Lightnews — Scholar-powered news

Mallory Freeberg @malloryfreeberg.bsky.social · 4h

Stay updated with the latest EGA news by signing up for the newly launched EGA Newsletter! 🤩

Providing easy access the latest highlights and insights from EGA including about #FederatedEGA, @ga4gh.org engagements, international projects, and more 🙌

✏️ Sign up here: mailchi.mp/4c1f9c3a3030...

EGA archive @egaarchive.bsky.social · 2d

📢 We are excited to announce the incoming launch of the EGA Newsletter!

Sign up now to stay updated on the latest news related to Federated EGA, Beacon, along with highlights and updates on the ongoing projects we are involved in 🙌

👉 mailchi.mp/4c1f9c3a3030...

2 3

Reposted by Mallory Freeberg

James Bonfield @jbonfield.bsky.social · 24d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

2 130 140

Reposted by Mallory Freeberg

Ensembl @ensembl.org · 27d

Heads up! The Ensembl Rapid Release site (zurl.co/2iF0U) will be archived very soon.
All links to it will redirect to our new site: zurl.co/PMirU
The original data will remain accessible at zurl.co/9IQJv.
Questions? Reach us at helpdesk [at] ensembl.org

Homepage of the Ensembl Rapid Release site http://rapid.ensembl.org

5 3

Reposted by Mallory Freeberg

Yasset Perez-Riverol @ypriverol.bsky.social · 26d

New release of pmultiqc v0.0.34 🚀🎉. github.com/bigbio/pmult..., highlights:
- A new contributor, Chris Bielow
- MaxDIA support, thanks @maxquant.bsky.social pmultiqc.quantms.org/MaxDIA/multi...
- DIANN reports way deeper thanks @vadim-demichev.bsky.social pmultiqc.quantms.org/DIANN/multiq...

Release v0.0.34 - DIANN and MaxDIA support · bigbio/pmultiqc

What's Changed fix bugs and add plots for mzid by @yueqixuan in #295 Multiple fix in mzidentml by @ypriverol in #296 MaxQuant: Fix NaN intensity errors by @cbielow in #304 Fix bug in proteobench_u...

github.com

3 5

Reposted by Mallory Freeberg

Global Alliance for Genomics and Health @ga4gh.org · 26d

Deadline approaching: register for GA4GH 13th Plenary in-person participation by 22 September.

Onsite registration will not be available. Virtual participation is free and open to all.

Learn more and register for the meeting: buff.ly/Iy5ocjo

Home

broadinstitute.swoogo.com

1 2 1

Mallory Freeberg @malloryfreeberg.bsky.social · 27d

💡Latest DECIPHER features!

⚛️ ProtVar (www.ebi.ac.uk/ProtVar/) links to functional annotations of missense variants
⚕️ ClinGen (clinicalgenome.org) VCEP Recommendations highlighted
📝 Descriptive names for gene & protein predictive scores

👉 More info www.deciphergenomics.org

#variantinterpretation

1 5

Reposted by Mallory Freeberg

Caroline Wright @carolinefwright.bsky.social · 29d

Very cool new feature in @deciphergenomics.bsky.social - direct link from any missense variant to ProtVar @ebi.embl.org. This variant is in the binding site and likely interacts with the ligand, predicted using AlphaFold with AlphaFill!

4 13

Reposted by Mallory Freeberg

Global Alliance for Genomics and Health @ga4gh.org · 28d

📣 GA4GH 13th Plenary panel spotlight: “Real-world implementation of GA4GH standards”

Learn about real-world examples highlighting how GA4GH tools and frameworks are powering interoperability and translating data sharing into action.

Register for GA4GH 13th Plenary: buff.ly/k1udEHJ

2 2

Reposted by Mallory Freeberg

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 20

Headed to #ASHG25?

Don’t miss HPRC’s workshop on the Human Pangenome: Data, Tools & Workflows.

📅 Oct 14 | 10AM–12PM

Learn how to access data & use pangenome tools!

www.ashg.org/product/ashg...

ASHG 2025 Workshop: The Human Pangenome: Data, Tools, and Workflows

Introducing participants to the new Human Pangenome Reference, how samples were chosen to maximize variation, & technologies used to build the pangenome

www.ashg.org

6 8

Reposted by Mallory Freeberg

EMBL-EBI @ebi.embl.org · Aug 12

Welcome @timcoorens.bsky.social ‪ ‬🇳🇱, our new Research Group Leader.

Find out how Tim’s group is exploring using large-scale single-cell and spatial data to trace cell lineages, understand cancer origins, and uncover how mutations drive disease.

www.ebi.ac.uk/about/news/p...
🖥️🧬

Welcome: Tim Coorens

EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.

www.ebi.ac.uk

2 10 48

Reposted by Mallory Freeberg

Andrea Ganna @andganna.bsky.social · Aug 5

The iPSYCH study represents a unique example to understand the ethical and legal challenges of using existing samples/data for health research. A thread 🧵

www.science.org/content/arti...

Blood taken from Danish babies ended up in huge genetic study—without consent

The iPsych project, which investigates the genetics of psychiatric disorders, has sent 140,000 opt-out notices amid backlash

www.science.org

1 4 12

Reposted by Mallory Freeberg

Jess Ewald @ewaldlab.org · Aug 7

Check out this opportunity to join my lab as a postdoc! www.ebi.ac.uk/research/pos...

