Publications
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2012. A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.. J Theor Biol. 292:71-7.
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2010. Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.. Applied and environmental microbiology. 76(13):4158-68.
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2010. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.. BMC bioinformatics. 11:213.
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2010. The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
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2010. The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
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2010. De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.. PloS one. 5(6):e10922.
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2010. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40.
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2010. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology. 4:140.
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2010. Drug off-target effects predicted using structural analysis in the context of a metabolic network model.. PLoS computational biology. 6(9):e1000938.
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2010. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81.
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2010. Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.. PLoS genetics. 6(11):e1001186.
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2010. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
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2010. Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85.
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2010. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
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2010. Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
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2010. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
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2010. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390.
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2010. A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.
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2010. Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
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2010. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5.
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2010. Structural and operational complexity of the Geobacter sulfurreducens genome.. Genome research. 20(9):1304-11.
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2010. Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12.
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2010. Towards genome-scale signalling network reconstructions.. Nature reviews. Genetics. 11(4):297-307.
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2010. What is flux balance analysis? Nature biotechnology. 28(3):245-8.
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2009. Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320.
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2009. Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Molecular cell. 35(3):255-6.
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2009. Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
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2009. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.. BMC systems biology. 3:38.
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2009. Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.. BMC systems biology. 3:30.
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2009. Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
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2009. Functional states of the genome-scale Escherichia coli transcriptional regulatory system.. PLoS computational biology. 5(6):e1000403.
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2009. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44.
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2009. Genome-scale network analysis of imprinted human metabolic genes.. Epigenetics : official journal of the DNA Methylation Society. 4(1):43-6.
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2009. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312.
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2009. Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292.
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2009. Metabolic systems biology.. FEBS letters. 583(24):3900-4.
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2009. Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6.
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2009. Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
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2009. Three-dimensional structural view of the central metabolic network of Thermotoga maritima.. Science (New York, N.Y.). 325(5947):1544-9.
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2009. The transcription unit architecture of the Escherichia coli genome.. Nature biotechnology. 27(11):1043-9.
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2009. Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
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2009. Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
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2009. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology. 3:44.
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2008. Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.. Applied and environmental microbiology. 74(24):7561-9.
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2008. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.. Nature biotechnology. 26(10):1155-60.
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2008. Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
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2008. Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171.
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2008. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.. BMC systems biology. 2:79.
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2008. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.. Applied microbiology and biotechnology. 80(5):849-62.
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2008. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.. Proceedings of the National Academy of Sciences of the United States of America. 105(49):19462-7.
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2008. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.. Genome research. 18(6):900-10.
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2008. Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.. Methods in molecular biology (Clifton, N.J.). 439:131-45.
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2008. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
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2008. Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.. Journal of bacteriology. 190(14):5087-94.
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2008. Network-based prediction of human tissue-specific metabolism.. Nature biotechnology. 26(9):1003-10.
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2008. Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57.
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2008. Three factors underlying incorrect in silico predictions of essential metabolic genes.. BMC systems biology. 2:14.
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2008. Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology. 4(9):e1000177.
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2007. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.. American journal of physiology. Cell physiology. 292(1):C164-77.
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2007. Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.. Biochemistry. 46(19):5722-31.
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2007. Estimation of the number of extreme pathways for metabolic networks.. BMC bioinformatics. 8(1):363.
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2007. An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.. BMC genomics. 8:274.
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2007. A genome-scale, constraint-based approach to systems biology of human metabolism.. Molecular bioSystems. 3(9):598-603.
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2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.. Molecular systems biology. 3:121.
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2007. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.. The Journal of biological chemistry. 282(39):28791-9.
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2007. Global reconstruction of the human metabolic network based on genomic and bibliomic data.. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1777-82.
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2007. In silico analysis of SNPs and other high-throughput data.. Methods in molecular biology (Clifton, N.J.). 366:267-85.
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2007. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.. BMC systems biology. 1:26.
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2007. Metabolic characterization of Escherichia coli strains adapted to growth on lactate.. Applied and environmental microbiology. 73(14):4639-47.
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2007. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.. PLoS computational biology. 3(10):1887-95.
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2007. Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4.
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2007. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.. Nature protocols. 2(3):727-38.
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2007. Systematic condition-dependent annotation of metabolic genes.. Genome research. 17(11):1626-33.
