Data-driven summarization of broadcasted cycling races by automatic team and rider recognition

The number of spectators for cycling races broadcasted on television is decreasing each year. More dynamic and personalized reporting formats are needed to keep the viewer interested. In this paper, we propose a methodology for data-driven summarization, which allows end-users to query for personalized stories of a race, tailored to their needs (such as the length of the clip and the riders and/or teams that they are interested in). The automatic summarization uses a combination of skeleton-based rider pose detection and pose-based recognition algorithms of the team jerseys and rider faces/numbers. Evaluation on both cyclocross and road cycling races show that there is certainly potential in this novel methodology

TXTGate: profiling gene groups with text-based information

We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database. Subclustering and links to external resources allow for in-depth analysis of the resulting term profiles

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH

<p>Abstract</p> <p>Background</p> <p>Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against a normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations.</p> <p>Results</p> <p>We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities.</p> <p>Conclusion</p> <p>The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies.</p

Text-mining assisted regulatory annotation

Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated cis-regulatory data

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

Background How to efficiently integrate the daily practice of molecular biologists, geneticists, and clinicians with the emerging computational strategies from systems biology is still much of an open question. Description We built on the recent advances in Wiki-based technologies to develop a collaborative knowledge base and gene prioritization portal aimed at mapping genes and genomic regions, and untangling their relations with corresponding human phenotypes, congenital heart defects (CHDs). This portal is not only an evolving community repository of current knowledge on the genetic basis of CHDs, but also a collaborative environment for the study of candidate genes potentially implicated in CHDs - in particular by integrating recent strategies for the statistical prioritization of candidate genes. It thus serves and connects the broad community that is facing CHDs, ranging from the pediatric cardiologist and clinical geneticist to the basic investigator of cardiogenesis. Conclusions This study describes the first specialized portal to collaboratively annotate and analyze gene-phenotype networks. Of broad interest to the biological community, we argue that such portals will play a significant role in systems biology studies of numerous complex biological processes. CHDWiki is accessible at http://www.esat.kuleuven.be/~bioiuser/chdwikistatus: publishe

EEAS 2.0: draft recommendations for the 2013 EEAS Review

This document offers recommendations for the amendment of Council Decision 2010/427/EU establishing the organisation and functioning of the European External Action Service (hereinafter ‘EEAS Decision’). These recommendations have been distilled from discussions between academics and practitioners during a two-day workshop held at the European University Institute in March 2013 in the framework of the so-called ‘EEAS 2.0’ project. This research project is a collaboration between independent scholars brought together by SIEPS, the EUI and CEPS. In February 2013, the team published a legal commentary on the EEAS Decision, available on the websites of the participating research centres. The current paper and its recommendations should be read in the light thereof. In formulating the recommendations, attention has been paid to policy papers, non-papers and recommendations that have been initiated by EU institutions, member states, think tanks and academia, notably in the context of the on-going review. As such, we hope to be able to inform, in a precise and legal way, the discussions in preparation of the High Representative’s own report. The current paper is work in progress and will be revisited for publication after the summer, taking into account the High Representative’s report of July and feedback from other stakeholders The current paper sheds light on possible adjustments in the operation of the Decision/Service ‘à droit constant’, but also includes proposals that could be considered in the context of an amendment of the EEAS Decision. With regard to the latter, several levels of revision may be envisaged: (i) a mere toilettage (e.g. deleting out-dated provisions and securing terminological consistency), (ii) technical changes in the text without reopening the political discussion that predated the adoption of the Decision and (iii) a more ambitious revision that could require more extensive legal modifications of collateral secondary measures (e.g. Staff and/or Financial regulations), if not of the founding treaties

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

BACKGROUND: The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. RESULTS: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. CONCLUSION: ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at

Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations

Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at http://www.esat.kuleuven.be/abandapart/

The Human Phenotype Ontology project:linking molecular biology and disease through phenotype data

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online