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Systems biology and bioinformatics
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Kinetic competition during the transcription cycle results in stochastic RNA processing. - Abstract - Europe PubMed Central

Abstract: Synthesis of mRNA in eukaryotes involves the coordinated action of many enzymatic processes, including initiation, elongation, splicing and...
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looks just amazing how they can totally measure all the processes in one gene

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Genome Medicine | Abstract | Modules, networks and systems medicine for understanding disease and aiding diagnosis

Genome Medicine | Abstract | Modules, networks and systems medicine for understanding disease and aiding diagnosis | Systems biology and bioinformatics | Scoop.it
Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.
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systems medicine in translation

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Rethinking “Enterotypes”

Rethinking “Enterotypes” | Systems biology and bioinformatics | Scoop.it
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Took Rob Knight a while to publish work 

we ssaw it in 2012 in Paris

http://www.cell.com/cell-host-microbe/pdfExtended/S1931-3128(14)00346-1 - here is full version

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Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory

Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory | Systems biology and bioinformatics | Scoop.it
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did not read it through yet - seems intresting

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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.
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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
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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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Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group

Biogeography and individuality shape function in the human skin metagenome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
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biogeography and reference free

 

we are getting deeper

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Abstract LB-155: Ovarian cancer-induced changes in the intestinal microbiota as potential biomarkers for early detection

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i actually doubt that microbiota can be a distinctive marker - unless we programm it

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Gut microbes and adverse food reactions: Focus on gluten related disorders

Gut microbes and adverse food reactions: Focus on gluten related disorders | Systems biology and bioinformatics | Scoop.it
Immediately following birth, the gastrointestinal tract is colonized with a complex community of bacteria, which helps shape the immune system. Under conditions of health, the immune system is able to differentiate between innocuous antigens, including food protein and commensals, and harmful antigens such as pathogens. However, patients with celiac disease (CD) develop an intolerance to gluten proteins which results in a pro-inflammatory T-cell mediated immune response with production of anti-g
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celiac disease summary - all concearning biota

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Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity

Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity | Systems biology and bioinformatics | Scoop.it
Alcohol dependence has traditionally been considered a brain disorder. Alteration in the composition of the gut microbiota has recently been shown to be present in psychiatric disorders, which suggests the possibility of gut-to-brain interactions in the development of alcohol dependence. The aim of the present study was to explore whether changes in gut permeability are linked to gut-microbiota composition and activity in alcohol-dependent subjects. We also investigated whether gut dysfunction is associated with the psychological symptoms of alcohol dependence. Finally, we tested the reversibility of the biological and behavioral parameters after a short-term detoxification program. We found that some, but not all, alcohol-dependent subjects developed gut leakiness, which was associated with higher scores of depression, anxiety, and alcohol craving after 3 wk of abstinence, which may be important psychological factors of relapse. Moreover, subjects with increased gut permeability also had altered composition and activity of the gut microbiota. These results suggest the existence of a gut–brain axis in alcohol dependence, which implicates the gut microbiota as an actor in the gut barrier and in behavioral disorders. Thus, the gut microbiota seems to be a previously unidentified target in the management of alcohol dependence.
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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
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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
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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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