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

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 Global Reach of the Proposed EU Financial Transaction Tax Directive: Creating momentum through internal legislation?

In the wake of the 2008 financial crisis, taxation of the financial sector has forcefully re-emerged on the European Union political agenda. One proposal – rightly or wrongly – received much political attention: a broad-based tax on financial transactions. What had for years existed as a utopia in the minds of grass roots movements, reached a legal and political milestone during Commission President Barosso’s State of the Union speech on 28 September 2011. There he presented a proposal for an EU Directive on a financial transaction tax installed across the 27 EU Member States. It was then an explicit objective of the Union that it would lead by example, and that its pan-European implementation would prove the global feasibility of a financial transaction tax (FTT). The Cannes G-20 Meeting early November 2011 under French chairmanship was expected to launch the global dimension of the FTT, using the momentum created by the proposed EU FTT Directive two months earlier. However, the European sovereign debt crisis caused the EU to teeter on the brink of political, financial and economic collapse, and momentum for a global FTT seemed utterly lost. Nonetheless, political discussions within the Union continued, and at the time of writing – Spring 2012 – discussions in the Council were on-going for some form of pan-EU. The global implementation of the EU FTT Directive is a tale of divided political views between Member States of the Union, the pursuit of an elusive single voice in the G-20, and the use of legal instruments for political reasons. In this paper, it will serve as a case-study for the EU seeking to shape global financial governance in the wake of the 2008 financial crisis, in line with its binding, law-oriented mission statement of Article 21 TEU. In light of this, this contribution investigates EU (im)potence to affect legal and institutional processes in global (financial) governance

A paradigm for coherence in EU external relations law : the European neighbourhood policy

Defence date: 31 May 2010Examining Board: Marise Cremona (Supervisor, EUI), Panos Koutrakos (University of Bristol), Ernst-Ulrich Petersmann (EUI), Ramses Wessel (University of Twente)Coherence is a powerful rhetorical device that is prevalent throughout decades of EU external relations discourse and practice. There is intuitiveness to coherence, an implied sense of ‘good fit’ between the different elements of an all-encompassing system. Yet, any attempt to concretize coherence will open up a plethora of context-specific legal and political questions. The European Neighbourhood Policy (ENP) is a recent example of an external policy drawn up explicitly with the objective of achieving coherence across different EU and Member State external policies. Positioning the ENP in the legalhistorical context of political Union, this thesis first argues why coherence is an issue at all in EU external relations, and why law is integral to attaining the ever-enigmatic single voice of the European Union. Subsequently, the text examines the role of EU external relations law in attaining a coherent neighbourhood policy. It is argued that the innovative nature of the ENP for coherence lies beyond the narrowly defined legal sphere, but stems mostly from its hybrid composition of hard legal, soft legal and nonlegal policy instruments. It is concluded that from a purely EU-internal and institutional perspective, this approach was reasonably successful in involving different actors towards common objectives in the neighbourhood. However, coherence should be more than rhetorical gloss, and agreeing that a wide range of initiatives should be included in soft legal instruments is no guarantee for coherence in actual policy substance. To examine the latter issue this thesis then moves beyond the realm of legal inquiry, and employs content analysis to investigate the extent to which the ENP is substantively coherent between the different norms, actors and instruments this policy encompasses

EU-EC External Competences after the Small Arms Judgment

On 20 May 2008, the Court of Justice handed down its long-awaited judgment in the Small Arms case (C-91/05). Two issues are addressed in this initial essay. First, three different approaches to the relationship between the Community and the Union as captured in Article 47 TEU are proposed, and it is argued that an overly strict interpretation of the ‘non-affectation clause’ could render the CFSP nugatory, whereas an exceedingly unrestricted interpretation could open up an escape route from the legal principles applicable to the Member States in their relationship with the Community. Second, the court’s judgment is assessed in the light of the various options and their underlying rationales. In the final paragraphs, the article concludes that the ECJ’s approach to the two CFSP instruments before it is incongruent, and therefore does not settle the dust that had been stirred up by this cross-pillar conflict. Noting the importance of this case, this contribution is the opening part of a diptych. Whereas this article discusses the case in the context of the post-Nice Treaty framework, a follow-up contribution will assess the case’s importance should the Lisbon Treaty be ratified