To Build a Microbial Factory: Investment Cost and Operating Cost Analysis of Metabolic Networks
Ross P. Carlson, Chemical and Biological Engineering, Montana State University, 315 Cobleigh Hall, Bozeman, MT 59717 |
Optimization of Stochastically-Simulated Gene Network Models
Jonathan R. Tomshine, Chemical Engineering and Materials Science, University of Minnesota -- Minneapolis, 421 Washington Ave SE, Box 78, Minneapolis, MN 55455 and Yiannis N. Kaznessis, Chemical Engineering. and Materials. Science, University of Minnesota, 499, Walter Library, 117, Pleasant St. SE, Minneapolis, MN 55455 |
How External Electrical Stimuli Can Act at Cellular Level in an in Vitro Culture: Mathematical Model and Experimental Analysis
Marina Flaibani and Nicola Elvassore, Department of Chemical Engeneering, University of Padova, via Marzolo, 9, Padova, 35131, Italy |
A Quantitative Model of Error Accumulation during Pcr Amplification with Application to Gene Synthesis
Hendrik J. Viljoen1, Elsje Pienaar1, Theresa Schinko2 and Reingard Grabherr2, (1)chemical engineering, University of Nebraska, 211 Othmer Hall, Lincoln, NE 68588, (2)Institut für Angewandte Mikrobiologie, Universitat für Bodenkultur, Vienna, Austria |
Studying the Mechanism of Transcriptional Regulation of Mesenchymal Stem Cell Proliferation and Differentiation
Linxia Zhang1, Tim Howes1, Neil Wright2 and Christina Chan1, (1)Chemical Engineering and Material Science, Michigan State University, 2527 Engineering Building, East Lansing, MI 48824, (2)Mechanical Engineering, Michigan State University, 2555 Engineering Building, East Lansing, MI 48824 |
Reverse Engineering of an Erythromycin Overproducing Strain
Chinping Chng, Amy M. Lum, Jonathan Vroom and Camilla M. Kao, Chemical Engineering, Stanford University, 381North-South Mall, Stanford, CA 94305 |
Simulation of Directed Evolution Experiments
Enrique T. Munoz, Rice University, 6100 Main St - MS 142, Houston, TX 77005-1892, Michael W. Deem, Bioengineering, Rice University, 6100 Main St - MS 142, Houston, TX 77005-1892 and K. Dane Wittrup, Chemical Engineering; Biological Engineering, MIT, Cambridge, MA 02139 |
Gene Expression Profiling of 3t3-L1 Adipocytes Expressing the Mitochondrial Uncoupling Protein 1
Fatih Senocak, Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX 77843, Yaguang Si, Biology, Tufts University, 4 Colby Street, Medford, MA 02155, Kyongbum Lee, Tufts University, 4 Colby Street, Room 142, Medford, MA 02155, U.S.A. and Arul Jayaraman, Department of Chemical Engineering,, Texas A& M University, College Station, TX 77843-3122 |
Complex Systems Analysis and Mathematical Modeling of Insulin Resistance in Skeletal Muscle Cells and the Impact of Plasma Free Fatty Acids
Baris U. Agar1, Ali Cinar1, Emmanuel C. Opara2 and Gary Reznik3, (1)Department of Chemical and Environmental Engineering, Illinois Institute of Technology, 10 W. 33rd Street, Chicago, IL 60616, (2)Department of Biomedical Engineering, Illinois Institute of Technology, 10 W. 32nd Street, Chicago, IL 60616, (3)Microbiology and Immunology Division, Illinois Institute of Technology Research Institute (IITRI), 10 W. 35th Street, Chicago, IL 60616 |
Combinatorial Engineering of Intergenic Regions to Tune Expression of Multiple Genes in Operons
Brian Pfleger1, Doug Pitera1, Christina Smolke2 and Jay D. Keasling1, (1)Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, (2)Chemistry & Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, MC 210-41, Pasadena, CA 91125 |
Identification of Succinic Acid Tolerance Genes in E.Coli
Amarjeet Singh, Chemical & Biological Engineering, University of Colorado at Boulder, 1111 Engineering Drive, Campus Box 424, Boulder, CO 80309 and Ryan T. Gill, Department of Chemical and Biological Engineering, University of Colorado, ECCH 111 Campus Box 424, Boulder, CO 80309 |
