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Article series : Nature Reviews Genetics

*Nature Genetics Series: Computational Tools for complex genetic and genomic data*

"The scale and complexity of genetic and genomic data are ever-expanding, requiring biologists to apply increasingly more sophisticated computational tools in the analysis, interpretation and storage of these data. This series contains articles that focus on the application of these software tools in genetics and genomics."

http://bit.ly/T82b2d

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Functional DNA Origami Devices

 

by
Michael S. Strano

"DNA is central to the existence of all life on Earth and uniquely encodes the instructions for producing such life. But it has another set of remarkable properties shared by a much larger class of molecules, most of which are yet to be invented. These “chemically sequenced polymers” (CSPs) are built by adding distinct monomers one at a time and can be programmed in such a way as to assemble into arbitrarily complex and three-dimensional shapes. Nature is far ahead of us in the creation and utility of such molecules, but on page 932 of this issue, Langecker et al. (1) provide a glimpse of the structural precision and functionality they offer for programmed assembly."
http://bit.ly/RH5awu

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Pluripotency re-centered around Esrrb : Abstract : The EMBO Journal

Pluripotency re-centered around Esrrb : Abstract : The EMBO Journal | SynBioFromLeukipposInstitute | Scoop.it

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Bernadett Papp and Kathrin Plath

"The orphan nuclear receptor estrogen-related receptor b (Esrrb) is a vital component of the core pluripotency network in embryonic stem cells (ESCs). However, its function is not clear and the identity of potential upstream regulators has remained elusive. Three elegant reports (Festuccia et al, 2012; Martello et al, 2012; Percharde et al, 2012) have now elucidated the role of Esrrb in ESC self-renewal and reprogramming."

http://bit.ly/XLK19c

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Frontiers in Systems and Synthetic Biology ’13 (FSSB’13) | Integrative BioSystems Institute at Georgia Tech

Frontiers in Systems and Synthetic Biology ’13 (FSSB’13) | Integrative BioSystems Institute at Georgia Tech | SynBioFromLeukipposInstitute | Scoop.it

Please join us for the International Conference Frontiers in Systems and Synthetic Biology ’13 , March 20-24, 2013 at Georgia Tech in Atlanta, Georgia. (Frontiers in Systems and Synthetic Biology ’13 (FSSB’13) in Georgia Tech.

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BBC - The Code - The Wisdom of the Crowd

*Why we need the crowd to do outstanding science?*

Have a look to this video: http://www.youtube.com/watch?feature=player_embedded&v=iOucwX7Z1HU

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Gen9 - 2012 G-Prize Contest Winners

Gen9 - 2012 G-Prize Contest Winners | SynBioFromLeukipposInstitute | Scoop.it

2012 Gen9 G-Prize
Rewarding innovators and disruptors who can transform an industry using synthesized DNA constructs.

The inaugural G-Prize contest, conceived and exclusively sponsored by Gen9, was launched to foster creative and innovative approaches for using synthetic DNA libraries to advance research in the production of pharmaceuticals, chemicals, biofuels and food.

The winners of the 2012 G-Prize are:

1st place (500 GeneBits, up to 500kb):
Tanja Kortemme, University of California, San Francisco
Computer-Aided Design of Sensor/Actuators

2nd place (300 GeneBits, up to 300kb):
Sarel Fleishman, Weizmann Institute (Rehovot, Israel)
Computational Design of Novel Binding Antibodies: Designing High-Specificity and High-Affinity Insulin Binders

3rd place (100 GeneBits, up to 100kb, two winners):
Alfonso Jaramillo, Institute of Systems & Synthetic Biology (Evry, France)
Combinatorial Synthesis of RNA Integrated Circuits to Program Living Cells

Xavier Duportet, Massachusetts Institute of Technology
Towards the Manipulation of Genomes On-Demand: High Throughput Discovery of New Recombination Sites

CEO’s Award (100 GeneBits, up to 100kb):
Lynn Rothschild, NASA
DNA Toolkit for Space Exploration

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Camein.com » People-Powered Medical Devices?

Camein.com » People-Powered Medical Devices? | SynBioFromLeukipposInstitute | Scoop.it

Medical devices seem to get smaller every year. Think of something as simple as a pacemaker or hearing aid. Like their bretheren PCs, these gadgets that help enhance and extend our lives continue to shrink.


Via petabush, LeapMind
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Tony Hardman's curator insight, August 14, 2013 11:31 AM
What Manufacturers Should Do to Build Secure Devices - http://bit.ly/19gsZUe
MPR PD Group's curator insight, September 10, 2014 8:48 AM

The itsy bitsy device that is powered by your body.

