Systems biology and bioinformatics
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Rescooped by Dmitry Alexeev from Complexity & Systems
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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)

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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)

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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

 

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CoNet

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

cytoscape tool for metagenomics networks

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22. Emergence and Complexity - YouTube

(May 21, 2010) Professor Robert Sapolsky gives a lecture on emergence and complexity. He details how a small difference at one place in nature can have a hug...
Dmitry Alexeev's insight:

butiful speaker

 

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António F Fonseca's curator insight, January 10, 2014 4:34 AM

A long but very interesting lecture about Emergence and Complexity from Stanford.

Rescooped by Dmitry Alexeev from Bioinformatics and holobiota
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PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access

Via Alexander Tyakht
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Alexander Tyakht's curator insight, December 26, 2013 4:46 AM

modelling gut microbiota behavior with differential equations

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BMC Bioinformatics | Abstract | A flexible statistical model for alignment of label-free proteomics data ¿ incorporating ion mobility and product ion information

The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions.
Dmitry Alexeev's insight:

few words on protein spectra alignment

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Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity

Constant activity of stationary-phase bacteria [Systems Biology] http://t.co/JEqohcTAJ3
Dmitry Alexeev's insight:

stationary phase single cell study

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PLOS ONE: A Metagenomic Framework for the Study of Airborne Microbial Communities

PLOS ONE: A Metagenomic Framework for the Study of Airborne Microbial Communities | 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:

metagenome is us)

 

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Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis

This apparently attracted much public attention, see http://www.scoop.it/t/statistical-omics/p/4012505889/2013/12/11/altmetric-2013-top-100

Dmitry Alexeev's insight:

however is you get meat and antibiotics - your risk is normal)

 

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Professional stuff - рабочие заметки

Professional stuff - рабочие заметки | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

just found out the our great friend Yuri has a wonderful blog which is a mix of science and life - which actually makes science so lively and life so scientific)

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Using networks to measure similarity between genes: association index selection : Nature Methods : Nature Publishing Group

Using networks to measure similarity between genes: association index selection : Nature Methods : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks.
Dmitry Alexeev's insight:

Fine measure of identity) - protein interaction partners
Tell me who your friends and i will tell you who you are) 

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Data deadline

Data deadline | Systems biology and bioinformatics | Scoop.it
Time is running out to comment on the NIH’s plan for sharing genomic data.
Dmitry Alexeev's insight:

well the decision will result in the future development of bioinformtaics 

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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!!!

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Alexander Tyakht's curator insight, January 15, 2014 1:59 AM

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

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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

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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)

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Discovery and saturation analysis of cancer genes across 21 tumour types : Nature : Nature Publishing Group

Discovery and saturation analysis of cancer genes across 21 tumour types : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

more NGS, more cancers more genes

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Cell - Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

Dmitry Alexeev's insight:

gee we are more of our guts then we ever thought

 

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Integration of Protein Abundance and Structure Data Reveals Competition in the ErbB Signaling Network -- Kiel et al. 6 (306): ra109 -- Science Signaling

Dmitry Alexeev's insight:

And this one is fantastic

really showing the possibility of global complex organization influencing the signalling

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DNA seen through the eyes of a coder

DNA seen through the eyes of a coder | Systems biology and bioinformatics | Scoop.it
DNA seen through the eyes of a coder http://t.co/RSc9hoLLb0 #genetics #bioinformatics #idiotsguide #codemonkeys
Dmitry Alexeev's insight:

if dna was a computer code

 

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BMC Bioinformatics | Full text | Processing gen...

BMC Bioinformatics | Full text | Processing gen... | Systems biology and bioinformatics | Scoop.it
“ Modern biological science generates a vast amount of data, the analysis of which presents a major challenge to researchers.” (BMC Bioinformatics | Full text | Processing genome scale tabular data with wormtable http://t.co/P8calM2A0B)...
Dmitry Alexeev's insight:

We introduce a new data format and software library called wormtable, which provides efficient access to tabular data in Python. Wormtable stores data in a compact binary format, provides random access to rows, and enables sophisticated indexing on columns within these tables. Files written in existing formats can be easily converted to wormtable format, and we provide conversion utilities for the VCF and GTF formats.

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PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

PLOS Computational Biology: Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

done on c difficile time series

 

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Metropolome | The Scientist Magazine®

Metropolome | The Scientist Magazine® | Systems biology and bioinformatics | Scoop.it
Researchers take advantage of rapid and cheap DNA sequencing technologies to map the bacterial microbiome of New York City.
Dmitry Alexeev's insight:

while new strains are in NY metro - i'm sure in Moscow we have new species

 

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The altered landscape of the human skin microbiome in patients with primary immunodeficiencies

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
Dmitry Alexeev's insight:

Thanks to Yuri - this is near to what we start to research

 

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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

what is a strain and waht is a species?

 

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