Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

Some time ago I gave a lecture "How to become a genius: An interpretation/adaptation of Altshuller’s Theory of Solutions of Inventive Problems (TRIZ)". It included interactive part "life as a chess game", but static slides may be also of interest. Putting it online generegulation.org/teaching/Tei...

Aging by the clock and yet without a program [perspective by David Meyer, Alexei Maklakov & Björn Schumacher] www.nature.com/articles/s43...

We are hiring! We are looking for a PDRA to study the epigenetics of breast cancer dormancy using chemical biology and genomics approaches. This is a 3-year position and is aimed at chemical biologists or biologists. Please share and apply using the link below 👇👇👇 www.imperial.ac.uk/jobs/search-...

Hsu et al., 2025. MNase stratification reveals heterogeneous 5hmC in naive B cells www.biorxiv.org/content/10.1...

Happy to announce that our department (School of Life Sciences at the University of Essex) is now ranked 6th out of 91 UK universities in the subject area Biology according to the Guardian University Guide 2026. This is our increase from 7th in 2025 www.theguardian.com/education/ng...

A random bit of history (for modern analogies). Lysenko set back genetics in USSR by ~50 years. Hundreds of geneticists imprisoned or died. Cybernetics was also named "reactionary pseudoscience", and about to undergo similar fate, but got lucky that this started close to the end of the Stalin era.

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

Peer-reviewers spend so much time to help journals that it would be only fair if academic publishers in return approve the sending of the textbooks that we request as free "instructor copies". There should be an option to get them as a *printed copy*, not just digital 📖

When biology and medicine overlap in the same paper 🙂🙃 TF - "transcription factor" vs "tumor fraction". NRL (nucleosome repeat length) vs NLR (neutrophil-to-lymphocyte ratio). Reads very similar and both on-topic :)

We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social! register here for the entire series: us06web.zoom.us/webinar/regi...

If you like transcription regulation and its mechanisms, this WIP list is for you. I'm sure I've forgotten lots of people, so don't hesitate to let me know so I can add you to the list. go.bsky.app/8vTgeXB

Contributions of local structural and energetic features of DNA to large-scale genomic organization [perspective by Wilma Olson & Co) www.sciencedirect.com/science/arti...

Looks like my book is available for pre-order: a.co/d/cTKIwBN #EpigeneticsBook

Saunders et al., 2025. HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone www.science.org/doi/full/10.... ▶️HMGB1 sites are away from where H1 binds ▶️HMGB1 increases nucleosomal DNA accessibility without displacing H1

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

When you get used to GPT5 and then unintentionally switch to GPT4, the difference is quite noticeable. It's unbelievable how, just several days ago, we thought that GPT4 was the state of the art, and now it's so outdated

The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat... My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.

Random thought. If more and more computer codes are going to be AI-generated, the roles of human programmers may shift to debugging/validation. This would require higher-level testing comparing expected/observed code behaviour, fishing out unrequested features, AI-planted exploits, etc.

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town. Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag. 🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41... 🧵Let’s break down what makes DynaTag so powerful (1/7)

Interesting use of ChatGPT: "we used... GPT-4o mini to analyze each [PubMed] abstract using the following query: ‘Your task is to identify genes associated with the hallmarks of aging... For each gene, annotate it with the corresponding hallmark of aging (genomic instability, telomere attrition...)’

Liu et al., 2025. An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin www.biorxiv.org/content/10.1... ▶️RoboATAC - automated ATAC-seq ▶️Deep learning models: motif orientation, spacing, flanking bases ▶️Nucleosome positioning analysis

Wang et al, 2025. Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq www.biorxiv.org/content/10.1...

SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...

Interested in developmental epigenetics? So are we! Apply now to join us for your postdoc! Multiple positions across multiple groups @mrc-lms.bsky.social Projects spanning germline demethylation, gene regulation, genome architecture in development & disease 👇👇 lms.mrc.ac.uk/work/vacanci...

Very happy to contribute to this CTCF-nucleosone paper in @narjournal.bsky.social, which was featured on the journal cover. This is mainly the work of @elenapugacheva.bsky.social. Exciting research and such a cool cover art!

The Chromatin And Development lab are hiring a postdoc! Come join us; we are a happy and hard working team @mrc-lms.bsky.social in London UK. Projects span the intersection of chromatin and transposon biology in dev't and disease. Email/DM for more info. Pls RT! lms.mrc.ac.uk/work/vacanci...

Do I have any BlueSky folks who might help advise me on how to generate a graph genome from dbSNP or 1000 Genomes data? Or advice on how to do variant-aware TF motif calling?

Is there a consensus in the field of gene regulation about whether enhancer names should be italicized like gene names, only in genotype contexts, or not at all?

FN is taking a summer vacation 🏖️, but we'll be back in September with more exciting talks on chromatin and transcription! If you've got a new story you'd like to share with the FN audience this fall, fill out the form here: docs.google.com/forms/d/e/1F...

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

NHS announced that it will start offering first liquid biopsy tests for diagnostics of lung and breast cancer; also planning expansion to pancreatic and gallbladder cancers www.england.nhs.uk/2025/05/nhs-...

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

I gave a talk at Pint of Science this year!! 2 anxiety attacks, 1 tequila, 1 espresso martini later... I made it. 😅 Talked liquid biopsies, cell death & early diagnosis. Grateful, tired, buzzing. 7 yrs ago I sat in the crowd—now I’m on stage. Full circle 🫶 #PintOfScience

Royal Society announces £30m fund to attract global talent over next two years royalsociety.org/news/2025/05...

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).

Native nucleosomes intrinsically encode genome organization principles www.nature.com/articles/s41... ▶️Condensed purified native mononucleosomes with polyamines ▶️Nucleosomes from A compartments have low condensability and those from B compartments have high condensability

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... 🧵

Kable et al., 2025. Compromised 2-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers www.biorxiv.org/content/10.1... ▶️In mature retina cells, the fraction of short-linker nucleosomes is lower -> stronger chromatin compaction.

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....

Data Sharing Statement in a paper that is based on whole-genone sequencing data for a large cohort of patients: "All data relevant to the study are included in the paper."

NIH funding cut by 40% will likely mean, among other things, the fall of sequencing providers and the rise of private-funded R&D

Funny thing happens at the intersection of liquid biopsy and chromatin research: "TF" means "transcription factor" in one part of the paper, and "tumor fraction" in another part :)

🧬My retrospective chromatin review is out @Proc Jpn Acad: doi.org/10.2183/pjab... The textbook view of #chromatin as 30-nm fibers is fading. A new paradigm: chromatin forms #liquid-like domains—locally dynamic, yet globally stable at the chromosome level (viscoelastic)—supporting genome function. ✨

We have a postdoctoral opening for a researcher with experience in bioinformatics of DNA sequencing and machine learning to work on the development of new methods for cancer diagnostics related to nucleosomes, chromatin and beyond www.jobs.ac.uk/job/DMK060/s.... Application deadline: 21st April 2025

~25 million lost lives, 2025-2040 www.nature.com/articles/d41...