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BMC Bioinformatics | Abstract | JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to...
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should be strainghtforward with genomic context analysis

 

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Genetic Diversity of Viable, Injured, and Dead Fecal Bacteria Assessed by Fluorescence-Activated Cell Sorting and 16S rRNA Gene Analysis

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are they dead or alive actually?

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PLOS Computational Biology: Chapter 12: Human Microbiome Analysis

PLOS Computational Biology: Chapter 12: Human Microbiome Analysis | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

chapter from the book - translational bioinformatics

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Straight talk with...Stephen O'Brien : Nature Medicine : Nature Publishing Group

Straight talk with...Stephen O'Brien : Nature Medicine : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
In December 2011, Stephen O'Brien stepped down as head of the US National Cancer Institute's Laboratory of Genomic Diversity and took up a three-year, $5 million 'megagrant' in Russia through a program started a year earlier...
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PLOS ONE: Disruption of the S41 Peptidase Gene in Mycoplasma mycoides capri Impacts Proteome Profile, H2O2 Production, and Sensitivity to Heat Shock

PLOS ONE: Disruption of the S41 Peptidase Gene in Mycoplasma mycoides capri Impacts Proteome Profile, H2O2 Production, and Sensitivity to Heat Shock | Systems biology and bioinformatics | 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.
Dmitry Alexeev's insight:

peptidase involved in stress response in mycoplasmas

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Simply Statistics

Simply Statistics | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

extensive blog of my teacheer a coursera

 

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Mycoplasma genitalium attaches to human spermatozoa

Mycoplasma genitalium attaches to human spermatozoa | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

whoa - mycoplasmas are travelling on spermatozoa - looks like they use every vessel available

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PLOS ONE: Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

PLOS ONE: Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data | Systems biology and bioinformatics | 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.
Dmitry Alexeev's insight:

following his promise Patricio published a paper on power calc - he was presenting in spring

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Translational Bioinformatics: PLOS Computational Biology presents an educational resource for an emerging field | PLOS Biologue

Translational Bioinformatics: PLOS Computational Biology presents an educational resource for an emerging field | PLOS Biologue | Systems biology and bioinformatics | Scoop.it
RT @Genomicsnew: Translational Bioinformatics: PLOS Computational Biology presents an ... - PLoS Blogs (blog) http://t.co/BnmhONXN
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Comprehensive effort and I like the name

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How did bacterial ancestors reproduce? Lessons from L-form cells and giant lipid vesicles - Briers - 2012 - BioEssays - Wiley Online Library

How did bacterial ancestors reproduce? Lessons from L-form cells and giant lipid vesicles - Briers - 2012 - BioEssays - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

from mycoplasma to L form only one step)

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PLOS ONE: Insights from Characterizing Extinct Human Gut Microbiomes

PLOS ONE: Insights from Characterizing Extinct Human Gut Microbiomes | Systems biology and bioinformatics | 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.
Dmitry Alexeev's insight:

it was very differnt 1000 of years before

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HTS mappers

HTS mappers | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

a lot of data for all mappers) - actually a good point for visualization

 

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Research methods: Know when your numbers are significant

Research methods: Know when your numbers are significant | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

this is a good motivation article - in spite of Tyakht coming statistics course

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uBiome -- Sequencing Your Microbiome

uBiome -- Sequencing Your Microbiome | Systems biology and bioinformatics | Scoop.it
World's FIRST citizen science project to sequence the human microbiome. Available INTERNATIONALLY in 196 countries. Learn about your health & change the world!
Dmitry Alexeev's insight:

Startup for microbiota sequencing based on crowd sourcing

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PLOS ONE: The Active Human Gut Microbiota Differs from the Total Microbiota

PLOS ONE: The Active Human Gut Microbiota Differs from the Total Microbiota | Systems biology and bioinformatics | 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.
Dmitry Alexeev's insight:

well lets see who is active in the end of the tunnel

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Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease : Nature Biotechnology : Nature Publishing Group

Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease : Nature Biotechnology : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Kwong et al. use nanoparticles coated with protease substrates to generate mass-encoded synthetic biomarkers for sensitive detection of fibrosis and cancer in mice.
Dmitry Alexeev's insight:

looks promising - sesarching for biomarkers you create yourself

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Detecting Novel Associations in Large Data Sets

Dmitry Alexeev's insight:

one year old publication of tool suitable for baseball as well as for biology/

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ScienceDirect.com - Journal of Proteomics - EasyProt — An easy-to-use graphical platform for proteomics data analysis

ScienceDirect.com - Journal of Proteomics - EasyProt — An easy-to-use graphical platform for proteomics data analysis | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

proteomics pipelines are seldom made - for there is already enough - however there is a new one

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Genome Biology | Abstract | Ray Meta: scalable de novo metagenome assembly and profiling

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling.
Dmitry Alexeev's insight:

metagenome assembley - while russia is sleeping everybody's working

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Landes Bioscience Journals: Mobile Genetic Elements

Landes Bioscience Journals: Mobile Genetic Elements | Systems biology and bioinformatics | Scoop.it
DNA methylation is one of the best studied epigenetic modifications observed in prokaryotes as well as eukaryotes. It affects nearby gene expression.
Dmitry Alexeev's insight:

Ischizo Kobayashi with a favorable hypothesys)

he is one of my favourites - so clear thinking

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Linking disease associations with regulatory information in the human genome

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms (RT @moorejh: #genomics #bioinformatics #GWAS RT @ENCODE_NIH: Linking human disease variants...
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Rescooped by Dmitry Alexeev from Bioinformatics Training
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BRAIN POWER: From Neurons to Networks

Directed by @tiffanyshlain Please share this film far and wide! Suggested ways below. Check out the #TEDBook that accompanies this film. Info at: http://www....

Via Pedro Fernandes
Dmitry Alexeev's insight:

This is actually the future  - still there is a chance to catch up)

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The ISME Journal - The chemical interactome space between the human host and the genetically defined gut metabotypes

The ISME Journal - The chemical interactome space between the human host and the genetically defined gut metabotypes | Systems biology and bioinformatics | 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...
Dmitry Alexeev's insight:

they go deeper and deeper
how do we catch up? 

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Rescooped by Dmitry Alexeev from Virology and Bioinformatics from Virology.ca
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PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species


Via Chris Upton + helpers
Dmitry Alexeev's insight:

tell me who your neighbours - and i will tell you who you are

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ROSALIND | Problems

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how many tasks have you done i wonder?

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