News archive 2016

December

20 Dec 2016

Happy anniversary, PDBe!

As PDBe looks back on its 20th year in operation, EMBL-EBI Director Ewan Birney reflects on nine proteins and complexes whose structures make life as we know it. Read more
A 3D printout of beta-galactosidase.
7 Dec 2016

ENA Release 130

Release 130 of ENA's assembled/annotated sequences now available Read more
5 Dec 2016

UniProt Release 2016_11

UniProt release 2016_11 offers over 71.5 million proteins! This month's headline article is "From mouth to gut: a new mechanism for fimbria assembly." Find out about updates to UniProt entries and news from UniProtKB. Read more
UniProt logo

November

27 Nov 2016

Omnipath: a clear view on signalling pathways

Combining signalling pathway data resources gives a clearer view on complex biological interactions. Read more
Illustration of a phoropter (lens mounter used in eye tests) through which known signalling pathways are seen in focus.
17 Nov 2016

What's an epigenome?

This short explainer gives an overview of the epigenome: the biological machinery that controls the genome. Read more
Artist's interpretation of the human epigenome.
17 Nov 2016

Data Coordination: Challenges and Solutions

Laura Clarke of EMBL-EBI, Data Coordinator for the BLUEPRINT project, shares some of the common pitfalls in large-scale research projects and how to manage them. Read more
Map of the world, with RADAR/rainbow overlay
17 Nov 2016

Blood, Big Data and Epigenetics

The BLUEPRINT project’s massive push to understand the blood epigenome is changing research, and EMBL-EBI is making it happen. Read more
The human epigenome
14 Nov 2016

ENA launches Browser and Advanced Search surveys

Have your say in future improvements to the ENA Browser and ENA's Advanced Search Read more
11 Nov 2016

Benchmarking data analysis software

A new software tool, LFQbench, helps researchers benchmark different instruments, acquisition methods and data-analysis software. Read more
LFQbench article workflow 2016
3 Nov 2016

UniProt release 2016_10

UniProt release 2016_10 offers over 71.2 million UniProtKB proteins! Our latest Headline article is about N-acyl amino acids and obesity. Read more
UniProt logo

October

28 Oct 2016

New releases: InterPro 60.0 and InterProScan 5.21-60.0

InterPro welcomes a new member database: MobiDB Lite! InterPro now offers residue annotation and hundreds of new methods, integrated from partner databases. InterProScan draws on 29,700 entries. Read more
InterPro logo
14 Oct 2016

Ewan Birney to lead Global Alliance for Genomics and Health

EMBL-EBI Director Ewan Birney has been selected to lead the Global Alliance for Genomics and Health. Read more
Global Alliance for Genomics and Health logo
13 Oct 2016

Drivers of evolution hidden in plain sight

A rapid, versatile mechanism that modifies proteins is revealed to be crucial for the evolutionary process Read more
An artist's interpretation of genetic diversity. Beltrao and colleagues in Science, 2016
7 Oct 2016

ENA release 129

Release 129 of ENA's assembled/annotated sequences now available Read more
5 Oct 2016

UniProt release 2016_09

Almost 68.5 million proteins in UniProt release 2016_09! Read our headline article on human protein Ki-67, a widely used marker for cell proliferation. Read more
UniProt logo

September

26 Sep 2016

Expression Atlas New Release

New in our Gene and Protein Expression data resources: embryonic development in mouse and zebrafish, keyword search, and heatmap sorting. Read more
Gene and Protein Expression data services
20 Sep 2016

Reactome milestone: 10,000 human protein records

Reactome has annotated and releases its 10,000th human protein record, making it the most comprehensive open-access knowledgebase of biological pathways. Read more
Reactome: 10,000 protein records
15 Sep 2016

New releases: InterPro 59.0 and InterProScan 5.20-59.0

InterPro welcomes a new member database: SFLD! This release of InterPro offers hundreds of new methods, integrated from partner databases. InterProScan now draws on over 29,600 entries. Read more
InterPro: protein sequence analysis & classification
14 Sep 2016

