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The genotype-phenotype map of an evolving digital organism

by Miguel A. Fortuna, Luis Zaman, Charles Ofria, Andreas WagnerTo understand how evolving systems bring forth novel and useful phenotypes, it is …

Biology

Scientists uncover genetic evidence that 'we are what we eat'

Researchers at the University of Oxford have demonstrated that the diets of organisms can affect the DNA sequences of their genes.<p>In a study on two …

How a researcher used big data to beat her own ovarian cancer

Academic scientists devote their lives to research, often toiling away on problems that few people outside their discipline fully understand. Perhaps …

Cancer

Genomic Data Processing on Google Cloud Platform

Posted by Dr. Stacey Gabriel, Director of the Genomics Platform at the Broad Institute of MIT and Harvard Today we hear from Broad Institute...

Long-read sequence assembly of the gorilla genome

• H. Y. K. Lam,<br>• M. J. Clark,<br>• R. Chen,<br>• R. Chen,<br>• G. Natsoulis,<br>• M. O’Huallachain,<br>• F. E. Dewey,<br>• L. Habegger,<br>• E. A. Ashley,<br>• M. B. Gerstein,<br>• A. J. Butte,<br>• H. P. Ji,<br>• M. …

Genetics

‘The whole field of nutrition is in the dark ages’: Dr Lee Hood

The implications and opportunities for ‘wellness’ are numerous, but the current thinking in nutrition research is holding the field back, …

Thought Leadership

A model for competition for ribosomes in the cell.

Related Articles<b>A model for competition for ribosomes in the cell.</b>J R Soc Interface. 2016 Mar;13(116)Authors: Raveh A, Margaliot M, Sontag ED, Tuller …

Atoms

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

Abstract<p>Recent work has shown that the accuracy of <i>ab initio</i> structure prediction can be significantly improved by integrating evolutionary …

Differential analysis of biological networks

Background: In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to …

Cancer

HMMvar-func: a new method for predicting the functional outcome of genetic variants

Background: Numerous tools have been developed to predict the fitness effects (i.e., neutral, deleterious, or beneficial) of genetic variants on …

Mutations

Iterative sub-network component analysis enables reconstruction of large scale genetic networks

Background: Network component analysis (NCA) became a popular tool to understand complex regulatory networks. The method uses high-throughput gene …

Machine Learning

TOGGLE: toolbox for generic NGS analyses

Background: The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The …

Bioinformatics

A new network representation of the metabolism to detect chemical transformation modules

Background: Metabolism is generally modeled by directed networks where nodes represent reactions and/or metabolites. In order to explore metabolic …

Algorithms

Reads2Type: a web application for rapid microbial taxonomy identification

Background: Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such …

Online Privacy

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate

Background: The high-throughput sequencing technology, RNA-Seq, has been widely used to quantify gene and isoform expression in the study of …

Algorithms

A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

1. Ramirez-Parra E, Desvoyes B, Gutierrez C. Balance between cell division and differentiation during plant development. Int J Dev Biol. …

Medicine

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

1. Depardieu F, Podglajen I, Leclercq R, Collatz E, Courvalin P (2007) Modes and modulations of antibiotic resistance gene expression. Clinical …

Biology

Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions

Abstract<p>In simple organisms like <i>E.coli</i>, the metabolic response to an external perturbation passes through a transient phase in which the activation …

Algorithms

Translational Bioinformatics Year In Review

Per tradition, Russ Altman gave his "Translational Bioinformatics: The Year in Review" presentation at the close of the AMIA Joint Summit on …

Object-oriented programming for scientists

22 Mar 2015<p>Introduction<p>For anyone not familiar with object-oriented programming it can sometimes come across as something mysterious that is used by …

Python Programming

BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data

User-friendly visualization and analysis<p>Despite the continuing high popularity of the BLAST algorithm and ever-increasing data loads, there is a …

Data Science

Investigating perturbed pathway modules from gene expression data via structural equation models

The above described method was applied to two gene expression microarrays datasets, one from a study on FTLD-U and the other on MS.<p>FTLD-U analysis<p>The …

Neuroscience

A web-based protein interaction network visualizer

Abstract<p>Background<p>Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these …

Data Visualization

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

To illustrate the capabilities of the methods presented here, a set of optimization problems, including cases from systems biology and …

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Methodology for the reconstruction of HMMER2 and HMMER3 scores<p>In the current implementation of the HMMER packages (HMMER2 [15, 38] and HMMER3 [16, …

Algorithms

RMaNI: Regulatory Module Network Inference framework. - PubMed

BACKGROUND:<p>Cell survival and development are orchestrated by complex interlocking programs of gene activation and repression. Understanding how this …

Administrative Law

A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity.

2014 Sep 15;23(18):4887-905. doi: 10.1093/hmg/ddu202. Epub 2014 May 2.<p>1Department of Pharmacology and Experimental Therapeutics and Wyss Institute …

Neuroscience

Systems genetics: From GWAS to disease pathways.

2014 Oct;1842(10):1903-1909. doi: 10.1016/j.bbadis.2014.04.025. Epub 2014 May 2.<p>1University of Groningen, University Medical Centre Groningen, …

Genetics

Nutrimetabonomics: nutritional applications of metabolic profiling. - PubMed

An individual's metabolic phenotype, and ultimately health, is significantly influenced by complex interactions between their genes and the diet. …

Biomarkers