Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches. www.biorxiv.org/content/10.1...

I feel incredibly privileged to share this study on Fanconi anaemia, based on a small but important cohort. This work describes the genetics and clinical outcomes of patients in Australia and New Zealand with a diagnosis of FA. www.sciencedirect.com/science/arti...

Thrilled to share our latest work on meiotic recombination, where we mapped rates and distributions by sequencing thousands of individual sperm. This study was led by Stevan Novakovic and @caitlinharris.bsky.social , in collaboration with @davisjmcc.bsky.social and Cynthia Liu.

Now that I've given my talk at today's excellent #ourdna symposium I can share this slide I put together for it. I knew these numbers, because I was the one paying for things, but still:

Valentine Svensson Negative binomial regression and inference using a pre-trained transformer https://arxiv.org/abs/2508.04111

When Jeffrey "graduated" from our lab to go to do a PhD at Cambridge I knew big things would come - and boy was I vindicated! Very exciting work - rigorous and insightful (exactly as I came to expect from Jeffrey) and immediately useful for a huge number of cool projects. Awesome 🌟, well done!

people don't actually want to test point-nulls in NHST, they want to test interval nulls and they rely on the structure of the test to define the "interval null" (*waves hands vaguely*) for them, rather than explicitly defining an interval null and testing it.

📢 Announcing the MOPITAS Autumn School on Spatial Transcriptomics Data Analysis – taking place November 12–14, in Munich. Don't miss this excellent opportunity to deepen your expertise in data science and multi-OMICS analysis - especially as a PhD student in the data science community.

The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025. Check it out and share widely: www.abacbs.org/abacbs2025 Registrations and abstract submissions open next week, with abstracts due in August!

Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/d...

Applications for this position will close on Friday 30 June So if you or anyone you know might be interested in applying, time to get your skates on!

🚨 New paper published in @natmethods.nature.com! We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics. 📰 Paper : nature.com/articles/s41... 💻 Code: github.com/MicTott/Spot... 📈 Website: mictott.github.io/SpotSweeper/ 🧵👇

Hey Australian genetics/genomics friends: the OurDNA Symposium will be in Sydney on 14 August, just before the HGSA meeting. Learn more about inclusive recruitment for genomics and get a preview of the OurDNA variant browser! events.humanitix.com/ourdna-sympo...

New preprint from the lab @tyagilab.bsky.social

I cannot recommend Davis’s group more highly! In addition to excellent research, he has been a great mentor!

📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics

Delighted that the 'flagship' manuscript on our @genesandhealth.bsky.social 44k exomes (British Pakistanis & Bangladeshis) is now preprinted. Great academic-industry collaboration. Lots of new associations (mostly additive, a few recessive) and new insights into homoz knockouts & drug discovery.

People always stop me in the street to ask: "Yoav, where are the disease-associated eQLTs? We found a lot in GTEx but we can't find anymore. Do you know where they are?" (For the record, no one has ever asked me this, but it is a really good question!) I think we know where they are.

My message to Trump’s NIH Director? No one in America wants us to do LESS cancer research. No one is asking Trump to make it harder to cure Alzheimer's disease. Yet Trump is cutting all of this NOW and demanding an $18 BILLION cut to NIH next year. Not on my watch.

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

I am so excited to share our most recent work & my first big project as a graduate student! We leveraged spatial transcriptomics to study the cell-cell communication involved in human lung development. Here’s the full study: www.biorxiv.org/content/10.1... (1/17)

Super happy and proud of this one. We and others have developed tools for dimensionality reduction for many years. MOFA (linear) and other non-linear generalisations, space/time. scDORI fuses this with GRN inference. It’s a nice and useful piece of software. Here applied to GBM biology.

My ongoing request: If your NSF or NIH grant was terminated--whether at Harvard or elsewhere--please report it here. NSF: grant-watch.us/submit-nsf.h... NIH: grant-watch.us/submit-nih.h... Our trackers are actively used in lawsuits and are often the only record that terminations ever occurred.

On Friday, my son stayed home from school because he had a sore throat and wasn’t feeling well. He went with my husband to his office for the morning while I handled our daughter. When he came back at lunch, he was not interested in eating, saying his throat hurt too much. 1/n

1/n 🚨Very excited to share our recent work!🚨 To understand gene regulation across diverse environmental conditions and cellular contexts, we treated a broad array of human cell types with three environmental exposures in vitro. www.biorxiv.org/content/10.1...

Australia should be doing this now and at a grander scale. Let’s reverse the brain drain and properly support the scientists we have @markbutlermp.bsky.social @edhusicmp.bsky.social

🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.

