofouling.

[53]  Raphael Gottardo,et al.  Automated gating of flow cytometry data via robust model‐based clustering , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[54]  W. Kelly,et al.  Using computational fluid dynamics to characterize and improve bioreactor performance , 2008, Biotechnology and applied biochemistry.

[55]  G J Lye,et al.  Scale‐up of Escherichia coli growth and recombinant protein expression conditions from microwell to laboratory and pilot scale based on matched kLa , 2008, Biotechnology and bioengineering.

[56]  M. Lidstrom,et al.  Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington , 2008, The ISME Journal.

[57]  Philip S. Stewart,et al.  Physiological heterogeneity in biofilms , 2008, Nature Reviews Microbiology.

[58]  E. Sherer,et al.  Identification of age‐structured models: Cell cycle phase transitions , 2008, Biotechnology and bioengineering.

[59]  Carsten Schultz,et al.  Fluorescence and bioluminescence procedures for functional proteomics , 2008, Proteomics.

[60]  J. Gasol,et al.  Evaluating the Flow-Cytometric Nucleic Acid Double-Staining Protocol in Realistic Situations of Planktonic Bacterial Death , 2008, Applied and Environmental Microbiology.

[61]  J. Marles-Wright,et al.  Stress responses of bacteria. , 2007, Current opinion in structural biology.

[62]  D. Otzen,et al.  Amyloid adhesins are abundant in natural biofilms. , 2007, Environmental microbiology.

[63]  K. Miyanaga,et al.  Optimization of distinction between viable and dead cells by fluorescent staining method and its application to bacterial consortia , 2007 .

[64]  A. Link,et al.  Beyond toothpicks: new methods for isolating mutant bacteria , 2007, Nature Reviews Microbiology.

[65]  S. Günther,et al.  Limits of propidium iodide as a cell viability indicator for environmental bacteria , 2007, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[66]  S. Sørensen,et al.  Establishment and Early Succession of a Multispecies Biofilm Composed of Soil Bacteria , 2007, Microbial Ecology.

[67]  Christophe Lacroix,et al.  Fermentation technologies for the production of probiotics with high viability and functionality. , 2007, Current opinion in biotechnology.

[68]  Frederik Hammes,et al.  Assessment and Interpretation of Bacterial Viability by Using the LIVE/DEAD BacLight Kit in Combination with Flow Cytometry , 2007, Applied and Environmental Microbiology.

[69]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[70]  M. Wagner,et al.  Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis , 2007, Applied Microbiology and Biotechnology.

[71]  J. Mckinney,et al.  Microbial phenotypic heterogeneity and antibiotic tolerance. , 2007, Current opinion in microbiology.

[72]  D. Porro,et al.  Towards understanding of the complex structure of growing yeast populations. , 2007, Journal of biotechnology.

[73]  M. Troussellier,et al.  Characterization of the Population of the Sulfur-Oxidizing Symbiont of Codakia orbicularis (Bivalvia, Lucinidae) by Single-Cell Analyses , 2007, Applied and Environmental Microbiology.

[74]  J. Gasol,et al.  Cytometric evidence reconciling the toxicity and usefulness of CTC as a marker of bacterial activity , 2007 .

[75]  Rasmus Bro,et al.  Real-time monitoring and chemical profiling of a cultivation process , 2006 .

[76]  Martina Micheletti,et al.  Microscale bioprocess optimisation. , 2006, Current opinion in biotechnology.

[77]  Robert J. Palmer,et al.  Use of Quantum Dot Luminescent Probes To Achieve Single-Cell Resolution of Human Oral Bacteria in Biofilms , 2006, Applied and Environmental Microbiology.

[78]  D. Kletsas,et al.  Acid Tolerance of Streptococcus macedonicus as Assessed by Flow Cytometry and Single-Cell Sorting , 2006, Applied and Environmental Microbiology.

[79]  Alvaro R. Lara,et al.  Living with heterogeneities in bioreactors , 2006, Molecular biotechnology.

[80]  Anne K Camper,et al.  Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. , 2006, Journal of microbiological methods.

[81]  F. Srienc,et al.  The cytostat: A new way to study cell physiology in a precisely defined environment. , 2006, Journal of biotechnology.

[82]  Elizabeth A Jares-Erijman,et al.  Imaging molecular interactions in living cells by FRET microscopy. , 2006, Current opinion in chemical biology.

