Recent SynBio papers

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Foundations for the design and implementation of synthetic genetic circuits : Abstract : Nature Reviews Genetics
Efficient and sequence-independent ... [Proc Natl Acad Sci U S A. 2012 <p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Sign in to NCBI PubMed US National Library of Medicine National Institutes of Health Efficient and sequence-independent ... [Proc Natl Acad Sci U S A. 2012
Foundations for the design and implementation of synthetic genetic circuits : Abstract : Nature Reviews Genetics
Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012 Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012 <p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p>
Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012
<p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012 Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012
Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Reprogramming the Genetic Code
Synthetic Biology: Mapping the Scientific Landscape Results The Rise of Synthetic Biology As of January 2012 a total of 1,255 publications were listed in Web of Science for synthetic biology and synthetic genomics in the period to the end of December 2011 (Figure 1). Synthetic Biology: Mapping the Scientific Landscape
Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage. Synthetic Genetic Polymers Capable of Heredity and Evolution Synthetic Genetic Polymers Capable of Heredity and Evolution
Synthetic Genetic Polymers Capable of Heredity and Evolution
Abstract Gene expression actualizes the organismal phenotypes encoded within the genome in an environment-dependent manner. Among all encoded phenotypes, cell population growth rate (fitness) is perhaps the most important, since it determines how well-adapted a genotype is in various environments. Traditional biological measurement techniques have revealed the connection between the environment and fitness based on the gene expression mean. Yet, recently it became clear that cells with identical genomes exposed to the same environment can differ dramatically from the population average in their gene expression and division rate (individual fitness). Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit
Trends in Biotechnology - Distributed computation: the new wave of synthetic biology devices Trends in Biotechnology - Distributed computation: the new wave of synthetic biology devices Distributed computation: the new wave of synthetic biology devices Volume 30, Issue 6 , Pages 342-349, Publication Date 18 April 2012 Copyright © 2012 Elsevier Ltd All rights reserved. DOI: 10.1016/j.tibtech.2012.03.006 Javier Macía
Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012 <p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012
A Biobrick Library for Cloning Custom Eukaryotic Plasmids Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. A Biobrick Library for Cloning Custom Eukaryotic Plasmids
MIT-CSAIL-TR-2012-008
Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency
Volume 23, Issue 6, December 2012, Pages 948–956 Phosphorus biotechnology • Pharmaceutical biotechnology Edited By Andrew N Shilton, Lars M Blank, Francis E Nano and José F Rodríguez iSSB, Institute of Systems and Synthetic Biology, CNRS UPS3509, University of Evry-Val-d’Essonne EA4527, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 Evry Cedex, France Current Opinion in Biotechnology - A retrosynthetic biology approach to therapeutics: from conception to delivery
Engineering Molecular Circuits Usin... [Annu Rev Chem Biomol Eng. 2012 <p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Sign in to NCBI PubMed US National Library of Medicine National Institutes of Health
Integrated Electromicrobial Conversion of CO2 to Higher Alcohols
1203808109.full
<p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Sign in to NCBI Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012
† School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States ‡ Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy § Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States A Sensitive Switch for Visualizing Natural Gene Silencing in Single Cells - ACS Synthetic Biology
Signaling-mediated bacterial persister formation. [Nat Chem Biol. 2012
Signaling-mediated bacterial persister formation. [Nat Chem Biol. 2012
Generation of a Synthetic Memory Trace
The Imaginary Mind of a Mouse
Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology
1108.3752
Phase transitions in the assembly of multivalent sign... [Nature. 2012
A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads
An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae
Synthetic biology: Simplifying design. [Nat Rev Genet. 2012
A sensing array of radically coupled genetic 'biopixels' [Nature. 2011
Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device : Nature Communications
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
Emerging biomedical applications of synthetic biology : Abstract : Nature Reviews Genetics
In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology
From DNA to Targeted Therapeutics: Bringing Synthetic Biology to the Clinic
Bayesian design of synthetic biological systems
Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology : Nature Communications
Arming yeast for synthetic biology : Nature Biotechnology
Sequential Establishment of Stripe Patterns in an Expanding Cell Population
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Yeast thrives with partially synthetic genome : Nature News
Entrainment of a Population of Synthetic Genetic Oscillators
Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells
Chemical and Genetic Engineering of Selective Ion Channel–Ligand Interactions
A Grand Challenge in Biology
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The Allure of Synthetic Biology
Expanding the Genetic Code of Escherichia coli with Phosphoserine
Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks
Bringing It Together with RNA
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Methods in Enzymology : Multiplexed Genome Engineering and Genotyping Methods : : Applications for Synthetic Biology and Metabolic Engineering
Chip chips away at the cost of a genome : Nature News
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Microfluidic technologies for synthetic biology. [Int J Mol Sci. 2011] - PubMed result
GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules
SCRM paper - revision draft 13 - Powered by Google Docs
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Synthetic Physiology
A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
Synthetic Biology | Mendeley Group
Amit_2010
Boston University: Applied BioDynamics Laboratory
Engineering microbial biofuel tolerance
tunable_signal
Informing Biological Design by Integration of Systems and Synthetic Biology
In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology
In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology
In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology