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Bioinformatics, Comparative Genomics and Molecular Evolution
A page dedicated at the dispersal of papers and facts related to these fascinating Scientific Endeavours
Curated by Arjen ten Have
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BioTechniques - Genetic Recoding in the Wild

BioTechniques - Genetic Recoding in the Wild | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
A new study finds that simple organisms commonly defy established DNA coding rules in the wild, recoding stop codons so that they command the addition of new amino acids to a developing protein instead of bringing construction to an...
Arjen ten Have's insight:

The genetic code is not so universal as we thought? Well, I am not surprised. The degeneracy of the code simply allows for more flexibility. The mechanism is well known and likely the basis of what is described here: a stopcodon slowly gets out of use, there are two other ones. Then, once no longer in use, you a codon as tour disposal. The same goes for all degenerate codons, 19 messages in total. Evolution at its best!

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A microbial ecosystem beneath the West Antarctic ice sheet : Nature : Nature Publishing Group

A microbial ecosystem beneath the West Antarctic ice sheet : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Liquid water has been known to occur beneath the Antarctic ice sheet for more than 40 years, but only recently have these subglacial aqueous environments been recognized as microbial ecosystems that may influence biogeochemical transformations on a global scale. Here we present the first geomicrobiological description of water and surficial sediments obtained from direct sampling of a subglacial Antarctic lake. Subglacial Lake Whillans (SLW) lies beneath approximately 800 m of ice on the lower portion of the Whillans Ice Stream (WIS) in West Antarctica and is part of an extensive and evolving subglacial drainage network. The water column of SLW contained metabolically active microorganisms and was derived primarily from glacial ice melt with solute sources from lithogenic weathering and a minor seawater component. Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. Our results confirm that aquatic environments beneath the Antarctic ice sheet support viable microbial ecosystems, corroborating previous reports suggesting that they contain globally relevant pools of carbon and microbes that can mobilize elements from the lithosphere and influence Southern Ocean geochemical and biological systems.
Arjen ten Have's insight:

NGS has gotten a well deserved and prominent role in evolution studies. This is an ecosystem that has been isolated for a very long time. The importance form being isolated comes the fact that it will be much easier to model it. A pity that due to the set-up only bacterial and archaeal life  was targetted. The rest soon to come? This will not stop with the ribosomal sequences: This is a metabolic pool that can be modelled!

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Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries

Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
With the ability to use next generation sequencing technology, researchers have a broadened understanding of the association of genetic changes and disease causation to a much greater resolution, driving new discoveries, said clinical geneticists...
Arjen ten Have's insight:
An important IMO is that of how we will share all that information. How will dr watson in Nigeria know of it? Breast cancer for instance we know now, thanks to NGS, can often be divided in subtypes that all should be treated differently. Many MD proof databases will need to be developed.
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From eons to seconds, proteins exploit the same forces

From eons to seconds, proteins exploit the same forces | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
(Phys.org) —Nature's artistic and engineering skills are evident in proteins, life's robust molecular machines. Scientists at Rice University have now employed their unique theories to show how the interplay between evolution and physics developed these skills.
Arjen ten Have's insight:

How proteins evolve depends on many aspects but according to this the energy landscape is extremely important. Nice combination of physics and evolution, at the heart of where biocomputation should be!

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GigaScience | Full text | Ten recommendations for creating usable bioinformatics command line software

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.
Arjen ten Have's insight:

An old one but of good help. Do you code? Then do it good and in a way anyone can use it!

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Computational identification of natural peptides based on analysis of molecular evolution

Computational identification of natural peptides based on analysis of molecular evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

There is a boom on these peptide identifiers, and this paper shows why. I suppose this is state of the art. 90% precision at only 50% recall, and that is based on what we know. As a real classifier performance will very likely be much worse. Much remains to be done!

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Genetic information transfer promotes cooperation in bacteria

Genetic information transfer promotes cooperation in bacteria | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014)

PLOS Genetics: Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution (2014) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.


Via Kamoun Lab @ TSL, Shaikhul Islam
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New tools advance bio-logic: Researchers build more sophisticated synthetic gene circuits

New tools advance bio-logic: Researchers build more sophisticated synthetic gene circuits | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
(Phys.org) —Researchers at Rice University and the University of Kansas Medical Center are making genetic circuits that can perform more complex tasks by swapping protein building blocks.
Arjen ten Have's insight:

Great stuff, if I was to start my science career right now....... Obviously we have no clue how complex the things can be without too much failure. Increasingly complex systems will have more errors and need complex error fixing. It is like a double layer...

