Featured Websites

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).

October 5, 2014 |

SUMMARY: We make the PCIT algorithm, used for detecting meaningful gene-gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modific...

Knottin database

October 5, 2014 |

Database of knottins - small proteins with an unusual "disulfide through disulfide" knot ...

iBioSim: a tool for the analysis and design of genetic circuits.

October 5, 2014 |

SUMMARY: Traditional methods of genetic study design and analysis work well under the scenario that a handful of single nucleotide polymorphisms (SNPs) independently contribute to the risk of disease. For complex diseases, susceptibility may be determined not by a single SNP, but rather a complex in...

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database.

October 5, 2014 |

MOTIVATION: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to det...

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.

October 5, 2014 |

MiSearch is an adaptive biomedical literature search tool that ranks citations based on a statistical model for the likelihood that a user will choose to view them. Citation selections are automatically acquired during browsing and used to dynamically update a likelihood model that includes authors...


October 5, 2014 |

Drosophila Testis Gene Expression Database ...

FACT: functional annotation transfer between proteins with similar feature architectures.

October 5, 2014 |

We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize...

A biosegmentation benchmark for evaluation of bioimage analysis methods.

October 5, 2014 |

SUMMARY: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of relate...

mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits.

October 5, 2014 |

SUMMARY: We describe mbmdr, an R package for implementing the model-based multifactor dimensionality reduction (MB-MDR) method. MB-MDR has been proposed by Calle et al. as a dimension reduction method for exploring gene-gene interactions in case-control association studies. It is an extension of the...


October 5, 2014 |

Evolutionary conserved regions, promoters, and transcription factor binding sites ...

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>