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Canadian horse shatters fossil genome record - Globe and Mail

Canadian horse shatters fossil genome record - Globe and Mail | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Design & Trend Canadian horse shatters fossil genome record Globe and Mail “The ability to watch genomes evolve is completely new, and we don't yet know what we're going to be able to learn,” said Beth Shapiro, an evolutionary molecular biologist...
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Hopefully many more of these really sequences will be dug out form the ice!

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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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Genome Biology | Full text | Genomic legacy of the African cheetah, Acinonyx jubatus

Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.
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Genome-wide patterns of selection in 230 ancient Eurasians : Nature : Nature Publishing Group

Genome-wide patterns of selection in 230 ancient Eurasians : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Creating a genetic algorithm for beginners

Creating a genetic algorithm for beginners | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
An introductory tutorial to genetic algorithms (GA) for beginners. Step by step guide of how to create a basic binary genetic algorithm (GA) in Java with example code.
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System that replaces human intuition with algorithms outperforms human teams

System that replaces human intuition with algorithms outperforms human teams | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Big-data analysis consists of searching for buried patterns that have some kind of predictive power. But choosing which "features" of the data to analyze usually requires some human intuition. In a database containing, say, the beginning and end dates of various sales promotions and weekly profits, the crucial data may not be the dates themselves but the spans between them, or not the total profits but the averages across those spans.
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First computational method based on evolutionary principles developed to predict protein dynamics

First computational method based on evolutionary principles developed to predict protein dynamics | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Researchers from the Structural Biology Computational Group of the Spanish National Cancer Research Centre, led by Alfonso Valencia, in collaboration with a group headed by Francesco Gervasio at the University College London (UK), have developed the first computational method based on evolutionary principles to predict protein dynamics, which explains the changes in the shape or dimensional structure that they experience in order to interact with other compounds or speed up chemical reactions.
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Intramolecular phenotypic capacitance in a modular RNA molecule

Intramolecular phenotypic capacitance in a modular RNA molecule | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

Another very nice piece of work by Andreas Wagner. Subject is related to his theory (I refuse to use hypothesis here) on reconciliation of drift and shift, but it goes way beyond that and it might have tremendous if picked up. They perform in vitro evolution experiments on a ribozyme including a valid determination of fitness. The idea is good, then they searched for a nice system to test their idea and they develop the complete thing in the wetlab. This is top science! Impact will be on how we understand early evolution, as such that this is yet another findings that explains why evolution happens so fast. It is also a very good instance of real evolution. I wonder if the Discovery Institute picked this up, they will hate it!

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Support for linguistic macrofamilies from weighted sequence alignment

Support for linguistic macrofamilies from weighted sequence alignment | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Who would have thought that MSA and phylogeny could successfully be applied to linguistics? Actually, it is not that weird, just a confirmation of the selfish meme.

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Straight up, with a twist: New model derives homochirality from basic life requirements

Straight up, with a twist: New model derives homochirality from basic life requirements | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Life is quirky. Although the molecules that make up all living things obey physical and chemical laws, they do so with a puzzling twist. How did the distinctive molecular features of life emerge, and what can they tell us about life on Earth and elsewhere in the universe?
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Maybe God doesn't throw dice, Nature does: New model derives homochirality from basic life requirements

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Mini DNA sequencer tests true - EMBL

Mini DNA sequencer tests true - EMBL | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The MinION miniature DNA sequencer has been evaluated by an open, international consortium and the results published in F1000Research.
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For those who laughed at Bones` tricorder........

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Control over overall shape and size in de novo designed proteins

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The next step where computational and synthetic biology go hand in hand.

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Scientists can now perform complete genome sequencing in 26 hours for emergencies

Scientists can now perform complete genome sequencing in 26 hours for emergencies | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Scientists have halved the amount of time it takes to perform genome sequence diagnoses in cases involving critically ill newborns. A new study published this week shows how physicians can diagnose genetic illnesses affecting babies in just 26...
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Widespread convergence in toxin resistance by predictable molecular evolution

Widespread convergence in toxin resistance by predictable molecular evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

Why is it that people that work in evolution make such terrible mistakes? Evolution predictable? You can only predict evolution if you actually know the functional constraints that obviously depend on the novel, hence unknown function. Just because there are X instances of convergent evolution does not allow for even suggesting predictable molecular evolution. Come on, this is Science.

