Luke Jostins-Dean
@lukejostins.bsky.social
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📥 106
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Data scientist at Nightingale Health, associate professor at University of Oxford
A lot of Auden, mostly
add a skeleton here at some point
4 days ago
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Luke Jostins-Dean
Nightingale Health
8 days ago
Our webinar “Multiomic insights into human disease” by
@lukejostins.bsky.social
is tomorrow! Join us on 3 December at 3 p.m. CET for an exploration of how integrating proteomics and metabolomics can deepen our understanding of human health and disease. Sign up:
www.lyyti.fi/reg/webinar-...
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reposted by
Luke Jostins-Dean
Yang Luo
12 days ago
🚨 New preprint from the lab! We’re excited to share “Improving population-scale disease prediction through multi-omics integration” by Ng et al.
www.medrxiv.org/content/10.1...
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Luke Jostins-Dean
Jonn Elledge
about 2 months ago
"The idea of deporting people with settled status is disgusting, and anyone proposing it should be immediately drummed out of polite society. Breaking promises made in good faith to our friends and neighbours is racist, extremist and immoral." I'm basically shouting at the sky here, but still.
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It’s racist, it’s extremist and it’s immoral
The right is still calling for deportations, and the government is still being cowardly about it. Also: London’s first green belt; some notes on a shark; and some news, on my next book.
https://jonn.substack.com/p/its-racist-its-extremist-and-its
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Luke Jostins-Dean
Yang Luo
3 months ago
This project is in close collaboration with the amazing
@lukejostins.bsky.social
, and the student will benefit from a multi-disciplinary team! 🌟🧬🧠
add a skeleton here at some point
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Luke Jostins-Dean
Kaur Alasoo
3 months ago
Parquet works really well with R as well. I use it all the time to work with GWAS summary statistics that won't fit into memory (our latest metabolite GWAS tested 95M+ variants in UKBB). Here's a minimal example of how to filter data on the fly while reading into R:
gist.github.com/kauralasoo/f...
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Filtering parquet files with dplyr
GitHub Gist: instantly share code, notes, and snippets.
https://gist.github.com/kauralasoo/f89288af71f3e5089be607689a561b6e
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reposted by
Luke Jostins-Dean
Yang Luo
3 months ago
🎓 New PhD opportunity in our lab
@kiroxford.bsky.social
@oxforduni.bsky.social
We're exploring host–microbiome genetic interactions in IBD using population-scale data 🧬🦠 🔗
kennedy.ox.ac.uk/.../deciphering-host2013microbiome-genetic-interactions-in-inflammatory-bowel-disease
#PhD
#Genetics
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https://kennedy.ox.ac.uk/.../deciphering-host2013microbiome-genetic-interactions-in-inflammatory-bowel-disease
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Luke Jostins-Dean
Pearl Freier
4 months ago
Novartis & Roche collaborated w/ Oxford researchers at the Big Data Institute 2 develop AI model using largest collection of clinical trial data (Novartis-Oxford MS dataset) from >8000 ppl living w/ multiple sclerosis (MS) to reclassify the progression of MS
www.ndm.ox.ac.uk/news/using-a...
#biosky
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Both sides of this debate made me feel very warmly about the people of France.
www.theguardian.com/society/2025...
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Call to ban ‘intolerant’ child-free resorts and hotels in France
Debate grows as Senator Laurence Rossignol says ‘we can’t organise society by separating children off’
https://www.theguardian.com/society/2025/aug/16/call-to-ban-intolerant-child-free-resorts-and-hotels-in-france
4 months ago
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reposted by
Luke Jostins-Dean
Nightingale Health
4 months ago
Welcome to our webinar “Multi-omic insights into human disease” by
@jeffbarrett.eu
on 4 September at 3 p.m. CEST! Join us for an exploration of how integrating proteomics and metabolomics can deepen our understanding of human health and disease. Learn more and sign up:
www.lyyti.fi/reg/multiomi...
