Functional Genomics At The EBI News Feed

Data manager position for a new project

Thu, 12 Apr 2012 00:00:00 GMT

A new job position working as a data manager for a large collaborative autism research project has opened up. Deadline for applications is April 22.

Semantic Web Atlas Project

Thu, 21 Jul 2011 00:00:00 GMT

RDF triplestore has been created from Gene Expression Atlas data. The total number of triples is ~170 million. Model consists of gene, p value, differential expression, and experimental factor connected to experiment accession.

New publication

Fri, 14 Jan 2011 00:00:00 GMT

A meta-analysis of human and mouse Affymetrix data has been published in Genome Biology, data is available from E-MTAB-27. Access data here

Downtime

Fri, 8 Jan 2011 00:00:00 GMT

Attention: All our services will be unavailable from Fri 7th Jan 1630 GMT until morning of Mon 10th Jan due to data centre maintenance. Sorry for the inconvenience.

ArrayExpress new infrastructure

Thu, 7 Jan 2011 00:00:00 GMT

The brand new infrastructure of the ArrayExpress Archive is going live on the 10th Jan. This will mean more streamlined submission processing and improved query speed, however, in short term some short delays in loading or releasing data are possible - please bear with us. Accession numbers will still be assigned and submissions will still be accepted and curated as normal.

New citation for ArrayExpress

Mon, 15 Nov 2010 00:00:00 GMT

Parkinson et al. 2010. ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucl. Acids Res., doi: 10.1093/nar/gkq1040. Pubmed ID 21071405.

Internship for a student project in human gene expression - Filled now

Wed, 20 Oct 2010 00:00:00 GMT

This student project is now taken.

Internship for a student project in human gene expression

Fri, 17 Sep 2010 00:00:00 GMT

A new student project has opened up in our group. For more details on applying, please see the file [ PDF - 40KB ]

New Atlas Data Release 10.8

Fri, 17 Sep 2010 00:00:00 GMT

A new release of Gene Expression Atlas has been made with 93 new experiments.

Global 'Expression Space'

Thu, 22 Apr 2010 00:00:00 GMT

EBI-Helsinki Team Integrates Array Data from Thousands of Samples to Map Global 'Expression Space'...more

A global map of human gene expression

Fri, 9 Apr 2010 00:00:00 GMT

By integrating gene expression data from a large variety of human tissue samples, a global map of human gene expression is produced. For more details, please see the Nature Biotechnology [PDF - 676KB] or EMBL press release [PDF - 148KB].

New Archive Browse Interface

Tue, 23 Mar 2010 00:00:00 GMT

A new interface is deployed with advanced query capabilities including using the EFO ontology for query expansion and synonym searches.

EFO Ontology Publication

Tue, 23 Mar 2010 00:00:00 GMT

An ontology paper describing building and applying an ontology of experimental variables in the ArrayExpress's Archive and Atlas interfaces has been published.

ArrayExpress Bioconductor package

Mon, 21 Dec 2009 00:00:00 GMT

The latest version of the ArrayExpress Bioconductor package is required to access the data file archives as the naming convention used has changed. There is more information in the new FAQ page.

Atlas article is a featured publication in NAR.

Mon, 23 Nov 2009 00:00:00 GMT

Featured Articles highlight the best papers published in NAR. These articles are chosen by the Executive Editors on the recommendation of Editorial Board Members and Referees. They represent the top 5% of papers in terms of originality, significance and scientific excellence.

GEO and ArrayExpress agree to exchange UHTS sequencing data.

Thu, 05 Nov 2009 00:00:00 GMT

ArrayExpress and GEO have entered into a metadata exchange agreement, meaning that ultra high throughput sequencing (UHTS) experiments will appear in both databases regardless of where they were submitted. This complements the exchange of underlying raw data between the short read archives, SRA and ERA. Raw sequencing data submitted to ArrayExpress or GEO will be sent to ERA or SRA respectively. You do not need to submit to the sequence repositories separately.

Student Project Placement

Sun, 04 Oct 2009 00:00:00 GMT

An exciting student project placement is available to develop an interface for the Human Gene Expression Map.

Functional Genomics and Systems Biology Workshop

Thu, 01 Oct 2009 00:00:00 GMT

30 Nov - 2 Dec, 2009, Wellcome Trust Conference Centre, Cambridge, UK.

MGED 12 - with student bursaries

Tue, 25 Aug 2009 00:00:00 GMT

Student bursaries are available for US and EC students attending the MGED 12 conference in Phoenix, Arizona, USA.

Gene Expression Atlas - Release 1.1.0

Tue, 16 Jun 2009 00:00:00 GMT

New features include an ontology driven interface using EFO, newly added datasets, expression profile similarity searching and top 10 variable genes per experiment.

Bioinformatician with ArrayExpress

Tue, 05 May 2009 00:00:00 GMT

A new job position working as a bioinformatician with ArrayExpress has opened up.

ArrayExpress Atlas - 1000 experiments

Tue, 05 May 2009 00:00:00 GMT

The latest release of ArrayExpress Atlas has grown to reach the milestone of 1000 experiments.

MGED 12 - Registration open

Tue, 05 May 2009 00:00:00 GMT

Registration is open for the MGED 12 conference in Phoenix, Arizona, USA.

ArrayExpress Atlas Student Masters Project

Mon, 02 Mar 2009 00:00:00 GMT

An MSc Masters project placement is available within the Microarray Group. It will involve developing an advanced ontology querying interface to ArrayExpress Atlas.

ArrayExpress Bioconductor Package

Fri, 14 Nov 2008 00:00:00 GMT

Use the ArrayExpress Bioconductor Package to access ArrayExpress data and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet. This package was developed with Emerald funding.

Sorting by Experiment Technology Type

Wed, 27 Aug 2008 00:00:00 GMT

Quickly identify ChIP-Chip or RNAi experiments using the new drop down filter.

Links to variably expressed genes in the Atlas from the browse interface

Wed, 27 Aug 2008 00:00:00 GMT

E.g. query E-GEOD-4262 and identify genes where expression varies with the experimental factors.