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Reposted by Joep de Ligt 🧬 PhD

Earlham Institute @earlhaminst.bsky.social · Jun 17

📑 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 🖥️ 🧬

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?

www.earlham.ac.uk

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Reposted by Joep de Ligt 🧬 PhD

tomjwebb @tomjwebb.bsky.social · Jun 5

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! 🌐🧪

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...

onlinelibrary.wiley.com

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 5

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

Paulien Hogeweg - Wikipedia

en.m.wikipedia.org

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Reposted by Joep de Ligt 🧬 PhD

ELIXIR Europe @elixir-europe.org · Jun 4

🌟 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)

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 4

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?

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Reposted by Joep de Ligt 🧬 PhD

Markus List @itisalist.bsky.social · Jun 3

🧬🖥️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.

Judith Bernett @judith-bernett.bsky.social · Jun 3

🧬🖥️So excited to show you the outcome of @pascivers.bsky.social and my latest project: "From Hype to Health Check: Critical Evaluation of Drug Response Prediction Models with DrEval" doi.org/10.1101/2025.05.26.655288, published with M. Picciani, M. Wilhelm, K. Baum & @itisalist.bsky.social.
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Overview of the DrEval framework. Via input options, implemented state-of-the-art models can be compared against baselines of varying complexity. We address obstacles to progress in the field at each point in our pipeline: Our framework is available on PyPI and nf-core and we follow FAIReR standards for optimal reproducibility. DrEval is easily extendable as demonstrated here with a pseudocode implementation of a proteomics-based random forest. Custom viability data can be preprocessed with CurveCurator, leading to more consistent data and metrics. DrEval supports five widely used datasets with application-aware train/test splits that enable detecting weak generalization. Models are free to use provided or custom cell line– and drug features. The pipeline supports randomization-based ablation studies and performs robust hyperparameter tuning for all models. Evaluation is conducted using meaningful, bias-resistant metrics to avoid inflated results from artifacts such as Simpson’s paradox. All results are compiled into an interactive HTML report. Created in https://BioRender.com.

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Reposted by Joep de Ligt 🧬 PhD

EASIGEN @easigen-eu.bsky.social · Jun 3

📢 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

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Reposted by Joep de Ligt 🧬 PhD

Quaid Morris @quaidmorris.bsky.social · Jun 3

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...

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 ...

www.biorxiv.org

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

#ELIXIR25 cancer use case example

Lost of links to demonstrator products and cBioPortal screenshot

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

Examples of projects #ELIXIR25

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Reposted by Joep de Ligt 🧬 PhD

ELIXIR Europe @elixir-europe.org · Jun 2

🔑 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

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Reposted by Joep de Ligt 🧬 PhD

British Pharmacological Society @britpharmsoc.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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

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Joep de Ligt 🧬 PhD @joepdel.bsky.social · Jun 2

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.

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Reposted by Joep de Ligt 🧬 PhD

Javier Santoyo @jsantoyo.bsky.social · May 30

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

academic.oup.com

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Reposted by Joep de Ligt 🧬 PhD

Victor Javier @vjsanchez.bsky.social · May 31

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

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

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

www.nature.com

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Reposted by Joep de Ligt 🧬 PhD

ELIXIR Europe @elixir-europe.org · May 30

📣 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...

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…

loom.ly

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