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2007. Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.. Molecular genetics and metabolism. 91(1):15-22.
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2007. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach.. Progress in drug research. Fortschritte der Arzneimittelforschung. Progrès des recherches pharmaceutiques. 64:265,267-309.
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2006. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.. Biophysical journal. 90(11):3919-28.
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2006. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.. Applied and environmental microbiology. 72(2):1558-68.
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2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.. Nature genetics. 38(12):1406-12.
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2006. Experimental and computational assessment of conditionally essential genes in Escherichia coli.. Journal of bacteriology. 188(23):8259-71.
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2006. Identification of genome-scale metabolic network models using experimentally measured flux profiles.. PLoS computational biology. 2(7):e72.
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2006. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.. Genome research. 16(5):627-35.
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2006. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.. Biotechnology and bioengineering. 95(5):972-83.
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2006. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.. PLoS computational biology. 2(5):e52.
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2006. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.. The Journal of biological chemistry. 281(12):8024-33.
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2006. Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.. PLoS computational biology. 2(1):e2.
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2006. Matrix formalism to describe functional states of transcriptional regulatory systems.. PLoS computational biology. 2(8):e101.
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2006. Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.. Biotechnology and bioengineering. 95(5):992-1002.
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2006. Metabolite coupling in genome-scale metabolic networks.. BMC bioinformatics. 7:111.
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2006. The model organism as a system: integrating 'omics' data sets.. Nature reviews. Molecular cell biology. 7(3):198-210.
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2006. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.. Molecular systems biology. 2:2006.0004.
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2006. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.. BMC bioinformatics. 7:132.
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2006. Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types.. Journal of biomedical optics. 11(1):014034.
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2006. PCR-based tandem epitope tagging system for Escherichia coli genome engineering.. BioTechniques. 40(1):67-72.
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2006. Systems approach to refining genome annotation.. Proceedings of the National Academy of Sciences of the United States of America. 103(46):17480-4.
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2006. Systems biology as a foundation for genome-scale synthetic biology.. Current opinion in biotechnology. 17(5):488-92.
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2006. Systems biology of SNPs.. Molecular systems biology. 2:38.
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2006. Systems biology of the human red blood cell.. Blood cells, molecules & diseases. 36(2):239-47.
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2006. Towards multidimensional genome annotation.. Nature reviews. Genetics. 7(2):130-41.
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2006. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.. Microbiology (Reading, England). 152(Pt 8):2207-19.
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2005. Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.. Biotechnology and bioengineering. 91(7):872-6.
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2005. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.. The Journal of biological chemistry. 280(12):11683-95.
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2005. The econometrics of evolution.. Nature chemical biology. 1(4):191-2.
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2005. Expa: a program for calculating extreme pathways in biochemical reaction networks.. Bioinformatics (Oxford, England). 21(8):1739-40.
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2005. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.. Journal of bacteriology. 187(16):5818-30.
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2005. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.. BMC microbiology. 5:8.
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2005. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.. Proceedings of the National Academy of Sciences of the United States of America. 102(52):19103-8.
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2005. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.. Journal of bacteriology. 187(17):6166-74.
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2005. In silico design and adaptive evolution of Escherichia coli for production of lactic acid.. Biotechnology and bioengineering. 91(5):643-8.
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2005. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.. Biophysical journal. 88(3):1616-25.
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2005. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.. Genome research. 15(10):1365-72.
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2005. Properties of metabolic networks: structure versus function.. Biophysical journal. 88(1):L07-9.
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2005. Reconstruction of cellular signalling networks and analysis of their properties.. Nature reviews. Molecular cell biology. 6(2):99-111.
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2005. Untangling the web of functional and physical interactions in yeast.. Journal of biology. 4(2):5.
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2004. Comparison of network-based pathway analysis methods.. Trends in biotechnology. 22(8):400-5.
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2004. The evolution of molecular biology into systems biology.. Nature biotechnology. 22(10):1249-52.
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2004. Flagellar biosynthesis in silico: building quantitative models of regulatory networks.. Cell. 117(6):689-90.
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2004. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.. Genome research. 14(9):1797-805.
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2004. Genome-scale models of microbial cells: evaluating the consequences of constraints.. Nature reviews. Microbiology. 2(11):886-97.
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2004. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.. Trends in biochemical sciences. 29(12):641-7.
