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Roxygen

Dmitry Alexeev's insight:

Google summer of code endeavour to make a self decribing code

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The Amordad database engine for metagenomics

The Amordad database engine for metagenomics | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

 Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.

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Controllability in protein interaction networks

Controllability in protein interaction networks | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we're back again after months of grant applications and writing a new paper on pp interaction and proteomics - this piece will be very handy

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Mathematics to improve running

Mathematics to improve running | Systems biology and bioinformatics | Scoop.it
How can runners improve their performance, weight and fitness? Researchers have produced a mathematical model to optimize running, which could lead to personal e-coaching customized to each individual's physiological state. It also confirms a well-known fact in the sports community: runners who vary their speed spend their energy better and thus run longer. Mathematics gives them the opportunity to switch from simple statistical tools to personalized sporting advice.
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Microbiology: Barriers to the spread of resistance : Nature : Nature Publishing Group

Microbiology: Barriers to the spread of resistance : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Despite identifying abundant genes capable of conferring antibiotic resistance in soil microorganisms, a study finds that few are shared by human pathogens and that there is little transfer of the genes within the soil communities. See Letter p.612
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Towards predictive models of the human gut microbiome

Towards predictive models of the human gut microbiome | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

fine review of modelling and way to go directions

 

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The proteomics quantification dilemma

The proteomics quantification dilemma | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

completely adore this author for his principial position on the subject - no to bottom up proteomics

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Mel Melendrez-Vallard's curator insight, April 14, 5:47 AM

For those that have access to the journal.

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Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

stream of knowledge lately has been working to keep us thinking tight

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Alexander Tyakht's curator insight, April 8, 11:42 PM

genomic diversity with focus on pathogen populations

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GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

it is becoming used more

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.

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Annual Progress Report - DOE Joint Genome Institute

Annual Progress Report - DOE Joint Genome Institute | Systems biology and bioinformatics | Scoop.it
The institute's annual report of its activities.
Dmitry Alexeev's insight:

cumulative of 1000 papaers Joint Genoe Institute report 2013

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No paradox, no progress: inverse cancer comorbidity in people with other complex diseases

Dmitry Alexeev's insight:

something good to know)

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Pathogens | Free Full-Text | Heat Shock Proteins: Intestinal Gatekeepers that Are Influenced by Dietary Components and the Gut Microbiota

Pathogens | Free Full-Text | Heat Shock Proteins: Intestinal Gatekeepers that Are Influenced by Dietary Components and the Gut Microbiota | Systems biology and bioinformatics | Scoop.it
Trillions of microorganisms that inhabit the intestinal tract form a diverse and intricate ecosystem with a deeply embedded symbiotic relationship with their hosts. As more detailed information on gut microbiota complexity and functional diversity accumulates, we are learning more about how diet-microbiota interactions can influence the immune system within and outside the gut and host health in general. Heat shock proteins are a set of highly conserved proteins that are present in all types of cells, from microbes to mammals. These proteins carry out crucial intracellular housekeeping functions and unexpected extracellular immuno-regulatory features in order to maintain the mucosal barrier integrity and gut homeostasis. It is becoming evident that the enteric microbiota is one of the major determinants of heat shock protein production in intestinal epithelial cells. This review will focus on the interactions between diet, gut microbiota and their role for regulating heat shock protein production and, furthermore, how these interactions influence the immune system and the integrity of the mucosal barrier.
Dmitry Alexeev's insight:

microbiota and heatshock - some of the topics we unite in our research

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Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

hey did we miss that one?

 

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Decontaminating Sequencing Samples - Bio-IT World

Decontaminating Sequencing Samples - Bio-IT World | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Appistry piplines 

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Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria : Article : Nature

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria : Article : Nature | Systems biology and bioinformatics | Scoop.it
Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.
Dmitry Alexeev's insight:

having a lot of data on metaaproteomics we are out to search all the possibilities data can provide

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Bioinformatics: Big data versus the big C : Nature : Nature Publishing Group

Bioinformatics: Big data versus the big C : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The torrents of data flowing out of cancer research and treatment are yielding fresh insight into the disease.
Dmitry Alexeev's insight:

yielding fresh insight

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Mass-spectrometry-based draft of the human proteome : Nature : Nature Publishing Group

Mass-spectrometry-based draft of the human proteome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
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Tribal gathering

Tribal gathering | Systems biology and bioinformatics | Scoop.it
Before they can construct a cell, researchers in synthetic biology must first build bridges between disciplines.
Dmitry Alexeev's insight:

amazing collection of papers and reviews and editorials on synbio by nature

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genoplotr

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

came across a nice package to R based gene plotting

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Network Biology

Network Biology | Systems biology and bioinformatics | Scoop.it
Network Biology
Dmitry Alexeev's insight:

the page camoe useful for me with marveloous collection of works and refernces

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Nalina Nagarajan's curator insight, April 23, 7:41 AM

Systems Biology?

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Global modeling of transcriptional responses in interaction networks

Global modeling of transcriptional responses in interaction networks | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues.

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Cell - A Whole-Cell Computational Model Predicts Phenotype from Genotype

Cell - A Whole-Cell Computational Model Predicts Phenotype from Genotype | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we are up into whole cell modelling)

and what are you up to today?))

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A Second-generation Protein-Protein Interaction Network of Helicobacter pylori

Dmitry Alexeev's insight:

This is exactly what we need now - a comprehensive wide network of PPI fro helicobacter pylori

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Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium | 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:

Medieval coprolites! Wonder is amount of pathogens found ... makes us think)

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Addendum: Enterotypes of the human gut microbiome : Nature : Nature Publishing Group

Addendum: Enterotypes of the human gut microbiome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

"It has been drawn to our attention that the methods described in the main text and the Supplementary Information of this Article have been considered by some researchers to be insufficient to enable them to identify enterotypes in their own data sets."

Good start for the Nature addendum - and yes we were among those researchers who were unable to identify )))



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Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies

Dmitry Alexeev's insight:

issues of biota manipulation

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