Genome-Wide Transcriptional Response of Staphylococcus Aureus to Hypochlorite-Induced Oxidative Stress
Wook Chang, Center for Biosystems Research, University of Maryland Biotechnology Institute, 701 Mapes Rd, Ft. Meade, MD 20755, Freshteh Toghrol, Office of Pesticide Programs, U.S. Environmental Protection Agency, 701 Mapes Rd, Ft. Meade, MD 20755 and William E. Bentley, Center for Biosystems Research, University of Maryland Biotechnology Institute, 6143 Plant Science Bldg, College Park, MD 20742 |
Optimal Combinatorial Library Design from a Computational Complexity Perspective
Wei Xie, Chemical and Biomolecular Engineering, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 and Nick Sahinidis, University of Illinois, Department of Chemical and Biomolecular Engineering, 600 South Mathews Avenue, Urbana, IL 61801 |
Control of Cell Growth and Glucose Uptake Rates by Controlled Expression of Phosphofructokinase (Pfk) in B. Subtilis
Zhiwei Pan1, Tao Zhu2, Richard Koepsel3, Michael Domach4 and Mohammad Ataai3, (1)Chemical and Petroluem Engineering, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, (2)Carnegie Mellon Univ., 5000 Forbes Ave., Pittsburgh, PA 15213, (3)Chemical and Petroleum Engineering, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, (4)Chemical Engineering, Carnegie Mellon University, 700 TECHNOLOGY DRIVE, Pittsburgh, PA 15219 |
Selections from Screens: a Novel Tool for the Selection of Overproducers
Michael D. Lynch, University of Colorado, ECCH 111, Campus Box 424, Boulder, CO 80309, Tirzah Ya'el Mills, Chemical Engineering, West Virginia University, 956 Ashton Place, Morgantown, WV 26508 and Ryan T. Gill, Department of Chemical and Biological Engineering, University of Colorado, Campus Box 424, Boulder, CO 80309 |
Setting up a High Throughput Screening Facility as Part of the Academic Experience
Parag P. Shah and Scott L. Diamond, Chemical and Biomolecular Engineering, University of Pennsylvania, 3340 Smith Walk, 1150 Vagelos Labs, Philadelphia, PA 19104 |
Regulating Phenotypic Variations Using Integrated Flux and Energy Balance Analysis Based Multiobjective Framework
Deepak Nagrath1, Marco Avila1, Francois Berthiaume2 and Martin L. Yarmush3, (1)Massachusetts General Hospital/Shriners Burn Hospital/Harvard Medical School, 51 Blossom Street, Boston, MA 02114, (2)Center for Engineering in Medicine, Harvard Medical School, 51 Blossom St, Boston, MA 02114, (3)Center for Engineering in Medicine, 51 Blossom Street, Boston, MA 02114 |
Usefulness of Rnase III Cleavage Sites for Tuning Relative Gene Expression
Wesley D. Marner II, University of California, Berkeley, 201 Gilman Hall, Berkeley, CA 94720, Brian Pfleger, University of California, Berkeley, Berkeley, CA 94720 and Jay D. Keasling, Department of Chemical Engineering, University of California, Berkeley, 201 Gilman Hall, Berkeley, CA 94720 |
Real-Time Detection of Tca Cycle Anaplerosis in Human Glioma Cells with 13c NMR Spectroscopy
Anthony Mancuso, Ralph J. Deberardinis and Craig B. Thompson, Cancer Biology, University of Pennsylvania, Room 445, BRB II/III, Philadelphia, PA 19104 |
Translational Coupling and Regulation in Prokaryotic Operons
Lon Chubiz, Chemical and Biomolecular Engineering, University of Illinois, 600 South Matthews Ave., 211 Roger Adams Laboratory, Box C-3, Urbana, IL 61801 and Christopher V. Rao, Department of Chemical and Biomolecular Engineering, University of Illinois, 600 South Matthews Ave., 211 Roger Adams Laboratory, Box C-3, Urbana, IL 61801 |
Quantifying the Metabolic Capabilities of Engineered Zymomonas Mobilis for Ethanol Production from Hexoses and Pentoses Using Linear Programming Analysis
