Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering.

[1]  M. Flickinger,et al.  A model of interorganelle monoclonal antibody transport and secretion in mouse hybridoma cells , 1991, Biotechnology and bioengineering.

[2]  M. Flickinger,et al.  A structured model for monoclonal antibody synthesis in exponentially growing and stationary phase hybridoma cells , 1991, Biotechnology and bioengineering.

[3]  Lyle H. Ungar,et al.  A hybrid neural network‐first principles approach to process modeling , 1992 .

[4]  Rimvydas Simutis,et al.  Hybrid modelling of yeast production processes – combination of a priori knowledge on different levels of sophistication , 1994 .

[5]  B. Palsson,et al.  Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.

[6]  Mark A. Kramer,et al.  Modeling chemical processes using prior knowledge and neural networks , 1994 .

[7]  J Morris,et al.  Neural-network contributions in biotechnology. , 1994, Trends in biotechnology.

[8]  A. Zeng.  Mathematical modeling and analysis of monoclonal antibody production by hybridoma cells , 1996, Biotechnology and bioengineering.

[9]  R. Simutis,et al.  THE USE OF HYBRID MODELLING FOR THE OPTIMIZATION OF THE PENICILLIN FERMENTATION PROCESS , 1996 .

[10]  T. Schäfer,et al.  Modelling hybridoma cell growth and metabolism--a comparison of selected models and data. , 1996, Journal of biotechnology.

[11]  H J van Can,et al.  An efficient model development strategy for bioprocesses based on neural networks in macroscopic balances. , 1997, Biotechnology and bioengineering.

[12]  H. Bonarius,et al.  Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. , 1997 .

[13]  Rimvydas Simutis,et al.  How to increase the performance of models for process optimization and control , 1997 .

[14]  J. Keasling,et al.  Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. , 1997, Biotechnology and bioengineering.

[15]  I. Grossmann,et al.  A disaggregation algorithm for the optimization of stochastic planning models , 1997 .

[16]  A. Zeng,et al.  Stoichiometry, Kinetics, and Regulation of Glucose and Amino Acid Metabolism of a Recombinant BHK Cell Line in Batch and Continuous Cultures , 1997, Biotechnology progress.

[17]  S. Feyo de Azevedo,et al.  Hybrid modelling of biochemical processes: A comparison with the conventional approach , 1997 .

[18]  A. Zeng,et al.  Determinants and rate laws of growth and death of hybridoma cells in continuous culture. , 1998, Biotechnology and bioengineering.

[19]  Henk B. Verbruggen,et al.  Semi-mechanistic modeling of chemical processes with neural networks , 1998 .

[20]  E. Martin,et al.  Non-linear projection to latent structures revisited: the quadratic PLS algorithm , 1999 .

[21]  Plamen Angelov,et al.  Hybrid modelling of biotechnological processes using neural networks , 1999 .

[22]  Bernhard Eikens,et al.  Process identification with multiple neural network models , 1999 .

[23]  D. Fell,et al.  Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.

[24]  A structured, dynamic model for animal cell culture systems: application to murine hybridoma , 1999 .

[25]  G. Stephanopoulos.  Metabolic fluxes and metabolic engineering. , 1999, Metabolic engineering.

[26]  S. Dhir,et al.  Dynamic optimization of hybridoma growth in a fed-batch bioreactor. , 2000, Biotechnology and bioengineering.

[27]  B. Palsson,et al.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  John P. Barford,et al.  An unstructured kinetic model of macromolecular metabolism in batch and fed-batch cultures of hybridoma cells producing monoclonal antibody , 2000 .

[29]  D. Fell,et al.  A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks , 2000, Nature Biotechnology.

[30]  Bernhard O. Palsson,et al.  Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions , 2000, BMC Bioinformatics.

[31]  B. Palsson,et al.  Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. , 2000, Biotechnology and bioengineering.

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

[33]  B. Palsson,et al.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.

[34]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[35]  B. Palsson,et al.  Metabolic modelling of microbes: the flux-balance approach. , 2002, Environmental microbiology.

[36]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[37]  G. Church,et al.  Genome-Scale Metabolic Model of Helicobacter pylori 26695 , 2002, Journal of bacteriology.

[38]  B. Palsson,et al.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .

[39]  Friedrich Srienc,et al.  Metabolic pathway analysis of a recombinant yeast for rational strain development. , 2002, Biotechnology and bioengineering.

[40]  G. Church,et al.  Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[41]  Bernhard O Palsson,et al.  Network-based analysis of metabolic regulation in the human red blood cell. , 2003, Journal of theoretical biology.

[42]  S. Lee,et al.  Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. , 2003, Biotechnology and bioengineering.

[43]  B. Palsson,et al.  Constraints-based models: regulation of gene expression reduces the steady-state solution space. , 2003, Journal of theoretical biology.

[44]  R. Aebersold,et al.  Proteomics: the first decade and beyond , 2003, Nature Genetics.

[45]  Steffen Klamt,et al.  FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps , 2003, Bioinform..

[46]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[47]  B. Palsson,et al.  Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli , 2003, Journal of bacteriology.

[48]  Jason A. Papin,et al.  Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.

[49]  Jason A. Papin,et al.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. , 2003, Biophysical journal.

[50]  Steffen Klamt,et al.  Two approaches for metabolic pathway analysis? , 2003, Trends in biotechnology.

[51]  C. Wittmann,et al.  In-Depth Profiling of Lysine-Producing Corynebacterium glutamicum by Combined Analysis of the Transcriptome, Metabolome, and Fluxome , 2004, Journal of bacteriology.

[52]  Homin K. Lee,et al.  Coexpression analysis of human genes across many microarray data sets. , 2004, Genome research.

[53]  Alfred O. Hero,et al.  Network constrained clustering for gene microarray data , 2005, Bioinform..

[54]  Gregory Stephanopoulos,et al.  High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts. , 2005, The Biochemical journal.

[55]  Ana P. Teixeira,et al.  Modelling and optimization of a recombinant BHK-21 cultivation process using hybrid grey-box systems. , 2005, Journal of biotechnology.

[56]  J. Nielsen,et al.  Mass spectrometry in metabolome analysis. , 2005, Mass spectrometry reviews.

[57]  W. Dunn,et al.  Measuring the metabolome: current analytical technologies. , 2005, The Analyst.

[58]  Steffen Klamt,et al.  A methodology for the structural and functional analysis of signaling and regulatory networks , 2006, BMC Bioinformatics.

[59]  Rui Oliveira,et al.  Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control , 2007, BMC Bioinformatics.

[60]  Y. Schneider,et al.  Metabolic design of macroscopic bioreaction models: application to Chinese hamster ovary cells , 2006, Bioprocess and biosystems engineering.

[61]  Stefan Schuster,et al.  Systems biology Metatool 5.0: fast and flexible elementary modes analysis , 2006 .

[62]  Konstantin Konstantinov,et al.  Towards industrial application of quasi real-time metabolic flux analysis for mammalian cell culture. , 2006, Advances in biochemical engineering/biotechnology.

[63]  Gang Wu,et al.  Integrative Analysis of Transcriptomic and Proteomic Data: Challenges, Solutions and Applications , 2007, Critical reviews in biotechnology.

[64]  Jianying Gao,et al.  Dynamic Metabolic Modeling for a MAB Bioprocess , 2007, Biotechnology progress.