Systems biology a...
Follow
Find
2.6K views | +1 today
Scooped by Dmitry Alexeev
onto Systems biology and bioinformatics
Scoop.it!

The mycoplasma virulence factor lipoprotein MslA is a novel polynucleotide binding protein

Dmitry Alexeev's insight:

We are sure the function is not transport - but regulation

more...
No comment yet.
Systems biology and bioinformatics
Your new post is loading...
Scooped by Dmitry Alexeev
Scoop.it!

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

 

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

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

For those that have access to the journal.

Scooped by Dmitry Alexeev
Scoop.it!

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

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

genomic diversity with focus on pathogen populations

Scooped by Dmitry Alexeev
Scoop.it!

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.

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

Dmitry Alexeev's insight:

something good to know)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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?

 

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Decontaminating Sequencing Samples - Bio-IT World

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

Appistry piplines 

more...
No comment yet.
Suggested by Alexander Tyakht
Scoop.it!

Evolution and transmission of drug-resistant tuberculosis in a Russian population : Nature Genetics : Nature Publishing Group

Evolution and transmission of drug-resistant tuberculosis in a Russian population : Nature Genetics : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Francis Drobniewski and colleagues report the whole-genome sequencing of 1,000 Mycobacterium tuberculosis strains obtained prospectively from patients over a 2-year period in Samara, Russia, a region with a high incidence of multidrug resistant...
Dmitry Alexeev's insight:

tubi from russia

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Human–microbe mismatch boosts risk of stomach cancer

Human–microbe mismatch boosts risk of stomach cancer | Systems biology and bioinformatics | Scoop.it
H. pylori strains more likely to cause tumours when they did not co-evolve with their hosts.
Dmitry Alexeev's insight:

This is AMAZING!!!

more...
Alexander Tyakht's curator insight, January 14, 10:59 PM

news about geo-tracked bacterium tracked by M. Achtman before.

Scooped by Dmitry Alexeev
Scoop.it!

Integrated metagenomics/metaproteomics reveals huma... [PLoS One. 2012] - PubMed - NCBI

Integrated metagenomics/metaproteomics reveals huma... [PLoS One. 2012] - PubMed - NCBI | Systems biology and bioinformatics | Scoop.it
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.
Dmitry Alexeev's insight:

crohn's metaproteomics - we'll save it for later

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

Dmitry Alexeev's insight:

all your base are belong to us! - metagenome controlling species hybrid survival - hologenome proofs)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

genoplotr

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

came across a nice package to R based gene plotting

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

more...
Nalina Nagarajan's curator insight, Today, 7:41 AM

Systems Biology?

Scooped by Dmitry Alexeev
Scoop.it!

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.

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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?))

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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 )))



more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

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

Dmitry Alexeev's insight:

issues of biota manipulation

more...
No comment yet.
Rescooped by Dmitry Alexeev from Papers
Scoop.it!

Molecular biology: A second layer of information in RNA

Molecular biology: A second layer of information in RNA | Systems biology and bioinformatics | Scoop.it

Three studies have characterized the full complement of RNA folding in cells. They find large numbers of secondary structures in RNA, some of which may have functional consequences for the cell.

 

Molecular biology: A second layer of information in RNA
Silvia B. V. Ramos & Alain Laederach

Nature 505, 621–622 (30 January 2014) http://dx.doi.org/10.1038/505621a


Via Complexity Digest
more...
No comment yet.
Rescooped by Dmitry Alexeev from Complexity - Complex Systems Theory
Scoop.it!

Marie Curie says stop hating on quilt plots already. | Simply Statistics

Marie Curie says stop hating on quilt plots already. | Simply Statistics | Systems biology and bioinformatics | Scoop.it

"There are sadistic scientists who hurry to hunt down error instead of establishing the truth." -Marie Curie (http://en.wikiquote.org/wiki/Marie_Curie)


Via Bernard Ryefield
Dmitry Alexeev's insight:

we support no ntrolling quiltplots)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Connecting the Dots between PubMed Abstracts

Connecting the Dots between PubMed Abstracts | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

somformulas but i like)

more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

Probabilistic inference of biochemical reac... [PLoS Comput Biol. 2013] - PubMed - NCBI

Probabilistic inference of biochemical reac... [PLoS Comput Biol. 2013] - PubMed - NCBI | Systems biology and bioinformatics | Scoop.it
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.
Dmitry Alexeev's insight:

have to read this one

 

more...
No comment yet.