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Course New to be offered Spring 2004 Instructor: Baltazar D. Aguda Title: Mechanisms and Models of Cellular Regulation Course Number: BE700 Course catalog description: Regulatory and control processes in cells are presented from a genetic and biochemical network perspective. Systems analysis of networks include logical (Boolean), deterministic (differential equations), and stochastic approaches. Case studies of gene regulatory networks as well as metabolic, signaling, cell survival, proliferation and death pathways are discussed. Existing modeling platforms of systems biology and bioinformatic pathways databases are introduced. Specific teaching goals: A primary goal of this course is to provide students with an integrated view of the regulatory and control mechanisms in a biological cell at the genetic and biochemical levels. This integration is essential for students in engineering and bioinformatics to appreciate the meaning and implications of the exploding fields of genomics, proteomics and other high-throughput data-generating technologies. The systems viewpoint emphasized in this course requires a sufficient overview of the molecular biology of the cell a requirement that will be carefully provided by the instructor. The coverage of this course is admittedly quite broad and the instructor should be aware of the danger that students could be swamped with biological details and end up not learning concrete or tangible research tools. The instructor will emphasize basic and well-developed modeling tools (mathematical and computational) for analyzing complex regulatory networks in general, as well as identify research areas that are still open for development. After sufficient introduction of the various cellular processes covered in this course, a case-study teaching approach (using examples from the recent literature) will be adopted so that students are exposed to the details and rigor of modeling complex systems. An important goal of this course is to make students aware of the existing and rapidly accumulating bioinformatics and systems biology resources, as well as biotechnological trends. Thus, an important component of this course is a set of invited lectures given by active researchers in the field (see syllabus). Syllabus: Week 1: Basic cell biology & levels of cellular regulation The cell as a unit of life: components and cell architecture Unicellular versus multicellular organisms What are the essential cellular processes? The big picture of what is covered in this course: gene expression, metabolism, signaling, cell division, cell death Levels in the complexity of gene expression: an overview of the basics The central dogma: DNA, RNA, proteins Transcription, RNA processing, translation, post-translational processes Week 2: Gene structure & transcription control elements Genetics, genomics Gene structure and regulatory elements Examples of prokaryotic and eukaryotic genomes Bioinformatics resources Weeks 3: Gene regulatory networks (GRNs) The fim genetic switch in E. coli illustrating the dynamic nature of the genome The bacteriophage lysis/lysogeny switch Operons, regulons, stimulons Transcriptional network in S. cerevisiae Weeks 4-6: Mathematical modeling and computer simulation of GRNs Boolean networks, generalized logical networks Nonlinear ordinary differential equations Qualitative differential equations Stochastic master equations Network analysis: stability, bifurcations Week 7-8: Engineering & control of GRNs Perturbation of GRNs: gene knock-outs/knock-ins, chemical genetics, RNAi Guest lecturer: try to invite Prof. S. Schreiber of Harvard (chemical genetics) Designer gene networks Guest lecturer: try to invite Prof. J. Collins of BU Week 9: Metabolic networks Overview of metabolism in cells, metabolic map of E. coli Metabolic control analysis Metabolic engineering Guest lecturer: try to invite Prof. Stephanopoulos of MIT Week 10: Signal transduction pathways Receptor tyrosine kinases, G-protein coupled receptors Ultrasensitivity in the MAP kinase cascade Proliferative, survival and death pathways Guest lecturer: try to invite Prof. Lauffenburger of MIT Week 11: Cell division and death (apoptosis) Models of the yeast cell cycle Checkpoints in the mammalian cell