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Accelerated growth in the absence of DNA replication origins : Nature : Nature Publishing Group

Accelerated growth in the absence of DNA replication origins : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery.
Dmitry Alexeev's insight:

never seen it before - you can guess the origins via normalization of readcounts in scyn and synced cells - and further you can get the insights 

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping: Cell

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping: Cell | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

holy crap)

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Ben Althouse on Diseases as Complex Systems

Ben Althouse on Diseases as Complex Systems | Systems biology and bioinformatics | Scoop.it

щлThis is the first in a series of interviews highlighting the work of experts in the field of complex systems science. Dr. Ben Althouse, an Omidyar Fellow at the Santa Fe Institute, is a mathematical epidemiologist focusing on the dynamics of infectious disease transmission. Ben holds both an ScM in Biostatistics and a PhD in Epidemiology from the Johns Hopkins Bloomberg School of Public Health where he focused on understanding Dengue fever and other sylvatic mosquito-borne viruses (arboviruses) in Senegal using mechanistic modeling and the SIR model. Dr. Althouse also attended the Santa Fe Institute’s Complex Systems Summer School during his graduate studies.


Via Jorge Louçã
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An enteric virus can replace the beneficial function of commensal bacteria : Nature : Nature Publishing Group

An enteric virus can replace the beneficial function of commensal bacteria : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Intestinal microbial communities have profound effects on host physiology. Whereas the symbiotic contribution of commensal bacteria is well established, the role of eukaryotic viruses that are present in the gastrointestinal tract under homeostatic conditions is undefined. Here we demonstrate that a common enteric RNA virus can replace the beneficial function of commensal bacteria in the intestine. Murine norovirus (MNV) infection of germ-free or antibiotic-treated mice restored intestinal morphology and lymphocyte function without inducing overt inflammation and disease. The presence of MNV also suppressed an expansion of group 2 innate lymphoid cells observed in the absence of bacteria, and induced transcriptional changes in the intestine associated with immune development and type I interferon (IFN) signalling. Consistent with this observation, the IFN-[agr] receptor was essential for the ability of MNV to compensate for bacterial depletion. Importantly, MNV infection offset the deleterious effect of treatment with antibiotics in models of intestinal injury and pathogenic bacterial infection. These data indicate that eukaryotic viruses have the capacity to support intestinal homeostasis and shape mucosal immunity, similarly to commensal bacteria.
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viral

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The metacommunity concept: a framework for multi-scale community ecology - Leibold - 2004 - Ecology Letters - Wiley Online Library

The metacommunity concept: a framework for multi-scale community ecology - Leibold - 2004 - Ecology Letters - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

we are quite excited about meta-community inside meta-community theory application to viruses living in bacteria living in human

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There Is No ‘Healthy’ Microbiome

There Is No ‘Healthy’ Microbiome | Systems biology and bioinformatics | Scoop.it

IN the late 17th century, the Dutch naturalist Anton van Leeuwenhoek looked at his own dental plaque through a microscope and saw a world of tiny cells “very prettily a-moving.” He could not have predicted that a few centuries later, the trillions of microbes that share our lives — collectively known as the microbiome — would rank among the hottest areas of biology.

These microscopic partners help us by digesting our food, training our immune systems and crowding out other harmful microbes that could cause disease. In return, everything from the food we eat to the medicines we take can shape our microbial communities — with important implications for our health. Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.


Via Complexity Digest
Dmitry Alexeev's insight:

Our microbes are truly part of us, and just as we are vast in our variety, so, too, are they. We must embrace this complexity if we hope to benefit from it.

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Rowan Norrie's curator insight, November 10, 6:14 AM

The fascinating world of the microbiome and the opportunities it heralds for future medicine

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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
Dmitry Alexeev's insight:

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

Dmitry Alexeev's insight:

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
Dmitry Alexeev's insight:

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
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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Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

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:

looks amazing on our data

 

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Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome | Systems biology and bioinformatics | Scoop.it
eding/fasting cycle influence host metabolism and contribute to obesity and metabolic diseases. However, fundamental characteristics of this relationship between the feeding/fasting cycle and the gut microbiome are unknown. Our studies show that the gut microbiome is highly dynamic, exhibiting daily cyclical fluctuations in composition. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes many of these cyclical fluctuations. Time-restricted feeding (TRF), in which feeding is consolidated to the nocturnal phase, partially restores these cyclical fluctuations. Furthermore, TRF, which protects against obesity and metabolic diseases, affects bacteria shown to influence host metabolism. Cyclical changes in the gut microbiome from feeding/fasting rhythms contribute to the diversity of gut microflora and likely represent a mechanism by which the gut microbiome affects host metabolism. Thus, feeding pattern and time of harvest, in addition to diet, are important parameters when assessing the microbiome’s contribution to host metabolism.
Dmitry Alexeev's insight:

fasting and microbiome dynamics

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Potential of fecal microbiota for early-stage detection of colorectal cancer - Zeller - 2014 - Molecular Systems Biology - Wiley Online Library

Potential of fecal microbiota for early-stage detection of colorectal cancer - Zeller - 2014 - Molecular Systems Biology - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

not that systematic - but the point is 20 per cent more sensitivity

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SciCurve - Understand your Field of Research.

SciCurve - Understand your Field of Research. | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

exactly what I was looking for today - graphs of keyword publishsing and citing

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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...
Dmitry Alexeev's insight:

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.
Dmitry Alexeev's insight:

systems medicine in translation

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Rethinking “Enterotypes”

Rethinking “Enterotypes” | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

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
Dmitry Alexeev's insight:

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.
Dmitry Alexeev's insight:

multi omics once again

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