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Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group

Understanding the interactions between bacteria in the human gut through metabolic modeling : Scientific Reports : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease.
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little bit on metabolomic modelling from gurus. Surprising is the journal chosen for that

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GEN | News Highlights:Alcohol-Dependence Gene Linked to Neurotransmitter

GEN | News Highlights:Alcohol-Dependence Gene Linked to Neurotransmitter | Systems biology and bioinformatics | Scoop.it
A multi-university group believes they have solved the mystery of why a specific signaling pathway can be associated with alcohol dependence.
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but where is microbes issue?

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Teaching Corporate in College

By applying the strengths of corporate models for effective teamwork, academic scientists can drive transdisciplinary research and accelerate biomedical translation.

Transdisciplinary (TD) investigations occur when individuals or teams from different disciplines converge to conduct research focused on solving a specific problem that cannot be solved by a single discipline. Working at the intersections of disciplines allows TD research teams to create new science while fostering a higher plane of enquiry—the unearthing of solutions to complex human health and societal problems. Academic medical centers are strategically positioned to drive local, national, and global TD biomedical research. However, academia’s disciplinary-bound culture—organized physically and conceptually around specific content areas—limits TD research and challenges scientists who are working within a university’s traditional department-based organization. In quest of solutions, we explore the characteristics of high-performing corporate teams that might be adapted for use in academic TD research and discuss the premise that collaborations between academic and industry teams present opportunities to harness the unique strengths of each.

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impressive how this is inline with what we are doing now in our team and it thought to the basis of interdisplinary research

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Arousal vs. Relaxation: A Comparison of the Neurophysiological and Cognitive Correlates of Vajrayana and Theravada Meditative Practices

Arousal vs. Relaxation: A Comparison of the Neurophysiological and Cognitive Correlates of Vajrayana and Theravada Meditative Practices | 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:

meditation brings benefit as scientists show

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Visualizing time-related data in biology, a review

Visualizing time-related data in biology, a review | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

fine one on time to 2d space mapping

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Systems Biology and New Technologies Enable Predictive and Preventative Medicine

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preventive medicine notion 

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Access : Software for systems biology: from tools to integrated platforms : Nature Reviews Genetics

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good review to remember

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Homeostasis and Inflammation in the Intestine

Homeostasis and Inflammation in the Intestine | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

for the sake of rememberin - while preparing to lecture on systems biology

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Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue | Systems biology and bioinformatics | Scoop.it
PLOS Computational Biology is an open-access
Dmitry Alexeev's insight:

more and more on metagnomics analysis

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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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GEN | News Highlights:Gut Feedings, Not Just Gut Feelings, Can Influence Our Minds

GEN | News Highlights:Gut Feedings, Not Just Gut Feelings, Can Influence Our Minds | Systems biology and bioinformatics | Scoop.it
Scientists from UCSF, Arizona State University, and the University of New Mexico concluded from a literature review that gut microbes influence human eating behavior and dietary choices.
Dmitry Alexeev's insight:

a good commentary on a good article on gut bacteria

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SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we start the hunt

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Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

it is altered microbiota per se and not the antibiotics that influence the organism

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A Whole-Cell Computational Model Predicts Phenotype from Genotype

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

old one but fits todays lecture

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Exploration and retrieval of whole-metagenome sequencing samples

Exploration and retrieval of whole-metagenome sequencing samples | Systems biology and bioinformatics | Scoop.it

ь

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metagenomes  and k-mers

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Robustness of metabolic networks: A review of existing definitions

Robustness of metabolic networks: A review of existing definitions | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

what do YOU mean robust?

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Over-optimism in bioinformatics research

Over-optimism in bioinformatics research | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

joyful reading

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An integrated catalog of reference genes in the human gut microbiome : Nature Biotechnology : Nature Publishing Group

An integrated catalog of reference genes in the human gut microbiome : Nature Biotechnology : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Li et al. provide the largest catalog of genes in the human gut microbiome based on samples from >1,200 individuals across three continents.
Dmitry Alexeev's insight:

nine millione genes

and nature group once agains)

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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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