Joep de Ligt 🧬 PhD

Day 2 at #AGBT2026 ☕

Join us 8:00–9:00 AM in the Palm Beach Suite:

• CoolMPS 600 — high accuracy + longer reads
• Stereo-seq spatial transcriptomics
• Disease microenvironments (Mayo Clinic)

🎤 ctDNA workshop at 2:40 PM
🏁 Final day of our F1 challenge

See you there.

#Genomics #SpatialBiology #

What’s the power of a pangenome? Here at the Earlham Institute a lot of people are very excited about pangenomes. But what are they? And how will they change genetics?

📑 Researchers are moving away from a single point of reference to compare multiple genomes against each other, providing a much greater picture of genetic diversity.

🔗 buff.ly/4Kwgz6N

#pangenome #genomics 🖥️ 🧬

MOBS 1.0: A Database of Interspecific Variation in Marine Organismal Body Sizes Motivation Body size is a fundamental trait influencing an organism's life history, ecology, physiology and evolutionary dynamics. While extensive body-size databases exist for terrestrial vertebrat...

For many marine species, all we have is a name. Now, thanks to a huge effort led by @drcraigmc.bsky.social, for 85,000 species we have body size as well. Version 1 of the MOBS database is published today: onlinelibrary.wiley.com/doi/10.1111/... Enjoy! 🌐🧪

And especially since the term bioinformatics was coined by/is attributed to a women. Paulien Hogeweg. en.m.wikipedia.org/wiki/Paulien...

🌟 A little recap from yesterday's #ELIXIR25:

Participants have a morning of fruitful discussion in workshops covering topics from #AI and #KnowledgeGraphs, #ResearchDataManagement resources 💾 to #Galaxy and #biodiversity and #FederatedEGA 🧬 and more! (🧵2/3)

It's always so cool to say people this involved with data and specimen collection, but having worked in Aotearoa NZ for a while means I also so a risk of biopiracy and colonial practices in this. Are volunteers are aware of local and Indigenous perspectives? How is benefit sharing done?

🧬🖥️Drug response prediction is a machine learning challenge with immense potential for precision medicine. Our latest preprint introduces DrEval, a comprehensive benchmarking framework to evaluate state-of-the-art methods, uncover widespread issues, and guide the development of more robust models.

📢 Meet the partners of the #EASIGEN-DS Consortium!

📍‪ UKSH is known for its clinical and research excellence, @uni-kiel.de is a top public research university and together they established IKMB to explore human diseases using genomic technologies. They serve as German node of #EASIGEN-DS

Damage and Misrepair Signatures: Compact Representations of Pan-cancer Mutational Processes Mutational signatures of single-base substitutions (SBSs) characterize somatic mutation processes which contribute to cancer development and progression. However, current mutational signatures do not ...

Please check out our new approach to modeling somatic mutation signatures.

DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪

www.biorxiv.org/content/10.1...

#ELIXIR25 next up we will be hearing from federated EGA.

Lost of links to demonstrator products and cBioPortal screenshot

#ELIXIR25 cancer use case example

#ELIXIR25 now a presentation from GDI (Genomics Data Infrastructure). Discovery by anonymous users but needs authentication before they can dig deeper

Mao of Europe showing most countries are engaged and a long list of projects

Examples of projects #ELIXIR25

#ELIXIR25 wide range of projects and stakeholders. Some key ones for cancer: EOSC cancer, CANDLE, GA4GH and B1MG.

🔑 For the keynote speech, Naveed Aziz from @genomecanada.ca shared Canada’s genomic strategy for collaboration through shared data, marking the importance of #globalcollaboration in #openscience.

#ELIXIR25

How has the 100k Genomes Project changed care for rare disease?
Hear from Dr Rich Scott (Genomics England) at #UKPGx2025.
📍 London | 🗓️ 18 June
🎟️ Register now: my.bps.ac.uk/events/detai...
#RareDisease #Genomics #HealthcareInnovation

#ELIXIR25 🖥️🧬🧪 next session: Human Genomes across borders at scale. "Federated analysis to solve real world problems."

#ELIXIR25 generational opportunity to build safe, fast and ethically governed (including indigenous voices) for data driven research and healthcare across borders.

#ELIXIR25 starting with a personal story about the value of genomics for rare diseases when data is shared globally.

#ELIXIR25 Naveed Aziz from @genomecanada.ca up now about collaboration through shared data.

#ELIXIR25 EOSC moving to a service delivery focus with nodes to deliver for health research.

#ELIXIR25 kicking off after the housekeeping. Looking forward to the Genome Canada keynote

Ready for #ELIXIR2025 @elixir-europe.org, looking forward to reconnecting with EU bioinformatics after my time in Aotearoa NZ. Will be posting about the sessions and workshops I have selected (mostly about cancer genomics and DREs) the coming days.

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. #PangenomeGraphs #Bioinformatics 💻 🧬
academic.oup.com/bioinformati...

MLOmics: Cancer Multi-Omics Database for Machine Learning - Scientific Data Scientific Data - MLOmics: Cancer Multi-Omics Database for Machine Learning

MLOmics: Cancer Multi-Omics Database for Machine Learning 🧪 🧬🖥️ www.nature.com/articles/s41...

ELIXIR releases new international strategy | ELIXIR ELIXIR has released an updated international strategy to guide its engagement and collaborations beyond Europe. The revised framework outlines how ELIXIR will work with international initiatives and…

📣 ELIXIR has released an updated international strategy to guide its engagement and #collaborations beyond Europe 🌍.
Find out how 🙌 ELIXIR will work with international initiatives and partner regions worldwide to address #lifescience data challenges 👉 elixir-europe.org/news/interna...

Trump administration halts Harvard’s ability to enroll international students Homeland security secretary Kristi Noem posts copy of department’s letter to university on X

www.theguardian.com/us-news/2025.... The attack on an academic institution like Harvard is very similar to what happened in the 1930s Germany. It needs to be stopped 🧪

🧪🌎🦑🐠🦈

YouTube video by studentsatcop15 Introduction to genomic resources by NCIG Deputy Director, Azure Hermes

Hear from @azurehermes.bsky.social on the importance of new culturally appropriate genomic resources for Aboriginal and Torres Strait Islander peoples.

🧬 Explore the resources: tinyurl.com/4s8vpyup

#Genomics #IndigenousGenomics #BridgingTheGap
@ncig2013.bsky.social @ausgenomics.bsky.social

What do nearly 300,000 American genomes reveal? Ancestry isn’t a box—it's a gradient. The All of Us cohort shows how deeply entangled our histories are. #Genomics #Anthropology #Admixture #HumanEvolution #PopulationGenetics