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Roxygen

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Google summer of code endeavour to make a self decribing code

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Systems biology and bioinformatics
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repubHub | iCopyright.com

repubHub | iCopyright.com | Systems biology and bioinformatics | Scoop.it
repubHub: Where editors, bloggers and marketers get licensed, republishable content.
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ots of samples in big data application

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Integrative Systems Approaches to Network Modeling of Biological Processes

Integrative Systems Approaches to Network Modeling of Biological Processes | Systems biology and bioinformatics | Scoop.it
Professor of Computational Biology and Bioinformatics, Department of Biostatistics, Harvard University, Dana-Farber Cancer Institute (Watch Webinar "Integrative Systems Approaches to Network Modeling of Biological Processes" by John Quackenbush,...
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well a prominent professor and comprehensive seminar

 

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Vaginal microbe yields novel antibiotic

Vaginal microbe yields novel antibiotic | Systems biology and bioinformatics | Scoop.it
Drug is one of thousands that may be produced by the human microbiome.
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and finally we go to Pharma!

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The ISME Journal - Abstract of article: High-fat diet alters gut microbiota physiology in mice

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Dmitry Alexeev's insight:

multi omics once again

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Gut microbiota disturbance during antibiotic therapy: a multi-omic approach -- Pérez-Cobas et al. 62 (11): 1591 -- Gut

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach -- Pérez-Cobas et al. 62 (11): 1591 -- Gut | Systems biology and bioinformatics | Scoop.it
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multiomics examples

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Identification of Related Peptides through the Analysis of Fragment Ion Mass Shifts - Journal of Proteome Research (ACS Publications)

Identification of Related Peptides through the Analysis of Fragment Ion Mass Shifts - Journal of Proteome Research (ACS Publications) | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

our main competitor for this week

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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.
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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
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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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Dubious commercial claims

Dubious commercial claims | Systems biology and bioinformatics | Scoop.it
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genetic ancestry critisized in vary agressive manner)

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The gut microbiota, bacterial metabolites and colorectal cancer : Nature Reviews Microbiology : Nature Publishing Group

The gut microbiota, bacterial metabolites and colorectal cancer : Nature Reviews Microbiology : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

crc and biota

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Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples - Journal of Proteome Research (ACS Publications)

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples - Journal of Proteome Research (ACS Publications) | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we have just invented the wheel? aren't we???

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Host-centric Proteomics of Stool: A Novel Strategy Focused on intestinal Responses to the Gut Microbiota

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traces of the host in the feces

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New IBD genetics: common pathways with other diseases -- Lees et al. 60 (12): 1739 -- Gut

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looks like a good summary on Crohn and IBD

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Mass Trees: A New Phylogenetic Approach and Algorithm to Chart Evolutionary History with Mass Spectrometry - Analytical Chemistry (ACS Publications)

Mass Trees: A New Phylogenetic Approach and Algorithm to Chart Evolutionary History with Mass Spectrometry - Analytical Chemistry (ACS Publications) | Systems biology and bioinformatics | Scoop.it

A new phylogenetics approach and algorithm with which to chart the evolutionary history of organisms is presented. It utilizes mass spectral data produced from the proteolytic digestion of proteins, rather than partial or complete gene or translated gene sequences. The concept and validity of the approach is demonstrated herein using both theoretical and experimental mass data, together with the translated gene sequences of the hemagglutinin protein of the influenza virus. A comparison of the mass trees with conventional sequenced-based phylogenetic trees, using two separate tree comparison algorithms, reveals a high degree of similarity and congruence among the trees. Given that the mass map data can be generated more rapidly than gene sequences, even when next generation parallel sequencing is employed, mass trees offer new opportunities and advantages for phylogenetic analysis.

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whoa good idea for ms phogenies

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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.
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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
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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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