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reposted by
Luke Jostins-Dean
Yang Luo
5 months ago
Amazing news! Excited to be part of this new direction of research.
add a skeleton here at some point
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reposted by
Luke Jostins-Dean
Tobi Alegbe
5 months ago
🚨New preprint just dropped 🚨
medrxiv.org/content/10.1101/2025.06.24.25330216
The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!
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Luke Jostins-Dean
Bradley Harris
5 months ago
To see which of these underpin susceptibility, we colocalised these with IBD GWAS. Remarkably, we nominate effector genes at an enormous 74 (❗) loci where one has not previously been nominated in @OpenTargets. This therefore SUBSTANTIALLY improves on previous efforts. 10/
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Luke Jostins-Dean
Helena Kilpinen
6 months ago
Job alert ‼️
@thomasdwkim.bsky.social
and I are recruiting a postdoc in single-cell genomics via the NORPOD program of the
@nordicembl.bsky.social
. Collaboration between
@fimm-uh.bsky.social
and
@dandrite.bsky.social
on multimodal data integration in neurodevelopment.
jobs.helsinki.fi/job/Helsinki...
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Postdoctoral Researcher in Single-Cell Genomics through the NORPOD program
Postdoctoral Researcher in Single-Cell Genomics through the NORPOD program
https://jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Single-Cell-Genomics-through-the-NORPOD-program/822625802/
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My 7-year-old just made a knife out of Lego, and did this: "I have a knife!" *Does a few slashes, then poses in a fighting stance" "and I am going to a gun fight" Is this from something, or did he make it up himself?
6 months ago
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reposted by
Luke Jostins-Dean
James Lee
6 months ago
📢 📢Job alert!📢📢 We have an exciting opportunity for a 4 year post-doc in my lab at
@crick.ac.uk
. This project will take a similar approach to our recent ETS2 paper, published in Nature, to better understand the mechanisms that contribute to IBD
tinyurl.com/yx43upnk
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Postdoctoral Fellow - Lee Lab
Salary for this Role: From £45,500 with benefits, subject to skills and experience. Job Title: Postdoctoral Fellow - Lee Lab Reports to: James Lee [C] Closing Date: 23.59 GMT Job Description: Job titl...
https://tinyurl.com/yx43upnk
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If you are interested to know why I have been weighing out 15 grams of butter for my bread, and what it has to do with the metabolomics of aging, sign up to this webinar tomorrow
add a skeleton here at some point
6 months ago
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reposted by
Luke Jostins-Dean
Nightingale Health
6 months ago
📣 Our webinar “Measuring the effects of aging with metabolomic profiling” by
@lukejostins.bsky.social
is tomorrow! Remember to sign up and join us tomorrow at 3 p.m. CEST. Sign up:
www.lyyti.fi/reg/aging_we...
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reposted by
Luke Jostins-Dean
Andrea Ganna
6 months ago
We have 2-3 group leader positions opening
@fimm-uh.bsky.social
!! We are looking for outstanding candidates in human genetics and precision medicine. This time we have a focus on population health data science. E.g. AI for EHR/health data Generous starting package 💰
shorturl.at/FAk6n
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FIMM-EMBL Group Leaders in Molecular Medicine
FIMM-EMBL Group Leaders in Molecular Medicine
https://jobs.helsinki.fi/job/Helsinki-FIMM-EMBL-Group-Leaders-in-Molecular-Medicine/821539302/
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reposted by
Luke Jostins-Dean
Mike Inouye
6 months ago
NB: The Polygenic Score Catalog has just lost its NIH funding. It was substantial. We are now on auxillary funding sources. If anyone has a spare £1m plz DM
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Luke Jostins-Dean
7 months ago
Considering a return to study in the life/environmental sciences at Masters/PhD level after time away? Working and wondering if full/part-time study is the next step for your career? Our RePOWER workshop on 13th June in Oxford/online will provide advice and support.
iles.web.ox.ac.uk/repower-retu...