[83]  Kim H. Esbensen,et al.  Representative sampling for process analytical characterization of heterogeneous bioslurry systems—a reference study of sampling issues in PAT , 2006 .

[84]  Alvaro R. Lara,et al.  Engineering Escherichia coli to improve culture performance and reduce formation of by‐products during recombinant protein production under transient intermittent anaerobic conditions , 2006, Biotechnology and bioengineering.

[85]  Simon V. Avery,et al.  Microbial cell individuality and the underlying sources of heterogeneity , 2006, Nature Reviews Microbiology.

[86]  D. Porro,et al.  Morphologically-structured models of growing budding yeast populations. , 2006, Journal of biotechnology.

[87]  Matthias Reuss,et al.  Modeling the dynamics of E. coli populations in the three-dimensional turbulent field of a stirred-tank bioreactor- : A structured-segregated approach , 2006 .

[88]  M. Drake,et al.  Stress Response of Escherichia coli , 2006 .

[89]  K. Jensen,et al.  Differential Gene Expression Profiles and Real‐Time Measurements of Growth Parameters in Saccharomyces cerevisiae Grown in Microliter‐Scale Bioreactors Equipped with Internal Stirring , 2006, Biotechnology progress.

[90]  L. Montastruc,et al.  CFD stimulation of gluconic acid production in a stirred gas-liquid fermenter , 2006 .

[91]  Marina G. Kalyuzhnaya,et al.  Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations , 2006, Applied and Environmental Microbiology.

[92]  F. Baganz,et al.  Miniature bioreactors: current practices and future opportunities , 2006, Microbial cell factories.

[93]  G. Stucky,et al.  Imaging Escherichia coli using functionalized core/shell CdSe/CdS quantum dots , 2006, JBIC Journal of Biological Inorganic Chemistry.

[94]  S. Sørensen,et al.  A flow cytometry-optimized assay using an SOS-green fluorescent protein (SOS-GFP) whole-cell biosensor for the detection of genotoxins in complex environments. , 2006, Mutation research.

[95]  Kalpathi R. Subramanian,et al.  Development of a Wireless Sensor Network for Monitoring a Bioreactor Landfill , 2006 .

[96]  K. Eidne,et al.  Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET) , 2006, Nature Methods.

[97]  Michael Wagner,et al.  daime, a novel image analysis program for microbial ecology and biofilm research. , 2006, Environmental microbiology.

[98]  Mette Burmølle,et al.  Making bio-sense of toxicity: new developments in whole-cell biosensors. , 2006, Current opinion in biotechnology.

[99]  U. Karsten,et al.  Bacterial Abundance, Activity, and Viability in the Eutrophic River Warnow, Northeast Germany , 2006, Microbial Ecology.

[100]  S. Sørensen,et al.  Use of a Whole-Cell Biosensor and Flow Cytometry to Detect AHL Production by an Indigenous Soil Community During Decomposition of Litter , 2005, Microbial Ecology.

[101]  J. Nielsen,et al.  Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge. , 2005, FEMS microbiology ecology.

[102]  W. D. de Vos,et al.  Genetic Diversity of Viable, Injured, and Dead Fecal Bacteria Assessed by Fluorescence-Activated Cell Sorting and 16S rRNA Gene Analysis , 2005, Applied and Environmental Microbiology.

[103]  A. Steinbüchel,et al.  Neutral Lipid Bodies in Prokaryotes: Recent Insights into Structure, Formation, and Relationship to Eukaryotic Lipid Depots , 2005, Journal of bacteriology.

[104]  J. L. Nadeau,et al.  Uptake of CdSe and CdSe/ZnS Quantum Dots into Bacteria via Purine-Dependent Mechanisms , 2005, Applied and Environmental Microbiology.

[105]  Jürgen Popp,et al.  Raman spectroscopic identification of single yeast cells , 2005 .

[106]  Søren J. Sørensen,et al.  Construction of a ColD cda Promoter-Based SOS-Green Fluorescent Protein Whole-Cell Biosensor with Higher Sensitivity toward Genotoxic Compounds than Constructs Based on recA, umuDC, or sulA Promoters , 2005, Applied and Environmental Microbiology.

[107]  Sandro Macchietto,et al.  Computational Issues in Hybrid Multizonal/Computational Fluid Dynamics Models , 2005 .

