Somethings Biotech
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Somethings Biotech
Observations of the world of biotechnology
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InteractiVenn - Interactive Venn Diagrams

InteractiVenn is an interactive visualization tool for analyzing lists of elements using Venn diagrams. The web tool supports up to six different sets. Moreover, union operations between sets can be made. The union operations are reflected to the Venn diagram. Other interactions are also available, such as color changing and export diagram in SVG and PNG format. We suggests the use of Inkscape to edit the Venn diagrams exported by InteractiVenn.
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Infectious disease hunter raises $30M to support epidemic risk management - MedCity News

Infectious disease hunter raises $30M to support epidemic risk management - MedCity News | Somethings Biotech | Scoop.it
Metabiota is applying big data analytics to help better predict and help companies insure against the impact of infectious disease outbreaks.
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Workshops (2015) | Bioinformatics.ca

Workshops (2015) | Bioinformatics.ca | Somethings Biotech | Scoop.it
bioinformatics.ca is home to all things bioinformatics in Canada. Hosted here are the Canadian Bioinformatics Workshops and a bioinformatics careers section, as well as bioinformatics community resources and information.
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SNPer: An R Library for Quantitative Variant Analysis on Single Nucleotide Polymorphisms among Influenza Virus Populations. - PLoS One

Influenza virus (IFV) can evolve rapidly leading to genetic drifts and shifts resulting in human and animal influenza epidemics and pandemics. The genetic shift that gave rise to the 2009 influenza A/H1N1 pandemic originated from a triple gene reassortment of avian, swine and human IFVs. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. Hence, a rapid tool to detect IFV mutations and the potential emergence of new virulent strains can better prepare us for seasonal influenza outbreaks as well as potential pandemics. Furthermore, identification of specific mutations by closely examining single nucleotide polymorphisms (SNPs) in IFV sequences is essential to classify potential genetic markers associated with potentially dangerous IFV phenotypes. In this study, we developed a novel R library called "SNPer" to analyze quantitative variants in SNPs among IFV subpopulations. The computational SNPer program was applied to three different subpopulations of published IFV genomic information. SNPer queried SNPs data and grouped the SNPs into (1) universal SNPs, (2) likely common SNPs, and (3) unique SNPs. SNPer outperformed manual visualization in terms of time and labor. SNPer took only three seconds with no errors in SNP comparison events compared with 40 hours with errors using manual visualization. The SNPer tool can accelerate the capacity to capture new and potentially dangerous IFV strains to mitigate future influenza outbreaks.


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Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification | Somethings Biotech | Scoop.it

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An Easy-to-follow Introductory Book on NGS Assembly Algorithms « Homolog.us – Bioinformatics

An Easy-to-follow Introductory Book on NGS Assembly Algorithms « Homolog.us – Bioinformatics | Somethings Biotech | Scoop.it

Via Mel Melendrez-Vallard
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SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation | Somethings Biotech | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies | Somethings Biotech | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing

Epstein-Barr Virus Cut Out Of Infected Human Cells By CRISPR-Cas9 Genome Editing | Somethings Biotech | Scoop.it

Researchers at Stanford exploited the newly developed precision gene editing technology known CRISPR-Cas9 into an anti-virus technology by cutting out Epstein-Barr virus from the host genome of infected cells.  Infected cells successfully treated this way scale back proliferation caused by viral programs and engage in a self-destruct program known as “apoptosis”, or controlled cell death.  EBV is known to express a “brake” protein that suppresses apoptosis, a way to evade natural defense mechanisms.  The researchers also show importantly that there was no toxic effect on non-infected cells.

 

Epstein-Barr virus (EBV) is most often associated with mononucleosis but is also a cause of more serious conditions such as Burkitt’s lymphoma, nasopharyngeal cancer, and even autoimmune diseases.   No therapy exists but the CRISPR-Cas9 study is a valuable avenue as it overcomes two challenges posed by the virus.

 

The first challenge is during the latent stage of its life cycle it integrates into the genome and exhibits few targets for intervention. In fact most therapeutics under development are focused on attacking the virus during its active “lytic” stage so are not expected to work for cells with virus in latent stage.  In the latent stage the virus is still “on”, running a latency program that prompts the cell to proliferate.

 

The second challenge is that the virus encodes and expresses with the help of the host cell a “brake” protein BHRF1that stops the self-destruct signal stimulated by immune cells in effort to rid the body of cells that have become compromised.   The “brake” signal is one reason why EBV is frequently found in cancers: under normal conditions cells that start off on the path to cancer by acquiring mutations get stopped by the cell’s natural ability to undergo “programmed cell death” but EBV halts this process.

 

The technology for CRISPR-Cas9 entails two parts.  The first is the “cutting” enzyme, which is able to cut out pieces of viral DNA that has integrated into the host genome.  The second is a “guide RNA” which is a nucleic acid template that matches the desired target, in this case parts of the EBV sequence.  The researchers designed a CRISPR-Cas9 system that targets EBV based on its sequence in computer databases.

