🎂This year we’re celebrating
@EMBL
’s 50th anniversary and 30 years of excellence in bioinformatics at EMBL-EBI!
We’re thrilled to unveil an anniversary edition of EMBL-EBI's Highlights report showcasing our achievements in 2023.
#EMBLEBI30
#EMBL50
Congratulations to our director,
@ewanbirney
, for being made a Commander of the British Empire (CBE) for services to computational
#genomics
and leadership across the
#lifesciences
🎉New
#AlphaFold
data! With
@DeepMind
, we’ve more than doubled the size of the database & added predictions for most of the manually-curated
@uniprot
entries in UniProtKB/SwissProt.
That's >400,000 new protein structure predictions for you to explore!
We are deeply saddened by the loss of Michael Ashburner, a pioneering co-founder and former Head of Research at EMBL-EBI.
His contributions to bioinformatics have been immeasurable. Our thoughts are with his family, colleagues and all those whose lives were enriched by his work.
AlphaFold DB will boldly go where no scientist has gone before.
With over 200 million protein structure predictions added to the database, AlphaFold DB now gives users open access to a 3D protein universe.
#AlphaFold
@DeepMind
AlphaFold has given us millions of protein structure predictions, but analysing these can be tricky due to computational limitations.
Foldseek Cluster is a new algorithm that can perform structural comparisons of every
#AlphaFoldDB
protein prediction.
Last year we teamed up with
@DeepMind
to launch the
#AlphaFold
database for protein structure predictions calculated using
#AI
. We’re now up to ~1 million predictions including proteins relevant to neglected tropical diseases & antimicrobial resistance 🦠
Huge congratulations to John Marioni for his appointment as our new Head of Research. 👏 🎉 Learn more about John’s vision for research at EMBL-EBI and his future plans.
@MarioniLab
@EMBL
.
AlphaFold DB marks its one year anniversary 🎉
To celebrate we look back at some of the exceptional advancements that
#AlphaFold
has made possible over the last 12 months and we invite you to add your own work in the replies.
@DeepMind
Comment below👇
#AI
for protein structure prediction is the
@ScienceMagazine
breakthrough and a
@Nature
top pick of the year 🎉
Thousands of protein structure predictions powered by
@Deepmind
's revolutionary AI are available in the
#openaccess
AlphaFoldDB
The
#AlphaFold
Database has levelled up 🚀
🔍 Sequence-based search: Find protein structures in the database using BLAST
🤝With
@thesteinegger
team, we bring structure similarity clusters for seamless navigation
A collaboration with
@GoogleDeepMind
Huge congratulations to
@ewanbirney
for being appointed Deputy Director General of
@embl
! 👏👏👏Ewan will also continue as EMBL-EBI Director and Research Group Leader
The
#AlphaFold
Protein Structure Database gives researchers
#openaccess
to an extensive collection of protein structure predictions.
Learn about this EMBL-EBI hosted resource and future plans from our scientists and
@DeepMind
to expand the database.
The new AlphaMissense catalogue from
@GoogleDeepMind
can be used with the
@ensembl
Variant Effect Predictor to predict variant pathogenicity and therefore aid interpretation.
Researchers compiled over 200 000 bacterial genomes & 170 million protein sequences from the human gut
#microbiome
into the most comprehensive catalogue to date 🦠. The international team was led our
@alexmsalmeida
&
@robdfinn
Building on the
#AlphaFold
buzz, scientists around the world teamed up to explore how accurate and useful the predictions are for a range of applications including function and ligand binding site predictions.
On Neglected Tropical Disease Day, we teamed up with
@DeepMind
to publish 190,000+ relevant protein structure predictions in the
#AlphaFold
database – freely available to all!
#WorldNTDDay
#beatNTD
To facilitate international data sharing + analysis of
#COVID19
research data, we’ll be setting up a COVID-19 Portal. We’ll start by sharing the data available at EMBL-EBI and working closely with collaborators to increase the scope 1/4
#coronavirus
Ever got a result back saying uncharacterised protein? 😩
@uniprot
and
@GoogleAI
have teamed up to create a natural language processing model that has generated over 40 million protein annotations to address this challenge.
Since its 2021 launch, the
#AlphaFold
database has had some major enhancements:
📈 600x increase in number of predicted structures
🗄 better data archiving
👩⚕️ inclusion of global health proteomes
🔍improved search
🙌integration with other data resources
Adaptive
@nanopore
sequencing can help save researchers time and cut down on unnecessary data acquisition.
BOSS-RUNS takes this one step further by adding an element of dynamic learning to the process in real-time 😎
Have questions about using
#AlphaFold
but are afraid to ask?
Check out the new practical guide to AlphaFold, co-developed with
@GoogleDeepMind
.
This free, modular course was created with input from the scientific community and is suitable for undergraduates and above.
In our newest practical guide, developed with
@GoogleDeepMind
and
@emblebi
, delve into the fundamentals of
#AlphaFold
, explore its strengths and limitations, and gain practical skills through hands-on exercises.
