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The Genotype-Tissue Expression (GTEx) project : Nature Genetics : Nature Publishing Group

The Genotype-Tissue Expression (GTEx) project : Nature Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

OK, 1st message: The finding that nearly 90% of these sites occur outside of protein-coding sequences2 suggests that many associated variants may instead have a role in gene regulation.

Obviously that explains a lot no? Then, don't we need another toold? Well this seems interesting enough

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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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Sex Determination: Why So Many Ways of Doing It?

Sex Determination: Why So Many Ways of Doing It? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromosomes in humans and other model species have led to the impression that sex determination mechanisms are old and conserved. In fact, males and females are determined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-determining signals is coupled with conserved molecular pathways that trigger male or female development. Conflicting selection on different parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determination mechanisms have been rigorously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research opportunities to characterize the evolutionary forces and molecular pathways underlying the evolution of sex determination.

 

Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, et al. (2014) Sex Determination: Why So Many Ways of Doing It? PLoS Biol 12(7): e1001899. http://dx.doi.org/10.1371/journal.pbio.1001899


Via Complexity Digest
Arjen ten Have's insight:

I am getting more and more bored by all these pretentious sounding papers in plos, although mostly in plosone. Here is another one, my question is Why is that even a question? Meaning it is rather obvious. One of things that apparently are still not clear is the difference between hard and soft selection. Hard being defined as having an impact irrespective of the environment, soft impact depending on the environment. Sexual selection is typically hard, hence any mutation that affects sex, like in "to have sex or not to have sex", is due to affect the offspring. Hence, if sex is an emergent property of evolution (and I for one believe it is), than many ways of sex signalling is a logic result of that emergent property. Or do I miss something?

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Scientists show bacteria can evolve a biological timer to survive antibiotics

Scientists show bacteria can evolve a biological timer to survive antibiotics | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Nanowerk is the leading nanotechnology portal, committed to educate, inform and inspire about nanotechnologies, nanosciences, and other emerging technologies
Arjen ten Have's insight:

Without having read the details this is just another example of how simple evolution works (to results in dazzling complexity). Again Donzhansky was right.

 

Look out of the box: A mathematical model of the process, it all makes sense and show Bioiformatics and Biocompuation are aplicable everywhere.

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Everything old is new again: (linc)RNAs make proteins!

Everything old is new again: (linc)RNAs make proteins! | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Multiple sequence alignment using partial order graphs

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Pity the abstract shows no reliable benchmark data. >5000 sequence datasets are hard to align......
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Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats

Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
PLOS Genetics is an open-access
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Evolution depends on rare chance events, 'molecular time travel' experiments show

Evolution depends on rare chance events, 'molecular time travel' experiments show | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Chance events may profoundly shape history. What if Franz Ferdinand's driver had not taken a wrong turn, bringing the Duke face to face with his assassin? Would World War I still have been fought? Would Hitler have risen to power decades later?
Arjen ten Have's insight:

Thornthon is one of my idols. He does the real thing in studying evolution. He resurrects ancient proteins and evolves them in the lab. Besides that it is scientifically interesting, he provides solid answers to IDiots.

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Frontiers | Analysis of plant microbe interactions in the era of next generation sequencing technologies | Plant Genetics and Genomics

Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the pant associated microbiota to demonstrate the worth of the new methods.
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Chemical Weapons: Engineering Enzymes to Neutralize Nerve Agents

Chemical Weapons: Engineering Enzymes to Neutralize Nerve Agents | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Researchers at The University of Tennessee are a step closer to creating a prophylactic drug that would neutralize the deadly effects of the chemical weapons used in Syria and elsewhere. Jeremy Smith, UT-ORNL Governor’s Chair and an expert in computational biology, is part of the team that is trying to engineer enzymes — called bioscavengers — so they work more efficiently against chemical weapons. 
Arjen ten Have's insight:

Combine Biomimicry and Synthetic biology!. Evolution does provide us (if we human beings realize biodiversity is a blessing from evolution) with many solutions. And sometimes evolution needs a helping hand. By the way: this is what we have been doing since the start of agriculture, just using different techniques.

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Interactome Analysis | The Scientist Magazine®

Interactome Analysis | The Scientist Magazine® | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Study examines tissue-specific protein interactions linked to hereditary diseases.
Arjen ten Have's insight:

Elegant is often found in simplicity. Not that this was an easy job but the idea behind is like, how to put it:  parsimonious! Filter! This might be the start for an important filter. You sequence a patient, apply Hapmap and related genome sequence comparison databases, then you check this!

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Microbes May Drive Evolution of New Animal Species | Science | WIRED

Microbes May Drive Evolution of New Animal Species | Science | WIRED | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Nice essay on how symbiosis might affect evolution. yet another way to look at evolution. There is more to it than just mutations and epistasis. If we want to understand the molecular events, we need to see the whole picture. And being in a symbiosis simply puts a constraint!
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Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer : Nature Biotechnology : Nature Publishing Group

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer : Nature Biotechnology : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Whole-exome sequencing of circulating tumor cells enables accurate and powered calling of somatic point mutations.
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PNAS | Mobile The predictability of molecular evolution during functional innovation

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We are the Borg, you will exapt!
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The hybrid nature of the Eukaryota and a consilient view of life on Earth : Nature Reviews Microbiology : Nature Publishing Group

The hybrid nature of the Eukaryota and a consilient view of life on Earth : Nature Reviews Microbiology : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

ion

Arjen ten Have's insight:

More and more we are faced with information that goes against Woese's brilliant idea of three superkingdoms. Basically we need to look at early prokaryotes as communities. Many prokaryotes and unicellular eukaryotes still heavily depend on lateral gene transfer. Hence, the whole idea of monophyly in taxonomy should be put aside. Horizontal gene transfer simply makes the whole hypothesis impossible.

