Systems biology and bioinformatics
4.9K views | +0 today
Follow
Systems biology and bioinformatics
Your new post is loading...
Your new post is loading...
Scooped by Dmitry Alexeev
Scoop.it!

Intestinal Microbiota Containing Barnesiella Sp... [Infect Immun. 2013] - PubMed - NCBI

Intestinal Microbiota Containing Barnesiella Sp... [Infect Immun. 2013] - PubMed - NCBI | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

there is more and more and fecal transplants 

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

The Human Microbiome Gets A Big Pharma Investment - Forbes

The Human Microbiome Gets A Big Pharma Investment - Forbes | Systems biology and bioinformatics | Scoop.it
The Human Microbiome Gets A Big Pharma Investment Forbes “This is an area of great importance for our R&D strategy for immunology because we believe it can bring in the mid-term and long-term value toward our goal of addressing unmet medical need,”...

Via Gilbert C FAURE, Clara Belzer
more...
No comment yet.
Rescooped by Dmitry Alexeev from Amazing Science
Scoop.it!

Earth is surrounded by a 'bubble' of live bacteria - at 33 000 feet

Earth is surrounded by a 'bubble' of live bacteria - at 33 000 feet | Systems biology and bioinformatics | Scoop.it

Earth’s upper atmosphere—below freezing, nearly without oxygen, flooded by UV radiation—is no place to live. But last winter, scientists from the Georgia Institute of Technology discovered that billions of bacteria actually thrive up there. Expecting only a smattering of microorganisms, the researchers flew six miles above Earth’s surface in a NASA jet plane. There, they pumped outside air through a filter to collect particles. Back on the ground, they tallied the organisms, and the count was staggering: 20 percent of what they had assumed to be just dust or other particles was alive. Earth, it seems, is surrounded by a bubble of bacteria.

 

Scientists don’t yet know what the bacteria are doing up there, but they may be essential to how the atmosphere functions, says Kostas Konstantinidis, an environmental microbiologist on the Georgia Tech team. For example, they could be responsible for recycling nutrients in the atmosphere, like they do on Earth. And similar to other particles, they could influence weather patterns by helping clouds form. However, they also may be transmitting diseases from one side of the globe to the other. The researchers found E. coli in their samples (which they think hurricanes lifted from cities), and they plan to investigate whether plagues are raining down on us. If we can find out more about the role of bacteria in the atmosphere, says Ann Womack, a microbial ecologist at the University of Oregon, scientists could even fight climate change by engineering the bacteria to break down greenhouse gases into other, less harmful compounds.


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

we are everywhere)

more...
Vloasis's curator insight, June 21, 2013 3:51 PM

Holy crap!  I never considered this...

Ed Rybicki's comment, June 25, 2013 3:39 AM
Hey, it's a microbial world - literally! From way above our heads, to way below our feet.
Dmitry Alexeev's curator insight, July 28, 2013 7:31 AM

we'll have that one in our book as well

 

Scooped by Dmitry Alexeev
Scoop.it!

New Measure of Human Brain Processing Speed | MIT Technology Review

New Measure of Human Brain Processing Speed | MIT Technology Review | Systems biology and bioinformatics | Scoop.it
A new way to analyze human reaction times shows that the brain processes data no faster than 60 bits per second.
Dmitry Alexeev's insight:

sorry it is not so fresh - from 2009)

but it is worth knowing

more...
No comment yet.
Rescooped by Dmitry Alexeev from Innovation and Science breakthroughs
Scoop.it!

Evidence that probiotics alter brain function

Evidence that probiotics alter brain function | Systems biology and bioinformatics | Scoop.it

In a discovery that carries significant implications for changing brain function through dietary interventions, UCLA researchers say they now have the first evidence that bacteria ingested in food can affect how the human brain works. The study, which focused on women who consumed yogurt containing the bacteria known as probiotics, appears in the journal Gastroenterology.


Via Pedro Barbosa
Dmitry Alexeev's insight:

Well this MRI studies are easI misinterpreted however - it is still a step towards 

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

Bio Journals From ACS Publications

Bio Journals From ACS Publications | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

includes a pdf guide from ACS on how to be found in modern science

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

Hive Plots - Linear Layout for Network Visualization - Visually Interpreting Network Structure and Content Made Possible

Hive Plots - Linear Layout for Network Visualization - Visually Interpreting Network Structure and Content Made Possible | Systems biology and bioinformatics | Scoop.it
more...
No comment yet.
Rescooped by Dmitry Alexeev from Microbes Inside
Scoop.it!

Ingestible gastrointestinal sampling device

Ingestible gastrointestinal sampling device | Systems biology and bioinformatics | Scoop.it

MONTREAL, April 26, 2013 /PRNewswire-iReach/ --Micropharma Limited, a pioneer in the development of innovative and effective products based on the human microbiome, today announced that after three years of development it has a timeline for launch of its ingestible gastrointestinal sampling technology.