 

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Playing with genes | COSMOS magazine

Playing with genes | COSMOS magazine | SynBioFromLeukipposInstitute | Scoop.it

Some people play sport, others play Xbox. And now there is a growing group of people who play with DNA sequences. http://bit.ly/X4FZts

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The Limits of De Novo DNA Motif Discovery

The Limits of De Novo DNA Motif Discovery | SynBioFromLeukipposInstitute | Scoop.it

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Simcha D, Price ND, Geman D.

"A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of the LR and ALR algorithms is available at http://code.google.com/p/likelihood-ratio-motifs/."

http://1.usa.gov/UmVxkw

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Craig Venter: Health, Genomics, Research and Power

Biologist and entrepreneur Craig Venter discusses the intersection between health, genomics, research and power.

 

For the full 46 minute interview go to 

http://fora.tv/2012/10/16/Craig_Venter_Health_Genomics_Research_and_Power

 

More previews of Many other interviews from the October 15-16 Living by Numbers Health Conference by WIRED and the Robert Wood Johnson Foundation

http://fora.tv/conference/wired_health_conference_living_by_numbers

 

"a new conversation on the future of healthcare with 200 expert leaders from the worlds of medicine, science, technology, and business.

....a clear, compelling argument that today there is a new opportunity to bring data into real-time decision-making for doctors, researchers, hospitals, and individuals. This combination has the potential to transform people's lives.

.....spanning the gap between healthcare and technology, connecting pioneering researchers with ambitious entrepreneurs. First and foremost, .... a forum for ideas. Expect new connections, new opportunities, and new insights in how better data is driving us all toward better health."

 

The full interviews are here:

http://fora.tv/conference/wired_health_conference_living_by_numbers/buy_programs


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Undergraduate Synthetic-Biology Contest Mixes Fun With Serious Warnings - Government - The Chronicle of Higher Education

Undergraduate Synthetic-Biology Contest Mixes Fun With Serious Warnings - Government - The Chronicle of Higher Education | SynBioFromLeukipposInstitute | Scoop.it
The range of projects at the International Genetically Engineered Machine meeting demonstrate the excitement and the anxiety inherent in the young discipline.
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The Role of Synthetic Biology for In Situ Resource Utilization (ISRU) | Abstract

The Role of Synthetic Biology for In Situ Resource Utilization (ISRU) | Abstract | SynBioFromLeukipposInstitute | Scoop.it

by

Michael Montague, George H. McArthur Charles S. Cockell, Jason Held, William Marshall, Louis A. Sherman, Norman Wang, Wayne L. Nicholson, Daniel R. Tarjan, and John Cumbers

"A persistent presence in space can either be supported from Earth or generate the required resources for human survival from material already present in space, so called “in situ material.” Likely, many of these resources such as water or oxygen can best be liberated from in situ material by conventional physical and chemical processes. However, there is one critical resource required for human life that can only be produced in quantity by biological processes: high-protein food. Here, recent data concerning the materials available on the Moon and common asteroid types is reviewed with regard to the necessary materials to support the production of food from material in situ to those environments. These materials and their suitability as feedstock for the biological production of food are reviewed in a broad and general way such that terminology that is often a barrier to understanding such material by interdisciplinary readers is avoided. The waste products available as in situ materials for feasibility studies on the International Space Station are also briefly discussed. The conclusion is that food production in space environments from in situ material proven to exist there is quite feasible. ..."

http://bit.ly/TwGvun

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Bristol University | News from the University | Synthetic biology funding

Bristol University | News from the University | Synthetic biology funding | SynBioFromLeukipposInstitute | Scoop.it
Scientists from the University of Bristol have been awarded a £1.1 million share of the Biotechnology and Biological Sciences Research Council (BBSRC)'s strategic Longer and Larger Awards in Synthetic Biology, announced today.
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Metabolic modelling in the development of cell factories by synthetic biology | Jouhten | Computational and Structural Biotechnology Journal

Metabolic modelling in the development of cell factories by synthetic biology | Jouhten | Computational and Structural Biotechnology Journal | SynBioFromLeukipposInstitute | Scoop.it

by

Paula Jouhten

"Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory."

http://bit.ly/ULykPe

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Science/AAAS | Special Issue: Biomaterials

Science/AAAS | Special Issue: Biomaterials | SynBioFromLeukipposInstitute | Scoop.it

*A great Science special about biomaterials*

"For biomaterials to move from the lab to clinical use, engineers, surgeons, physicists, and biologists all increasingly need to work together."

http://bit.ly/WegXa3

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Keystone Symposia Conference | Precision Genome Engineering and Synthetic Biology: Designing Genomes and Pathways - Program

Keystone Symposia, a non-profit organization dedicated to connecting the scientific community for the benefit of the world community and accelerating life science discovery, conducts scientific conferences on biomedical and life science topics in...
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These mini-bots were made for walking: Cells power biological machines

These mini-bots were made for walking: Cells power biological machines | SynBioFromLeukipposInstitute | Scoop.it
They're soft, biocompatible, about 7 millimeters long -- and, incredibly, able to walk by themselves. Miniature "bio-bots" are making tracks in synthetic biology.
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SynBioBeta - About

SynBioBeta - About | SynBioFromLeukipposInstitute | Scoop.it

SynBioBeta is an industry conference dedicated to synthetic biology startups. This is the opportunity to meet the up and coming synthetic biology companies, founders, investors and service providers.

