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James Tisdall, Beginning Perl for Bioinformatics | ShareBookFree.Com

James Tisdall, Beginning Perl for Bioinformatics | ShareBookFree.Com | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
James Tisdall, Beginning Perl for Bioinformatics ISBN: 0596000804 | edition 2001 | PDF | 394 pages | 13 mb With its highly developed capacity to detect (James Tisdall, Beginning Perl for Bioinformatics http://t.co/dgDPc4Y2N3)...
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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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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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Human genome was shaped by an evolutionary arms race with itself

Human genome was shaped by an evolutionary arms race with itself | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Some description goes here.("Human genome was shaped by an evolutionary ar..." Sent from the ScienceDaily app http://t.co/RjWCMvwON7 #genomics @hgp)...
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And still people deny Dawkins! The principal unit of selection is the gene. Selection at higher levels of organization can be explained by gene selection. That does not mean that for instance individue selection does not affect gene selection. It does but in the end it is always the gene and the interaction with its environment. That is a crucial point in interactions. Here we know whether it is the chicken or the egg.
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Experts provide much-needed policy analysis for clinical integration of next-generation sequencing

Experts provide much-needed policy analysis for clinical integration of next-generation sequencing | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
As genetic sequencing technologies continue to evolve rapidly, becoming part of clinical care, there is a critical need to establish appropriate policies and regulatory frameworks to address potential challenges, legal and ethical experts have said.
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Frontiers: Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors (2014)

Frontiers: Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors (2014) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.


Via Kamoun Lab @ TSL
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Ten Simple Rules for Better Figures

PLOS Computational Biology is an open-access
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You Can't Have Science 2.0 Without Statistics - Or Big Data Either

You Can't Have Science 2.0 Without Statistics - Or Big Data Either | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Arjen ten Have's insight:
Sooooo true. I need a biostatician in my team, and they simply do not exist!
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An association analysis between psychophysical characteristics and genome ... - Nature.com

An association analysis between psychophysical characteristics and genome ...
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The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers

The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The GOBLET Training Portal: A Global Repository of #Bioinformatics Training Materials, Courses and Trainers http://t.co/mHZNgWk1ip
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The ISME Journal - Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease

The ISME Journal - Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in...
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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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Origins of major archaeal clades correspond to gene acquisitions from bacteria : Nature : Nature Publishing Group

Origins of major archaeal clades correspond to gene acquisitions from bacteria : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms[mdash]ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.
Arjen ten Have's insight:

HGT is for prokaryotes as sex is for eukaryotes. They form the  most interesting emergent property of evolution. But this goes beyond the fact that HGT is pretty normal in prokaryotes: This paper actually shows it drives evolution and speciation, and indirectly substantiates the hypothesis that early and prokaryote evolution is communal, which explains the evolution of the genetic code. Oh my, this is YUMMIIE!

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In-depth introduction to machine learning in 15 hours of expert videos

In-depth introduction to machine learning in 15 hours of expert videos | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
In January 2014, Stanford University professors Trevor Hastie and Rob Tibshirani (authors of the legendary Elements of Statistical Learning textbook) taught an online course based on their newest textbook, An Introduction to Statistical Learning...
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PLOS Collections : Article collections published by the Public Library of Science

PLOS Collections : Article collections published by the Public Library of Science | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
PLOS Collections: Article collections published by the Public Library of Science
Arjen ten Have's insight:
Often I find it difficult to get proper insights into theoretical and practial aspects of novel techniques and technology. This is nice start page to look for some.
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The robustness and innovability of protein folds

Arjen ten Have's insight:
This provides a nice introduction to the topics of protein robustness and evolvability. I found it somewhat confusing, but I guess that was part of the purpose of this opinion. Basically they introduce scaffold-active site polarity. The more the active site can be seen separate from the scaffold, the more robust and the more innovable it is. Certainly makes sense, but how does one define scaffold and do we determine separateness? Likely, this should be seen as a principle, conceptual or even metaphorical, rather than that one should think in the BI tool.
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The changing face of the molecular evolutionary clock: Trends in Ecology & Evolution

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Studying the co-evolution of protein families with the Mirrortree web server

Studying the co-evolution of protein families with the Mirrortree web server | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
RT @RomainStuder: #eccb14 MirrorTree Server http://t.co/fRtgqyteFM is based on the primary work from Pazos and @Alfons_Valencia http://t.co
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Sequencing 100,000 genomes is exciting but how will it transform care for patients?

Sequencing 100,000 genomes is exciting but how will it transform care for patients? | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The 100,000 Genomes Project has just sequenced the 100th genome.
Arjen ten Have's insight:
basically we need easily accesible databases and a proper understanding of statistics for MDs. In addition, decisions will improve if they are made by groups of MD and scientists. Hospitals need to hire trained bioanalysts.
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BioTechniques - Library construction for next-generation sequencing: Overviews and challenges

BioTechniques - Library construction for next-generation sequencing: Overviews and challenges | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of...
Arjen ten Have's insight:
Very nice review on library prep for NGS. This and other papers by biotehniques are really important sonce it opens the door for biologists to this powerful technology.
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The changing face of the molecular evolutionary clock: Trends in Ecology & Evolution

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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.