UniProt release 2016_08

With UniProt release 2016_08, the UniProt Knowledgebase now has over 67 million proteins! This month's headline article: 'Butterfly fashion: all they need is cortex'. Read more
UniProt: the Universal Protein Resource
14 Sep 2016

‘Essential genes’ help focus research

Study identifies 410 genes that are essential to life in the mouse, potentially good candidates for research on human diseases. Read more
IMPC: a resource connecting genotype and phenotype
5 Sep 2016

BioStudies: The Data Bento Box

A new database at EMBL-EBI gives a home to all the data supporting a study. Read more
BioStudies logo

August

23 Aug 2016

Maintaining our data centres

Data Centre Maintenance in Hinxton, UK will start on the afternoon of Friday 26 August and finish on the evening of Tuesday 30 August 2016. Every five years, EMBL-EBI's on-campus data centre, located in Hinxton, has to be shut down for mandatory electrical safety checks. We have scheduled this year's shut-down over the UK's public holiday weekend to minimise disruption. Read more
Hinxton Data Centre will be closed for maintenance 26-30 August 2016
3 Aug 2016

Projects and studies merged in the ENA browser

Projects and studies have now been merged within the ENA browser so that there is a single landing page. Read more
2 Aug 2016

Scheduled disruption to ENA services

All services are back to normal after the planned electrical maintenance work at EBI 26th - 30th August. Read more

July

29 Jul 2016

European Variation Archive release 3: over 540 million unique variants

The third release of the European Variation Archive (EVA) features over 540 million unique variants and 25 new datasets. The data is enriched with dbSNP links. Read more
European Variation Archive news
21 Jul 2016

Ensembl 85 is out!

New features and updates in Ensembl version 85 include new human epigenomes from the Roadmap Epigenomics Project, improved visualisation using Wasabi Tree viewer, human and mouse CRISPR sites and many more. Read more
Ensembl genome explorer logo
20 Jul 2016

GO, slim, GO!

Comparing sample data in EBI Metagenomics is easier than ever, thanks to a new, specialised Gene Ontology 'slim' that creates a high-level visualisation of your sample's functional profile. Read more
EBI Metagenomics refactors its analysis pipeline
11 Jul 2016

New Protein Data REST API

A new API from EMBL-EBI provides access to key biological data from UniProt and Large Scale Studies data mapped to UniProt. Read more
New protein API from EMBL-EBI
6 Jul 2016

UniProt release 2016_07

UniProt release 2016_07 is out now with close to 66 million proteins! New this month: changes to the controlled vocabulary of human diseases and a headline article on '(Bacterial) immigration under control'. Read more
UniProt: the universal protein resource
5 Jul 2016

Cancer cell lines predict drug response

Patient-derived cancer cell lines harbour most of the same genetic changes found in patients’ tumours, and could be used to learn how tumours are likely to respond to new drugs. Read more
Puzzling out drug response [Graphic concept by Francesco Iorio, Illustration by Spencer Phillips, EMBL-EBI]
5 Jul 2016

Anatomy of a decision: mapping early development

A new atlas of gene expression during the earliest stages of life boosts studies of development. Read more
Early embryonic development study by Marioni, Gottgens in Nature, 2016

June

28 Jun 2016

RESTful RNA-seq Analysis API version 1.2 is out

Access analyses of 265,000 RNA-seq runs in 264 organisms (including 38 new entries from WormBase ParaSite) as well as aggregated baseline gene expression in tissues, cell types, developmental stages, sex and strains in 61 organisms Read more
Gene and protein expression services at EMBL-EBI
24 Jun 2016

Expression Atlas: new release, new species, new features!