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Study reveals declining influence of high impact factor journals - UdeMNouvelles

Study reveals declining influence of high impact factor journals - UdeMNouvelles | SynBioFromLeukipposInstitute | Scoop.it

Study reveals declining influence of high impact factor journals

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Department of Energy’s ESnet Rolls Out World’s Fastest Science Network « Berkeley Lab News Center

Department of Energy’s ESnet Rolls Out World’s Fastest Science Network « Berkeley Lab News Center | SynBioFromLeukipposInstitute | Scoop.it

The era of extreme data has arrived! http://1.usa.gov/X4JUGz

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Designer nucleic acids to probe and program the cell

by

Krishnan Y, Bathe M.

"Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone."

http://bit.ly/STwZ3s

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*Chemistry with spatial control using particles and streams*

by

Kalinin YV, Murali A, Gracias DH.

"Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis."

http://1.usa.gov/THfnZt

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Community links for the GenoCon2 Synthetic Biology Genomic Design Contest | Facebook

Community links for the GenoCon2 Synthetic Biology Genomic Design Contest | Facebook | SynBioFromLeukipposInstitute | Scoop.it

1. The http://GenoCon.org website containing

- GenoCon2 Challenges with backgrounds,measurement concept, basic science, and manuals

- GenoCon2 Timelines Contest Procedure Overview  GenoCon News About Us

  

2. The http://LinkData.org database  Using LinkData.org you can make an account, find useful data for GenoCon2 and upload your own data.

Using the LinkDataApp programing space http://app.linkdata.org/

you can: 

a) Find useful programs to analyze and process GenoCon2 data,

b) Make your own forked program copy to customize and design your own programs from scratch to enter to GenoCon2

c) Enter The GenoCon2 Contest

d) Write your reports explaining how your programs and designs work 

e) Share and Collaborate using your programs with other GenoCon2 community members

 

3.The GenoCon.org facebook page

 http://www.facebook.com/GenoCon.org/

and GenoCon2 facebook group 

http://www.facebook.com/groups/genocon

 

The GenoCon.org facebook page provides news and interesting links and a place to post community information The GenoCon facebook group provides a forum for questions and answers with the organizers and participants in the GenoCon Community

The LinkData App page http://on.fb.me/VehmUw

in the GenoCon.org facebook page provides links to and descriptions of design tools and entries to the GenoCon contest Challenges shared openly with the the GenoCon 2 Community. 

 

4. GenoCon2 on Scoop.it provides additional news and interesting links.

 http://www.scoop.it/t/genocon-2

 

5. @GenoCcon2 on Twitter for the latest headlines and links.

https://twitter.com/GenoCon2


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Team:Slovenia - 2012.igem.org

Team:Slovenia - 2012.igem.org | SynBioFromLeukipposInstitute | Scoop.it

*Bistable toggle switch in mammalian cells*

- great iGem project from Slovenia

"Biological drugs are being used ever more often as advanced drugs for the treatment of numerous diseases, due to their more specific mode of action. In current therapies the biological drugs are usually distributed more or less throughout the whole body, although each function should often be restricted to a specific organ or tissue. This can cause serious side effects, requires larger dosages and consequently raises the price of therapy. Our solution to this problem was to implant cells producing biological drugs inside the very tissue where the drug is required. The drug producing cells are safely sealed inside microcapsules that prevent cells from spreading throughout the body and protect them from destruction by cells of the host immune system. We constructed a device that allows implanted cells to produce different types of drugs while switching between those production states can be controlled from the outside by a physician, depending on the stage of the disease. We designed our device specifically for the therapy of hepatitis C or heart attack. Against hepatitis C the engineered cells produce a protein with antiviral activity, whose biological activity we have tested and confirmed. After the state of the cells is switched, a protein that improves liver regeneration would be produced. For the therapy after a heart attack we designed cells to suppress local inflammation and promote formation of new blood vessels only around the affected tissue. A physician may initiate self-destruction of the therapeutic cells and capsules by an outside stimulus when the therapy is complete or at any other given time. We believe our system to be safe, effective and applicable in the real world for the therapy of different types of diseases."
http://bit.ly/QbjlN5

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£20m boost for university research projects

£20m boost for university research projects | SynBioFromLeukipposInstitute | Scoop.it

A project at the University of Warwick is one of six to have secured a share of £20m to research synthetic biology http://bit.ly/RTdhWj

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