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Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator–prey system

Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator–prey system | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator–prey (rotifer–algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

Via Ashish Umre
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Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns

Fluctuation-Driven Neural Dynamics Reproduce  Drosophila  Locomotor Patterns | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Author Summary The brain is never quiet. Even in the absence of environmental cues, neurons receive and produce an ongoing barrage of fluctuating signals. These fluctuations are well studied in the sensory periphery but their potential influence on central circuits and behavior are unknown. In particular, activity fluctuations in action selection circuits—neural populations that drive an animal’s actions from moment to moment—may strongly influence behavior. To shed light on the influence of
Arjen ten Have's insight:

This is not only a research that has direct biological impact. More importantly it shows how complexity can arise and it is yet another step in explaining how evolution of complex organisms, doing even more complex things as driving a car through a busy city center, can actually have taken place!

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FDA starts beta-testing 'the most advanced bioinformatics platform in the world'

FDA starts beta-testing 'the most advanced bioinformatics platform in the world' | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The FDA has started testing the precisionFDA platform it developed with DNAnexus. The closed beta test phase is the precursor to a more widespread rollout of the system, which the CEO of DNAnexus has described as being "the most advanced bioinformatics platform in the world."
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This sounds about right but I think we need to see what it actually is. Typically these platforms are more genomics than bioinformatics/biocomputation...

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Big data: The power of petabytes : Nature : Nature Publishing Group

Big data: The power of petabytes : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Researchers are struggling to analyse the steadily swelling troves of '-omic' data in the quest for patient-centred health care.
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Glia-derived neurons are required for sex-specific learning in C. elegans : Nature : Nature Publishing Group

Glia-derived neurons are required for sex-specific learning in C. elegans : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

Luckily we are not worms. Or are we? The message is that males prefer sex over a meal and that women prefer sustenance. In terms of evolution this does make sense. Does that explain why men are better cooks? A Dutch proverb goes "The love of a man comes through the stomach" Well, that is apparently not the best way of putting it.

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Accelerating molecular simulations of proteins using Bayesian inference on weak information

Accelerating molecular simulations of proteins using Bayesian inference on weak information | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Not exactly my cup of tea but this might be a major breakthrough

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BioTechniques - A Complete Map of the Human Proteome

In a similar vein to the Human Genome Project, researchers working on the Human BioPlex Project aim to complete a map of the colossal complex web of protein-protein interactions within human cells. The first results of this...
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Did Convergent Protein Evolution Enable Phytoplasmas to Generate ‘Zombie Plants’?

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I am not so sure this is indeed the result of convergent evolution. Could be HGT?

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BMC Genomics | Full text | Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus.
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Potentially interesting this might be an oversimplification.

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Fate of a mutation in a fluctuating environment

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This might seem as too obvious but this is more about how the dynamics of negative, neutral and positive selection. An on the average negative mutation will behave differfently than that that is on the average positive.

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Intramolecular phenotypic capacitance in a modular RNA molecule

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Excellent work again of Andreas Wagner, builiding upon his hypothesis (which IMO should be theory) of neutral evolution paving the way for positive selection. Basically, the hypothesis says that many neutral substitutions are connected in protein solution space, thereby gaining access to more mutations that might give advantage. Not only does this explain why evolution is so fast, it also explains why so many susbstitutions are detected as positive, neutral steps become positive when the last positive mutation kicks in. Simple and elegant!

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Real-time analysis of metabolic products

Real-time analysis of metabolic products | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Biologists at ETH Zurich have developed a method that, for the first time, makes it possible to measure concentration changes of several hundred metabolic products simultaneously and almost in real time. The technique could inspire basic biological research and the search for new pharmaceutical agents.
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dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
#bioinformatics Tutorial: An open-source R package for ontology analysis http://t.co/ns6GdtoJ4I
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