The latest release of our Expression Atlas features baseline and differential data on tomato, a new heatmap style and a feature for retrieving genes with similar expression patterns across baseline conditions. Read more
Expression Atlas logo
24 Jun 2016

EMBL-EBI and the UK referendum

Statement from our Directors on the impact of the ‘leave’ decision. Read more
European Union and Union Jack flags
24 Jun 2016

Unidentified spectra detector

Detecting millions of consistently unidentified spectra in vast tracts of proteomics data is possible with a new algorithm developed at EMBL-EBI. Read more
Proteomics data: the tip of the iceberg. Illustration by Spencer Phillips, EMBL-EBI
22 Jun 2016

ENA Release 128

Release 128 of ENA's assembled/annotated sequences now available Read more
15 Jun 2016

RESTful RNA-seq Analysis API version 1.1 is out

Access analyses of 250,000 RNA-seq runs in 221 organisms, now with TPM gene counts, bedGraph and bigWig track files! Read more
Gene and protein expression services at EMBL-EBI
9 Jun 2016

New releases: InterPro 58.0 and InterProScan 5.19-58.0

InterPro now features a new member database: CDD! This release of InterPro offers hundreds of new methods integrated from partner databases, and InterProScan now draws on over 29,000 entries. Read more
InterPro: protein sequence analysis & classification
9 Jun 2016

Sharing genomic, clinical data

A perspective by the Global Alliance for Genomics and Health calls for responsible, effective data sharing and proposes practical solutions. Read more
Global Alliance for Genomics and Health logo, EMBL-EBI website
8 Jun 2016

UniProt 2016_06 release

UniProt 2016_06 release is now available with over 64.5 million UniProtKB proteins! With this release we bring you a headline article, 'Strength through unity,' about the curation of pseudokinases FAM20A and FAM20B. Read more
UniProt logo
8 Jun 2016

Acute Myeloid Leukaemia is 11 diseases

Large-scale genetic analysis of leukaemia patients reveals that AML is at least 11 different diseases. Read more
Leukaemia study by Papaemmanuil and Gerstung reveals AML is 11 different diseases

May

20 May 2016

New: RESTful On-the-fly Gene Set Overlap Analysis API

Are you interested in finding out how your set of genes overlaps with over 7500 differential comparisons in Expression Atlas? It's all there for you, just one REST API call away. Our Gene Expression team has published a free tool to perform this analysis in seconds - for up to 100 Ensembl gene identifiers. See documentation for more details. Read more
Gene and protein expression services at EMBL-EBI
12 May 2016

What's a microbiome?

Microbiomes: Our humble overlords Microbes drive almost every food chain on Earth, using just about anything for energy and interacting with one another in countless ways. But how on Earth do they work? In the seas, in the soil, on our skin, in our gut – even in sewage treatment plants –microbes play pivotal roles in health and disease. To decipher how they work and how they influence each other, their hosts and the environment, scientists throughout the world are sharing and comparing vast amounts of information, all supported by EMBL-EBI. Read more
Microbiota illustration
12 May 2016

UniProt release 2016_05

The latest UniProt release 2016_05 offers over 62.5 million proteins in the knowledge base! Our headline article this month: Slow/White and the 6 DWORFs. Read more
UniProt: the universal protein resource
9 May 2016

Proteomics data on the rise: how can you take part?

When you contribute your experimental datasets to PRIDE Archive, you are helping research in this fascinating area of molecular biology by making your data openly available. Read more
Sharing your proteomics data helps make science better
5 May 2016

ExpressionAtlas: New R package for search and download

The ExpressionAtlas Bioconductor package is out! Now, it's easier than ever to search and download from our differential and baseline expression data resources. Read more
3 May 2016

ChEBI highlight: phorbol

Phorbol is at the core of many of the active compounds that make the manchineel tree the most dangerous in the world. It is also at the core of several new anti-cancer agents. ChEBI's entity of the month explains Read more
"Death apple": machineel fruit

April

29 Apr 2016

Breast cancer study: towards personalised treatment

Largest-ever study of breast cancer genomes, led by Wellcome Genome Campus researchers, reveals new genes and mutations involved in the disease. Read more
Largest-ever study of breast cancer genomes, 2 May 2016
22 Apr 2016

Expression Atlas: new release is out!

