Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!

Since 2020, we were running a practical introducing year 2 students to a hypothetical situation requiring to diagnose a patient placed in ICU based on real-time analysis of cfDNA. This new paper shows that it works in actual ICU at a bedside-relevant sequencing depth www.nature.com/articles/s41...

Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬 IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable. @NatureComms: www.nature.com/articles/s41... Thread 🧵👇 1/

Bercovich et al., 2025. IceQream: Quantitative chromosome accessibility analysis using physical TF models www.nature.com/articles/s41... ▶️spatially integrates sequences and localises them relative to the target locus ▶️infers effective TF concentrations ▶️supplements with pairwise TF interactions

We lack clear guidelines for AI use by our students. My attempt: Encouraged (when used responsibly): ✅Exploration, brainstorming and troubleshooting ✅Controlled software development and debugging Discouraged (in most cases): 🚫Writing or "improving" academic texts 🚫Creating academic illustrations

we are recruiting a postdoc with interest in using genomics and molecular biology to study transcription factors. We have an R35 to fund the project/salary.

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Just received a notification that our university is renegotiating #openaccess agreements with the “big five” publishers (Springer, Elsevier, etc), and it is highly likely that we will lose some of these agreements. If we do, this will be a big problem since we do not have budgets to pay OA fees

Remember this paper "Low overlap of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...) well, well, well 🍿 ⬇️ www.biorxiv.org/content/10.1...

Sequencing advice sought: Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing? Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing. Please share 🙏 #epigenetics

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians! The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

Interesting paper from Gernot Längst & Co. They calculated nucleosome repeat length in Plasmodium falciparum, the malaria-causing parasite, and showed that it follows a smooth continuous function of time (the numbers on the X axis below are hours post-invasion) www.biorxiv.org/content/10.1...

Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells. In a new preprint, we share some clues about when, how, and why this happens! www.biorxiv.org/content/10.1...

Polletti et al, 2025. Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing www.cell.com/immunity/abs... ▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF

📣 New preprint from the lab - Endogenous fluctuations of transcription factor levels shape their occupancy in unexpected ways www.biorxiv.org/content/10.1...

We have space for two postdoctoral fellows in the Taipale Lab at the @sangerinstitute.bsky.social. This is a core-funded open position! Come with your ideas and interests and we can develop a project together. sanger.wd103.myworkdayjobs.com/en-US/Wellco...

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?