[108]  Michael Schmitt,et al.  Chemotaxonomic Identification of Single Bacteria by Micro-Raman Spectroscopy: Application to Clean-Room-Relevant Biological Contaminations , 2005, Applied and Environmental Microbiology.

[109]  Michael A. Henson,et al.  Cell ensemble modeling of metabolic oscillations in continuous yeast cultures , 2005, Comput. Chem. Eng..

[110]  S. Gambhir,et al.  Quantum Dots for Live Cells, in Vivo Imaging, and Diagnostics , 2005, Science.

[111]  S. Generalis,et al.  Modelling a Biochemical Reaction with Computational Fluid Dynamics , 2005 .

[112]  Michael A Henson,et al.  Modeling the synchronization of yeast respiratory oscillations. , 2004, Journal of theoretical biology.

[113]  O. Kuipers,et al.  Visualization of Differential Gene Expression by Improved Cyan Fluorescent Protein and Yellow Fluorescent Protein Production in Bacillus subtilis , 2004, Applied and Environmental Microbiology.

[114]  Doraiswami Ramkrishna,et al.  Cybernetic modeling of metabolism: towards a framework for rational design of recombinant organisms , 2004 .

[115]  Lisa R. Hilliard,et al.  A rapid bioassay for single bacterial cell quantitation using bioconjugated nanoparticles. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[116]  Prodromos Daoutidis,et al.  Cell population balance modeling and control in continuous bioreactors , 2004 .

[117]  J. Stelling Mathematical models in microbial systems biology. , 2004, Current opinion in microbiology.

[118]  S. Leibler,et al.  Bacterial Persistence as a Phenotypic Switch , 2004, Science.

[119]  Krist V. Gernaey,et al.  Activated sludge wastewater treatment plant modelling and simulation: state of the art , 2004, Environ. Model. Softw..

[120]  Byron F. Brehm-Stecher,et al.  Single-Cell Microbiology: Tools, Technologies, and Applications , 2004, Microbiology and Molecular Biology Reviews.

[121]  Matthias Reuss,et al.  Dynamic Behavior of Microbial Populations in Stirred Bioreactors Simulated with Euler−Lagrange Methods: Traveling along the Lifelines of Single Cells† , 2004 .

[122]  Rajeev J Ram,et al.  In situ bioprocess monitoring of Escherichia coli bioreactions using Raman spectroscopy , 2004 .

[123]  S. Sørensen,et al.  Quantification of plasmid loss in Escherichia coli cells by use of flow cytometry. , 2004, FEMS microbiology letters.

[124]  H. Kitano Cancer as a robust system: implications for anticancer therapy , 2004, Nature Reviews Cancer.

[125]  H. Shapiro,et al.  The evolution of cytometers , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[126]  A. Aertsen,et al.  Stress and How Bacteria Cope with Death and Survival , 2004, Critical reviews in microbiology.

[127]  Daniel Hoefel,et al.  Enumeration of water-borne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques. , 2003, Journal of microbiological methods.

[128]  Alvin W Nienow,et al.  Further studies related to the scale‐up of high cell density escherichia coli fed‐batch fermentations: , 2003, Biotechnology and bioengineering.

[129]  J. Derksen Numerical Simulation of Solids Suspension in a Stirred Tank , 2003 .

[130]  M. A. Henson Dynamic modeling of microbial cell populations. , 2003, Current opinion in biotechnology.

[131]  S. Sørensen,et al.  Direct Detection and Quantification of Horizontal Gene Transfer by Using Flow Cytometry and gfp as a Reporter Gene , 2003, Current Microbiology.

[132]  Sandro Macchietto,et al.  General hybrid multizonal/CFD approach for bioreactor modeling , 2003 .

[133]  K. H. Nealson,et al.  Quantum Dots as Strain- and Metabolism-Specific Microbiological Labels , 2003, Applied and Environmental Microbiology.

[134]  M. Wagner,et al.  Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. , 2003, Current opinion in microbiology.

[135]  L. Raaska,et al.  Methodologies for the characterization of microbes in industrial environments: a review , 2003, Journal of Industrial Microbiology and Biotechnology.

[136]  Roland Ulber,et al.  Optical sensor systems for bioprocess monitoring , 2003, Analytical and bioanalytical chemistry.

[137]  A. G. Fredrickson,et al.  Population balance equations for cell and microbial cultures revisited , 2003 .