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2004. High-throughput laser-mediated in situ cell purification with high purity and yield.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 61(2):153-61.
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2004. High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.. Genome research. 14(12):2495-502.
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2004. In silico biotechnology. Era of reconstruction and interrogation.. Current opinion in biotechnology. 15(1):50-1.
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2004. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.. Omics : a journal of integrative biology. 8(1):25-41.
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2004. Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.. BMC genomics. 5:63.
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2004. Integrating high-throughput and computational data elucidates bacterial networks.. Nature. 429(6987):92-6.
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2004. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.. Biophysical journal. 87(1):37-46.
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2004. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.. Nature genetics. 36(10):1056-8.
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2004. Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.. Journal of theoretical biology. 228(4):437-47.
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2004. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.. The Journal of biological chemistry. 279(38):39532-40.
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2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.. Genome research. 14(7):1298-309.
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2004. Reconstruction of microbial transcriptional regulatory networks.. Current opinion in biotechnology. 15(1):70-7.
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2004. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk.. Journal of theoretical biology. 227(2):283-97.
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2004. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.. Biophysical journal. 87(4):2172-86.
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2004. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.. Biotechnology and bioengineering. 86(3):317-31.
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2003. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.. Biophysical journal. 84(2 Pt 1):794-804.
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2003. Constraints-based models: regulation of gene expression reduces the steady-state solution space.. Journal of theoretical biology. 221(3):309-25.
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2003. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.. Biophysical journal. 85(1):16-26.
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2003. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.. Journal of bacteriology. 185(21):6400-8.
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2003. Development of network-based pathway definitions: the need to analyze real metabolic networks.. Trends in biotechnology. 21(5):195-8.
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2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).. Genome biology. 4(9):R54.
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2003. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.. Journal of bacteriology. 185(21):6392-9.
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2003. Genome-scale microbial in silico models: the constraints-based approach.. Trends in biotechnology. 21(4):162-9.
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2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.. Genome research. 13(2):244-53.
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2003. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and bioengineering. 84(7):763-72.
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2003. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.. Journal of bacteriology. 185(15):4593-602.
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2003. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.. Omics : a journal of integrative biology. 7(2):193-202.
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2003. Metabolic pathways in the post-genome era.. Trends in biochemical sciences. 28(5):250-8.
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2003. Network-based analysis of metabolic regulation in the human red blood cell.. Journal of theoretical biology. 225(2):185-94.
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2003. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes.. Journal of molecular microbiology and biotechnology. 6(2):101-8.
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2003. Reconciling gene expression data with known genome-scale regulatory network structures.. Genome research. 13(11):2423-34.
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2003. Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.. Journal of theoretical biology. 224(3):313-24.
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2003. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.. Proceedings of the National Academy of Sciences of the United States of America. 100(23):13134-9.
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2003. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.. Biotechnology letters. 25(5):435-41.
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2003. Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.. Journal of theoretical biology. 220(1):1-18.
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2003. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.. Journal of theoretical biology. 224(1):87-96.
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2003. Thirteen years of building constraint-based in silico models of Escherichia coli.. Journal of bacteriology. 185(9):2692-9.
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2002. Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line.. In vitro cellular & developmental biology. Animal. 38(2):90-6.
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2002. Characterizing the metabolic phenotype: a phenotype phase plane analysis.. Biotechnology and bioengineering. 77(1):27-36.
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2002. Description and analysis of metabolic connectivity and dynamics in the human red blood cell.. Biophysical journal. 83(2):646-62.
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2002. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.. Genome research. 12(5):760-9.
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2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.. Nature. 420(6912):186-9.
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2002. Extreme pathway analysis of human red blood cell metabolism.. Biophysical journal. 83(2):808-18.
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2002. Extreme pathway lengths and reaction participation in genome-scale metabolic networks.. Genome research. 12(12):1889-900.
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2002. Extreme pathways and Kirchhoff's second law.. Biophysical journal. 83(5):2879-82.
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2002. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.. Journal of theoretical biology. 215(1):67-82.
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2002. Genome-scale metabolic model of Helicobacter pylori 26695.. Journal of bacteriology. 184(16):4582-93.
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2002. H. influenzae Consortium: integrative study of H. influenzae-human interactions.. Omics : a journal of integrative biology. 6(4):341-8.