Ivi C. Tsantili, Faculty of Mathematics, School of Applied Mathematics & Physical Sciences (S.A.M.P.S),, National Technical University of Athens (N.T.U.A), Zografou Campus, Athens, Greece, M. Nazmul Karim, Chemical Engineering Department, Texas Tech University, Lubbock, TX 79409-3121 and Maria I. Klapa, Institute of Chemical Engineering and High-Temperature Chemical Processes (ICEHT), Foundation for Research and Technology-Hellas (FORTH), PATRAS, Greece |
Genomic-Based Identification of the Sporulation Restoring Gene in Degenerate Clostridium Acetobutylicum Strains
Bryan P. Tracy, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 and Eleftherios T. Papoutsakis, Chemical and Biological Engineering, Northwestern University, 2145 N. Sheridan Rd., Tech E136, Evanston, IL 60208 |
Magnetically Driven Mixing within a Microarray Geometry Using Functionalized Magnetic Nanoparticles
Sandip Agarwal and Paul E. Laibinis, Rice University, 6100 S. Main Street, Houston, TX 77005 |
Nuclear Receptors Based Modulation of Hepatic Lipid and Glucose Metabolism
Deepak Nagrath1, Yoko Tanimura1, Hongzhi Xu1, Francois Berthiaume2 and Martin L. Yarmush3, (1)Massachusetts General Hospital/Shriners Burn Hospital/Harvard Medical School, 51 Blossom Street, Boston, MA 02114, (2)Center for Engineering in Medicine, Harvard Medical School, 51 Blossom St, Boston, MA 02114, (3)Harvard Medical School, Center for Engineering in Medicine, Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114 |
Biosynthesis of Lovastatin in a Heterologous Host
Suzanne M. Ma, Xinkai Xie, Wladyslaw A. Wojcicki and Yi Tang, Chemical and BioMolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095 |
“Retrobiosyntethic” Design for the Microbial Production of an Organic Compound
Collin Martin and Kristala Jones Prather, Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Room 66-458, Cambridge, MA 02139 |
Significance Analysis of Time-Series High-Throughput Transcriptional Profiling Data: Applied to Arabidopsis Thaliana Liquid Cultures Subjected to Environmental Stresses
Bhaskar Dutta1, Robert W. Snyder2 and Maria I. Klapa1, (1)University of Maryland, 2113 Chemical and Nuclear Engineering Building, College Park, MD 20742-2111, (2)Department of Chemical and Biomolecular Engineering, University of Maryland College Park, College Park, MD 20742 |
Design of Isotope Labeling Experiments for Metabolic Flux Analysis in Escherichia Coli under Anaerobic Condition
Madhuresh Choudhary, Chemical and Biological Engineering, Iowa State University, 2114 Sweeney Hall, Ames, IA 50011, Yandi Dharmadi, Chemical and Biomolecular Engineering, Rice University, Houston, TX 77251-1892, Ramon Gonzalez, Chemical and Biomolecular Engineering, Rice University, MS-362, P.O. Box 1892, Houston, TX 77251-1892, Ka-Yiu San, Department of Bioengineering, Rice University, MS-142, PO Box 1892, Houston, TX 77005 and Jacqueline V. Shanks, Chemical and Biological Engineering, Iowa State University, 3031 Sweeney Hall, Iowa State University, Ames, IA 50011 |
Development of a Database Tool for Novel Biosynthetic Pathway Design
Kristala Jones Prather, Amanda Lanza and Wei Chan, Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Room 66-458, Cambridge, MA 02139 |
Data Correction, Normalization and Validation for Enhanced Accuracy of Gc-MS Metabolomic Analysis:
Time Series Metabolomic Analysis of Arabidopsis Thaliana Response to Elevated Co2 a Case Study
Harin H. Kanani and Maria I. Klapa, University of Maryland, 2113 Chemical and Nuclear Engineering Building, College Park, MD 20742-2111 |
User-Controlled Changes in Fluorescence Distribution in Cells with Oscillatory Genetic Network Dynamics
