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Research methods: Know when your numbers are significant

Research methods: Know when your numbers are significant | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

this is a good motivation article - in spite of Tyakht coming statistics course

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Journal of Biomedical Semantics

Journal of Biomedical Semantics | Systems biology and bioinformatics | Scoop.it
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Decline in ribosomal fidelity contributes to the accumulation and stabilization of the master stress response regulator σS upon carbon starvation

A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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How to sequence a bacterial genome at the end of 2012

A potential user (‘customer’) of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to write this post. The suggestion...
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well a comprehensive guide - the only thing missing is price

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Rescooped by Dmitry Alexeev from Microbial World
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TEDx Delft: My microbial self & I

TEDx Delft: My microbial self & I | Systems biology and bioinformatics | Scoop.it

We live in a microbial world; both from an evolutionary, biochemical, and an ecological perspective.
Our bodies are no exception. The mammalian gut harbors microorganisms (the microbiota) of vast phylogentic, genomic, and metabolic diversity, and recent years have seen a rapid development in the techniques for studying these complex microbial ecosystems. It is increasingly apparent that the GIT microbiota plays an intricate role in human health and disease.
In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience.


Via Guus Roeselers
Dmitry Alexeev's insight:

this one is popular on microbes

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Gut microbiota disturbance during antibiotic therapy: a multi-omic approach -- Pérez-Cobas et al. -- Gut

Dmitry Alexeev's insight:

Multiomics analysis for microbiota - not so many examples so far

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Fast stochastic algorithm for simulating evolutionary population dynamics

Fast stochastic algorithm for simulating evolutionary population dynamics | Systems biology and bioinformatics | Scoop.it
We introduce a new exact algorithm for fast fully stochastic simulations of evolutionary dynamics that include birth, death and mutation events.
Dmitry Alexeev's insight:

would probably be of use in microbiotic dynamics

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ScienceDirect.com - Biotechnology Advances - On the functional and structural characterization of hubs in protein–protein interaction networks

ScienceDirect.com - Biotechnology Advances - On the functional and structural characterization of hubs in protein–protein interaction networks | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

one more on hubs

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Ensembl Plants

Ensembl Plants | Systems biology and bioinformatics | Scoop.it
Ensembl Plants is a genome-centric portal for plant species of scientific interest
Dmitry Alexeev's insight:

If you are ever ruined under heaps of genes and proteins in plants - this should be very useful!

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Rescooped by Dmitry Alexeev from Virology and Bioinformatics from Virology.ca
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VideoStream for biocodershub

useful videos


Via Chris Upton + helpers
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Tim Berners-Lee on the next Web | Video on TED.com

TED Talks 20 years ago, Tim Berners-Lee invented the World Wide Web.
Dmitry Alexeev's insight:

linked data - is the new way for molecular biology and bioinformatics?

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Rescooped by Dmitry Alexeev from Microbiome
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PLoS ONE: Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

PLoS ONE: Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics | Systems biology and bioinformatics | Scoop.it
Abstract Top
We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These vectors are generated from one of a finite number of Dirichlet mixture components each with different hyperparameters. Observed samples are generated through multinomial sampling. The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. The model can also deduce the impact of a treatment and be used for classification. We wrote software for the fitting of DMM models using the ‘evidence framework’ (http://code.google.com/p/microbedmm/). This includes the Laplace approximation of the model evidence. We applied the DMM model to human gut microbe genera frequencies from Obese and Lean twins. From the model evidence four clusters fit this data best. Two clusters were dominated by Bacteroides and were homogenous; two had a more variable community composition. We could not find a significant impact of body mass on community structure. However, Obese twins were more likely to derive from the high variance clusters. We propose that obesity is not associated with a distinct microbiota but increases the chance that an individual derives from a disturbed enterotype. This is an example of the ‘Anna Karenina principle (AKP)’ applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community.

Via David Guttman
Dmitry Alexeev's insight:

i wonder if model explains some of the abnormalties we observed earlier

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Are You Living in a Computer Simulation?

Are You Living in a Computer Simulation? | Systems biology and bioinformatics | Scoop.it
examines the idea that we live in an "ancestor simulation", a computer simulation run by some technologically advanced civilization. The original paper, interviews, further research
Dmitry Alexeev's insight:

are really living in a computer simulation?

there is a chance and there are... proofs)

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Brain Games & Brain Training - Lumosity

Brain Games & Brain Training - Lumosity | Systems biology and bioinformatics | Scoop.it
Improve memory and attention with scientific brain games. Play games and train your brain to boost overall mental power and performance.
Dmitry Alexeev's insight:

it will be harder to catch us

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Metabolic gene regulation in a dynamically changing environment : Abstract : Nature

This suggests that although certain characteristics of the complex networks may differ when probed in a static environment, the system has been optimized for a robust response to a dynamically changing environment.
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exploring husty and tsering)

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ScienceDirect.com - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics - Utilization of Protein Intrinsic Disorder Knowledge in Structural Proteomics

ScienceDirect.com - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics - Utilization of Protein Intrinsic Disorder Knowledge in Structural Proteomics | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

still not so much order in knowledge on disordered proteins

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An integrated map of genetic variation from 1,092 human genomes : Nature : Nature Publishing Group

An integrated map of genetic variation from 1,092 human genomes : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
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Vova discussing the article on SNP variation during the seminar

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Molecular Systems Biology

Molecular Systems Biology | Systems biology and bioinformatics | Scoop.it
Queueing up for enzymatic processing: correlated signaling through coupled degradation
Dmitry Alexeev's insight:
Well one more piece in our collection of complex proitein interactions
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