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RePOWER: Returning to Postgraduate Study in the Life and Environmental Sciences
https://iles.web.ox.ac.uk/repower-returning-postgraduate-study-life-and-environmental-sciences
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Goodbye
#ESHG2025
and goodbye Milano! A great conference and a lovely city.
7 months ago
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Luke Jostins-Dean
Annique Claringbould
7 months ago
Justified standing ovation for Nobel laureate Katalin Karikó at
#ESHG2025
She shared her adventurous scientific life and life lessons like "If you want to do something, you find a way. If not, you find excuses", and reminded us scientists to thank our near and dear because "they suffer a little bit"
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Daniel MacArthur
@dgmacarthur.bsky.social
, practically twitching with imposter syndrome, is giving the ESHG Award Lecture
#eshg2025
7 months ago
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reposted by
Luke Jostins-Dean
Yang Luo
7 months ago
Ciao
#eshg2025
! We had a good time!
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Annique Claringbould
@anniquec.bsky.social
is talking about CRISPR interference in primary CD4 T cells for ~1000 GWAS-implicated enhancers, reading out ~2000 genes. Interfering with some key enhancers (CD28, IL2RA) impact basically every CD4-expressed gene.
#eshg2025
7 months ago
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reposted by
Luke Jostins-Dean
Eric Fauman (he/him)
7 months ago
From Adam Butterworth: worth getting embroidered:
add a skeleton here at some point
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A very pleasant poster session, lots of friendly people came to talk about our work. I took
@jeffbarrett.eu
's advice to ask everyone who visited my poster what they work on, to get some actual convos rather than spending an hour repeating my spiel over and over
#ESHG2025
7 months ago
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More circadian phenotypes from Clara Albiñana. Gold standard for circadian dysfunction requires 24 hour saliva melatonin assay. Can you do it using a cross-sectional blood assay in UKB?
#eshg2025
7 months ago
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Lea Urpa is giving a talk on the interaction between genetics and circadian rhythm on blood glucose. Satisfyingly relevant top hits: CRY2 (blue light sensor) and MTNR1B (melatonin receptor). Leads to higher glucose in the morning and lower in the evening.
#eshg2025
7 months ago
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reposted by
Luke Jostins-Dean
Yang Luo
7 months ago
We are
#eshg2025
! Here's where you can find us.
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It is 10.30am in Finland, but nonetheless Helena Kilpinen
@hkilpinen.bsky.social
has also fallen asleep at the podium. She is talking about looking beyond gene expression to downstream cell phenotypes, such as cell morphology.
#ESHG2025
7 months ago
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Luke Jostins-Dean
Yang Luo
7 months ago
Amazing population-level single cell RNAseq showcases at
#eshg2025
-TenK10K (Powell, Australia) and 6.5K donors (Soranzo,UK). lots of interesting findings:cell-type specific eQTLs, disease-associated cell compositions, eGenes enrichment for drug developments, etc. Crucially - they're *open source*!
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Nicole Soranzo lives in Milan, but it is still first thing in the morning on a Sunday so she has also fallen asleep at the podium. She is talking about the Cardinal study, single cell RNA-seq 6.5k UK participants with genetics and EHR (UKB and Genes and Health)
#ESHG2025
7 months ago
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Early morning session on single cell genetics at
#ESHG2025
. Joseph Powell just flew in from Australia, and may be the first person to fall asleep at the podium.
7 months ago
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Aitzkoa Lopez de Lapuente Portilla (called Aitzkoa Lopez de Lapuente Portilla by her friends) has run high resolution flow cytometry in 12k Swedes. Genetics explains more variance in immune cells traits than does age or sex in this study.
#eshg2025
7 months ago
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Austin Argentieri (
@austinargen.bsky.social
) has built a proteomic aging score in UKB. They have also built a polygenic risk score for having a younger proteomic than chronological age, and run it in FinnGen - it has an odds ratio of 1.44 for living to 95.
