I'm super excited to announce that registrations are now open for the 19th Australian Cell Cycle, DNA Repair and Telomere Workshop. Awesome international speaker line-up, with plenty of locals being invited! Book now to secure your earlybird rate. www.australiancellcycle.org

“In all my discussions with scientists across every sector, exactly zero think the journal system works well.” Some will disagree with aspects of Seemay’s analysis but this point is undoubtedly true open.substack.com/pub/asterain...?

2nd Meeting on Epigenetics & Epigenomics - 24th - 26th September, Brussels 🇧🇪 Speakers Line-up looks fantastic including @adelmanlab.bsky.social @kjarmache.bsky.social @mariekeoudelaar.bsky.social @tinekelenstra.bsky.social @lucianodicroce.bsky.social www.xcellsconferences.com/epigenetics2...

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020. It's a very cool method for adding chromatin accessibility data to native LRS experiments. You should definitely check out the original paper: www.science.org/doi/10.1126/...

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social www.cell.com/cell/fulltex...

New review paper written by Jess Chitty in the team just out in Trends in Cancer (@cp-trendscancer.bsky.social) (OpenAccess) The extracellular matrix in cancer: from understanding to targeting | → www.sciencedirect.com/science/arti... ← |

Fun writing this piece with @bartegiani.bsky.social!

Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...

This is very interesting!

(1/n) New preprint from @claricehongky.bsky.social Fan Fang Varshini Ramanathan in collab w Jie Liu. Q: How do we get ultra-high-res 3D genome maps? A: New deep learning model, Cleopatra. Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.

@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social Paper here: genome.cshlp.org/content/35/5... See below for more details 🧵

I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal haematopoietic processes and haematological cancers. www.nature.com/articles/s41...

Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...

📣 A reminder about an open postdoctoral position in our group! 🧫 Are you interested in mechanisms of gene regulation, human facial development and disease? How our DNA shapes the way we look? Do you love chromatin and enhancers? 🧬 If so, reach out for an informal chat! 💬 longlab.co.uk

A beautiful example of how cautious interpretation of an artifact leads to important results for the scientific community👇Congrats @konrad-chudzik.bsky.social @drmrobson.bsky.social and all authors!

Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n) doi.org/10.1093/bioi...

Colossal is back with their totally BS claims. They reverse engineered snps into 14 GENES and claim they changed a grey wolf into a dire wolf. 1/n time.com/7274542/colo...

Interesting paper on using long-read sequencing to consider accessibility at repetitive elements. Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2 www.science.org/doi/full/10....

Good Lord. EWAS w/ n's in the tens? This nonsense has to stop. Trauma leaves marks across generations but they're not epigenetic.

I can't believe we're still allowing completely inadequate and uninterpretable Epigenome-Wide Association Studies (EWAS) to be published. I don't care that this study is probably well-intentioned, and probably trying to draw attention to awful events in Syria. www.nature.com/articles/s41...

Mine in today’s @newyorker.com

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6...

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

#mRNA meets Tardigrades! Delivery of an mRNA encoding a protein from the famously tough animal can protect healthy tissue from damaging radiation. Very creative! #RNAsky www.nature.com/articles/s41...

Telomeric transposons are pervasive in linear bacterial genomes | Science www.science.org/doi/10.1126/...

Did you know that two jumping sequences (LINE-1 and Alu) make up nearly 30% of our genomes? Ever wonder how they jump into new genomic sites? We have some exciting discoveries to share new in @science.org on the structural mechanisms of LINE-1 retrotransposition (aka jumping 🧬➡️🧬) 🧪 #ScienceResearch

Review from our lab out today: "Roles for the 3D Genome In the cell cycle, DNA replication, and double strand break repair." Written by @scientistkate.bsky.social, with her co-supervisor @piptaberlay.bsky.social and collaborator Mat Jones. www.frontiersin.org/journals/cel...

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...

Program is out for our first EMBL #singlemolecule gene regulation meeting! Check out the dedicated panel sessions on single molecule genomics, single molecule imaging and theory where we would like to brainstorm the future of the field: Registration is open! 👇 www.embl.org/about/info/c...

Paper out !!🥳big thanks to all authors @marliesoomen.bsky.social @diego-rt.bsky.social @kaessmannlab.bsky.social @jonathangoeke.bsky.social @lorenzamottes.bsky.social & 'bluesky-less' Lots of interesting new TE (& genes) biology Data fully browsable💻 👉 embryo.helmholtz-munich.de/shiny_embryo/

I have created a Bsky account just in time for #LorneGenome25 so that I can post from (and about) the meeting. I am very proud of the program that the Organising Committee has pulled together (www.lornegenome.org) and can't wait to see you all on Sunday! Looking forward to some science by the beach!

