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Synthetic Biology Journal Club

Welcome to the Synthetic Biology Journal Club page.

**Meetings for the 2011 Winter Quarter will be held every Monday from 3:00-4:00pm in Foege N230.

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.

Individual Schedules

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 Ryan or Herbert.

Theme Reviewer
Jan 17 Holiday
Jan 24 Experimental Update Will
Jan 31 Paper Kyung
Feb 7 Paper Deepak
Feb 14 Paper Ryan
Feb 21 Holiday
Feb 28 Autodesk Maya Group Discussion
Mar 7
Mar 14 Paper Timo

Future journal club papers?

Distributed biological computation with multicellular engineered networks

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

BioCoder: A programming language for standardizing and automating biology protocols

Environments that Induce Synthetic Microbial Ecosystems

Watch the clock—engineering biological systems to be on time

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

Design, construction and characterization of a set of insulated bacterial promoters

Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data

Multichromatic Control of Gene Expression in Escherichia coli

Chemical synthesis of the mouse mitochondrial genome

Engineering of a synthetic electron conduit in living cells

PCRless library mutagenesis via oligonucleotide recombination in yeast

Minimal genetic device with multiple tunable functions

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

Cellodextrin Transport in Yeast for Improved Biofuel Production

A General Mechanism for Network-Dosage Compensation in Gene Circuits

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

Fundamental limits on the suppression of molecular fluctuations

Oscillating Gene Expression Determines Competence for Periodic Arabidopsis Root Branching

Functional roles for noise in genetic circuits

Emergent cooperation in microbial metabolism

Reconstruction and flux-balance analysis of thePlasmodium falciparum metabolic network

Bacterial charity work leads to population-wide resistance

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

Programming cells: towards an automated ‘Genetic Compiler’

An engineered mammalian band-pass network

Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

A synthetic three-color scaffold for monitoring genetic regulation and noise

"The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world"

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

Kinetic flux profiling for quantitation of cellular metabolic fluxes

Simulating plant metabolic pathways with enzyme-kinetic models

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

Winter 2009: Changes to Journal Club

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.

Previous Journal Clubs (Archive)

Autumn Quarter 2010

Spring Quarter 2010

Winter Quarter 2010

Fall Quarter 2009

Spring Quarter 2009

Winter Quarter 2009

Fall Quarter 2008

Summer Quarter 2008

Spring Quarter 2008

Useful Synthetic Biology Readings and Links

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

Animations of transcription, translation, etc.

For an introduction to synthetic biology...

Recent synthetic biology reviews

journalclub.txt · Last modified: 2011/03/02 15:25 (external edit)

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