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Joep de Ligt 🧬 PhD

@joepdel.bsky.social
868 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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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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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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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 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
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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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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Reposted by Joep de Ligt 🧬 PhD
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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Reposted by Joep de Ligt 🧬 PhD
BF Francis Ouellette @bffo.bsky.social · 01/04/2025
Vence Bonham, acting chief of National Human Genome Research Institute 'unexpectedly' put on leave 🧬 🖥️ 🧪 ⬇️ www.statnews.com/2025/03/31/t... via @statnews.com
statnews.com
Vence Bonham, acting chief of National Human Genome Research Institute, 'unexpectedly' put on leave
Vence Bonham, who became acting director of the National Human Genome Research Institute less than two weeks ago, is "unexpectedly" placed on leave.
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Reposted by Joep de Ligt 🧬 PhD
Robin Rohwer @robinrohwer.bsky.social · 01/04/2025
I have been seeing a lot of packages published in the journal of open source software recently. JOSS looks neat because the reviews are of the code + documentation and the paper itself is minimal. 💻🧬 joss.theoj.org
joss.theoj.org
Journal of Open Source Software
Journal of Open Source Software (JOSS) is a developer friendly, open access journal for research software packages.
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Reposted by Joep de Ligt 🧬 PhD
European Cancer Organisation @europeancancer.bsky.social · 02/04/2025
Rising cancer cases, ageing populations & rapid tech shifts are creating urgent skills gaps in cancer care It’s time to make skilling the #CancerWorkforce a political priority Scroll down to learn how Europe is catching up #WHWWeek #HealthWorkersSaveLives
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BC Genome Sciences Centre @bcgsc.ca · 02/04/2025
📢 A major milestone for international biomedical research - Canada joins Federated EGA! We are proud to host the new Canadian node, which strengthens research collaboration & global access to secure genomic & health data while upholding privacy & compliance. 🔽Link Below🔽
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The Conversation U.S. @us.theconversation.com · 01/04/2025
Bird flu is showing signs of possible human-to-human transmission. An anthropologist explores the history of infectious diseases, revealing how human behavior has shaped viral evolution for thousands of years. buff.ly/upaUHGm Ron Barrett @macalestercollege.bsky.social 🩺#medsky #birdflu 🧪 #H5N1
buff.ly
Bird flu could be on the cusp of transmitting between humans − but there are ways to slow down viral evolution
At the viral chatter stage of an outbreak, pathogens are just starting to infect people in sporadic bursts. It’s a sign that a pandemic may be on the horizon.
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Reposted by Joep de Ligt 🧬 PhD
james stevenson @jsstevenson.bsky.social · 30/03/2025
The 2.0 release of the @ga4gh.org Variation Representation Specification (VRS) is signed, sealed, and delivered! It provides powerful ways to describe genomic variation and enhances alignment with other important standards. 🧪 🖥️ 🧬 www.ga4gh.org/news_item/va...
ga4gh.org
Variation Representation Specification (VRS) v2.0 is an approved GA4GH product
A newly approved GA4GH product, the Variation Representation Specification (VRS) v2.0 establishes standardised descriptions of variant evidence across different sequence collections used by resources ...
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Reposted by Joep de Ligt 🧬 PhD
ELIXIR Europe @elixir-europe.org · 25/03/2025
Do you have a #bioinformatics project idea that needs a little stimulus⚡? Submit your project proposal for #BioHackEU25 to get the chance to meet with experts 💨 to drive the project forward. 📥 Submit your proposal by 14 April: biohackathon-europe.org/projects/
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Reposted by Joep de Ligt 🧬 PhD
Darragh Duffy @darraghduffy.bsky.social · 24/03/2025
13 chair positions open @inserm.fr to lead a junior research group in France covering #neuroscience, #immunology, #bioinformatics, #bioengineering, #biotherapy, #public health pro.inserm.fr/rubriques/co... 🧪🔬
pro.inserm.fr
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Genome BC @genomebc.bsky.social · 27/03/2025
BC's economy & health get a $49M booster shot! 📈❤️ Genome BC secured funding for 5 precision health projects, driving innovation & improving cancer, child safety, & heart health. More: bit.ly/GBCCPHI #BCEconomy #BCHealth #Genomics
bit.ly
BC Researchers Awarded Over $49 Million for Advancements in Hereditary Cancer Care, Child Drug Safety and Heart Health - Genome BC
BC led research to transform early disease detection, treatment and health equity using cutting edge genomic technologies.   Vancouver, BC—Genome BC has helped secure more than $49 million for researc...
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Stephen Turner @stephenturner.us · 27/03/2025
Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/MoinSebi/gfa... (MIT, Rust 🦀)
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Reposted by Joep de Ligt 🧬 PhD
Alice Manuzzi @alicemanuzzi.bsky.social · 27/03/2025
#PopGen Great opportunity for a postdoc on #Genomics and #ancientDNA with a fantastic team at DTU Aqua, Denmark!
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Reposted by Joep de Ligt 🧬 PhD
Kai Kupferschmidt @kakape.bsky.social · 26/03/2025
When the US reported a year ago that the H5N1 avian influenza virus had infected dairy cattle, it seemed some rare confluence of factors had allowed the virus to infect the cows’ udders. Then it happened again. And again. Story in @science.org on some questions about the origins of H5N1 in cows… 🧪
science.org
Mysteries surrounding cow flu have scientists concerned about future outbreaks
One year after the first infections were reported, it's still unclear how H5N1 virus jumped into U.S. cattle—and why it keeps doing so
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Stephen Turner @stephenturner.us · 24/03/2025
Benchmarking of Human Read Removal Strategies for Viral and Microbial Metagenomics www.biorxiv.org/content/10.1... 🧬🖥️🧪 Nextflow github.com/wtsi-npg/hrr...
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