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Joep de Ligt 🧬 PhD

@joepdel.bsky.social
872 followers 2.5K following 226 posts

Lead data @HartwigMedicalFoundation, Amsterdam, Netherlands. Honorary fellow @OtagoUniversity. Active in the field of Bioinformatics and Genetics with a focus on human diseases. Lover of nature and (book) nerd. he/him orcid.org/0000-0002-0348-419X

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Reposted by Joep de Ligt 🧬 PhD
completegenomics.bsky.social @completegenomics.bsky.social · 25/02/2026
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 #
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Reposted by Joep de Ligt 🧬 PhD
Earlham Institute @earlhaminst.bsky.social · 17/06/2025
📑 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 🖥️ 🧬
earlham.ac.uk
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?
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Reposted by Joep de Ligt 🧬 PhD
tomjwebb @tomjwebb.bsky.social · 05/06/2025
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! 🌐🧪
onlinelibrary.wiley.com
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...
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 05/06/2025
And especially since the term bioinformatics was coined by/is attributed to a women. Paulien Hogeweg. en.m.wikipedia.org/wiki/Paulien...
en.m.wikipedia.org
Paulien Hogeweg - Wikipedia
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Reposted by Joep de Ligt 🧬 PhD
ELIXIR Europe @elixir-europe.org · 04/06/2025
🌟 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 · 04/06/2025
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 · 03/06/2025
🧬🖥️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.
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Reposted by Joep de Ligt 🧬 PhD
EASIGEN @easigen-eu.bsky.social · 03/06/2025
📢 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 · 03/06/2025
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...
biorxiv.org
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 ...
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
#ELIXIR25 next up we will be hearing from federated EGA.
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
#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 · 02/06/2025
#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 · 02/06/2025
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 · 02/06/2025
#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 · 02/06/2025
🔑 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 · 02/06/2025
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 · 02/06/2025
#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 · 02/06/2025
#ELIXIR25 generational opportunity to build safe, fast and ethically governed (including indigenous voices) for data driven research and healthcare across borders.
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
#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 · 02/06/2025
#ELIXIR25 Naveed Aziz from @genomecanada.ca up now about collaboration through shared data.
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
#ELIXIR25 EOSC moving to a service delivery focus with nodes to deliver for health research.
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
#ELIXIR25 kicking off after the housekeeping. Looking forward to the Genome Canada keynote
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 02/06/2025
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 · 30/05/2025
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 · 31/05/2025
MLOmics: Cancer Multi-Omics Database for Machine Learning 🧪 🧬🖥️ www.nature.com/articles/s41...
nature.com
MLOmics: Cancer Multi-Omics Database for Machine Learning - Scientific Data
Scientific Data - MLOmics: Cancer Multi-Omics Database for Machine Learning
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Reposted by Joep de Ligt 🧬 PhD
ELIXIR Europe @elixir-europe.org · 30/05/2025
📣 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...
loom.ly
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…
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Reposted by Joep de Ligt 🧬 PhD
Prof Tom Cotter @proftomcotter.bsky.social · 23/05/2025
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 🧪
theguardian.com
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
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Reposted by Joep de Ligt 🧬 PhD
David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 14/05/2025
🧪🌎🦑🐠🦈
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Reposted by Joep de Ligt 🧬 PhD
Australian Genomics @ausgenomics.bsky.social · 14/05/2025
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
youtu.be
Introduction to genomic resources by NCIG Deputy Director, Azure Hermes
YouTube video by studentsatcop15
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Reposted by Joep de Ligt 🧬 PhD
Anthropology.net @anthropology.net · 12/05/2025
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
anthropology.net
Mapping the Genome of a Multi-Ethnic Nation
How a U.S.-wide study of nearly 300,000 genomes is rewriting what we thought we knew about ancestry, identity, and the story of human variation
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Reposted by Joep de Ligt 🧬 PhD
The Washington Post @washingtonpost.com · 24/04/2025
Breaking news: The United States faces millions of measles cases over the next 25 years if vaccination rates for the disease drop 10 percent, according to new research published Thursday.
washingtonpost.com
Millions of U.S. measles cases forecast over 25 years if shots decline
Measles, once virtually wiped out in the United States, could become commonplace again if declining vaccination rates continue, a new model shows.
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Reposted by Joep de Ligt 🧬 PhD
Gavin Foster @thefosterlab.bsky.social · 23/04/2025
A stark reminder, if we needed it, we need climate action now: 🧪🌊🪸 www.theguardian.com/environment/...
theguardian.com
More than 80% of the world’s reefs hit by bleaching after worst global event on record
An ashen pallor and an eerie stillness all that remains where there should fluttering fish and vibrant colours in the reefscape, one conservationist says
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Reposted by Joep de Ligt 🧬 PhD
