Joanna Achinger

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

Scientific Publishing: Enough is Enough Why we're no longer funding journal publications

“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...?

Epigenetics 2025 | Xcells Conferences

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...

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

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

Single-molecule regulatory architectures captured by chromatin fiber sequencing Fiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin.

🧬🧪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...

The extracellular matrix in cancer: from understanding to targeting Significant advances in matrix biology research have enhanced our understanding of individual matrix components and extracellular matrix (ECM) signall…

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!

GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain types of data visualization - What are they and why are they bad. Friends don't let friends make certain types of data visualization - What are they and why are they bad. - GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain ty...

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 🧵

Transposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer Journal Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis

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...

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data Abstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu

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!

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu

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...

The Return of the Dire Wolf Colossal Biosciences has genetically engineered the first dire wolf to live in over 10,000 years. Here's what that means for other extinct species.

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.

Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees - Scientific Reports Scientific Reports - Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees

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...

Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte

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 🧵👇

Radioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades - Nature Biomedical Engineering Radiation-therapy-induced DNA damage in oral and rectal epithelial cells can be reduced via the nanoparticle-mediated local delivery of messenger RNA encoding for a damage-suppressor protein found in ...

#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 Eukaryotes have linear DNA and their telomeres are hotspots for transposons, which in some cases took over telomere maintenance. Here we identify several families of independently evolved telomeric tr...

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...

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

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...