#eshg2025
7 months ago
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Dalia Kasperaviciute is reporting on the first few thousand of the NHS newborn screening Generation Study. 27 mutations identified (0.5% of cases), of which 19 would be missed by the current blood spots screening program.
#eshg2025
7 months ago
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Luke Jostins-Dean
Aleena M Stolworthy
7 months ago
Who licks bones found in excavation sites? Archaeologists! To test if it's a bone or a stone. Johannes Krause at
#eshg2025
on tackling modern human DNA contamination of samples from archaeological sites.
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Steven McCarroll talking about repeat expansion in Huntington's at
#ESHG2025
. I remember being blown away by Bob Handsaker's talk on this at
#ASHG2023
. I really hope the next time I see this talked about it ends with plans for inhibition trials in humans.
7 months ago
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reposted by
Luke Jostins-Dean
Kaur Alasoo
7 months ago
Finally, some genes are truly pheripheral that have weak indirect effects on many traits. Distinguishing between these scenarios is challenging (unless biology already known), but I believe that varous readouts of cis-effects of variant effects on protein function (including molQTLs) can help.
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Eric Abner
@genomicsdoge.bsky.social
is talking about Tartu's lovely big GWAS meta-analysis of
@nightingalehealth.com
metabolite data in UKB and Estonian biobank. 600k individuals, 249 metabolites, 8.7k lead variants. About 1000 are low frequency (<0.5%)
#eshg2025
7 months ago
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Interesting finding from
@ambermluckett.bsky.social
- the non-HLA GWAS of HLA DR3+ and DR4+ type 1 diabetes are surprisingly different (coheritability is only 0.68). Some evidence of less adaptive (CD4) and more innate (mast cell) enrichment in DR3 genetics.
#eshg2025
7 months ago
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At
#eshg2025
. Some nice talks on longitudinal GWAS of childhood traits (in Japan Environment and Children's study) and of hospital lab values (in FinnGen). Nice plots of polygenic prediction of trajectories (eg childhood BMI curves, rises vs fallers for LDL with age).
7 months ago
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reposted by
Luke Jostins-Dean
Nightingale Health
7 months ago
Welcome to our webinar “Measuring the effects of aging with metabolomic profiling” on 3 June at 3 p.m. CEST by our Principal Scientist Dr.
@lukejostins.bsky.social
. Learn more and sign up:
www.lyyti.fi/reg/aging_we...
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reposted by
Luke Jostins-Dean
Nightingale Health
7 months ago
Are you coming to
@eshg.bsky.social
Conference 2025 on May 24-27? Our Principal Scientist,
@lukejostins.bsky.social
, will have a poster presentation, and you can also meet our team at booth 134 during the event.
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reposted by
Luke Jostins-Dean
Mike Inouye
7 months ago
Big news for health data research and population diversity: The Mexico City Prospective Study data are now available securely to approved researchers worldwide.
www.ndph.ox.ac.uk/news/latin-a...
Cohort description:
www.ctsu.ox.ac.uk/research/pro...
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Latin-American genetic data available securely to approved researchers worldwide/Datos genéticos latinoamericanos disponibles para investigadores de todo el mundo
https://www.ndph.ox.ac.uk/news/latin-american-genetic-data-available-securely-to-approved-researchers-worldwide
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reposted by
Luke Jostins-Dean
Kaur Alasoo
8 months ago
We've just posted an updated version of our metabolic trait GWAS preprint. The GWAS summary statistics are still the same as in October, but we've included several new follow-up analyses and completely rewritten the manuscript! See thread below for some highlights.
www.medrxiv.org/content/10.1...
add a skeleton here at some point
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reposted by
Luke Jostins-Dean
Yang Luo
9 months ago
Great poster sessions today
#BSI
Oxford 2025
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