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Mallory Freeberg

@malloryfreeberg.bsky.social
398 followers 437 following 31 posts

🧬 Human Data Sharing Expert 🌱 Community & Collaboration Builder 👩‍💻 Bioinformatics & Metadata Enthusiast 🙌 Open Science Advocate 🇺🇸 in 🇬🇧

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Reposted by Mallory Freeberg
EGA archive @egaarchive.bsky.social · 18/02/2026
The second EGA newsletter is out! 🚀 Discover the insights from the #FederatedEGA Swedish Node (@nbis.se) 💥 Introducing FEGA Affiliate: a new way to become part of Federated EGA 💡 The Beacon Template UI is now available There is much more to read in the latest issue! ➡️ mailchi.mp/130c2186dfd1...
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Reposted by Mallory Freeberg
deciphergenomics.bsky.social @deciphergenomics.bsky.social · 28/01/2026
Links to IEMbase and Treatable ID have moved – they can now be found on the new Therapies tab
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Reposted by Mallory Freeberg
deciphergenomics.bsky.social @deciphergenomics.bsky.social · 28/01/2026
Approved genetic drugs/therapies, from the @n1collaborative.bsky.social, N1C Gene Registry are now displayed in DECIPHER on a new Therapies tab - available from gene pages and patient records.
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Reposted by Mallory Freeberg
deciphergenomics.bsky.social @deciphergenomics.bsky.social · 28/01/2026
Links to @uniquecharity.bsky.social single gene disorder guides are now displayed in DECIPHER on gene pages, therapies tabs and patient records #inclusion #informationforeveryone
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Reposted by Mallory Freeberg
EMBL @embl.org · 05/01/2026
EMBL’s Sabbatical Fellowship Programme is slowly growing, attracting participants from around the world with its collaborative insights and access to world-class technologies. www.embl.org/news/connect...
embl.org
A lab away from home | EMBL
The EMBL Sabbatical Fellowship Programme keeps growing, offering participants collaborative insights and access to world-class technology.
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Reposted by Mallory Freeberg
EMBL-EBI @ebi.embl.org · 18/12/2025
The new ShapeEmbed deep learning method helps quantify shapes in bioimages 🔬 It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations. Great for robust cell shape analysis, classification & exploring phenotypes. neurips.cc/virtual/2025...
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Reposted by Mallory Freeberg
HEREDITARY @hereditaryeu.bsky.social · 10/12/2025
🧬 HEREDITARY #XMAS Giveaway! ✨ To thank you all for your support throughout the year, the HEREDITARY project is celebrating the holiday season with a special giveaway of exclusive project materials! Good luck to all, and happy holidays! ❄️🎁
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Reposted by Mallory Freeberg
ELIXIR Europe @elixir-europe.org · 23/10/2025
✨ #ELIXIR is looking for a Head of Operations to lead the Operations team at the ELIXIR Hub and 🤝 coordinate the implementation of our scientific programme. Apply by 15 November 👉 loom.ly/0lpqg88 #ResearchInfrastructures #hiring
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Mallory Freeberg @malloryfreeberg.bsky.social · 23/10/2025
📣 Check out this cool new work to better represent and integrate growth data, including in the @deciphergenomics.bsky.social platform, to help children with rare genetic conditions 🧬💻
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Reposted by Mallory Freeberg
European Commission @ec.europa.eu · 23/10/2025
🇪🇬 Egypt is a new strategic partner for the EU. During the first EU-Egypt summit, the EU committed to: 💰€4 billion in Macro-Financial Assistance 💶€75 million to support of socio-economic reforms Egypt joins #HorizonEU, unlocking opportunities for local researchers. 🔗 link.europa.eu/RphYTp
A traditional sailboat on the Nile river with palm trees and desert mountains in the background. EU and Egypt flags appear above, with the text ‘EU-EGYPT. HORIZON EUROPE’ below symbolizing their partnership.
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Reposted by Mallory Freeberg
Rare Disease Research UK @rdrukhub.bsky.social · 17/10/2025
🏅 There’s less than a month left to apply for the ECR Award in PPIE — a great opportunity to recognise and celebrate early career researchers who are making real impact through patient and public involvement and engagement. 📣 Don’t miss out. Spread the word and share this with your networks!
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Reposted by Mallory Freeberg
GWAS Catalog @gwascatalog.bsky.social · 14/10/2025
🚨 Countdown to #ASHG25: Predicted Effector Gene standard is coming! 🚨 Join us and be part of the conversation! 📌 Poster Oct 16 | 2:30–4:30 | Poster Hall 🗓️ Session Oct 17 | 11:45–1:15 | Room 259A Learn more: kpnashg2025.wordpress.com/pegs-workshop/
kpnashg2025.wordpress.com
PEGs Workshop
Friday, October 17th | 11:45AM – 1:15PM | Convention Center room 259A The meeting will open with an introduction (Noel Burtt), include a recap of the landscape analysis (Laura Harris), presentation…
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Reposted by Mallory Freeberg
EGA archive @egaarchive.bsky.social · 15/10/2025
🧬💬 Tomorrow, Abeer Fadda, bioinformatics lead at the EGA - @crg.eu team and researcher in the @hereditaryeu.bsky.social project, will be participating in a roundtable on genomic medicine at #RIES2025 Check out the agenda ➡️ forumries.com/programa/
forumries.com
Programa | RIES
RIES X Forum es el evento de referencia a nivel nacional e internacional para abordar los retos y oportunidades del ecosistema de la salud.