UC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 22/04/2025
🧪🧬🖥️ Our variation graphs (vg) version 1.65.0 (code name "Carfon") is out now! It has all the fixes from v1.64.1, plus a fix for consistent ref allele traversals in vg call -v. github.com/vgteam/vg/re...
vg logo
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 23/04/2025
Small context notes: -Germline variant calling -Not all frameworks tested (was expecting UK biobank workflow since they are one of the largest sources of germline data out there)
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Joep de Ligt 🧬 PhD @joepdel.bsky.social · 22/04/2025
Found it in the feed so seems to work just fine
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Reposted by Joep de Ligt 🧬 PhD
Maria Dzunkova @dzunkovam.bsky.social · 22/04/2025
We can celebrate the #EarthDay 🌍 with our paper contributing to the Earth Biogenome Project published in Ecology and Evolution! We aimed to identify the best DNA extraction protocol for long-read #sequencing of #nudibranch #genome ...⬇️ 🧬🖥️ 🦑🧪 🐟🪸 #MarineLife 🌐 onlinelibrary.wiley.com/doi/full/10....
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Reposted by Joep de Ligt 🧬 PhD
Healthcare Infection Society @hisinfection.bsky.social · 13/04/2025
Great talk at #ESCMID2025 by HIS Secretary Dr James Price on how #WGS can optimise #IPC & tackle #HCAIs — insights from the GENOTIPE study, research funded by HIS platinum partner Genpax. Learn more about HIS partners: lnkd.in/eEGfBmZv #Genomics #InfectionControl
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Reposted by Joep de Ligt 🧬 PhD
Stephen Turner @stephenturner.us · 21/04/2025
The impact of long-read sequencing on human population-scale genomics genome.cshlp.org/content/35/4... 🧬🖥️🧪
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Reposted by Joep de Ligt 🧬 PhD
Hannah Harris Green @whatsitlike.me · 18/04/2025
The review found consensus that cannabis is effective for treating symptoms of cancer and chemo like pain and nausea. Perhaps more surprisingly, it also found consensus that cannabis can fight cancerous cells. But a lot more research is needed to show that would work in human patients.
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Reposted by Joep de Ligt 🧬 PhD
Cancer Survivors Club 📙 @thecancersurvivorsclub.com · 15/04/2025
Genetic data could revolutionise #CancerCare! Testing a patient’s DNA may help personalise #Radiotherapy—like choosing longer treatment courses for better outcomes. #TCSC #Oncology #Genomics #CancerResearch www.cancernetwork.com/view/genetic...
cancernetwork.com
Genetic Data May Inform Personalized Radiotherapy Strategies for Cancer Care
Testing a patient’s genetics may influence decisions such as using longer courses of radiotherapy, says Rachit Kumar, MD.
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Reposted by Joep de Ligt 🧬 PhD
Bloomberg News @bloomberg.com · 15/04/2025
Some major public institutions in Canada, including a pension management firm and a leading hospital, are advising staff against traveling to the US.
bloomberg.com
Avoid US or Take Burner Devices, Canadian Executives Tell Staff
Some major public institutions in Canada, including a pension management firm and a leading hospital, are advising staff against traveling to the US, marking a greater erosion in the country’s longsta...
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Reposted by Joep de Ligt 🧬 PhD
juli g pausas @jgpausas.bsky.social · 14/04/2025
"the quality of input data is more important when improving forecasts than the complexity of the ML architecture" @fdg10371.bsky.social Although it may seem obvious, it deserves reiteration, and it applies to other fields, not only global fires www.nature.com/articles/s41... 🧪🌎🔥🌲🔥🌿 wildfire
nature.com
Global data-driven prediction of fire activity - Nature Communications
The ability to predict wildfires-such as those that recently devastated Los Angeles and Canada-is advancing rapidly with the help of AI. This study shows that to improve accuracy and reliability, we m...
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Reposted by Joep de Ligt 🧬 PhD
Stephen Turner @stephenturner.us · 07/04/2025
Integrating experimental feedback improves generative models for biological sequences www.biorxiv.org/content/10.1... 🧬🖥️🧪
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Reposted by Joep de Ligt 🧬 PhD
Tamim Ahsan @tamim-ahsan.bsky.social · 08/04/2025
This is a big one! A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat. #genomics #transcriptomics #proteomics #multiomics #evolution #wheat doi.org/10.1038/s415...
doi.org
A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat - Nature Genetics
A telomere-to-telomere genome assembly of allohexaploid bread wheat cv. Chinese Spring (CS-IAAS), along with transcriptomic and proteomic data, highlights wheat genome complexity and its structural an...
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Reposted by Joep de Ligt 🧬 PhD
Martin Smith @martinalexsmith.bsky.social · 09/04/2025
🚨Scoop: Keynote speakers announced for the Australasian Genomic Technologies Association #AGTA25 Annual Conference #genomics #Sydney #Australia
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Reposted by Joep de Ligt 🧬 PhD
Dan Chibnall @bookowl.bsky.social · 07/04/2025
Important read about the current measles outbreak in the U.S. from Dr. @kkjetelina.bsky.social 🧪 yourlocalepidemiologist.substack.com/p/third-meas...
yourlocalepidemiologist.substack.com
Third measles death
This is not normal. For three reasons.
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Reposted by Joep de Ligt 🧬 PhD
Stephen Turner @stephenturner.us · 07/04/2025
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing www.nature.com/articles/s41... (read free: rdcu.be/egGj6) 🧬🖥️🧪 github.com/KolmogorovLa...
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BioSB Research School @biosb.bsky.social · 03/04/2025
🚀 The BioSB 2025 Scientific Programme is LIVE! 🚀 Whether you’re a researcher, industry professional or student, BioSB 2025 offers invaluable insights and networking opportunities: www.aanmelder.nl/biosb2025/pr... #BioSB2025 #Conference #Bioinformatics #SystemsBiology #IndustryPartnerships
aanmelder.nl
BioSB 2025 - Programme 2025
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