 

Once the cells were treated the researches found that latently infected cells no longer proliferated.  To ensure that this was not a toxic effect of treatment, the same CRISPR-Cas9 system was applied to cells that lack EBV, in which case there was no effect on proliferation.  This is an important point as some criticize CRISPR-Cas9 for its off-target effects in which unintentional cutting occurs.


Via Dr. Stefan Gruenwald
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CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure

Summary: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions.

Availability and implementation: CorMut is released under the GNU General Public License within bioconductor project, and freely available athttp://bioconductor.org/packages/release/bioc/html/CorMut.html.

Contact: mal@chinaaids.cn or yshao08@gmail.com


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Ebola virus protein offers potential drug target

Ebola virus protein offers potential drug target | Somethings Biotech | Scoop.it
An Ebola protein that is key to virus replication has a unique and unusual structure not seen in other human viral diseases. Researchers suggest it could be a new drug target.
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How the Ebola outbreak compares to other killers

How the Ebola outbreak compares to other killers | Somethings Biotech | Scoop.it
The Ebola outbreak centered in West Africa continues to expand its reach, with the World Health Organization recently announcing the infectious disease could  afflict more than 20,000 people within the next nine months.

Via Aid & Development
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Graph Theory – Ways to Uncover Valuable Insights About Data

Graph Theory – Ways to Uncover Valuable Insights About Data | Somethings Biotech | Scoop.it
Graph theory provides analytic tools to find relationships in any information in the system to get new, more actionable and relevant answers (Graph Theory – Ways to Uncover Valuable Insights About Data http://t.co/ogXqrhQeXR)...
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A Unique Virulence Gene Occupies a Principal Position in Immune Evasion by the Malaria Parasite Plasmodium falciparum. - PubMed - NCBI

A Unique Virulence Gene Occupies a Principal Position in Immune Evasion by the Malaria Parasite Plasmodium falciparum. - PubMed - NCBI | Somethings Biotech | Scoop.it
PLoS Genet. 2015 May 19;11(5):e1005234. doi: 10.1371/journal.pgen.1005234. eCollection 2015.
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Center for Infectious Disease Research Hosts “Rally for Global Health” | Business Wire

Center for Infectious Disease Research Hosts “Rally for Global Health” | Business Wire | Somethings Biotech | Scoop.it
The Center for Infectious Disease Research (formerly Seattle BioMed) hosted the “Rally for Global Health” today to raise awareness for the
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Combatting Viruses with RNA-Targeted CRISPR | The Scientist Magazine®

Combatting Viruses with RNA-Targeted CRISPR | The Scientist Magazine® | Somethings Biotech | Scoop.it
Scientists reengineer a Cas9 enzyme that naturally targets bacterial RNA to stymie hepatitis C inside human cells.
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Malaria - Life Cycle of Plasmodium [HD Animation] - YouTube

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/
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Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data

Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data | Somethings Biotech | Scoop.it
Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data Michael Gilchrist, Wei-Chen Chen, Premal Shah, Russell Zaretz...
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DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis

Background: Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets.
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transphylo - Bayesian inference of infectious disease transmission from a phylogeny - Google Project Hosting

transphylo - Bayesian inference of infectious disease transmission from a phylogeny - Google Project Hosting | Somethings Biotech | Scoop.it

This is the homepage of TransPhylo, a software package for the Bayesian inference of infectious disease transmission from a phylogeny. The input is a dated phylogeny, where leaves correspond to pathogens isolated from the infected hosts. The main output is a transmission tree which indicates who infected whom. Such reconstruction can be achieved by colouring the branches of the phylogeny using a separate colour for each host, and such that the subtree coloured in a given colour represents the evolution happening within the corresponding host. Changes of colours on branches therefore correspond to transmission events from one host to another.


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Conserved and host-specific features of influenza virion architecture : Nature Communications : Nature Publishing Group

Conserved and host-specific features of influenza virion architecture : Nature Communications : Nature Publishing Group | Somethings Biotech | Scoop.it

Viruses use virions to spread between hosts, and virion composition is therefore the primary determinant of viral transmissibility and immunogenicity. However, the virions of many viruses are complex and pleomorphic, making them difficult to analyse in detail. Here we address this by identifying and quantifying virion proteins with mass spectrometry, producing a complete and quantified model of the hundreds of host-encoded and viral proteins that make up the pleomorphic virions of influenza viruses. We show that a conserved influenza virion architecture is maintained across diverse combinations of virus and host. This ‘core’ architecture, which includes substantial quantities of host proteins as well as the viral protein NS1, is elaborated with abundant host-dependent features. As a result, influenza virions produced by mammalian and avian hosts have distinct protein compositions. Finally, we note that influenza virions share an underlying protein composition with exosomes, suggesting that influenza virions form by subverting microvesicle production.


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IBM Watson Analytics...Hunting for Tableau??

IBM Watson Analytics...Hunting for Tableau?? | Somethings Biotech | Scoop.it
Increase customer retention and advocacy by harnessing all the data at your disposal to make smarter predictions about their needs and behaviors.
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Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis | Chemistry

Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis | Chemistry | Somethings Biotech | Scoop.it
Effects of essential oil treatments on the secondary protein structure of Vicia faba: http://t.co/VZ5Fw2gFv2
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