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Mallory Freeberg @malloryfreeberg.bsky.social · 09/10/2025
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...
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Reposted by Mallory Freeberg
James Bonfield @jbonfield.bsky.social · 15/09/2025
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
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Reposted by Mallory Freeberg
Ensembl @ensembl.org · 12/09/2025
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
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Reposted by Mallory Freeberg
Yasset Perez-Riverol @ypriverol.bsky.social · 12/09/2025
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...
github.com
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...
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Reposted by Mallory Freeberg
Global Alliance for Genomics and Health @ga4gh.org · 12/09/2025
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
broadinstitute.swoogo.com
Home
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Mallory Freeberg @malloryfreeberg.bsky.social · 11/09/2025
💡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
ebi.ac.uk
EMBL-EBI ProtVar - Contextualising human missense variation
ProtVar: A tool to contextualise and interpret human missense variation
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Reposted by Mallory Freeberg
Caroline Wright @carolinefwright.bsky.social · 10/09/2025
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!
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Reposted by Mallory Freeberg
Global Alliance for Genomics and Health @ga4gh.org · 10/09/2025
📣 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
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Reposted by Mallory Freeberg
Human Pangenome Reference Consortium @humanpangenome.bsky.social · 20/08/2025
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.org
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
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Reposted by Mallory Freeberg
EMBL-EBI @ebi.embl.org · 12/08/2025
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... 🖥️🧬
ebi.ac.uk
Welcome: Tim Coorens
EMBL-EBI’s newest Research Group Leader is investigating how somatic mutations reveal the hidden histories of human cells.
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Reposted by Mallory Freeberg
Andrea Ganna @andganna.bsky.social · 05/08/2025
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...
science.org
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
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Reposted by Mallory Freeberg
Jess Ewald @ewaldlab.org · 07/08/2025
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.
ebi.ac.uk
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...
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Reposted by Mallory Freeberg
María Chavero-Díez @mariachdiez.bsky.social · 31/07/2025
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
rdcu.be
Communicating clearly about data sharing in genomics | Human Genomics
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Nicky Whiffin @nickywhiffin.bsky.social · 31/07/2025
📣 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'
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Eileen Furlong @eileen-furlong.bsky.social · 30/07/2025
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...
embl.wd103.myworkdayjobs.com
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...
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Reposted by Mallory Freeberg
Stephen Turner @stephenturner.us · 28/07/2025
A draft UAE-based Arab pangenome reference www.nature.com/articles/s41... 🧬🖥️🧪
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Reposted by Mallory Freeberg
Atlas of Variant Effects Alliance @varianteffect.bsky.social · 23/07/2025
🧬 Interested in variant interpretation? #FunctionalGenomics #Pharmacogenetics #MutationalScanning #VariantEffectPredictor #RareDisease #Collaboration #PrecisionMedicine Check out our list of publications! 📖 www.varianteffect.org/publications/
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Mallory Freeberg @malloryfreeberg.bsky.social · 26/07/2025
🧬💻 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
embl.wd103.myworkdayjobs.com
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,...
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Mallory Freeberg @malloryfreeberg.bsky.social · 26/07/2025
🧬💻 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
embl.wd103.myworkdayjobs.com
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 ...
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Mallory Freeberg @malloryfreeberg.bsky.social · 23/07/2025
So proud to represent our amazing teams and resources in the Human Genomics Team and beyond 🫶🏼
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EMBL-EBI @ebi.embl.org · 23/07/2025
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... 🧬🖥️
ebi.ac.uk
New platform integrates gene perturbation data
The Perturbation Catalogue provides user-friendly access to human gene perturbation, variant analysis, and expression data.
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Mallory Freeberg @malloryfreeberg.bsky.social · 23/07/2025
🧬 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
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EMBL-EBI @ebi.embl.org · 14/07/2025
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.
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Mike Inouye @mikeinouye.bsky.social · 04/07/2025
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...
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Saez-Rodriguez Group @saezlab.bsky.social · 02/07/2025
Postdoc position in our group at @ebi.embl.org about analyzing single cell data sets to better understand and treat neurodegen diseases, in collab with A Bassett, M Lotfollahi, @bayraktarlab.bsky.social, M Strauss and others within Open Targets. Deadline 20/07. Please share tinyurl.com/87wj466m
tinyurl.com
Postdoctoral Fellow in computational modelling of NeuroImmune Mechanisms of Neurodegeneration (Open Targets)
Your role As a Postdoctoral Fellow on the NeuroImmune Open Targets project, you will develop and apply integrative computational pipelines to dissect immune-cell phenotypes and cell–cell interactions ...
