Bioinformatics, Comparative Genomics and Molecular Evolution
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Why Simulate?

Why Simulate? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
RT @moorejh: Why simulate? http://t.co/f6UX6TmKGk #bioinformatics #complexity This opens a whole new line of research. Socioinformatics
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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
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Rescooped by Arjen ten Have from Plant Pathogenomics
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Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016)

Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.


Via Steve Marek, Kamoun Lab @ TSL
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Encore une fois

Encore une fois | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The genomic era arrives. And this time it’s probably real
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Convergent evolution of the genomes of marine mammals : Nature Genetics : Nature Publishing Group

Convergent evolution of the genomes of marine mammals : Nature Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Andrew Foote and colleagues report the whole-genome sequences and de novo assemblies of three marine mammal species[mdash]the walrus, killer whale and manatee[mdash]and an improved bottlenose dolphin genome. Their comparative genomic analysis finds evidence of parallel evolution across the marine mammal genomes.
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This company wants to sequence your DNA and tell you your risk for 8 different cancers for $249

This company wants to sequence your DNA and tell you your risk for 8 different cancers for $249 | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The test now includes results for your hereditary risk for eight types of cancer.
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Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Publishing Group

Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
We are bacteria, YOUR resistance is futile since we will exapt. Must be a scary episode of Star Trek. This makes a lot of sense, microbes do not have sex, hence they must transfer material otherwise. These kind of studies show us how vast and how fast resistance spreads. There is even no need for direct transfer, the community will solve it. Just like the Borg they simply exapt resistance. Yet another demonstation of the fact that adatation is meaningless in terms of evolution. It is exaptation of existing plasticity.
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PLOS Computational Biology: The Maximum Entropy Fallacy Redux?

PLOS Computational Biology: The Maximum Entropy Fallacy Redux? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Reliable modelling without threading? PLOS Computational Biology: The Maximum Entropy Fallacy Redux?
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Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation

Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Evolutionary Trace combined with Mutual Information, now where did I see that before?
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Realizing privacy preserving genome-wide association studies

Realizing privacy preserving genome-wide association studies | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
I kind of liked Craig Venters new venture with Discovery but maybe they can learn things from this
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NMR Methods to Study Dynamic Allostery

NMR Methods to Study Dynamic Allostery | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach.
Arjen ten Have's insight:
Still one of the most interesting issues in protein biochemistry
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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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BMC Genomics: Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements (2016)

BMC Genomics: Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Background. Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one from foxtail millet (Setaria italica), three from wild foxtail millet S. viridis, and one isolate each from finger millet (Eleusine coracana), wheat (Triticum aestivum) and oat (Avena sativa), in addition to an isolate of a sister species M. grisea, that infects the wild grass Digitaria sanguinalis.

 

Results. Whole genome sequence comparison confirmed that M. oryzae Oryza and Setaria isolates form a monophyletic and close to another monophyletic group consisting of isolates from Triticum and Avena. This supports previous phylogenetic analysis based on a small number of genes and molecular markers. When comparing the host specific subgroups, 1.2–3.5 % of genes showed presence/absence polymorphisms and 0–6.5 % showed an excess of non-synonymous substitutions. Most of these genes encoded proteins whose functional domains are present in multiple copies in each genome. Therefore, the deleterious effects of these mutations could potentially be compensated by functional redundancy. Unlike the accumulation of nonsynonymous nucleotide substitutions, gene loss appeared to be independent of divergence time. Interestingly, the loss and gain of genes in pathogens from the Oryza and Setaria infecting lineages occurred more frequently when compared to those infecting Triticum and Avena even though the genetic distance between Oryza and Setaria lineages was smaller than that between Triticum and Avena lineages. In addition, genes showing gain/loss and nucleotide polymorphisms are linked to transposable elements highlighting the relationship between genome position and gene evolution in this pathogen species.

 

Conclusion. Our comparative genomics analyses of host-specific M. oryzae isolates revealed gain and loss of genes as a major evolutionary mechanism driving specialization to Oryza and Setaria. Transposable elements appear to facilitate gene evolution possibly by enhancing chromosomal rearrangements and other forms of genetic variation.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
So for all of you that keep thinking of transposable elements and alike as mere selfish genes that do not contribute to the other replicators of its host, maybe you should read this. Bummer that this happens in a pathogen.
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Detection of convergent and parallel evolution at the amino acid sequence level.

Detection of convergent and parallel evolution at the amino acid sequence level. | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Computational Modeling, Formal Analysis, and Tools for Systems Biology

Computational Modeling, Formal Analysis, and Tools for Systems Biology | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
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Next Generation Sequencing Library Preparation: Concepts, Tips and Tricks

Next Generation Sequencing Library Preparation: Concepts, Tips and Tricks | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
In this webinar, you will learn the core steps in preparing DNA/RNA NGS libraries.
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Rescooped by Arjen ten Have from Papers
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The evolution of cooperation within the gut microbiota

Little is known about cooperative behaviour among the gut microbiota; here, limited cooperation is demonstrated for Bacteroides thetaiotaomicron, but Bacteroides ovatus is found to extracellularly digest a polysaccharide not for its own use, but to cooperatively feed other species such as Bacteroides vulgatus from which it receives return benefits.

 

The evolution of cooperation within the gut microbiota
Seth Rakoff-Nahoum, Kevin R. Foster & Laurie E. Comstock

Nature 533, 255–259 (12 May 2016) http://dx.doi.org/10.1038/nature17626


Via Complexity Digest
Arjen ten Have's insight:
This is cool stuff, and once again is shows the basics of evolution: all you need is an Evolutionary Stable Strategy and it will evolve. Unclear yes is what the benefit is (or was?).
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Functional Implications of Human-Specific Changes in Great Ape microRNAs

Functional Implications of Human-Specific Changes in Great Ape microRNAs | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans. We explored the strength of purifying selection among microRNA regions and found that the seed and mature regions are under similar and stronger constraint than the precursor region. We further constructed a comprehensive catalogue of microRNA species-specific nucleotide substitutions among great apes and, for the first time, investigated the biological relevance that human-specific changes in microRNAs may have had in great ape evolution. Expression and functional analyses of four microRNAs (miR-299-3p, miR-503-3p, miR-508-3p and miR-541-3p) revealed that lineage-specific nucleotide substitutions and changes in the length of these microRNAs alter their expression as well as the repertoires of target genes and regulatory networks. We suggest that the studied molecular changes could have modified crucial microRNA functions shaping phenotypes that, ultimately, became human-specific. Our work provides a frame to study the impact that regulatory changes may have in the recent evolution of our species.
Arjen ten Have's insight:
The authors do not claim this was the trigger for speciation but IMO this does demonstrate how sympatric speciation can occur.
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MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Web resource: 1000 Fungal Genomes Project (2016)

Web resource: 1000 Fungal Genomes Project (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Sequencing unsampled fungal diversity


Via Kamoun Lab @ TSL
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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."
Arjen ten Have's insight:

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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