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A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.

October 5, 2014 |

The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools. Complementing existing software for comparison and exploration of genomics data, genoPlotR automatically creates publication-grade linear maps of gene and geno...

The Gene Set Builder: collation, curation, and distribution of sets of genes.

October 5, 2014 |

BACKGROUND: In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools attempt to reveal sequential, functional, and expressional ties. However, while tremendous effort has been invested in deve...


October 5, 2014 |

Database for dinucleotide properties ...

A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly.

October 5, 2014 |

SUMMARY: LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networ...


October 5, 2014 |

Comparative analysis of metazoan mitochondrial genomes ...

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.

October 5, 2014 |

MOTIVATION: Cross-species meta-analyses of microarray data usually require prior affiliation of genes based on orthology information that often relies on sequence similarity. RESULTS: We present an algorithm merging microarray datasets on the basis of co-expression alone, without any requirement for...

NestedMICA as an ab initio protein motif discovery tool.

October 5, 2014 |

MOTIVATION: With the rapid accumulation of genetic data for a multitude of different species, the availability of intuitive comparative genomic tools becomes an important requirement for the research community. Here we describe a web-based comparative viewer for mapping data, including genetic, phys...

VEGA: variational segmentation for copy number detection.

October 5, 2014 |

SUMMARY: Current challenges in microRNA (miRNA) research are to improve the identification of in vivo mRNA targets and clarify the complex interplay existing between a specific miRNA and multiple biological networks. MiRonTop is an online java web tool that integrates DNA microarrays or high-through...

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

October 5, 2014 |

SUMMARY: Our RNA-As-Graph-Pools (RagPools) web server offers a theoretical companion tool for RNA in vitro selection and related problems. Specifically, it suggests how to construct RNA sequence/structure pools with user-specified properties and assists in analyzing resulting distributions. This uti...

DDN: a caBIG® analytical tool for differential network analysis.

October 5, 2014 |

Differential dependency network (DDN) is a caBIG® (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks representing two biological conditions. Developed under caBIG®s In Silico Research Centers ...

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>