[138]  S. Sørensen,et al.  Presence of N-Acyl Homoserine Lactones in Soil Detected by a Whole-Cell Biosensor and Flow Cytometry , 2003, Microbial Ecology.

[139]  Hanjing Huang,et al.  A segregated model for heterologous amylase production by Bacillus subtilis , 2003 .

[140]  G. W. Harrington,et al.  Simultaneous determination of bacterial viability and identity in biofilms using ethidium monoazide and fluorescent in situ hybridization. , 2003, Water science and technology : a journal of the International Association on Water Pollution Research.

[141]  M. Coelho,et al.  An age-structured population balance model for microbial dynamics , 2003 .

[142]  J. Nielsen,et al.  Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. , 2003, Environmental microbiology.

[143]  J. Nielsen,et al.  Evaluation of the Redox Dye 5-Cyano-2,3-Tolyl-Tetrazolium Chloride for Activity Studies by Simultaneous Use of Microautoradiography and Fluorescence In Situ Hybridization , 2003, Applied and Environmental Microbiology.

[144]  Shaoyou Chu,et al.  Green fluorescent protein variants as ratiometric dual emission pH sensors. 1. Structural characterization and preliminary application. , 2002, Biochemistry.

[145]  Matthias Reuss,et al.  Cell population modelling of yeast glycolytic oscillations. , 2002, The Biochemical journal.

[146]  Hilary M. Lappin-Scott,et al.  Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria , 2002, Applied and Environmental Microbiology.

[147]  I. Booth,et al.  Stress and the single cell: intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. , 2002, International journal of food microbiology.

[148]  Michael A. Henson,et al.  Dynamics analysis of an age distribution model of oscillating yeast cultures , 2002 .

[149]  A. G. Fredrickson,et al.  A new set of population balance equations for microbial and cell cultures , 2002 .

[150]  Chang‐Deng Hu,et al.  Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. , 2002, Molecular cell.

[151]  S. Sørensen,et al.  Inducible Gene Expression by Nonculturable Bacteria in Milk after Pasteurization , 2002, Applied and Environmental Microbiology.

[152]  Edward R Sumner,et al.  Phenotypic heterogeneity: differential stress resistance among individual cells of the yeast Saccharomyces cerevisiae. , 2002, Microbiology.

[153]  R. Ye,et al.  Applications of DNA microarrays in microbial systems. , 2001, Journal of microbiological methods.

[154]  P. Daoutidis,et al.  Numerical solution of multi-variable cell population balance models. II. Spectral methods , 2001 .

[155]  Prodromos Daoutidis,et al.  Numerical solution of multi-variable cell population balance models. III. Finite element methods , 2001 .

[156]  Thomas Scheper,et al.  Flow cytometry in biotechnology , 2001, Applied Microbiology and Biotechnology.

[157]  L. Bini,et al.  The acid-stress response in Lactobacillus sanfranciscensis CB1. , 2001, Microbiology.

[158]  M. Wagner,et al.  16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. , 2001, Environmental microbiology.

[159]  C. McFarlane,et al.  Scale-down model to simulate spatial pH variations in large-scale bioreactors. , 2001, Biotechnology and bioengineering.

[160]  Doraiswami Ramkrishna,et al.  On modeling of bioreactors for control , 2001 .

[161]  J. Bertrand,et al.  Eulerian simulation of dense solid-liquid suspension in multi-stage stirred vessel , 2001 .

[162]  D. Veal,et al.  Heterogeneity of stress gene expression and stress resistance among individual cells of Saccharomyces cerevisiae , 2001, Molecular microbiology.

[163]  D. Naumann,et al.  Investigating Microbial (Micro)colony Heterogeneity by Vibrational Spectroscopy , 2001, Applied and Environmental Microbiology.

[164]  J. Nielsen,et al.  In situ detection of cell surface hydrophobicity of probe-defined bacteria in activated sludge. , 2001, Water science and technology : a journal of the International Association on Water Pollution Research.

[165]  C. Hewitt,et al.  Physiological responses to mixing in large scale bioreactors. , 2001, Journal of biotechnology.

[166]  John F. Hunt,et al.  Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein , 2001, Nature Biotechnology.

[167]  J. Wimpenny,et al.  Heterogeneity in biofilms. , 2000, FEMS microbiology reviews.

[168]  Michael A. Henson,et al.  Model predictive control of continuous yeast bioreactors using cell population balance models , 2000 .