The latest release of EMBL-EBI's Expression Atlas features over 2700 experiments and updates to Ensembl 84 and Ensembl Genomes 31 gene annotation mappings. Read more
Expression Atlas: Differential and baseline expression data
19 Apr 2016

Open Targets: new name, new data

The Centre for Therapeutic Target Validation, now called ‘Open Targets’, releases its first experimental datasets and a new API. Read more
Open Targets: home of the Target Validation platform
13 Apr 2016

UniProt release 2016_04: over 64 million proteins

UniProt release 2016_04 offers data on over 64 million proteins! Read 'Small changes, big effects', our Headline story about SYT7 proteins, in our latest news item. Read more
UniProt: the universal protein resource
13 Apr 2016

Learn ArrayExpress with our new Train online course

How can you get the most out of ArrayExpress? Our new Train online course gives you tips on how to mine functional genomics data. Read more
ArrayExpress: an archive of functional genomics data
6 Apr 2016

ENA Release 127

Release 127 of ENA's assembled/annotated sequences now available Read more
6 Apr 2016

New releases: InterPro 57.0 and InterProScan 5.18-57.0

InterPro version 57.0 and InterProScan 5.18-57.0 are now available! InterPro now features hundreds of new methods integrated from partner databases, and InterProScan draws on over 29,000 entries. Read more
InterPro: protein sequence analysis & classification
6 Apr 2016

Expression Atlas: now with over 2600 datasets

This release contains our reanalyses of data sets from the BLUEPRINT epigenomes project, baseline data sets from ENCODE on 13 different human tissues, human immunihistochemistry data on normal cell types generated by the Human Protein Atlas and much more. Read more
Expression Atlas: Differential and baseline expression data

March

29 Mar 2016

EnsemblGenomes 31 is out!

Ensembl Protists now includes 158 genomes from 104 species and Ensembl Bacteria has been updated to include the latest versions of 39,584 genomes (39,183 bacteria and 401 archaea) from the INSDC archives. Read more
EnsemblGenomes
25 Mar 2016

Happy anniversary, Swiss-Prot!

A unique collaboration that unifies the world of protein data: reflections on UniProtKB/Swiss-Prot, 30 years on. Read more
Swiss-Prot 30th anniversary
23 Mar 2016

Foetus, or placenta?

Research published in Cell shows subtle differences between seemingly identical cells at a very early stage of development. Read more
Goolam et al., Cell 2016: Foetus, or placenta?
23 Mar 2016

European Variation Archive release 2: new data, new features

EVA release 2 offers more than 290 million unique variants for you to browse, query or download! Improved performance makes it easier than ever to visit the EVA on the go. Read more
21 Mar 2016

Supporting the bioimaging revolution

The rapid rise of high-resolution 3D cellular imaging techniques in biology demands data solutions – and EMBL is there to provide them. Read more
EMPIAR: raw 2D data from bioimaging studies at EMBL-EBI
18 Mar 2016

UniProt release 2016_03

UniProt release 2016_03 offers data and information on over 63 million proteins. This release of the Knowledge Base includes an expertly curated reference proteome for the Zika virus. Read more
UniProt release 2016_03: search over 63 million proteins
9 Mar 2016

Ensembl 84 is out!