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2002. In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism.. Genome research. 12(11):1687-92.
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2002. Metabolic modelling of microbes: the flux-balance approach.. Environmental microbiology. 4(3):133-40.
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2002. Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.. Experimental hematology. 30(5):460-3.
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2002. Transcriptional regulation in constraints-based metabolic models of Escherichia coli.. The Journal of biological chemistry. 277(31):28058-64.
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2001. Dynamic simulation of the human red blood cell metabolic network.. Bioinformatics (Oxford, England). 17(3):286-7.
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2001. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.. American journal of physiology. Regulatory, integrative and comparative physiology. 280(3):R695-704.
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2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.. Nature biotechnology. 19(2):125-30.
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2001. Metabolic modeling of microbial strains in silico.. Trends in biochemical sciences. 26(3):179-86.
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2001. Regulation of gene expression in flux balance models of metabolism.. Journal of theoretical biology. 213(1):73-88.
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2000. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.. Journal of theoretical biology. 203(3):249-83.
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2000. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.. Biotechnology and bioengineering. 71(4):286-306.
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2000. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.. Proceedings of the National Academy of Sciences of the United States of America. 97(10):5528-33.
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2000. Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium.. Cytometry. 40(2):109-18.
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2000. In situ labeling of adherent cells with PKH26.. In vitro cellular & developmental biology. Animal. 36(1):4-6.
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2000. Intercellular adhesion can be visualized using fluorescently labeled fibrosarcoma HT1080 cells cocultured with hematopoietic cell lines or CD34(+) enriched human mobilized peripheral blood cells.. Cytometry. 40(2):119-25.
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2000. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.. BMC bioinformatics. 1:1.
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2000. Multiple steady states in kinetic models of red cell metabolism.. Journal of theoretical biology. 207(1):125-7.
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2000. Robustness analysis of the Escherichia coli metabolic network.. Biotechnology progress. 16(6):927-39.
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2000. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.. Journal of theoretical biology. 203(3):229-48.
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1999. Key adhesion molecules are present on long podia extended by hematopoietic cells.. Cytometry. 37(3):171-7.
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1999. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.. Biotechnology progress. 15(3):296-303.
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1999. Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line.. Cytometry. 36(4):312-8.
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1999. Symmetry of initial cell divisions among primitive hematopoietic progenitors is independent of ontogenic age and regulatory molecules.. Blood. 94(8):2595-604.
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1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype.. The Journal of biological chemistry. 274(25):17410-6.
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1999. Toward metabolic phenomics: analysis of genomic data using flux balances.. Biotechnology progress. 15(3):288-95.
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1998. Cell cycle dependence of retroviral transduction: An issue of overlapping time scales.. Biotechnology and bioengineering. 58(2-3):272-81.
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1998. Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures.. Biotechnology and bioengineering. 59(5):605-11.
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1998. How will bioinformatics influence metabolic engineering? Biotechnology and bioengineering. 58(2-3):162-9.
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1998. Tissue culture surface characteristics influence the expansion of human bone marrow cells.. Biomaterials. 19(21):1963-72.
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1998. Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells.. Blood. 92(10):3616-23.
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1998. The underlying pathway structure of biochemical reaction networks.. Proceedings of the National Academy of Sciences of the United States of America. 95(8):4193-8.
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1997. Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors.. Human gene therapy. 8(3):285-91.
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1997. Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion.. Proceedings of the National Academy of Sciences of the United States of America. 94(23):12258-62.
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1997. Importance of parenchymal:stromal cell ratio for the ex vivo reconstitution of human hematopoiesis.. Stem cells (Dayton, Ohio). 15(4):305-13.
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1997. Moloney murine leukemia virus-derived retroviral vectors decay intracellularly with a half-life in the range of 5.5 to 7.5 hours.. Journal of virology. 71(10):7541-8.
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1997. What lies beyond bioinformatics? Nature biotechnology. 15(1):3-4.
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1996. Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.. Biotechnology and bioengineering. 50(5):479-92.
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1996. Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.. Human gene therapy. 7(6):743-50.
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1996. Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design.. Annals of biomedical engineering. 24(3):373-81.
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1996. Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions.. Biotechnology and bioengineering. 50(5):505-13.