Start the free, self-paced tutorial today:
Genomes differ slightly among individuals and so using one standard reference genome has limitations.
Researchers from
@HumanPangenome
have released a more complete collection of genome sequences – the human pangenome – to better capture human diversity.
As our Director Emeritus, Prof Dame Janet Thornton retires, we take a look back at how she shaped the world of
#bioinformatics
and computational biology.
Thank you Janet for your leadership and happy retirement!
@ELIXIREurope
A 25th anniversary is the perfect time to celebrate the past and reminisce. Today we look back on the early days of EMBL-EBI, before our first web servers and the incredible rise of genomics
#emblebi25
#genomics
#bioinformatics
Two decades after the unveiling of the human genome, our understanding of genomic complexity continues to evolve.
Find out more and what the future holds for the comprehensive annotation of human genes.
We’re pleased to announce that
@PaulFlicek
and
@jomcentyre
will be taking up the roles of Associate Directors of EMBL-EBI Services. Many congratulations to the both of them!
Big congrats to
@VirginieUhlmann
for being appointed as our Deputy Head of Research! 🎉
Virginie will support the coordination of our research groups, while continuing to lead her own group focusing on bioimage analysis.
Happy International Day of Women and Girls in Science! Help us celebrate by taking a selfie, posting it using
#WomenOfEMBL
and captioning it with who/what got you into science. We can't wait to see your selfies!
🚨Molecular data for over 200,000 pathogen species and strains are now available in our new Pathogens Portal, launched today.
An indispensable resource for healthcare research, global pandemic surveillance, and food security.
#pathogensportal
Huge congratulations to our Director Emeritus, Professor Dame Janet Thornton, for winning the 2021
@BiochemSoc
Award 🏆 in recognition of her work using
#computational
methods to advance
#biomolecular
science! 👏👏👏
International collaboration is essential for the future of
#science
and has been at our core from the very beginning. Our research & data resources are serving scientists around the world and we will continue championing
#openscience
for all.
Pleased to announce that we are among the 10 organisations who have received funding from
@WellcomeTrust
to sequence 2000 species on the British Isles as part of the
#DarwinTreeofLife
project
The new
@EMDB_EMPIAR
cryo-electron tomography (cryo-ET) browser allows you to see proteins up close in the cellular environment.
Over 1,800 high-resolution reconstructed tomograms from cryo-plasma-FIB milled Chlamydomonas reinhardtii cells are available.
The last of our 12 molecular machines allows us to edit genomes. It is, of course, the famous
#CRISPR
! Thank you for watching. Happy holidays and may 2020 bring you joy, kindness and many exciting discoveries!🥳
@ewanbirney
#merrymolecularxmas
#MerryChristmas
#AI
is revolutionising protein science. Can it add to our knowledge of protein function?
New
@NatureBiotech
research shows how deep learning models can be used to improve protein annotations within
@PfamDB
and help predict protein function.
Researchers have identified protein
#phosphorylation
sites which have been conserved for hundreds of millions of years across the
#eukaryotic
tree of life:
Our premises have closed in order to protect staff & visitors during the
#coronavirus
outbreak, but our virtual presence is as strong as ever. We will be working remotely to ensure our data resources are available to the community as usual.
#COVID19
Exciting news from
@DeepMind
at
#CASP14
. Great to see how knowledge exchange can help researchers address one of biology’s biggest mysteries - the protein folding problem - using
#ArtificialIntelligence
There are different versions of the human genome annotation but which do you use?
The Matched Annotation from
@NCBI
and EMBL-EBI (MANE) collaboration is the answer and brings new meaning to the phrase: two heads are better than one.
Do you annotate bacterial genomes? 🦠
The new ggCaller tool from
@johnlees6
and
@SamuelHorsfield
helps you annotate thousands of bacterial genomes using genome graphs, and connects these into a pangenome.
If you’re after microbiome data, our
@MGnifyDB
protein database just got bigger: 3 billion non-redundant sequences, freely-available.
MGnify’s high-quality open datasets have already been used in the development of AI systems
#AlphaFold
and
#ESMAtlas
.
This week is all about saying
#thanksOA
& celebrating everything
#OpenAccess
! Open data is at the heart of what we do, creating opportunities for scientists everywhere + fuelling innovation, so here’s to the freely-available resources that make open life science possible
#OAweek
What proteins are hiding in the dark? 🫣
A new study published today in
@Nature
shows how the
@PfamDB
team is helping to illuminate the "dark matter" of unannotated proteins.
Find out more in the full paper 👇
Our teams are working hard to make
#COVID19
data accessible to the scientific community. This is a round-up of the most notable data resources, tools and datasets we released in the last month. We hope these are useful to researchers working on
#SARSCoV2
(👇thread)
The first draft of the human genome was published
#OTD
20 years ago. Check out these five little-known facts about this monumental achievement! They might prove handy at your next quiz night. 🧬
#HumanGenomeProject
#HumanGenome20
When will RNA get its
#AlphaFold
moment?