cycle Modeling apoptosis Week 12: Platforms of Systems Biology Whole-cell modeling computer software: E-Cell, Virtual SBW/SBML(Caltech) Cell, Pathways database systems Institutes of Systems Biology Week 13: Pathway inference & pathways databases Reverse engineering from microarray gene expression data analysis Bayesian networks Pathways databases: KEGG, PathDB, EcoCyc, BIND, etc. Guest lecturers: TBA Week 14: Biotechnology trends Proteomics, mass spectrometry, the omics industry Guest lecturer: try to invite Dr. Stephen Naylor of Beyond Genomics Week 15: Course summary (1 lecture) Grading System: One term paper/project Homework assignments One midterm exam Final exam 30% 20% 20% 30% Target audience & Pre-requisites: Graduate students in BME, Bioinformatics; ordinary differential equations and at least one course in computer programming. Representative References: Aguda BD. Instabilities in phosphorylation-dephosphorylation cascades and cell cycle checkpoints. Oncogene. 1999 May 6;18(18):2846-51. Asthagiri A, Lauffenburger D. Bioengineering Models of Cell Signaling. Annual Review of Biomedical Engineering, 2:31-53, 2000. Bolouri H, Davidson EH. (2002) Modeling transcriptional regulatory networks , BioEssays 24: 11181129. Bower JM, Bolouri H (Eds.) Computational modeling of genetic and biochemical networks (Computational molecular biology). MIT Press, 2001. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell. 2000 Jan;11(1):369-91. De Jong H. (2002) Modeling and simulation of genetic regulatory systems: A literature review , J. Computational Biology 9: 67-103. Deutsch A (Ed.) Function and regulation of cellular systems: Experiments and models (Mathematics and Biosciences in interaction). Birkhauser (Architectural), August 2003. ISBN 3764369256 Fussenegger M, Bailey JE, Varner J. A mathematical model of caspase function in apoptosis. Nat Biotechnol. 2000 Jul;18(7):768-74. Erratum in: Nat Biotechnol 2001 Feb;19(2):173. Comment in: Nat Biotechnol. 2000 Jul;18(7):717-8. Gilman A, Arkin AP. (2002) Genetic Code : Representations and dynamical models of genetic components and networks , Annu. Rev. Genomics Hum. Genet. 3:341-369. Hasty J, McMillen D, Isaacs F, Collins JJ. (2001) Computational studies of gene regulatory networks: in numero molecular biology , Nature Reviews Genetics 2: 268-279. Hasty J, McMillen D, Collins JJ. (2002) Engineered Gene Circuits , Nature 420: 224-230. Heinrich R, Schuster S. The regulation of cellular systems. Chapman & Hall, 1996. Ideker T, Galitski T, Hood L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2: 343-72. Koffas M, Roberge C, Lee K, Stephanopoulos G. (1999) Metabolic engineering , Annu. Rev. Biomed. Eng. 1: 535-57. Kohane IS, Kho A, Butte AJ. Microarrays for an integrative genomics (Computational molecular biology). MIT Press, 2002. ISBN 026211271X. McAdams HH, Arkin A. (1998) Simulation of prokaryotic genetic circuits . Annu. Rev. Biophys. Biomol. Struct. 27: 199-224. McAdams HH, Arkin A. (2000) Towards a circuit engineering discipline . Curr. Biol. 10: R318-20. Ouzounis CA, Karp PD. (2000) Global properties of the metabolic map of Escherichia coli. Genome Res. 2000: 568-678. Palsson B. (2000) The challenges of in silico biology. Nat. Biotechnol. 18: 1147-50. Ptashne M. A Genetic Switch Phage Lambda and Higher Organisms. 2nd Ed. Cell Press & Blackwell Scientific Publications, c1986. Ptashne M, Gann A. Genes & Signals. Cold Spring Harbor Lab Press, c2002. Rao CV, Arkin AP. (2001) Control motifs for intracellular regulatory networks. Annu. Rev. Biomed. Eng. 3: 391-419. Schilling C, S. Schuster, B. Palsson and R. Heinrich. Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era. Biotechnology Progress, 15:296-303, 1999. Smolen P, Baxter DA, Byrne JH. (2000) Modeling transcriptional control in gene networks methods, recent results, and future directions. Bull. Math. Biol. 62: 247-92. Torres NV, Voit EO. Pathway analysis and optimization in metabolic engineering. Cambridge U.P., 2002. Tomita M, Hashimoto K, Takahashi K, Simizu TS,Matsuzaki Y et al. (1999) E-CELL: software environment for whole-cell simulation , Bioinformatics 15: 72-84. Tyson JJ, Csikasz-Nagy A, Novak B. The dynamics of cell cycle regulation. Bioessays. 2002 Dec;24(12):1095-109.

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