This is an awesome opportunity to do large-scale genomic data science with direct, meaningful impact on the lives of patients. This program has already returned over 450 genetic diagnoses to families affected by rare genetic disease; help us help more families!

📢 new preprint alert: So so excited to share our analysis on the impact of common and rare variants on single-cell gene expression in blood, using WGS and scRNA-seq data from nearly 2,000 individuals and 5.4m cells as part of TenK10K phase 1 🧬 www.medrxiv.org/content/10.1... 🧵👇 (1/n)

Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses! @davisjmcc.bsky.social www.biorxiv.org/content/10.1...

First 🇺🇸 targeted research in our unis, now going after our national scientific organisation. We need to diversify our research partnerships & increase R&D spending but 🇦🇺 govt should also stand up for agreements that are beneficial for BOTH countries. www.smh.com.au/national/sug...

1. For the past thirty years I've had the best job in the world. 
I've had the opportunity to follow my curiosity; explore the workings of nature and society; mentor students and junior colleagues in the same process; and teach generations of students about it all.

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...

By Arthur Caplan: "many scientists and administrators now seem to think that the best response to the war on DEI is to keep their heads low and wait out four hard years." "the only way forward is speaking truth to power."

My story: I’m a single father and cancer researcher whose wife died of a rare cancer. Science and biomedical research is personal to me. Here is my op-ed in my hometown newspaper. Pls fwd. www.vindy.com/opinion/edit...

I second this strong recommendation! I attended in 2014 (? what is time, who remembers) and it was a fantastic experience - got to have some deep conversations with some amazing people, both tutors and PhD students. The cohort of tutors this year is straight fire

Come and set up a lab and work with us at @petermaccc.bsky.social

Hi everyone, I’m the graduate student here. I’ve never felt a worse feeling than this moment. There is no way to justify what’s been happening. I wasn’t even notified that my study section wasn’t meeting. I still haven’t been notified. I’ve effectively been ghosted by the NIH - make it make sense.

📣 New from the lab: The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes www.nature.com/articles/s41... Check out the INTERVAL RNAseq portal www.intervalrna.org.uk Led by @alextokolyi.bsky.social & Elodie Persyn!

A few weeks ago, I had an incredibly emotional call with James Coney, a writer for the Sunday Times whose son Charlie was in the @genomicsengland.bsky.social 100k project and was recently diagnosed with ReNU syndrome. This beautiful article tells their story ❤️ www.thetimes.com/article/0bcc...

📢 Thrilled to see this out, an atlas of e/sQTL across multiple tissues and diverse ancestries in 14,324 TOPMed participants: www.medrxiv.org/content/10.1... Grateful to the #TOPMed #Omics WG for giving me an opportunity to learn and contribute to this important work 🧬

📣 Registrations and Abstract submissions are now open for Cancer Bioinformatics Australia 2025! Abstracts, due 11th April: cancerbioinformatics.au/abstracts Registration: cancerbioinformatics.au/register Further info: cancerbioinformatics.au See flyer for our amazing invited speakers!

Our new paper examining how to analyse longread RNA-seq with no reference genome. We compare approaches for assembly and downstream analysis, from transcript accuracy to differential expression. Lead by @alexyfyf.bsky.social. Thnx to all contributors incl. @qgouil.bsky.social for the pea data!

WOW!! 🤩 Congrats to Banovich et al. on the LARGEST imaging-based spatial transcriptomic study of the human lung to date! This study discovers conserved spatial pathological signatures and alveolar remodeling in pulmonary fibrosis disease progression.

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

Many thanks to my supervisors @davisjmcc.bsky.social and Heejung who encouraged me to write this piece up! It is not a style of writing that I am the most familiar with so it took a lot of experimenting and also valuable feedback from @jeffreypullin.bsky.social on some earlier versions

Have you been thinking hard about statistical modelling of scATAC-seq data? (No.) Luckily for you, @aaronkwc.bsky.social has! Aaron will help you grok: What's going on? What is TF-IDF? Is there really single-cell level chromatin information? Check it out 👇 www.biorxiv.org/content/10.1... 🧪🧬💻

Now new and improved and out on Genome Medicine! link.springer.com/article/10.1...

A commonly inherited genetic variant of human PCSK9 drives breast cancer metastasis and associates with reduced patient survival in @cellcellpress.bsky.social PCSK9 drives pro-metastatic gene expression by repressing LRP1. Anti-PCSK9 antibody suppresses Br mets. sciencedirect.com/science/arti...

We've been doing this for a few years - except we call them "one minute updates" (actual time may be 30s to 5+ mins) and just go round the table It's been great and would wholeheartedly recommend - I didn't know about the "flashlight" concept/version of this until now