Ensembl version 84 incorporates data from the BLUEPRINT epigenome project, and many others. New pairwise LD calculation gives you more flexibility in exploring variation data. Read more
Ensembl genome explorer
7 Mar 2016

Immunology meets single-cell sequencing

A new computational approach in single-cell genomics reveals how different types of T cells detect, destroy and remember invaders. Read more
TraCeR: a new approach to single-cell genomics
7 Mar 2016

Leading the way for gender equality

Robert Petryszak of EMBL-EBI and Sumana Sharma of the Sanger Institute acknowledged for leadership in gender equality with the Wellcome Genome Campus with Sex in Science Best Practice Award 2016. Read more
Best Practice for Supporting Women in Science 2016
2 Mar 2016

New: RESTful RNA-seq Analysis API

Access analyses of 200,000 RNA-seq runs in 185 organisms! Read more
Gene and protein expression services at EMBL-EBI

February

25 Feb 2016

A new view on proteins

UniProt has launched the first protein sequence viewer to integrate all publicly available information about proteins, helping researchers visualise and interpret large volumes of biological data. Read more
UniProt feature viewer: a new way to look at proteins
24 Feb 2016

DREAM shadows: chasing down disease networks

A community effort to assess the performance of computational methods for ‘learning’ the structure of molecular networks shows that solutions may be within reach. Read more
HPN-DREAM breast cancer network inference challenge
19 Feb 2016

New releases: InterPro 56.0 and InterProScan 5.17-56.0

The latest release of InterPro integrates 281 new methods from the SUPERFAMILY, PROSITE profiles and PANTHER databases. Read more
InterPro: protein sequence analysis & classification
17 Feb 2016

UniProt release 2016_02

UniProt release 2016_02 is now available with 61,522,041 proteins in the UniProt Knowledgebase! Our headline article: "Another one (antibiotic) bites the dust" describes the story of the Mcr-1 gene, which is available in UniProtKB. Read more
UniProt: the universal protein resource
15 Feb 2016

Environmental data curation: new publication

In our new publication, "Value, but high costs in post-deposition data curation”, we explore the curation of environmental sample information in the European Nucleotide Archive. Read more
European Nucleotide Archive
11 Feb 2016

Impact: independent evaluation of EMBL-EBI

An independent analysis of EMBL-EBI underscores the value and impact of open data in the life sciences. Read more
"The Value and Impact of the European Bioinformatics Institute" report
8 Feb 2016

Changes to WGS and TSA sequences in the ENA browser

Changes are being made to WGS and TSA sequences in the ENA browser. Read more
8 Feb 2016

Biogen Joins Pioneering Target Validation Collaboration

Cambridge, US and Cambridge, UK, 8 February 2016 – Biogen  (NASDAQ: BIIB) has joined the Centre for Therapeutic Target Validation (CTTV), the pioneering public-private collaboration to improve the success rate for discovering new medicines. Read more
Biogen joins the CTTV - www.targetvalidation.org
5 Feb 2016

ChEBI entity of the month: S-Propyl propanethiosulfinate and plants

As part of a newly-discovered defence mechanism, the roots of some plants have been found to release the foul-smelling sulfur compound S-propyl propanethiosulfinate when they are disturbed by potential predators. ChEBI's 'entity of the month' explains. Read more
Mimosa pudica flowers (Wikimedia Commons)

January

25 Jan 2016

Open Author Profiles at Europe PMC: ORCIDs in Action

Europe PMC has launched author profile pages, which provide a graphical overview of your publications in Europe PMC and your citation rate over time based on your ORCID record. Read more
22 Jan 2016

UniProt 2016_01 release

Wish you a happy new year! UniProt's first release this year 2016_01 is now available with 60,268,458 proteins! This release's headline article is about 'cGAMP, a welcome stowaway' and related updates in this release to cGAS entries as of this release.. You can read more about that and the latest news at http://www.uniprot.org/help/2016/01/20/release! Read more
13 Jan 2016

Assembly XML now available from ENA

As the first step to improvements into genome assembly data access, XML files describing each assembly version are now available from the ENA browser. Read more
11 Jan 2016

Parallel single-cell profiling

New method makes it possible to study the direct relationship between DNA methylation and gene expression in the same cells. Read more
Angermueller et al., Nature Methods 2016: Parallel single-cell profiling. Image: Spencer Phillips, EMBL-EBI
7 Jan 2016

ENA launches comprehensive CRAM indexing

ENA has launched a new service to provide reference coordinate-based indices for CRAM data. Read more