 

Manipulation of the gut microbiome is becoming an important way to treat immune, gastrointestinal and metabolic disease.  Probiotic therapies affecting the human gut microbiome have gained regulatory approval and are now included as part of clinical guidelines for a wide range of indications.  Further, there are now a number of microbiome focused companies actively developing microbiome based diagnostics, identifying uses for small molecules acting through the microbiome and developing GMO stains to affect the microbiome. 


Via Clara Belzer
Dmitry Alexeev's insight:

You swallow - it collects the sample along the way - and here it is the microbiota from the inner part of yours) 

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

Systems biology technologies series

Systems biology technologies series | Systems biology and bioinformatics | Scoop.it
Molecular Systems Biology is a peer-reviewed author-pays online journal that publishes full-length papers and accompanying synopses describing original research in the field of molecular systems biology and which focuses on the analysis,...
Dmitry Alexeev's insight:

i started with metabolic reconstruction and went on further

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

Genome Biology | Full text | Genomic DNA k-mer spectra: models and modalities

The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with...
Dmitry Alexeev's insight:
K mers and genomes
more...
No comment yet.
Scooped by Dmitry Alexeev
Scoop.it!

periodic table of bioinformatic tools

Dmitry Alexeev's insight:

thanks to sergey musienko - periodic table of bioinformatic tools

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

The Emergence of Proactive P4 Medicine: A Revolution in Healthcare - Leroy Hood

Dr. Leroy Hood with the Institute of Systems Biology will focus on their efforts at taking a systems approach to diseases—looking at a neurodegenerative (pri...

Via Pedro Fernandes
Dmitry Alexeev's insight:

Leroy Hood is the master

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

Gut microbiota or gut flora? Prof. Joël Doré explains which term is best

We interviewed Prof.Joël Doré, Head of Research at the French National Institute for Agricultural Research (INRA - Institut National de la Recherche Agronomique), at the 2nd Gut Microbiota for Health Summit, in order to find out more about gut...

Via Clara Belzer
more...
Clara Belzer's curator insight, April 8, 2013 4:27 PM

I agree we should use the term microbiota to indicate the microorganisms in our intestine because microbes are not teh same as plants . Also be aware that microbiome is not the same as  microbiota. Microbiome is all microorgansims including their genetic content.

Scooped by Dmitry Alexeev
Scoop.it!

New book series on emergence, complexity, and computation.

New book series on emergence, complexity, and computation. | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

oh i want this book)

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

Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer

Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer | Systems biology and bioinformatics | Scoop.it

Evidence from twin and family studies suggests an inherited genetic component to epithelial ovarian cancer (EOC) risk. Rare, high-penetrance alleles of genes such as BRCA1 and BRCA2 account for about 40% of excess familial risk, and GWAS have recently identified common risk alleles at 9p22, 8q24, 2q31 and 19p13, with two additional loci at 3q25 and 17q21 that approached genome-wide significance. However these alleles only explain 4% of excess familial risk, and more risk loci probably exist.

 

A study group therefore recently pooled the data from two GWAS to inform the selection of SNPs for a large-scale replication. The North American study comprised 4 independent case-control studies that included 1,952 cases and 2,052 controls. The second study was a 2-phase multicenter GWAS that included 1,817 cases and 2,354 controls in the first phase and 4,162 cases and 4,810 controls in the second phase.

 

The researchers carried out a fixed-effects meta-analysis from the two GWAS for ~2.5 million genotyped or imputed SNPs. They selected 24,551 SNPs associated with the risk of either all-histology (11,647 SNPs) or serous (12,904 SNPs) ovarian cancer on the basis of ranked P values. They designed assays for 23,239 SNPs and included them on a custom Illumina Infinium iSelect array (iCOGS) comprising 211,155 SNPs designed by the Collaborative Oncological Gene-environment Study (COGS) to evaluate genetic variants for association with risk of breast, ovarian and prostate cancers. They then genotyped these SNPs in cases and controls from 43 individual studies from the Ovarian Cancer Association Consortium (OCAC) that were grouped into 34 case-control strata. These included most of the samples genotyped in the initial GWAS. An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility and implicated CHMP4C in the pathogenesis of ovarian cancer.  


Via Dr. Stefan Gruenwald
Dmitry Alexeev's insight:

is that a new method, Vova)?

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

PLOS Genetics: Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers

PLOS Genetics: Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers | Systems biology and bioinformatics | Scoop.it
PLOS Genetics is an open-access
Dmitry Alexeev's insight:

this one we are going to dig deeper in ontologies

 

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

Aid and Complex Systems cont'd: Timelines, Incubation Periods and ...

Aid and Complex Systems cont'd: Timelines, Incubation Periods and ... | Systems biology and bioinformatics | Scoop.it
I'm at one of those moments where all conversations seem to link to each other, I see complex systems everywhere, and I'm wondering whether I'm starting to lose my marbles. Happily, lots of other people seem to be suffering ...
Dmitry Alexeev's insight:

Very profound view on complexity 

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

ScienceDirect.com - Cell Host & Microbe - The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

ScienceDirect.com - Cell Host & Microbe - The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Mtb quantified - this is really a lot - work of system tb consortia

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

The Deadly Genomes - Genome Size and Structure of Harmful Bacteria and Viruses

The Deadly Genomes - Genome Size and Structure of Harmful Bacteria and Viruses | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Wow wow wow

this is amazing infographics back from 2009

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

ScienceDirect.com - Cell - Microbiota Keep the Intestinal Clock Ticking

ScienceDirect.com - Cell - Microbiota Keep the Intestinal Clock Ticking | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

is it at lunch time you want to eat?