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Global Alliance for Genomics and Health @ga4gh.org · 23/06/2025
Join us for our upcoming Fireside Chat on 11 July 2025 at 13:00 UTC with Tim Hubbard and Serena Scollen of @elixir-europe.org‬! Register for the event:
buff.ly
Welcome! You are invited to join a webinar: Fireside Chat with Tim Hubbard and Serena Scollen. After registering, you will receive a confirmation email about joining the webinar.
Welcome! You are invited to join a webinar: Fireside Chat with Tim Hubbard and Serena Scollen. After registering, you will receive a confirmation email about joining the webinar.
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Atlas of Variant Effects Alliance @varianteffect.bsky.social · 23/06/2025
We have co-organized a MAVE course with Wellcome Connecting Science! Meeting is in November, but the 🗓️📝Application deadline is 18 August 2025 ⏰https://coursesandconferences.wellcomeconnectingscience.org/event/multiplex-assays-of-variant-effects-maves-approaches-analysis-and-interpretation-20251123/
coursesandconferences.wellcomeconnectingscience.org
Multiplex assays of variant effects (MAVEs): Approaches, Analysis, and Interpretation — 20251123
.Learn how to analyse, assess, and interpret MAVE data for clinical and research applications
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Reposted by Mallory Freeberg
Ensembl @ensembl.org · 09/06/2025
Two exciting jobs open now: 🧬 Genebuild Project Leader Apply: www.ensembl.info/2025/06/02/j... ⏳ Closes: 30 June 2025 🔗 Dataflow Coordinator Apply: www.ensembl.info/2025/06/09/j... ⏳ Closes: 6 July 2025 #Genomics #Bioinformatics #Jobs
ensembl.info
Job: Ensembl Genebuild Project Leader – Ensembl Blog
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Reposted by Mallory Freeberg
Christina Ernst @christinaernst.bsky.social · 17/06/2025
Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬 Now’s your turn: tell us how you’ve used them + why they matter. It takes 15 mins and helps keep these services open and free for all. 👉 tinyurl.com/bdf73zpp Closes 16 July #opendata #FAIRdata
tinyurl.com
EMBL-EBI Value and Impact Survey 2025
Take this survey powered by surveymonkey.com. Create your own surveys for free.
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Global Alliance for Genomics and Health @ga4gh.org · 17/06/2025
Policy Brief: will the UK participate in the European Health Data Space? In this brief, Miranda Mourby discusses questions that remain, following publication of the European Health Data Space Regulation text, related to participation from outside of the EU. Read more: www.ga4gh.org/news_item/po...
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Mallory Freeberg @malloryfreeberg.bsky.social · 12/06/2025
#Genes #variants #phenotypes, oh my! @ebi.embl.org Human Genomics Team services presented at #CCG2025: 🔍@gene2phenotype.bsky.social (G2P) - accelerating genomic medicine w/ high-confidence, evidence-based gene-disease models www.ebi.ac.uk/gene2phenoty...
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Saez-Rodriguez Group @saezlab.bsky.social · 12/06/2025
🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇 decoupler.readthedocs.io/en/latest/
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Mallory Freeberg @malloryfreeberg.bsky.social · 12/06/2025
Today is Day 2 of Curating the Clinical Genome organised by @deciphergenomics.bsky.social and hosted by @eventswcs.bsky.social 🫶 Come visit poster 15 - I would love to talk to you about how the fabulous members of the @ga4gh.org community are accelerating clinical genomics! 🌱 #CCG2025
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Mallory Freeberg @malloryfreeberg.bsky.social · 11/06/2025
👋 I'll be in Exeter for the @uk-fgx.bsky.social Inaugural Scientific Symposium 16 June & London for the @genomicsengland.bsky.social Research Summit 17 June. I'd love to chat about @ebi.embl.org resources like @ensembl.bsky.social, @deciphergenomics.bsky.social, and the Perturbation Catalog! 🧬 💻
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Stephen Turner @stephenturner.us · 09/06/2025
Pangenome-aware DeepVariant www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/google/deepv...
biorxiv.org
Pangenome-aware DeepVariant
Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome…
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Anshul Kundaje @anshulkundaje.bsky.social · 09/06/2025
Please sign the Bethesda Declaration: A Call for NIH and HHS Leadership to Deliver on Promises of Academic Freedom and Scientific Excellence www.standupforscience.net/bethesda-dec... Stand up for science!
standupforscience.net
Bethesda Declaration — STAND UP FOR SCIENCE
Support NIH Staff Now!
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Yasset Perez-Riverol @ypriverol.bsky.social · 06/06/2025
We recently released a tool to help you with this. 🚀 Say hello to pridepy — your Python for grabbing data from the @pride-ebi.bsky.social! To search metadata or download files via FTP, Aspera, Globus, or S3, and is perfect for bioinfo workflows. Check it out 👉 github.com/PRIDE-Archiv...
github.com
GitHub - PRIDE-Archive/pridepy: Python client for PRIDE Archive Rest API.
Python client for PRIDE Archive Rest API. . Contribute to PRIDE-Archive/pridepy development by creating an account on GitHub.
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