Welcome to the Synthetic Biology Journal Club page.

Meetings for the 2010 Summer Quarter will be held every Friday from 1:30-2:30pm in Foege N303.

Below are the synthetic biology papers we will discuss each week and the person who chose the paper. Please email Ryan if you have questions.

If you can't make a schedule you must let Ryan or Herbert know. There may be adjustments made to the schedule depending on whether the person is in Seattle or whether it is a holiday. If someone hasn't been added but would like to have a slot email Sean or Herbert.

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

Simple molecular networks that respond optimally to time-periodic stimulation

Measuring the Activity of BioBrick Promoters Using an In Vivo Reference Standard

To save Sean some effort we are gong to change the way Journal club works. For now, the table at the end of this page will indicate who's responsibility it is to choose and present a journal club paper. In addition, papers will be considered every three weeks of the month and on the forth week, the selected person will instead choose and discuss a method of interest, this can be a computational or experimental method used in synthetic or systems biology. See the table at the end of the page for details.

June 18 - Programming cells by multiplex genome engineering and accelerated evolution (Sean)

June 11 - Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks (Bryan)

June 4 - Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors (Ryan)

May 28 - Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expressionControl of stochasticity in eukaryotic gene expressionPhenotypic consequences of promoter-mediated transcriptional noise (Kyung)

May 21 - Reprogramming bacteria to seek and destroy an herbicide (Will)

May 7 - Synthesis of Methyl Halides from Biomass Using Engineered Microbes (Sean)

Apr 23 - BioPAX (Michal)

Apr 16 - Estimating the Stochastic Bifurcation Structure of Cellular Networks (Deepak)

Apr 9 - A synthetic low-frequency mammalian oscillator (Ryan)

Apr 2 - Microbial production of fatty-acid-derived fuels and chemicals from plant biomass (Bryan)

Mar 12 - Beyond directed evolution: Darwinian selection as a tool for synthetic biology (Jeff)

Mar 5 - Standard Virtual Biological Parts: A Repository of Modular Modeling Components for Synthetic Biology (Lucian)

Feb 26 - Growth Rate-Dependent Global Effects on Gene Expression in Bacteria (Will)

Feb 19 - Next-generation synthetic gene networks (Song)

Feb 5 - Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter (Ryan)

Jan 29 - A “crash course” in multivariate statistics, principal components analysis and Fisher discriminants (Deepak)

Jan 22 - Signal Differentiation by Differential Regulation of Protein Stability in Quorum Sensing (Bryan)

Dec 18 - Slow growth leads to a switch and Emergent bistability by a growth-modulating positive feedback circuit (Deepak)

Dec 11 - Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits (Mike)

Dec 4 - Review of interesting iGEM projects (Sean)

Nov 20 - Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast (Ryan)

Nov 13 - Engineering the Salmonella type III secretion system to export spider silk monomers (Kyung)

Nov 6 - Microfluidic devices for measuring gene network dynamics in single cells (Will)

Oct 23 - Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture (Deepak)

June 5 - (Lucian)

May 29 - Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise (Brian)

May 14 - Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3 (Song)

May 1 - Diversity-based, model-guided construction of synthetic gene networks with predicted functions

April 17 - Lessons from the DREAM2 Challenges (Frank)

March 19 - Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination (Austin)

March 12 - Presentation of ChIP-chip analysis (Will)

March 5 - Higher-Order Cellular Information Processing with Synthetic RNA Devices (Alec)

February 26 - A tunable synthetic mammalian oscillator (Song)

February 19 - (Paper 1) Environment-specific combinatorial cis-regulation in synthetic promoters (Deepak)

February 19 - (Paper 2) Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures (Deepak)

February 5 - Self-Sustained Replication of an RNA Enzyme (Bryan)

January 29 - (Paper 1) A genetically encoded fluorescent reporter of ATP:ADP ratio (James)

January 29 - (Paper 2) Understanding the Dynamic Behavior of Genetic Regulatory Networks by Functional Decomposition (Herbert)

January 22 - Toward scalable parts families for predictable design of biological circuits (Mike)

January 8 - Multistable Decision Switches for Flexible Control of Epigenetic Differentiation (Deepak)

December 12 -

Top 3 and Peking iGEM 2008 Projects

#1 Slovenia - Immunobricks

#2 Freiburg - Modular Synthetic Receptor System

#3 Caltech - Engineering multi-functional probiotic bacteria

Peking - A Genetic Circuit for Directed Evolution in vivo

November 21 - Adaptive Response of a Gene Network to Environmental Changes by Fitness-Induced Attractor Selection (Sean)

November 14 - A fast, robust and tunable synthetic gene oscillator (Sean)

November 4 - Effects of topology on network evolution (Deepak)

October 31 - (Paper 1) Probing transcription factor dynamics at the single-molecule level in a living cell (Kyung)

October 31 - (Paper 2) A stochastic single-molecule event triggers phenotype switching of a bacterial cell (Kyung)

September 25 - Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops (Kyung)

September 18 - (Paper 1) Protein engineering: The fate of fingers (Mike)

September 18 - (Paper 2) Rapid "Open-Source" Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification (Mike)

September 11 - (Paper 1) A strategy for increasing an in vivo flux by genetic manipulations. The tryptophan system of yeast (Herbert)

September 11 - (Paper 2) Dynamics and Design Principles of a Basic Regulatory Architecture Controlling Metabolic Pathways (Herbert)

September 4 - Construction of a genetic toggle switch in Escherichia coli (Sean)

August 28 - Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat (Sean)

August 21 - Programming gene expression with combinatorial promoters (Sean)

July 31 - (Paper 1) Targeted Development of Registries of Biological Parts (Param)

July 31 - (Paper 2) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts (Param)

July 24 - Refinement and standardization of synthetic biological parts and devices (Sean)

July 17 - (Paper 1) Asmparts: assembly of biological model parts (Alex)

July 17 - (Paper 2) Computational design of digital and memory biological devices (Alex)

July 10 - (Paper 1) Gene synthesis by circular assembly amplification (Deepak)

July 10 - (Paper 2) Recursive construction of perfect DNA molecules from imperfect oligonucleotides (Deepak)

June 26 - Gene network shaping of inherent noise spectra (Kyung)

June 13 - Engineering BioBrick vectors from BioBrick parts (Sean)

June 6 - TABASCO: A single molecule, base-pair resolved gene expression simulator (Deepak)

May 30 - Construction of an in vitro bistable circuit from synthetic transcriptional switches (Josh)

May 23 (Paper 1) - Genetdes: automatic design of transcriptional networks (Deepak)

May 23 (Paper 2) - Deriving structure from evolution: metazoan segmentation (Deepak)

May 16 - Evolvability and hierarchy in rewired bacterial gene networks (Mike)

May 9 - Discussion on BioBrick measurement kits (Sean and Ingrid)

May 2 - Darwinian Evolution on a Chip (Herbert)

April 18 - Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics (Dan)

April 11 - A synthetic oscillatory network of transcriptional regulators (Sean)

For those of you with little or no background in molecular biology and genetics, or want a quick refresher in these subjects, check out excerpts from The Cartoon Guide to Genetics below.

Cartoon Guide to Genetics, Part 1

Cartoon Guide to Genetics, Part 2

Biostudio animations

Molecular Movies

Adventures in synthetic biology (comic)

Foundations for engineering biology

Synthetic biology: new engineering rules for an emerging discipline

Reconstruction of Genetic Circuits

Genetic Parts To Program Bacteria

Design of Gene Circuits: Lessons from Bacteria