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Genotype calling in tetraploid species from bi-allelic marker data using mixture models.

October 5, 2014 |

SUMMARY: An essential element when analysing the structure, function, and dynamics of biological networks is the identification of communities of related nodes. An algorithm proposed recently enhances this process by clustering the links between nodes, rather than the nodes themselves, thereby allow...

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

October 5, 2014 |

OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data m...

Galaxy CloudMan: delivering cloud compute clusters.

October 5, 2014 |

Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites fro...


October 5, 2014 |

Variation in drug response based on human variation ...

OnEX: Exploring changes in life science ontologies.

October 5, 2014 |

PopABC is a computer package for inferring the pattern of demographic divergence of closely related populations and species. The software performs coalescent simulation in the framework of approximate Bayesian computation (ABC). PopABC can also be used to perform Bayesian model choice to discriminat...

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.

October 5, 2014 |

Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools. We describe novel computat...

MolMovDB - Database of Macromolecular Movements

October 5, 2014 |

Descriptions of protein and macromolecular motions, including movies ...

K-SPMM: a database of murine spermatogenic promoters modules & motifs.

October 5, 2014 |

BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stochastic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools an...

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.

October 5, 2014 |

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, ...

NPRD - Nucleosome Positioning Region Database

October 5, 2014 |

Nucleosome positioning region database ...

Protein-protein binding affinity prediction on a diverse set of structures.

MOTIVATION: Accurate binding free energy functions for protein-protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes. RESULTS: We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein-protein binding. AVAILABILITY: The molecular descriptor set and descriptor values for all complexes are available in the supplementary. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/%7EAffinity CONTACT: paul.bates@cancer.org.uk.

Reconstructing transcription factor activities in hierarchical transcription network motifs.

MOTIVATION: A knowledge of the dynamics of transcription factors is fundamental to understand the transcriptional regulation mechanism. Nowadays an experimental measure of transcription factor activities in vivo represents a challenge. Several methods have been developed to infer these activities from easily measurable quantities such as mRNA expression of target genes. A limitation of these methods is represented by the fact that they rely on very simple single-layer structures, typically consisting of one or more transcription factors regulating a number of target genes. RESULTS: We present a novel statistical inference methodology to reverse engineer the dynamics of transcription factors in hierarchical network motifs such as feed-forward loops. The approach we present is based on a continuous time representation of the system where the high level master transcription factor is represented as a two state Markov jump process driving a system of differential equations. We solve the inference problem using an efficient variational approach and demonstrate our method on simulated data and two real datasets. The results on real data show that the predictions of our approach can capture biological behaviours in a more effective way than single-layer models of transcription, and can lead to novel biological insights. AVAILABILITY: http://homepages.inf.ed.ac.uk/gsanguin/software.html CONTACT: g.sanguinetti@ed.ac.uk.

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.

SUMMARY: The survcomp package provides functions to assess and statistically compare the performance of survival/risk prediction models. It implements state-of-the-art statistics to (i) measure the performance of risk prediction models, (ii) combine these statistical estimates from multiple datasets using a meta-analytical framework, and (iii) statistically compare the performance of competitive models. AVAILABILITY: The R/Bioconductor package survcomp is provided open source under the Artistic-2.0 License with a user manual containing installation, operating instructions and use case scenarios on real datasets. survcomp requires R version 2.13.0 or higher.URL: http://bioconductor.org/packages/release/bioc/html/survcomp.html CONTACT: Benjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>, Markus Schröder <mschroed@jimmy.harvard.edu>