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A New Online Computational Biology Curriculum

A New Online Computational Biology Curriculum | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
PLOS Computational Biology is an open-access
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Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:

Not black not white. That is the message, although likely it is even more complicated I like this message. Induced fit and conformational selection are models and models help us understand reality but do not let them restrict your reality to Platoon's cave!

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A structural perspective of compensatory evolution

Arjen ten Have's insight:
Is this a trend? To combine evolutionary and structural biology seems avery good idea and it will again show new biological aspects of siimilarity: there is more to similarity then just physico-chemical forces, much more.
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Fingerprinting protein structures effectively and efficiently

Fingerprinting protein structures effectively and efficiently | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Unpronounceable — why can't people give bioinformatics tools sensible names?

Thoughts on biology, genomics, and the ongoing threat to humanity from the bogus use of bioinformatics acronyms

Arjen ten Have's insight:

This goes beyond the JABBA cases Just Another Bogus Bioinformatics Acronym.

 

Well, lets not get too serious on reading papers the whole day.

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Public needs to be engaged in biotech, animal welfare issues

Public needs to be engaged in biotech, animal welfare issues | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Need for transparency and open conversations between ag industry and public over issues like biotechnology and animal welfare
Arjen ten Have's insight:

Science is politically neutral, contrarily to what many alpha-scientists will claim, at least the exact sciences are. But that does not mean scientists should not engage in these things. Very important actually since otherwise pseudoscientist will do this. Thanks to Greenpeace The golden rice cultivar cannot save l many lifes , that is the kind of issue at stake. It is a difficult task though and looking into these apparent successful programs can help.

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Burst of Mutations During Initial Infection Allows Bacteria to Evade Human Immune Response

Burst of Mutations During Initial Infection Allows Bacteria to Evade Human Immune Response | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Bacteria that cause ulcers in humans undergo accelerated evolution during the initial stages of infection, allowing them to evade the immune system, according to new research by an international team of researchers including Penn State scientists. The study shows, for the first time, and in real-time, the interplay between the human immune system and invading bacteria that allows the bacteria to counter the immune response by quickly evolving. A paper describing the research is published in the June 13, 2014 issue of the journal Nature Communications.
Arjen ten Have's insight:

Now this is how evolution works. Well, one of the many ways. If it makes sense, it will evolve Dobzhansky was right.

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Diagnosing Infections With Next-Generation Sequencing

Diagnosing Infections With Next-Generation Sequencing | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
A new study used next-generation sequencing to diagnose a rare infection. Can this success help drive this technology into routine clinical use?
Arjen ten Have's insight:

For sure House MD's team would look quite different these days. After a fierce fight with Cuddy, they finally bought a sequencer, he fired all of his team, hired two bioinformaticians and a bioanalist. Wilson will likely also be quite happy!

 

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Context effects produced by question orders reveal quantum nature of human judgments

Arjen ten Have's insight:
So do you still believe in free will? I must say, this flabbergasts me but this is just sooooooooooo nice. Good start of the week! In recent years, quantum probability theory has been used to explain a range of seemingly irrational human decision-making behaviors. The quantum models generally outperform traditional models in fitting human data, but both modeling approaches require optimizing parameter values. However, quantum theory makes a universal, nonparametric prediction for differing outcomes when two successive questions (e.g., attitude judgments) are asked in different orders. Quite remarkably, this prediction was strongly upheld in 70 national surveys carried out over the last decade (and in two laboratory experiments) and is not one derivable by any known cognitive constraints. The findings lend strong support to the idea that human decision making may be based on quantum probability
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Mel Melendrez-Vallard's curator insight, June 17, 5:17 AM

Great Insight from Arjen ten Have's:

"So do you still believe in free will? I must say, this flabbergasts me but this is just sooooooooooo nice. Good start of the week! In recent years, quantum probability theory has been used to explain a range of seemingly irrational human decision-making behaviors. The quantum models generally outperform traditional models in fitting human data, but both modeling approaches require optimizing parameter values. However, quantum theory makes a universal, nonparametric prediction for differing outcomes when two successive questions (e.g., attitude judgments) are asked in different orders. Quite remarkably, this prediction was strongly upheld in 70 national surveys carried out over the last decade (and in two laboratory experiments) and is not one derivable by any known cognitive constraints. The findings lend strong support to the idea that human decision making may be based on quantum probability"
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Directory of in silico Drug Design tools

Directory of in silico Drug Design tools | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Directory of in silico drug design tools
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Processed pseudogenes acquired somatically during cancer development : Nature Communications : Nature Publishing Group

Processed pseudogenes acquired somatically during cancer development : Nature Communications : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Is Evolution Predictable?

Is Evolution Predictable? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Stick insects show that evolution is more random than some biologists believed

Arjen ten Have's insight:

Stick insects show that evolution is more random than some biologists believed. That is the conclusion of journal Science, I wonder. I would agree for this case but I also think it will really depend on the possibilities. Imagine a trait that involves only 1 gene and a trait that depends on 20 genes. It will be clear that if you put a constraint related to these two traits, in the simple case, evolution will have to change that one gene, whereas in second complex case there might me many solutions. I can make it stronger by restricting further the example: the one locus case needs to evolve an enzyme with a larger substrate binding cleft. Would we be really surprised to find enzymes with a larger substrate binding cleft?  The authors are correct in this case but it will always depend on the case. Certain cases will have a very restricted solution space whereas others might have a very large solution space.

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