📢 An exciting #Postdoc position opened in our laboratory for a junior #Bioinformatician! Developing #Bioinformatic and #AI tools to advance precision oncology using the available #singlecell / #spatial data universe. careers.adelaide.edu.au/cw/en/job/51... Pls share! 🙏 #postdocposition

Heading to #lornegenome25 #LorneCancerConference ? Looking for a computational postdoc to work on spatial and single nuclei transcriptomics of poor prognosis cancers, please DM me or see me at Lorne. We will be advertising soon. @ozsinglecell.bsky.social #LorneCancer2025 #Lorne2025

Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that: 1) active histone mods occur independently of transcription 2) transcription coordinates histone deacetylation at active promoters www.science.org/doi/10.1126/...

🚨𝐌𝐚𝐣𝐨𝐫 𝐉𝐨𝐛 𝐀𝐥𝐞𝐫𝐭!🚨The Groth @groth-anja.bsky.social, Mailand, Nilsson @nilssonlab.bsky.social & Krietenstein @nilskrietenstein.bsky.social labs are hiring 𝟔 𝐏𝐡𝐃&𝐩𝐨𝐬𝐭𝐝𝐨𝐜𝐬 to join the new Center for Epigenetic Cell Memory (EpiC) in Copenhagen, Denmark. Apply here: tinyurl.com/yvd93na2 & please share!

Delighted to share our 'Androgen clock' paper in #PNAS ow.ly/Guts50ULghF - the first way to predict long-term androgen exposure using DNA alone. We so much more than the sequence we are born with! Stellar work (and animation - SOUND ON) by Dr Victoria Sugrue youtu.be/GL55yjMalII

We're #hiring a #postdoc to join our lab 🧪 in Melbourne 🇦🇺🦘 in #StemCell and #Cancer #Epigenetics. Great opportunity to lead a research project within the broader vision of the lab, with plenty of scope to develop as an independent leader 👩‍🔬🔬 Apply by 27 Feb careers.petermac.org/job/MELBOURN...

Long-read sequencing just got an upgrade. 📢 Genome, methylome, epigenome & transcriptome in one go—haplotype-resolved & at single-molecule resolution. 🔥

Genetic coupling of enhancer activity and connectivity in gene expression control https://www.nature.com/articles/s41467-025-55900-3 🧬🖥️🧪 ...beautiful plots made with #Rstats plotgardner https://phanstiellab.github.io/plotgardener/

CTCF stall DNA 🧬 loop ➰ extrusion by cohesin - but exactly how it pulls this off is a 'mechanistic mystery' (to cite @andersshansen.bsky.social, Nucleus, 2020). We just preprinted 📜 a new study @biorxivpreprint.bsky.social that provides some answers to this enigma: www.biorxiv.org/content/10.1...

Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41... ▶️Footprints of DNA–protein interactions from bulk & single-cell ATAC-seq ⤵️ ▶️Deep learning to infer transcription factor and nucleosome binding ▶️Age-associated reduction of nucleosome footprints

If there's something we don't understand I assume transposons are responsible unless proven otherwise

An interesting link between 5mC and m6A; when #epigenetics meets #epitranscriptomics! www.cell.com/cell/abstrac...

[📢 BIG ANNOUNCEMENT] We're partnering with @network-alba.bsky.social for their season 2. Worried about going from post-doc to group leader? In this new mini-series, we'll dive into this critical career stage with stories and experts 💌Subscribe to their newsletter : www.alba.network/diversity-po...

There’s a lot to unpack in our recent Science Advances paper - come check it out! Here’s a thread on what we found. #chromatin #genomics #biophotonics #dna #epigenetics #imaging #northwestern #science #biology #aging #longevity #biomedicine #cpge www.science.org/doi/10.1126/...

I promised to write an end-to-end tutorial to replicate this genomics figure during the holidays. Now it is ready 👇

Yes, they can hallucinate papers that don't exist, discuss results that seem to be imaginary, and can be confusing and inconsistent. But talking to tenured professors may still be helpful

The recent discussion on X with @mbeisen.bsky.social about how grad students are selected made me reflect on my own journey. I often wonder about who it was that made the life-changing decision to approve my grad school app, and what it was about me that pushed them over the edge. 1/ #AcademicSky