Secondary Papers
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BMC Evolutionary Biology | Abstract | Phage-induced diversification improves host evolvability

Bacteriophage (viruses that infect bacteria) are of key importance in ecological processes at scales
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BioPAX support in CellDesigner

Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.


Via jameslz
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Synthetic Biology: Drew Endy

Long Now Synthetic Biology Debate: Drew Endy Drew Endy is a biological engineer at Stanford University and a leading voice in the field of synthetic biology.
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Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates | Secondary Papers | Scoop.it
Most protein substitution models use a single amino acid replacement matrix summarizing the biochemical properties of amino acids. However, site evolution is highly heterogeneous and depends on many factors that influence the substitution patterns.
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BMC Evolutionary Biology | Full text | Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus

When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them.
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The new drug circuit

The new drug circuit | Secondary Papers | Scoop.it

by Daniel Grushkin

"Synthetic biology has historically relied on bacteria as a testing ground for engineering cell behavior through genetic signals. But a small group of researchers have their sights set on redesigning mammalian cells, which have more complex genetic machinery. Daniel Grushkin meets the scientists aiming to reprogram our bodies' cells for a new generation of tailor-made treatments."

http://bit.ly/Rq7oON


Via Gerd Moe-Behrens, jameslz
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ScienceDirect.com - Physics of Life Reviews - Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments

ScienceDirect.com - Physics of Life Reviews - Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments | Secondary Papers | Scoop.it
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Metabolomics-assisted synthetic biology. [Curr Opin Biotechnol. 2012] - PubMed - NCBI

As the world progresses from a fossil-fuel based economy to a more sustainable one, synthetic biology will become increasingly important for the production of high-value fine chemicals as well as low-value commodities in bulk. The integration of metabolomics and fluxomics within synthetic biology projects will be vital at all levels, including the initial design of the pathways to be generated, through to the optimisation of those pathways so that more efficient conversion of low-cost starting materials into highly desirable products can be achieved. This review highlights these areas and details the most important and exciting advances being made in this area.

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The relationship between the hierarchical position ofproteins in the human signal transduction networkand their rate of evolution

Background:
Proteins evolve at disparate rates, as a result of the action of different types and strengths ofevolutionary forces. An open question in evolutionary biology is what factors are responsiblefor this variability.
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