[169]  C. Hewitt,et al.  Studies related to the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow cytometry: effect of a changing microenvironment with respect to glucose and dissolved oxygen concentration. , 2000, Biotechnology and bioengineering.

[170]  B. Lendl,et al.  Multidimensional information on the chemical composition of single bacterial cells by confocal Raman microspectroscopy. , 2000, Analytical chemistry.

[171]  P. Lebaron,et al.  Use of fluorescent probes to assess physiological functions of bacteria at single-cell level. , 2000, Microbes and infection.

[172]  S. Avery,et al.  Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry , 2000, Yeast.

[173]  A. B. Lyons,et al.  Analysing cell division in vivo and in vitro using flow cytometric measurement of CFSE dye dilution. , 2000, Journal of immunological methods.

[174]  D. Veal,et al.  Fluorescence staining and flow cytometry for monitoring microbial cells. , 2000, Journal of immunological methods.

[175]  C. Hewitt,et al.  Analysis of bacterial function by multi-colour fluorescence flow cytometry and single cell sorting. , 2000, Journal of microbiological methods.

[176]  H M Shapiro,et al.  Microbial analysis at the single-cell level: tasks and techniques. , 2000, Journal of microbiological methods.

[177]  K. Schuster,et al.  Single-cell analysis of bacteria by Raman microscopy: spectral information on the chemical composition of cells and on the heterogeneity in a culture. , 2000, Journal of microbiological methods.

[178]  Doraiswami Ramkrishna,et al.  Population Balances: Theory and Applications to Particulate Systems in Engineering , 2000 .

[179]  J. Joung,et al.  A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[180]  Daniel B. Oerther,et al.  Monitoring Precursor 16S rRNAs ofAcinetobacter spp. in Activated Sludge Wastewater Treatment Systems , 2000, Applied and Environmental Microbiology.

[181]  J. C. Godfrey,et al.  CFD Simulation of Particle Distribution in Stirred Vessels , 2000 .

[182]  J. Nielsen,et al.  Mathematical modelling of metabolism. , 2000, Current opinion in biotechnology.

[183]  S. Müller,et al.  Flow cytometric techniques to characterise physiological states of Acinetobacter calcoaceticus. , 2000, Journal of microbiological methods.

[184]  G. Geesey,et al.  Localization and Identification of Populations of Phosphatase-Active Bacterial Cells Associated with Activated Sludge Flocs , 1999, Microbial Ecology.

[185]  Matthias Reuss,et al.  A critical assessment on the use of k–ε turbulence models for simulation of the turbulent liquid flow induced by a Rushton-turbine in baffled stirred-tank reactors , 1999 .

[186]  E. Sherr,et al.  Estimating abundunce and single-cell characteristics of respiring bacteria via the redox dye CTC , 1999 .

[187]  C. Bunthof,et al.  Rapid Fluorescence Assessment of the Viability of Stressed Lactococcus lactis , 1999, Applied and Environmental Microbiology.

[188]  R. Desjardins,et al.  LIVE/DEAD BacLight : application of a new rapid staining method for direct enumeration of viable and total bacteria in drinking water. , 1999, Journal of microbiological methods.

[189]  T. Terwilliger,et al.  Rapid protein-folding assay using green fluorescent protein , 1999, Nature Biotechnology.

[190]  J. Lisle,et al.  The use of multiple indices of physiological activity to access viability in chlorine disinfected Escherichia coli O157:H7 , 1999, Letters in applied microbiology.

[191]  Prodromos Daoutidis,et al.  Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration , 1999 .

[192]  D. Kompala,et al.  Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures. , 1999, Journal of biotechnology.

[193]  R. Kolter,et al.  Evolution of microbial diversity during prolonged starvation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[194]  K. Schleifer,et al.  Combination of Fluorescent In Situ Hybridization and Microautoradiography—a New Tool for Structure-Function Analyses in Microbial Ecology , 1999, Applied and Environmental Microbiology.

[195]  D. Cooper,et al.  Development and solution of a cell mass population balance model applied to the SCF process , 1999 .

[196]  L. Fuchs,et al.  Large eddy simulations of the turbulent flow in a stirred reactor , 1998 .

[197]  Michael J. Kurtz,et al.  Control of oscillating microbial cultures described by population balance models , 1998 .

[198]  Lilia Alberghina,et al.  Control by Nutrients of Growth and Cell Cycle Progression in Budding Yeast, Analyzed by Double-Tag Flow Cytometry , 1998, Journal of bacteriology.

[199]  Gero Miesenböck,et al.  Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins , 1998, Nature.

[200]  Lilly,et al.  Reactor heterogeneity with saccharopolyspora erythraea airlift fermentations , 1998, Biotechnology and bioengineering.

[201]  I. Stagljar,et al.  A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[202]  M. Thoma,et al.  Effect of the dilution rate on the mode of oscillation in continuous cultures of Saccharomyces cerevisiae. , 1998, Journal of biotechnology.

[203]  E. Collet,et al.  Substrate gradient formation in the large-scale bioreactor lowers cell yield and increases by-product formation , 1998 .

[204]  A S Verkman,et al.  Green fluorescent protein as a noninvasive intracellular pH indicator. , 1998, Biophysical journal.

[205]  Gen Larsson,et al.  Comparison of the Baker's yeast process performance in laboratory and production scale , 1998 .

[206]  M Carlsen,et al.  Growth and product formation of Aspergillus oryzae during submerged cultivations: verification of a morphologically structured model using fluorescent probes. , 1998, Biotechnology and bioengineering.

[207]  G. Patterson,et al.  Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. , 1997, Biophysical journal.

[208]  A. Bos,et al.  Flow cytometric analysis of Lactobacillus plantarum to monitor lag times, cell divisionand injury , 1997 .

[209]  M. Reuss,et al.  In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae : I. Experimental observations. , 1997, Biotechnology and bioengineering.

[210]  M. Hermansson,et al.  Determination of bacterial cell surface hydrophobicity of single cells in cultures and in wastewater in situ. , 1997, FEMS microbiology letters.

[211]  G. Cangelosi,et al.  Depletion of pre-16S rRNA in starved Escherichia coli cells , 1997, Journal of bacteriology.

[212]  James J. Smith,et al.  Mechanisms of INT (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride), and CTC (5-cyano-2,3-ditolyl tetrazolium chloride) reduction in Escherichia coli K-12 , 1997 .

[213]  Friedrich Srienc,et al.  Solutions of population balance models based on a successive generations approach , 1997 .

[214]  D. Kell,et al.  Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. , 1996, Microbiological reviews.

[215]  S. Kain,et al.  Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. , 1996, Nucleic acids research.

[216]  J. Hegemann,et al.  Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast , 1996, Yeast.

[217]  H. Noorman,et al.  Substrate gradients in bioreactors: origin and consequences , 1996 .

[218]  W. Page,et al.  Quantitation of poly-β-hydroxybutyrate by fluorescence of bacteria and granules stained with Nile blue A , 1996 .

[219]  W. Stemmer,et al.  Improved Green Fluorescent Protein by Molecular Evolution Using DNA Shuffling , 1996, Nature Biotechnology.

[220]  A. Alivisatos Semiconductor Clusters, Nanocrystals, and Quantum Dots , 1996, Science.

[221]  R. Tsien,et al.  Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer , 1996, Current Biology.

[222]  D. Grunwald [Principles of flow cytometry]. , 1995, Bulletin du cancer.

[223]  G. McFeters,et al.  Factors affecting the determination of respiratory activity on the basis of cyanoditolyl tetrazolium chloride reduction with membrane filtration , 1995, Applied and environmental microbiology.

[224]  J. Nielsen,et al.  Population balance models of autonomous microbial oscillations. , 1995, Journal of biotechnology.

[225]  M. Hjortso Solution and properties of age population balance models which assume discrete division ages. , 1995, Journal of biotechnology.

[226]  P. Silver,et al.  Kinetics of spindle pole body separation in budding yeast. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[227]  R Y Tsien,et al.  Wavelength mutations and posttranslational autoxidation of green fluorescent protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[228]  T. Naas,et al.  Generation of genetic diversity by DNA rearrangements in resting bacteria , 1994 .

[229]  R. Lenski,et al.  Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[230]  K. Bellgardt Analysis of synchronous growth of baker's yeast. Part II: Comparison of model prediction and experimental data , 1994 .

[231]  K. Bellgardt Analysis of synchronous growth of baker's yeast. Part I: Development of a theoretical model for sustained oscillations , 1994 .

[232]  Ritzka,et al.  Fermentation monitoring and process control. , 1994, Current opinion in biotechnology.

