Joep de Ligt 🧬 PhD
@joepdel.bsky.social
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
https://orcid.org/0000-0002-0348-419X
https://orcid.org/0000-0002-0348-419X
Reposted by Joep de Ligt 🧬 PhD
📑 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 🖥️ 🧬
🔗 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
June 17, 2025 at 2:11 PM
📑 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 🖥️ 🧬
🔗 buff.ly/4Kwgz6N
#pangenome #genomics 🖥️ 🧬
Reposted by Joep de Ligt 🧬 PhD
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
June 5, 2025 at 8:42 AM
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! 🌐🧪
Reposted by Joep de Ligt 🧬 PhD
🌟 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)
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)
June 4, 2025 at 8:42 AM
🌟 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)
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)
Reposted by Joep de Ligt 🧬 PhD
🧬🖥️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.
🧬🖥️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.
🧵1/10
🧵1/10
June 3, 2025 at 5:43 PM
🧬🖥️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.
Reposted by Joep de Ligt 🧬 PhD
📢 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
📍 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
June 3, 2025 at 8:30 AM
📢 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
📍 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
Reposted by Joep de Ligt 🧬 PhD
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...
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
June 3, 2025 at 12:34 AM
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...
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...
Reposted by Joep de Ligt 🧬 PhD
🔑 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
#ELIXIR25
June 2, 2025 at 12:56 PM
🔑 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
#ELIXIR25
Reposted by Joep de Ligt 🧬 PhD
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
Hear from Dr Rich Scott (Genomics England) at #UKPGx2025.
📍 London | 🗓️ 18 June
🎟️ Register now: my.bps.ac.uk/events/detai...
#RareDisease #Genomics #HealthcareInnovation
June 2, 2025 at 12:46 PM
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
Hear from Dr Rich Scott (Genomics England) at #UKPGx2025.
📍 London | 🗓️ 18 June
🎟️ Register now: my.bps.ac.uk/events/detai...
#RareDisease #Genomics #HealthcareInnovation
#ELIXIR25 Naveed Aziz from @genomecanada.ca up now about collaboration through shared data.
June 2, 2025 at 11:36 AM
#ELIXIR25 Naveed Aziz from @genomecanada.ca up now about collaboration through shared data.
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.
June 2, 2025 at 7:08 AM
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.
Reposted by Joep de Ligt 🧬 PhD
Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. #PangenomeGraphs #Bioinformatics 💻 🧬
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
academic.oup.com
May 30, 2025 at 6:13 PM
Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. #PangenomeGraphs #Bioinformatics 💻 🧬
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Joep de Ligt 🧬 PhD
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
May 31, 2025 at 7:13 AM
MLOmics: Cancer Multi-Omics Database for Machine Learning 🧪 🧬🖥️ www.nature.com/articles/s41...
Reposted by Joep de Ligt 🧬 PhD
📣 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...
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
May 30, 2025 at 11:45 AM
📣 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...
Find out how 🙌 ELIXIR will work with international initiatives and partner regions worldwide to address #lifescience data challenges 👉 elixir-europe.org/news/interna...
Reposted by Joep de Ligt 🧬 PhD
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 🧪
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
May 23, 2025 at 9:04 AM
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 🧪
Reposted by Joep de Ligt 🧬 PhD
🧪🌎🦑🐠🦈
Last call ⏳🚨
If you have any elasmobranch and killer whale interaction records we want to hear about it!
Please reach our team with the email below, would love to include them in our global review!
If you have any elasmobranch and killer whale interaction records we want to hear about it!
Please reach our team with the email below, would love to include them in our global review!
May 14, 2025 at 10:27 AM
🧪🌎🦑🐠🦈
Reposted by Joep de Ligt 🧬 PhD
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
🧬 Explore the resources: tinyurl.com/4s8vpyup
#Genomics #IndigenousGenomics #BridgingTheGap
@ncig2013.bsky.social @ausgenomics.bsky.social
Introduction to genomic resources by NCIG Deputy Director, Azure Hermes
YouTube video by studentsatcop15
youtu.be
May 14, 2025 at 4:37 AM
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
🧬 Explore the resources: tinyurl.com/4s8vpyup
#Genomics #IndigenousGenomics #BridgingTheGap
@ncig2013.bsky.social @ausgenomics.bsky.social
Reposted by Joep de Ligt 🧬 PhD
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
May 12, 2025 at 1:45 PM
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
Reposted by Joep de Ligt 🧬 PhD
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.
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.
www.washingtonpost.com
April 24, 2025 at 3:21 PM
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.
Reposted by Joep de Ligt 🧬 PhD
A stark reminder, if we needed it, we need climate action now: 🧪🌊🪸 www.theguardian.com/environment/...
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
www.theguardian.com
April 23, 2025 at 6:43 AM
A stark reminder, if we needed it, we need climate action now: 🧪🌊🪸 www.theguardian.com/environment/...
Reposted by Joep de Ligt 🧬 PhD
🧪🧬🖥️ 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...
github.com/vgteam/vg/re...
April 22, 2025 at 4:05 PM
🧪🧬🖥️ 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...
github.com/vgteam/vg/re...
Reposted by Joep de Ligt 🧬 PhD
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....
🌐 onlinelibrary.wiley.com/doi/full/10....
April 22, 2025 at 8:45 AM
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....
🌐 onlinelibrary.wiley.com/doi/full/10....
Reposted by Joep de Ligt 🧬 PhD
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
Learn more about HIS partners: lnkd.in/eEGfBmZv
#Genomics #InfectionControl
April 13, 2025 at 9:13 AM
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
Learn more about HIS partners: lnkd.in/eEGfBmZv
#Genomics #InfectionControl
Reposted by Joep de Ligt 🧬 PhD
The impact of long-read sequencing on human population-scale genomics genome.cshlp.org/content/35/4... 🧬🖥️🧪
April 21, 2025 at 6:30 PM
The impact of long-read sequencing on human population-scale genomics genome.cshlp.org/content/35/4... 🧬🖥️🧪
Reposted by Joep de Ligt 🧬 PhD
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.
April 18, 2025 at 3:58 PM
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.