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1996. Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.. Experimental hematology. 24(5):597-604.
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1996. flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion.. Journal of hematotherapy. 5(5):449-59.
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1996. Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses.. Journal of theoretical biology. 182(1):1-20.
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1996. Membrane adsorption characteristics determine the kinetics of flow-through transductions.. Biotechnology and bioengineering. 51(3):260-70.
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1996. Retroviral infection is limited by Brownian motion.. Human gene therapy. 7(13):1527-34.
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1996. Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data.. Biotechnology and bioengineering. 52(1):24-33.
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1995. Bioreactor expansion of human bone marrow: comparison of unprocessed, density-separated, and CD34-enriched cells.. Journal of hematotherapy. 4(3):159-69.
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1995. Growth factor consumption and production in perfusion cultures of human bone marrow correlate with specific cell production.. Experimental hematology. 23(12):1275-83.
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1995. In vitro expansion of hematopoietic cells for clinical application.. Cancer treatment and research. 76:215-23.
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1995. Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects.. Blood. 86(5):1784-93.
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1995. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism.. Biotechnology and bioengineering. 45(1):69-79.
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1995. Retroviral-mediated gene transfer in human bone marrow cells growth in continuous perfusion culture vessels.. Blood. 86(10):3754-62.
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1994. Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific.. Cytotechnology. 16(1):1-15.
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1994. Frequent harvesting from perfused bone marrow cultures results in increased overall cell and progenitor expansion.. Biotechnology and bioengineering. 44(5):609-16.
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1994. High-density algal photobioreactors using light-emitting diodes.. Biotechnology and bioengineering. 44(10):1161-7.
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1994. Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells.. Biotechnology and bioengineering. 43(8):734-9.
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1994. Monoclonal antibody production using free-suspended and entrapped hybridoma cells.. Biotechnology & genetic engineering reviews. 12:509-33.
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1994. Predictions for oxygen supply control to enhance population stability of engineered production strains.. Biotechnology and bioengineering. 43(4):275-85.
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1994. Preface. Tissue engineering and cell therapies.. Biotechnology and bioengineering. 43(7):541.
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1994. Preface: Tissue engineering and cell therapies: II.. Biotechnology and bioengineering. 43(8):683.
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1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.. Applied and environmental microbiology. 60(10):3724-31.
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1993. Biochemical production capabilities of Escherichia coli.. Biotechnology and bioengineering. 42(1):59-73.
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1993. Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells.. Biotechnology and bioengineering. 41(3):330-40.
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1993. Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system.. Bio/technology (Nature Publishing Company). 11(3):368-72.
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1993. Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures.. Blood. 82(2):378-84.
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1993. Loss of antibody productivity is highly reproducible in multiple hybridoma subclones.. Biotechnology and bioengineering. 42(2):247-50.
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1993. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.. Journal of theoretical biology. 165(4):477-502.
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1993. Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients.. Journal of theoretical biology. 161(3):299-315.
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1993. Review: tissue engineering: reconstitution of human hematopoiesis ex vivo.. Biotechnology and bioengineering. 42(8):909-30.
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1993. Simultaneous determination of ammonia nitrogen and L-glutamine in bioreactor media using flow injection.. The Analyst. 118(11):1361-5.
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1993. Simultaneous enzymatic/electrochemical determination of glucose and L-glutamine in hybridoma media by flow-injection analysis.. Biotechnology and bioengineering. 41(10):964-9.
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1993. Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads.. Biotechnology and bioengineering. 42(9):1131-5.
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1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.. Applied and environmental microbiology. 59(8):2465-73.
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1992. Continuous photoautotrophic cultures of the eukaryotic alga Chlorella vulgaris can exhibit stable oscillatory dynamics.. Biotechnology and bioengineering. 39(5):487-97.
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1992. A Macintosh software package for simulation of human red blood cell metabolism.. Computer methods and programs in biomedicine. 38(4):195-226.
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1992. Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods.. Journal of theoretical biology. 155(2):201-14.
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1992. Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.. Journal of theoretical biology. 155(2):215-42.
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1992. Replication of mini-F plasmids during the bacterial division cycle.. Research in microbiology. 143(6):541-8.
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1992. Replication of prophage P1 is cell-cycle specific.. Journal of bacteriology. 174(13):4457-62.