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BioTechniques - Don’t Let the Name Fool You: Long Non-Coding RNAs Sometimes Code Proteins

BioTechniques - Don’t Let the Name Fool You: Long Non-Coding RNAs Sometimes Code Proteins | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
New studies suggest that some sequences dubbed long non-coding RNA may require a rechristening—or at least a thorough reexamination. In fruit flies, zebra fish, and humans, some long non-coding RNAs appear to be translated into...
Arjen ten Have's insight:
Peptides, small peptides or smorfs, there are many of them, yet another expansion of knowledge, cool!
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Biome | Psychiatric genomics

Biome | Psychiatric genomics | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
How will genomic insights into the overlap between psychiatric disorders effect diagnosis and future research?
Arjen ten Have's insight:

Bioinformatics will soon be applied to many other aspects of science. Psychoinformatics or even Socioinformatics. The difference is that it gets more complex, hence, predictions will have lower value but that does not mean it will not be developed.

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Computer Models Reveal Quantum Effects in Biological Oxygen Transport - Scientific Computing

Computer Models Reveal Quantum Effects in Biological Oxygen Transport - Scientific Computing | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Scientific Computing Computer Models Reveal Quantum Effects in Biological Oxygen Transport Scientific Computing Until now, computational scientists have been unable to come to a good understanding of exactly why such protein poisoning is not more...
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Major revision of the NCBI genomes FTP site this summer

Major structural changes are coming to the NCBI #genomes FTP site. Details at NCBI News http://t.co/rUExQUnpmP #bioinformatics
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Encyclopedia of how genomes function gets much bigger

a_big_step_in_understanding_the_mysteries_of_the_human_genome_was_unveiled_today_in_the_form_of_three_analyses_that_provide_the_most_detailed_comparison_yet_of_how_the_genomes_of_the_fruit_fly_roundworm_and_human_function_
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EBI: Next Generation Sequencing Practical Course | Train online

15 hours of #NGS free online practical course by @EMBLorg http://t.co/oa2W8RFRjg
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Will the real synthetic biology please stand up?

Will the real synthetic biology please stand up? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Biotechnology processes are inherently cleaner and healthier for the environment than petrochemical processes.
Arjen ten Have's insight:

What's in a name?

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Terry Hill's curator insight, August 15, 8:34 AM

There is no doubt about the efficacy of bio over petro. 

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BioTechniques - Thousands of New Protein Isoforms Hiding in Plain Sight

BioTechniques - Thousands of New Protein Isoforms Hiding in Plain Sight | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
By combing through gene databases in a new way, researchers found more than 2000 human and mouse protein variants never before reported. Learn more...
Arjen ten Have's insight:

If an accidentally novel produced splicing isoform is functional and contributes to survival and offspring, it will simply be selected for. Alternative splicing is very important. It tells us why microarray are not that informative and why we need better algorithms for RNAseq contigging and why it is important to have longer reads in the first place! For RNAseq I would go for a long read method!

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How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes

How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
Arjen ten Have's insight:

Evolution at work!

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Algorithms, games, and evolution

Algorithms, games, and evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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5 Simple Bioinformatics Tips That Will Improve Your Research |

5 Simple Bioinformatics Tips That Will Improve Your Research | | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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New Study Looks at How Epigenetic Effects are Passed Down

New Study Looks at How Epigenetic Effects are Passed Down | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
A new study demonstrates that the ‘memory’ of nutrition during pregnancy can be passed through sperm of male offspring to the next generation, increasing risk of disease for grandchildren as well. In other words, to adapt an old maxim, ‘you are what your grandmother ate.’
Arjen ten Have's insight:

This is another area of interest for Bioinformaticians and evolutionists. Epigenetics and evolution of acquired traits. The way epigenetics works seems to make a lot of sense, it functions like finetuning: starvation results in methylation of bits of DNA, this is transferred to the offspring. Methylation will likely be maintained under starvation conditions and relieved upon relaxation of starvation. This relief is required since the methylation results in an organims with a different metabolism, that is therefore more sensitive to diabetes. Trade-off!

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An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

Arjen ten Have's insight:
This sounds very interesting, I am actually a bit dwarfed by all these adjustments. I do get the idea of gamma distribution and better the dirichlet probability models but on the other: I am lost if you combine all these things. Here it seems the author actually adjusts its phylogeny using the phyologeny. would even be better if it includes a loop with the MSA.
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Scientists find protein-building enzymes have metamorphosed & evolved new ... - Science Codex

Scientists find protein-building enzymes have metamorphosed & evolved new ...
Arjen ten Have's insight:

Functional diversification is apparently not only the result of birth and death evolution, alternative CDS are yet another resource of function. 

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Computational identification of natural peptides based on analysis of molecular evolution

Computational identification of natural peptides based on analysis of molecular evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
OB: Computational identification of natural peptides based on analysis of molecular evolution: Motivation: Man... http://t.co/M6uLfh5Dji
Arjen ten Have's insight:

Peptides are one of the underestimated biomolecules. Why? They are encoded and synthesized, once synthesized they will pick up a function, that is how evolution works. Hence, this kind of research is really important.

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You're not allowed bioinformatics anymore

You're not allowed bioinformatics anymore | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
"Ah welcome! Come in, come in!” said the institute director as Professor Smith appeared for their scheduled 2pm meeting. “I want to talk to you about your latest proposal”, the director continued. ...
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Fun but a bit obnoxious as well

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