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Table of contents

IEEE Trans. Neural Netw. Blake, W. Noise in eukaryotic gene expression. Bleris, L. Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Bloom, J. In the light of directed evolution: pathways of adaptive protein evolution. Bonnet, E. BiNoM 2. BMC Syst. Bowsher, C.

Journal of Integrative Bioinformatics

Stochastic kinetic models: dynamic independence, modularity and graphs. Buetow, K. Science , — Canton, B. Refinement and standardization of synthetic biological parts and devices. Carothers, J. Model-driven engineering of RNA devices to quantitatively program gene expression.

Chandran, D. Mathematical modeling and synthetic biology. Drug Discov. Today Dis. Models 5, — Chen, B. Robust design of biological circuits: evolutionary systems biology approach. Cheng, T. Moore's law meets the life sciences. IEEE Des. Test Comput. Chopra, P. Engineering life through synthetic biology.

In Silico Biol. Chung, K. Automated on-chip rapid microscopy, phenotyping and sorting of C. Methods 5, — Ellis, T. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Elowitz, M. A synthetic oscillatory network of transcriptional regulators. Stochastic gene expression in a single cell.

Endler, L. Designing and encoding models for synthetic biology. Interface 6, S—S Endy, D. Foundations for engineering biology. Feret, J. Internal coarse-graining of molecular systems. Gahan, P. Life: the science of biology 7th edn W. Purves, D. Sadava, G. Orians and H. Heller, W. Freeman and Co, pp. Cell Biochem. Gardner, T. Construction of a genetic toggle switch in Escherichia coli. Gersbach, C. Genetic engineering for skeletal regenerative medicine. Gibson, D. Creation of a bacterial cell controlled by a chemically synthesized genome. Science , 52— Gillespie, D.

Stochastic simulation of chemical kinetics.

About synthetic and systems biology

Haeuptle, M. Effect of cell shape change on the function and differentiation of rabbit mammary cells in culture. Cell Biol. Hallinan, J. Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. IEEE Eng. Harold, F. Biochemical topology: from vectorial metabolism to morphogenesis.

Hooshangi, S. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Hornung, G. Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput. Huang, S. Deisboeck and J. Kresh Springer , — Jeong, H. Lethality and centrality in protein networks. Nature , 41— The large-scale organization of metabolic networks. Kardas, D. Computational model for the cell-mechanical response of the osteocyte cytoskeleton based on self-stabilizing tensegrity structures. Karr, J. A whole-cell computational model predicts phenotype from genotype.

Cell , — Kestler, H. From individual Wnt pathways towards a Wnt signalling network. B Biol. Khalil, A. Synthetic biology: applications come of age. Kitano, H. Foundations of Systems Biology. Systems biology: a brief overview. Computational systems biology.

Klann, M. Spatial simulations in systems biology: from molecules to cells. Kobayashi, H. Araki, M. Programmable cells: interfacing natural and engineered gene networks. Kramer, B. An engineered epigenetic transgene switch in mammalian cells. Kwok, R. Five hard truths for synthetic biology. Nature , Lee, H. Spatial organization of enzymes for metabolic engineering. Liou, S. Cellular ability to sense spatial gradients in the presence of multiple competitive ligands.

E Stat. Soft Matter Phys. Long, B. Lu, T. Next-generation synthetic gene networks. Luengo-Oroz, M. ISBI Ma'ayan, A. Toward predictive models of mammalian cells. Marcotte, E. The path not taken. Michelotti, N. Beyond DNA origami: a look on the bright future of nucleic acid nanotechnology. Miller, M. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity.

Mitchell, M. An Introduction to Genetic Algorithms. Mobashir, M. Simulated evolution of signal transduction networks. Mukherji, S. Synthetic biology: understanding biological design from synthetic circuits. Neumann, H. Synthetic biology approaches in drug discovery and pharmaceutical biotechnology. Nevozhay, D. Transferring a synthetic gene circuit from yeast to mammalian cells. Ozbudak, E. Regulation of noise in the expression of a single gene. Pedraza, J. Noise propagation in gene networks. Science , Pe'er, D. Bayesian network analysis of signaling networks: a primer.

STKE pl4. Pfaendtner, J. Pothen, J. The inflammatory twitch as a general strategy for controlling the host response. Purnick, P. The second wave of synthetic biology: from modules to systems. Qutub, A. Multiscale models of angiogenesis: integration of molecular mechanisms with cell- and organ-level models. Rapaport, D. The Art of Molecular Dynamics Simulation. Ro, D. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Roze, L. Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes. Fungal Genet.

Ruder, W. Synthetic biology moving into the clinic. Ryan, D.

Scarselli, F. Computational capabilities of graph neural networks. Schaller, G. Multicellular tumor spheroid in an off-lattice Voronoi-Delaunay cell model. Singhvi, R. Effects of substratum morphology on cell physiology. Slusarczyk, A. Foundations for the design and implementation of synthetic genetic circuits. Smolke, C.

Informing biological design by integration of systems and synthetic biology. Song, H. Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Sozzani, R. High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype. Spicher, A. Dubitzky, J. Southgate, and H. Stricker, J. A fast, robust and tunable synthetic gene oscillator. Tabor, J. A synthetic genetic edge detection program. Cell , Takahashi, K. Space in systems biology of signaling pathways—towards intracellular molecular crowding in silico. FEBS Lett. Tanaka, H.

Synthetic morphology using alternative inputs. Thattai, M. Intrinsic noise in gene regulatory networks. Vendruscolo, M. Protein dynamics: Moore's law in molecular biology. Walker, D. The modulatory effect of cell—cell contact on the tumourigenic potential of pre-malignant epithelial cells: a computational exploration. Interface 10, 1— Wang, B. Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology.

Wang, Z. Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model. Benders, Michael G. Montague, Li Ma, Monzia M.

Primary Sidebar

Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Smith, and J. Craig Venter. A13 Engineering Scalable Biological Systems. A14 Metabolic Systems Biology. A15 Systems Vaccinology. Helder I. Nakaya, Jens Wrammert, Eva K. Nicholas Haining, Anthony R. Means, Sudhir P. A22 The Silicon Trypanosome. Barbara M. Bakker, R. Westerhoff , Paul A. Michels, Ranier Breitling, and Michael P. B Agenda. C Acronyms. D Glossary. E Forum Member Biographies.

F Speaker Biographies. WO Self-sustained amplification of a population of cross-replicating RNA enzymes, resulting in selection of the fittest replicators. WO Is it alive? WO Phases and data used to generate a metabolic reconstruction. WO Schematic for theoretical construction of a generic vaccine chip. WO A framework for systems vaccinology. WO Adoptive T-cell immunotherapy. WO Clinical trial timeline on patient 5. WO The effectiveness of T-cells based upon their functionality is reflected in this analogy. WO Gyrase inhibitors induce an oxidative damage cellular death pathway.

WO A common mechanism induced by bactericidal antibiotics. WO Overview of steps in making a cell controlled by a synthetic genome. WO Targeting bacterial defense networks. WO A simple biofilm biosensor. A Understanding the mechanism of uncultivability.


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A A high-throughput screen for antimicrobials in an animal model. Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, , the Institute of Medicine's IOM's Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases.

The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants.

Computational Systems Biology – Laboratory of Systems and Synthetic Biology

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