- no, it is not you - they make you to want)

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

ProScope Micro Mobile Turns Any Apple iOS Device into Professional Microscope (w/video)

ProScope Micro Mobile Turns Any Apple iOS Device into Professional Microscope (w/video) | Systems biology and bioinformatics | Scoop.it

Bodelin Technologies (Lake Oswego, OR) is about to start shipping a new microscope compatible with just about all iOS devices, including iPhones, iPads, and iPod touches of recent generations.


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

Assembly-Free Metagenomic Analysis Reveals New Metabolic Capabilities in Surface Ocean Bacterioplankton - Luo - Environmental Microbiology Reports - Wiley Online Library

Assembly-Free Metagenomic Analysis Reveals New Metabolic Capabilities in Surface Ocean Bacterioplankton - Luo - Environmental Microbiology Reports - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Well it makes a lot of sense - if assembley is ever needed at all? Or we can operate in reads
more...
No comment yet.
Rescooped by Dmitry Alexeev from Papers
Scoop.it!

Stephen Hawking’s advice for twenty-first century grads: Embrace complexity

 A few years ago, Hawking was asked what he thought of the common opinion that the twentieth century was that of biology and the twenty-first century would be that of physics. Hawking replied that in his opinion the twenty-first century would be the “century of complexity”. That remark probably holds more useful advice for contemporary students than they realize since it points to at least two skills which are going to be essential for new college grads in the age of complexity: statistics and data visualization.


Via Complexity Digest
Dmitry Alexeev's insight:

Complexity is us)

more...
Harshal Hayatnagarkar's curator insight, April 25, 2013 2:17 PM
Exactly, Sir !
Murray McKercher's curator insight, April 30, 2013 7:39 AM

"century of complexity" sounds like we should therefore concentrate on simplicity in all things mobile...

Rescooped by Dmitry Alexeev from Innovation and Science breakthroughs
Scoop.it!

Bacteria selectively accelerate their own evolution by replication

Bacteria selectively accelerate their own evolution by replication | Systems biology and bioinformatics | Scoop.it

Several mechanisms that increase the rate of mutagenesis across the entire genome have been identified; however, how the rate of evolution might be promoted in individual genes is unclear. Most genes in bacteria are encoded on the leading strand of replication. This presumably avoids the potentially detrimental head-on collisions that occur between the replication and transcription machineries when genes are encoded on the lagging strand.

 

A new study now describes the ubiquitous (core) genes in Bacillus subtilis and determine that 17% of them are on the lagging strand. The scientists find a higher rate of point mutations in the core genes on the lagging strand compared with those on the leading strand, with this difference being primarily in the amino-acid-changing (nonsynonymous) mutations. They determine that, overall, the genes under strong negative selection against amino-acid-changing mutations tend to be on the leading strand, co-oriented with replication. In contrast, on the basis of the rate of convergent mutations, genes under positive selection for amino-acid-changing mutations are more commonly found on the lagging strand, indicating faster adaptive evolution in many genes in the head-on orientation. Increased gene length and gene expression amounts are positively correlated with the rate of accumulation of nonsynonymous mutations in the head-on genes, suggesting that the conflict between replication and transcription could be a driving force behind these mutations. Indeed, using reversion assays, the scientists show that the difference in the rate of mutagenesis of genes in the two orientations is transcription dependent. Altogether, their findings indicate that head-on replication–transcription conflicts are more mutagenic than co-directional conflicts and that these encounters can significantly increase adaptive structural variation in the coded proteins. The researchers propose that bacteria, and potentially other organisms, promote faster evolution of specific genes through orientation-dependent encounters between DNA replication and transcription.


Via Dr. Stefan Gruenwald, Pedro Barbosa
Dmitry Alexeev's insight:

Video is amasing!!!

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

PLOS ONE: Complex Carbohydrate Utilization by the Healthy Human Microbiome

PLOS ONE: Complex Carbohydrate Utilization by the Healthy Human Microbiome | 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.

Via Clara Belzer
Dmitry Alexeev's insight:

as we just start thinking of carb utilization - the issue a paper)

more...
Clara Belzer's curator insight, April 4, 2013 9:35 AM

When broad sugar utilization was compared within the five major body sites, the gastrointestinal track contained the highest potential for total sugar degradation, while dextran and peptidoglycan degradation were highest in oral and vaginal sites respectively.

 

The analysis suggests that the carbohydrate composition of each body site has a profound influence and probably constitutes one of the major driving forces that shapes the community composition and therefore the CAZyme profile of the local microbial communities, which in turn reflects the microbiome fitness to a body site.