Stephanie Portle, Rice University, Chemical and Biomolecular Engineering Department, Houston, TX 77005, Ka-Yiu San, Department of Bioengineering, Rice University, MS-142, PO Box 1892, Houston, TX 77005, George N. Bennett, Biochemistry and Cell Biology, Rice University, 6100 Main st, Houston, TX 77005 and Nikos Mantzaris, Chemical & Biomolecular Engineering, Rice University, 6100 Main Street MS#362, Houston, TX 77005 |
Escherichia Coli Autoinducer 2 Uptake Is Induced by Intracellular Factors Such as Luxs Transcription Rate but Not Necessarily by the Cell Density: Analysis of the Network Using Bifurcation Analysis and Stochastic Approach
Andres Fernando Gonzalez Barrios, Chemical Engineering, University of Connecticut, Dept. of Chemical Engineering, Unit 3222, 191 Auditorium Road, Storrs, CT 06269 and Luke E. K. Achenie, University of Connecticut, Dept. of Chemical Engineering, Unit 3222, 191 Auditorium Road, Storrs, CT 06269 |
Sensitivity Analysis on Ms2 Viral Dynamics Using Interval Mathematics
Ozlem Yilmaz, University of Connecticut, 191 Auditorium Rd. Unit 3222, Storrs, CT 06269, Luke E. K. Achenie, University of Connecticut, Dept. of Chemical Engineering, Unit 3222, 191 Auditorium Road, Storrs, CT 06269 and Ranjan Srivastava, University of Connecticut, 191 Auditorium Rd., Unit 3222, Storrs, CT 06269 |
Computational and Recombination Based Methods for Directed Evolution
Bernard Loo1, Anshul Dubey2, Karen M. Polizzi2, Javier Chaparro-Riggers3 and Andreas S. Bommarius4, (1)Chemical & Biomolecular Engineering, Georgia Institute of Technology, IBB 3428, 315 Ferst Dr, Atlanta, GA 30332, (2)School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Dr, Atlanta, GA 30332, (3)School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, IBB 3428, 315 Ferst Dr, Atlanta, GA 30332, (4)Chemical & Biomolecular Engineering, Georgia Tech, 315 Ferst Dr, Atlanta, GA 30332-0363 |
A Metabolic Modeling Approach to Optimizing Recombinant Protein Production in L. Lactis Fermentations
Gian M. Oddone, Chemical Engineering, University of California, Davis, Bainer Hall, One Shields Ave, Davis, CA 95616, David A. Mills, Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 and David E. Block, Department of Chemical Engineering and Materials Science and Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 |
Design of Transient Isotopic Labeling Studies for the Experimental Measurement of Autotrophic Metabolic Fluxes
Avantika A. Shastri, Purdue University, 480 Stadium Mall Dr, West Lafayette, IN 47907 and John A. Morgan, School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., 1160 FRNY,, West Lafayette, IN 47907 |
The Bioactivity of Il-12: There's More to the Story Than P70 or P40
David Klinke, Department of Chemical Engineering, West Virginia University, P.O. Box 6102, Morgantown, WV 26506-6102 |
Shotgun DNA Microarray-Based Transcriptional Analysis of the Clostridium Tyrobutyricum Wildtype and Mutants
Yali Zhang1, Xiaoguang Liu2 and Shang-Tian Yang2, (1)The Ohio State Biochemistry Program, The Ohio State University, 140 w. 19th Ave, Columbus, OH 43210, (2)Chemical and Biomolecular Engineering Department, The Ohio State University, 140 w. 19th Ave, Columbus, OH 43210 |
An Age-Structured Model of Dendritic Cell Trafficking in the Lung
David Klinke, Department of Chemical Engineering, West Virginia University, P.O. Box 6102, Morgantown, WV 26506-6102 |
Modeling of Glycolytic Pathway Using in Vitro Kinetics
Haluk Hamamci, Food Engineering, Middle East Technical University, Inonu Bulvari, Ankara, Turkey, Banu Ozturk-Temur, Biotechnology Department, Middle East Technical University, Inonu Bulvari, Ankara, Turkey and A. Palazoglu, Department of Chemical Engineering and Materials Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 |
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