Every year, faculty from EMBL-EBI and the Wellcome Sanger Institute co-develop projects that allow fellows to be part of ✨both✨ of these amazing research institutes.

EMBL-EBI-Sanger postdoctoral fellowships (ESPOD)

The ESPOD fellowship builds on the collaborative relationship between EMBL-EBI and the Wellcome Sanger Institute, offering projects that combine experimental (wet-lab) and computational (dry-lab) appr...

www.ebi.ac.uk

3 14 11

Reposted by Mallory Freeberg

María Chavero-Díez @mariachdiez.bsky.social · Jul 31

Really cool read if you're into federated analysis in genomics 🧬 It clears up a lot of the jargon and makes it easier to get the bigger picture! rdcu.be/eyKGr

Communicating clearly about data sharing in genomics | Human Genomics

rdcu.be

2 1

Reposted by Mallory Freeberg

Nicky Whiffin @nickywhiffin.bsky.social · Jul 31

📣 We are recruiting! Please share!!

Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺

We have two roles available 👇

🧵 1/4

Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'

1 43 43

Reposted by Mallory Freeberg

Eileen Furlong @eileen-furlong.bsky.social · Jul 30

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Group Leader - Genome Biology Unit

Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

embl.wd103.myworkdayjobs.com

230 190

Reposted by Mallory Freeberg

Stephen Turner @stephenturner.us · Jul 28

A draft UAE-based Arab pangenome reference www.nature.com/articles/s41... 🧬🖥️🧪

2 4

Reposted by Mallory Freeberg

Atlas of Variant Effects Alliance @varianteffect.bsky.social · Jul 23

🧬 Interested in variant interpretation?
#FunctionalGenomics #Pharmacogenetics #MutationalScanning #VariantEffectPredictor #RareDisease #Collaboration #PrecisionMedicine
Check out our list of publications!
📖 www.varianteffect.org/publications/

2 5

Mallory Freeberg @malloryfreeberg.bsky.social · Jul 26

🧬💻 We're hiring a #Software #Developer @emblebi.bsky.social! Join the @deciphergenomics.bsky.social team building tools for global rare disease diagnosis & research. Work that matters, in a collaborative environment.
👉 Apply: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
⏰ Deadline: 10 August

Software Developer

In this role, you will have the opportunity to develop domain area expertise in human genetics while working with a modern technology stack. You will design, develop and support the DECIPHER platform,...

embl.wd103.myworkdayjobs.com

2 3

Mallory Freeberg @malloryfreeberg.bsky.social · Jul 26

🧬💻 We're hiring a #Bioinformatics #Developer @emblebi.bsky.social! Join the @ensembl.bsky.social Variation team building open-source tools to support global research & clinical genomics. Collaborative team; real impact.
👉 Apply: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
⏰ Deadline: 10 August

Bioinformatics Developer

About the team and role The Ensembl Project based at the European Bioinformatics Institute (EMBL-EBI) develops free, comprehensive genome data services for a worldwide audience, distributing gene and ...

embl.wd103.myworkdayjobs.com

14 20

Mallory Freeberg @malloryfreeberg.bsky.social · Jul 24

As an American living in the UK, I'll admit I'm split on the issue ;) But, when in Rome!

1

Mallory Freeberg @malloryfreeberg.bsky.social · Jul 23

So proud to represent our amazing teams and resources in the Human Genomics Team and beyond 🫶🏼

Ensembl @ensembl.org · Jul 23

Did you attend @iscb.bsky.social's #ismbeccb2025 🇬🇧? @ebi.embl.org colleagues (including reps from #Ensembl, @deciphergenomics.bsky.social, @training.ebi.embl.org, @pdbeurope.bsky.social and @expressionatlas.bsky.social) surely did! 🧬

We snapped some pics of @malloryfreeberg.bsky.social in action 🎤

A photograph of a speaker on a stage and a screen projecting presentation slides.

A photograph of an EMBL-EBI booth at a conference.

A photograph of a speaker on stage with a screen projecting presentation slides and an audience looking towards the stage.

1 1 9

Reposted by Mallory Freeberg

EMBL-EBI @ebi.embl.org · Jul 23

The Perturbation Catalogue is here!

A new platform unifying perturbation data from CRISPR screens, multiplexed variant effect assays and gene expression data in one place.

The beta version is now live. Find out more and try the platform:

www.ebi.ac.uk/about/news/u...
🧬🖥️

New platform integrates gene perturbation data

The Perturbation Catalogue provides user-friendly access to human gene perturbation, variant analysis, and expression data.

www.ebi.ac.uk

1 6 17

Mallory Freeberg @malloryfreeberg.bsky.social · Jul 23

🧬 New @emblebi.bsky.social service beta launched:
Perturbation Catalogue

🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies

Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...

Funded by @opentargets.org

1 18 44

Reposted by Mallory Freeberg

EMBL-EBI @ebi.embl.org · Jul 14

EMBL-EBI will be at #ISMB2025!

Visit us at our booth, meet our scientists, and find out about our latest training, services, research highlights and more.

1 3 13

Reposted by Mallory Freeberg

Mike Inouye @mikeinouye.bsky.social · Jul 4

The UK Govt just released its 10 year plan for the NHS and it is legitimately ambitious and exciting. Genomic population health features heavily... on the cover even! assets.publishing.service.gov.uk/media/686638...

9 37