A recent paper explores how to overcome obstacles such as data quality and volume, usage of data beyond simple sequence alignments and more.
@RNAcentral
Excited to announce we have started work on our new Thornton building, named after our Director Emeritus and inspirational scientist, Prof Dame Janet Thornton.
We are grateful to
@UKRI_News
&
@wellcometrust
for their amazing support for this project!
This month marks 20 years since
@nature
&
@ScienceMagazine
published the first draft of the human genome. Take a look back at the project that changed the life sciences forever.
#HumanGenome20
The new
@EMBL
Programme has launched!
We're proud to be a part of
@EMBL
and we're looking forward to contributing our
#bioinformatics
expertise to this exciting new scientific programme that ushers in a new era in the life sciences.
EMBL embarks on a new era of molecular biology.
EMBL research will expand to study life in context – from molecules to ecosystems. Broad in scope, our next programme encompasses fundamental research, services & multidisciplinary collaboration.
Happy 10th anniversary to
@ChEMBL
, our prolific database of bioactive molecules with drug-like properties! Big congratulations to the team (past and present) that have made this database such an amazing success! 🥳🎂
#chembl10yrs
#chembl10years
Biological data can be used to answer fundamental questions about
#biodiversity
, to identify species at risk of extinction & help preserve genetic information about life on Earth. On
#BiodiversityDay
see these
#opendata
resources that may help further your biodiversity research.
We’re extremely grateful to
@UKRI_News
for confirming £80.7 million to help transform our technical infrastructure & continue to meet the growing data needs of the life sciences 🎉
#Bioimaging
data have significant potential for reuse but this requires systematic archiving & metadata. Today we propose Recommended Metadata for Biological Images (REMBI) & we need your feedback to develop these guidelines!
@naturemethods
#microscopy
When submitting scRNA-Seq data to public databases it’s crucial to provide sufficient
#metadata
to ensure reproducibility. Find out more in these guidelines from researchers at EMBL-EBI,
@ucscgenomics
,
@HarvardDBMI
,
@sangerinstitute
, and colleagues
Last month we received over a billion requests to our data resources marking a new record!🎉🎉🎉 Many thanks to all of our hard-working staff for their dedication, whether on-site or
#WFH
, and to our partners for their continuous support in these trying times!
#StrongerTogether
In only 6 months, the
#COVID19
Data Platform united research efforts across Europe & beyond. It secured valuable data submissions & made crucial data available to all who are working towards stopping
#SARSCoV2
in its tracks. Lots more to do, but working together is key.
#OAWeek
Welcome Sarah Dyer, our new Non-Vertebrate Genomics Team Leader! With a wealth of experience in
#bioinformatics
and a passion for plant 🌱 and crop 🌾 genomes, we’re excited to see what Sarah will bring to the
@ensembl
Plants and Metazoa teams.
Introducing
@ProteomicsML
, a community-driven resource for proteomics data sets and tutorials across most of the currently explored physicochemical peptide properties.
The perfect starting point for your
#proteomics
#machinelearning
endeavours.
The Global Biodiversity Portal has launched!
Get access to raw data, genome assemblies, and annotations, and track the status of your species of interest sequenced as part of
@EBPgenome
.
AlphaFold DB launched 2 years ago 🎂
But did you know this incredible resource wouldn’t exist without your data?
Learn about the journey your data takes from submission, training the
@GoogleDeepMind
#AlphaFold
algorithm, to integrating AlphaFold predictions across our databases
Long-read sequencing is
@naturemethods
Method of the Year 2022! 🎉
Nature Methods’
@metricausa
got the inside scoop from our experts about the benefits of using this technology for cancer genomics and producing high-quality genome annotations.
Microbes are everywhere, including the surface of our skin. Find out how skin
#microbiome
research from
@NIH
@genome_gov
and EMBL-EBI can help further our understanding of skin health and disease.
@NatureMicrobiol
New service alert! Our colleagues in the
@ExpressionAtlas
have been working hard behind the scenes to bring you the Single Cell Expression Atlas – a new home for your
#singlecell
RNA-seq data for all species
#nextgenseq
One year ago today, we launched the European
#COVID19
Data Platform to facilitate
#opendata
sharing & analysis, and accelerate coronavirus research. The scientific community’s response was incredible, and the Platform has been growing ever since. A few noteworthy highlights 👇
New
#singlecellanalysis
technique lets you detect changes in three ‘layers’ of molecular activity simultaneously: nucleosome, DNA methylation and transcription. Could reveal new mechanisms of
#generegulation
in development and disease
Today marks one year since the launch of the BioImage Archive, our dedicated data resource for biological images 🥳 Huge thanks to our
@EMDB_EMPIAR
, BioStudies and technical services teams for all their hard work behind the scenes!
#bioimaging