[233]  M. Chalfie,et al.  Green fluorescent protein as a marker for gene expression. , 1994, Science.

[234]  D. Ramkrishna,et al.  Toward a self‐similar theory of microbial populations , 1994, Biotechnology and bioengineering.

[235]  K. Schügerl,et al.  Transient behaviour of baker's yeast during enforced periodical variation of dissolved oxygen concentration. , 1994, Journal of biotechnology.

[236]  I. Herskowitz,et al.  Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. , 1993, Science.

[237]  D A Stahl,et al.  Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms , 1993, Applied and environmental microbiology.

[238]  H Håkanson,et al.  Sampling and sample handling--crucial steps in process monitoring and control. , 1993, Trends in biotechnology.

[239]  John Villadsen,et al.  Modelling of microbial kinetics , 1992 .

[240]  E. Fearon,et al.  Karyoplasmic interaction selection strategy: a general strategy to detect protein-protein interactions in mammalian cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[241]  H. Ridgway,et al.  Use of a fluorescent redox probe for direct visualization of actively respiring bacteria , 1992, Applied and environmental microbiology.

[242]  S. Fields,et al.  The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[243]  Lilia Alberghina,et al.  Structured segregated models and analysis of self-oscillating yeast continuous cultures , 1990 .

[244]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[245]  L. Mariani,et al.  A simulation program based on a structured population model for biotechnological yeast processes , 1988, Applied Microbiology and Biotechnology.

[246]  K. Luyben,et al.  Experimental simulation of oxygen profiles and their influence on baker's yeast production: I. One‐fermentor system , 1988, Biotechnology and bioengineering.

[247]  G. Honderd,et al.  Modelling the dynamic behaviour ofSaccharomyces cerevisiae and its application in control experiments , 1988, Applied Microbiology and Biotechnology.

[248]  E. Fiolitakis Ein altersstrukturiertes Populationsmodell zur Beschreibung instationärer mikrobieller Prozesse, Teil I: Theorie , 1987 .

[249]  E. Fiolitakis Ein altersstrukturiertes Populationsmodell zur Beschreibung instationärer mikrobieller Prozesse, Teil II: Modell‐Verifikation am Beispiel der Glucose‐Fermentation mit Zymomonas mobilis , 1987 .

[250]  J M Masson,et al.  Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions. , 1987, Genes & development.

[251]  E. Stadtman,et al.  Use of fluorescein hydrazide and fluorescein thiosemicarbazide reagents for the fluorometric determination of protein carbonyl groups and for the detection of oxidized protein on polyacrylamide gels. , 1987, Analytical biochemistry.

[252]  Lilia Alberghina,et al.  Yeast population models for monitoring and control of biotechnical processes , 1986 .

[253]  J. Beckwith,et al.  Uses of lac fusions for the study of biological problems. , 1985, Microbiological reviews.

[254]  James E. Bailey,et al.  Transient responses of budding yeast populations , 1983 .

[255]  W. Ward,et al.  Reversible denaturation of Aequorea green-fluorescent protein: physical separation and characterization of the renatured protein. , 1982, Biochemistry.

[256]  J G Holt,et al.  Nile blue A as a fluorescent stain for poly-beta-hydroxybutyrate , 1982, Applied and environmental microbiology.

[257]  A. Wheals Size control models of Saccharomyces cerevisiae cell proliferation , 1982, Molecular and cellular biology.

[258]  J. W. Hastings,et al.  BIOLUMINESCENCE AND CHEMILUMINESCENCE , 1976, Photochemistry and photobiology.

[259]  W. Reznikoff,et al.  Fusions of the lac and trp Regions of the Escherichia coli Chromosome , 1970, Journal of bacteriology.

[260]  H. M. Tsuchiya,et al.  On the mass distribution model for microbial cell populations. , 1970, The Bulletin of mathematical biophysics.

[261]  Doraiswami Ramkrishna,et al.  Statistics and dynamics of procaryotic cell populations , 1967 .

[262]  T. D. Brock,et al.  Autoradiography as a Tool in Microbial Ecology , 1966, Nature.

[263]  S. Benzer,et al.  An active cistron fragment. , 1962, Journal of molecular biology.

[264]  H. Davey,et al.  Multivariate data analysis methods for the interpretation of microbial flow cytometric data. , 2011, Advances in biochemical engineering/biotechnology.

