A appraisal of PRS informed prostate cancer screening by @amitsud.bsky.social, showing that the PRS approach resulted in more biopsies, fewer detections of clinically significant cancers, and increased overdiagnosis of low-grade tumours www.sciencedirect.com/science/arti...

Our paper on mutational signatures was published earlier this week in @natgenet.nature.com We investigated mutations from #WGS in over 10k patients with 16 different cancers, from the @genomicsengland.bsky.social 100k Genomes Project www.nature.com/articles/s41... #cancer #genomics #signatures

We are excited to announce our latest publication in #BloodCancerJournal of our Two-Sample MR analysis to investigate causal relationships between 446 immune cell traits and 6 B-cell malignancies 📄 www.nature.com/articles/s41... #cancer #genetics #Bcell #bloodcancer #drugdiscovery #MR

It's not all work and no play in the Houlston Lab. We had our annual #Easter taste test! Returning to hot cross buns this year. We went a bit maverick and allowed some more ... unconventional varieties! #hotcrossbuns #tastetests 📸: @jessicamayh.bsky.social

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵

Spatial transcriptomics holds great promise to understand biological tissue function, but the assignment of transcripts to cells has been a substantial bottleneck. For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger. www.biorxiv.org/content/10.1...

Using a photonic network interface, scientists from Oxford University have successfully linked two separate quantum processors to form a single, fully connected quantum computer, paving the way to tackling computational challenges previously out of reach. More info ⬇️

Delighted to share our latest paper describing a method to read the levels of hundreds of metabolites or drugs in parallel using DNA sequencing. This method, which we call ‘smol-seq’ (Small MOLecule sequencing), harnesses the power of DNA sequencing for metabolite detection: rdcu.be/d8xLv (1/6)

Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment. www.science.org/doi/10.1126/...

Beware! AAV libraries prone to length & homology dependent chimerism! Our latest preprint, from the brilliant @jblalanne.bsky.social‬, was a true surprise as related phenomena are textbook for lentivirus (highly relevant to HIV & Perturb-seq) yet to our reading not known for AAV tinyurl.com/5amc562a

We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church. www.science.org/doi/10.1126/...

Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵 www.medrxiv.org/content/10.1...

I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq. Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵 [work led by @minetoota.bsky.social ] bsky.app/profile/jkpr...

How population stratification makes environments look like genes. A short 🧵:

The death of the surrealist film and television director David Lynch inspired tributes from fellow filmmakers, celebrities and past collaborators, who praised his visionary work and singular voice.

Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE. www.nature.com/articles/s41...

I've written a lot about polygenic risk scores in DNA testing, which, for at least the time being, are regarded as largely unhelpful (at best). That's because these tests analyze many genes to predict risk of a condition. With our current knowledge of the genome, that's just tough to do.

In science, we often see weird blips in the data. The question: is it artefact (usually!), or something new & exciting? We don’t always have time to dig deep. Our paper in @nature.com today came from just such a blip. So don’t ignore the weird stuff. Pull on that thread...

Osteosarcoma, an aggressive bone cancer, most commonly affects children and young adults. New research solves the mystery of what drives the genomic rearrangements causing the aggressive development and evolution of osteosarcoma tumours. www.ebi.ac.uk/about/news/r... 🧪

We held a great launch meeting at @cpmoxford.bsky.social last week for our award from #RHO to research health #inequalities and #ethnicity in the NHS genomic medicine service. Great discussions from @medesh.bsky.social @bughayleyw.pharmsky.app and many others [apols 4 ltd knowledge bsk addrs] 1/8

Happy New Year! (and first post here 😀) Excited to share the final version of our work where we combine deep mutational scanning, cryo-EM, and molecular dynamics to further resolve the mechanisms of pH sensing in GPCRs. 🧵(1/n) www.cell.com/cell/fulltex...

BBC Radio4 is celebrating a hundred years of the Shipping Forecast this New Year’s Day - as loyal listeners, here’s our contribution damonandnaomi.bandcamp.com/track/sailin...

From @nytopinion.nytimes.com Jimmy Carter “described his second career as ‘waging peace.’ That work remains far from finished, and it remains for those who admired Mr. Carter to continue,” the editorial board writes.

Our final paper of 2024 is a great collaborative effort between multiple genome stability groups (Steve Roberts & David Cortez). Kudos to the extremely talented scientists - @tmweaver.bsky.social @k4v1.bsky.social, Justin Ling, and Cameron Cordero. www.nature.com/articles/s41...

I'm going to repost a #thread here about a recent #paper from my group together with the labs of Marketa Tomkova and Skirmantas Kriaucionis: nature.com/articles/s41588-024-01945-x In it, we show that epigenetic DNA methylation causes errors during DNA replication! #epigenetics #mutations 1/🧵

This work finds that costly foundation models are outperformed by CNNs in genomics benchmarks, and are outperformed by *linear* autoregression in time-series benchmarks. 👀

Check out long-read sequencing results in human IGH! HUGE duplications in constant gene regions...and 7 copies of IGHV3-23 on one haplotype! @lossiusandreas.bsky.social @williamlees.bsky.social www.biorxiv.org/content/10.1...

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

Prof @alucassen.bsky.social is the new Academic Champion for Public and Community Engagement with Research!👏 With expertise in integrating community engagement into translational research, Prof Anneke will pioneer the 2024-2029 strategy. Read more 👉 https://buff.ly/4ivFnIj

Beautiful work led by Maya Arce from Marson lab reveals a fascinating story about rewiring of a critical gene regulatory circuit in different T cell types: T effectors and Tregs www.nature.com/articles/s41...

High Pacific surface temperatures fuel record warm year 📊 https://www.ft.com/content/54401156-2a87-4397-b9d1-8341cb895855

Climate graphic of the week: First ice-free day in the Arctic Ocean may come before 2030, study shows 📊 https://www.ft.com/content/63fbcf2b-9acc-4ccb-ac12-9f3b78e85b68

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8

Check out our (Emil Pedersen, Theresa Wimberley, and me) news and views out today in Nature Genetics, highlighting the importance of selection bias and information bias in genetic studies. #statgen #genepi #selectionbias eur01.safelinks.protection.outlook.com?url=https%3A...

1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

Marcella Hazan’s bolognese has been called “the gold standard” and has more than 20,000 5-star reviews. Try it and see for yourself. nyti.ms/40X1mla

📣 Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in Nature 📣 Co-first authoring with the brilliant Qinqin Huang🌟—proof that teamwork does make the dream work. 💪 www.nature.com/articles/s41...

New here and excited to share our new paper on transcriptional effectors! Interested to discuss context-specificity of gene regulation? Or how to get CRISPRi/a working in new contexts? 👋 www.nature.com/articles/s41...

A reminder that polygenic risk scores (#PRS) are calculated, not measured, risk factors. Results will vary. jamanetwork.com/journals/jam...

I am posting on Bluesky the piece I wrote about Bluesky for the @theatlantic.bsky.social. The short version is that it seems very nice here but also it is bad that it seems nice because social media is bad and we need to abandon it. Further thoughts follow 👇 www.theatlantic.com/technology/a...