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Nanopore sequencing technology lands licensing deal | UW Today

Nanopore sequencing technology lands licensing deal | UW Today | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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It seems Illumina will become the leading factor in NGS!

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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 - 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...
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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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Stepwise Threshold Clustering: A New Method for Gen... [PLoS One. 2014] - PubMed - NCBI

PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Towards the Standard Model of Evolution

Towards the Standard Model of Evolution | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The so-called Modern Synthesis of Evolution was shaped by men like Fisher, Dobzhansky, and Wright, somewhere in the mid 20th century. A lot has happened since then but I cannot say things have become
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Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online

Ewan's Blog: bioinformatician at large: Scaling up bioinformatics training online | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Scaling bioinformatics training online. Blog post on @emblebi's train online portal http://t.co/xYXxAp4vUl
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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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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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RNA determination opens up the possibility of evolutionary discoveries

RNA determination opens up the possibility of evolutionary discoveries | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Researchers from the University of Dundee have defined the structure of a recently discovered enzyme, raising the possibility of learning more about the evolution of organisms over billions of years.
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Cell membrane proteins give up their secrets

Cell membrane proteins give up their secrets | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Rice University scientists have succeeded in analyzing transmembrane protein folding in the same way they study the proteins' free-floating, globular cousins.
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Computational Cell Biology: Mechanistic Modeling for Experimentalists

Computational Cell Biology: Mechanistic Modeling for Experimentalists | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Cold Spring Harbor Laboratory 2014 Course - Computational Cell Biology: Mechanistic Modeling for Experimentalists, Jul 22, 2014 - Aug 11, 2014 (Computational Cell Biology: Mechanistic Modeling for Experimentalists
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Biological applications of the theory of birth-and-death processes

Biological applications of the theory of birth-and-death processes | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
“Biological applications of the theory of birth-and-death processes”, emphasis on evol. genomics - http://t.co/7nuOS7RI1E
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Review applying birth and death evolution to systematics

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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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