[265]  Thomas Bley,et al.  From single cells to microbial population dynamics: modelling in biotechnology based on measurements of individual cells. , 2011, Advances in biochemical engineering/biotechnology.

[266]  S. Mukherjee,et al.  Review: biofunctionalized quantum dots in biology and medicine , 2009 .

[267]  Matthew J. Brauer,et al.  Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. , 2008, Molecular biology of the cell.

[268]  J. Schenk,et al.  The ongoing quest for truly on-line bioprocess monitoring using spectroscopy , 2008 .

[269]  J. Lay,et al.  (Applied Microbiology and Biotechnology, 74(5):1126-1134)Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target , 2007 .

[270]  E. Ron Bacterial Stress Response , 2006 .

[271]  Bas Teusink,et al.  Modelling strategies for the industrial exploitation of lactic acid bacteria , 2006, Nature Reviews Microbiology.

[272]  J. Nielsen,et al.  Advances in microscopy: microautoradiography of single cells. , 2005, Methods in enzymology.

[273]  T. Terwilliger,et al.  Recent Advances in GFP Folding Reporter and Split-GFP Solubility Reporter Technologies. Application to Improving the Folding and Solubility of Recalcitrant Proteins from Mycobacterium tuberculosis , 2005, Journal of Structural and Functional Genomics.

[274]  Thomas Egli,et al.  Molecular components of physiological stress responses in Escherichia coli. , 2004, Advances in biochemical engineering/biotechnology.

[275]  A. Giacomini,et al.  Optimization of fluorescence microscopy techniques for the detection of total and viable lactic acid bacteria in whey starter cultures , 2004 .

[276]  Maria Papagianni,et al.  Fungal morphology and metabolite production in submerged mycelial processes. , 2004, Biotechnology advances.

[277]  Hazel M Davey,et al.  Using flow cytometry to quantify microbial heterogeneity. , 2003, Current issues in molecular biology.

[278]  V. Créach,et al.  Direct estimate of active bacteria: CTC use and limitations. , 2003, Journal of microbiological methods.

[279]  Prodromos Daoutidis,et al.  Dynamics and Control of Cell Populations in Continuous Bioreactors , 2002 .

[280]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[281]  Prodromos Daoutidis,et al.  Nonlinear productivity control using a multi-staged cell population balance model , 2002 .

[282]  Prashant Mhaskar,et al.  Cell Population Modeling and Parameter Estimation for Continuous Cultures of Saccharomyces cerevisiae , 2002, Biotechnology progress.

[283]  U. Stockar,et al.  Modeling of oscillating cultivations of Saccharomyces cerevisiae: Identification of population structure and expansion kinetics based on on-line measurements , 2000 .

[284]  M. Wickens,et al.  Yeast three-hybrid system to detect and analyze interactions between RNA and protein. , 1999, Methods in enzymology.

[285]  H. Shapiro,et al.  Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique. , 1999, Cytometry.

[286]  Pierre Gy,et al.  Sampling for analytical purposes , 1998 .

[287]  J E Bailey,et al.  Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities , 1998, Biotechnology progress.

[288]  G. Caetano-Anollés,et al.  DNA markers : protocols, applications, and overviews , 1997 .

[289]  B. Christensen,et al.  Bacterial plasmid conjugation on semi-solid surfaces monitored with the green fluorescent protein (GFP) from Aequorea victoria as a marker. , 1996, Gene.

[290]  A G Fredrickson,et al.  Multistaged corpuscular models of microbial growth: Monte Carlo simulations. , 1995, Bio Systems.

[291]  C. Stewart,et al.  Use of a photolabeling technique to identify nonviable cells in fixed homologous or heterologous cell populations. , 1991, Cytometry.

[292]  R. Tsien Fluorescent probes of cell signaling. , 1989, Annual review of neuroscience.

[293]  Suteaki Shioya,et al.  Comparison of simple population models in a baker's yeast fed-batch culture , 1985 .

[294]  W. Ward PROPERTIES OF THE COELENTERATE GREEN-FLUORESCENT PROTEINS , 1981 .

[295]  H. M. Tsuchiya,et al.  Mathematical Models for Fermentation Processes , 1970 .

[296]  A. Ravna,et al.  Theoretical Biology and Medical Modelling Open Access Molecular Model of the Outward Facing State of the Human P-glycoprotein (abcb1), and Comparison to a Model of the Human Mrp5 (abcc5) , 2022 .