iiinova — where your digital self keeps evolving

Finally: nucleosome positioning as highlighting with a marker in a book. Just as highlighted words or sentences stand out differently, where nucleosomes sit can make parts of the genome easier or harder to read. This analogy took me a while to come up with! 4/4

020

Next: DNA methylation as accents on letters. In languages like French, an accent can change how a letter or word is read; methylation marks can change how cells read DNA, without changing the underlying sequence. Has anyone seen this analogy used before? 3/4

First: the genome as a book. DNA sequence is the text, written with four letters - A, T, G and C. This is a standard analogy, but it gives students a clear starting point before introducing gene regulation. 2/4

100

Teif lab @teiflab.bsky.social · 07/07/2026

Yesterday I gave a webinar for Year 12 students titled “Genomics meets AI: can we detect cancer earlier?” Alongside the science, I found a few useful ways to explain gene regulation to people without a biology background. Sharing in case useful to others. 1/4

240

Chen et al 2026. Genome-wide rotational and translational phasing of nucleosomes with human transcription factors www.cell.com/molecular-ce... ▶️ In vivo nucleosome phasing measured on the same TF-bound DNA molecule ▶️ Phasing around CTCF sites is DNA encoded ▶️ FoxA and NFIA phase adjacent nucleosomes

How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here, we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells and enhance chromatin immunoprecipitation (ChIP)-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes, and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Upon examining 40 TF classes, unbound sites were found to be phased either inward or outward or to lack phasing. In all examined cases, TF binding (e.g., NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.

0155

Teif lab @teiflab.bsky.social · 05/07/2026

Gaspa-Toneu et al, 2026. Single molecule footprinting measures low nucleosome occupancy in mature spermatozoa of mice and men www.biorxiv.org/content/10.6... ▶️ NOMe-seq at 103 and 163 genomic sites in spermatozoa of mice and human ▶️ nucleosome occupancy ∼1.2 to 1.7% in mice; ∼2.3 to 4.5% in human

biorxiv.org

Single molecule footprinting measures low nucleosome occupancy in mature spermatozoa of mice and men

Nucleosomes are fundamental units of DNA packaging and gene regulation in eukaryotes. In mammalian sperm, most nucleosomes are replaced by protamines causing extreme chromatin compaction. Various epig...

030

Teif lab @teiflab.bsky.social · 03/07/2026

It's important to distinguish, what this process is not: - not asking AI to draft a text for you - not asking it to fix your text for you - not giving up your own style, even if imperfect - not agreeing blindly with all its suggestions

Teif lab @teiflab.bsky.social · 03/07/2026

A good use of AI in text editing is interactive: it highlights issues, you try different approaches, it disagrees, you push back, and the two of you have a dialogue much as you would with a human coauthor. A refined text emerges iteratively, and you learn from the process. The process itself matters

280

9/9 The model and ranking criteria need to be transparent. If multiple AI-based evaluation systems emerge, which seems likely, their assumptions, limitations, and outputs should be easy to compare and interpret. At the same time, no AI model should be fully autonomous without human supervision, IMO

020

8/9 The cohort of experts providing feedback for model training probably needs to be diverse and balanced. That also means there should be broad agreement on its composition. One possible approach could be to include, for example, all scientists with a PhD, or the whole current peer-reviewer pool.

131

7/9 A score based on an AI model trained with feedback from many human experts is likely more stable than a score created by one person. But how many experts are enough? My guess is: having just several experts is not enough. For most fields, likely thousands would be needed.

6/9 On the technical side, no single score is perfect, and one can envision many different AI scores. You can already experiment with ChatGPT to define a score (I tried it on some of my own papers). Scaling this to many manuscripts would need a bit more programming, but it is already doable.

5/9 If we post preprints knowing they may be ranked, it becomes a different game from posting preprints simply to share quick, often important, results that may not yet have matured into a solid story. This may have implications for open science, not necessarily positive ones.

130

4/9 My sense is that all research that is out there in the open can already be scrutinised by anyone, with or without AI. We cannot really “consent” to our work being ranked. Any openly available work can potentially be evaluated for different purposes.

3/9 This could have major financial and policy implications. For example, the UK’s national research evaluation exercise (REF 2021) cost an estimated £471 million, most of it borne by universities. AI assistance could make parts of this process cheaper.

110

2/9 It seems to me that Pandora’s box is open and cannot really be closed, potentially leading to many unintended consequences. AI can, conceptually, assist in evaluating research, e.g. in the form of papers or preprints. You can already ask ChatGPT to do this, or develop a more specialist model.

Teif lab @teiflab.bsky.social · 26/06/2026

1/9 A few thoughts and personal opinions on the use of AI in research evaluation. I suspect many of these changes may be inevitable, so the real question may not be whether this will happen, but how we shape it responsibly 🧵

2124

So with this cmarification, looking at your table, if someone is a beginner in Python, you'd tell them never start writing functions with AI. I think this is a bit harsh. It takes away a major benefit of AI for coding. Agree with other aspects (writing text, etc).

100

Teif lab @teiflab.bsky.social · 26/06/2026

Good idea. Question- how do you define who is an expert and who is intermediate? Do you map this at career stages?

200

Reposted by Teif lab

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/06/2026

After reading @blekhernia.bsky.social's great blog post on lab AI usage policy (blekhman.substack.com/p/you-need-t...), we made one in lab meeting. Feedback welcome! rilab.ucdavis.edu/ai_expectati...

rilab.ucdavis.edu

Ross-Ibarra Lab Policy on AI Usage

45124

Teif lab @teiflab.bsky.social · 24/06/2026

The idea is conceptually good. Interestingly, I noticed that the top paper in genetics from your list (a great paper, by the way) is authored by one of the 15 experts whom you selected for human peer-review, it's a funny coincidence 😄 www.biorxiv.org/content/10.1...

biorxiv.org

Protamine lacunae preserve the paternal chromatin landscape in sperm

The transmission of the paternal genome requires extensive chromatin reorganization, in which nucleosomes are largely replaced by protamines that drive extreme condensation of the genome in the sperm ...

180

Teif lab @teiflab.bsky.social · 21/06/2026

Deskilling associated with AI is a real danger for our students as well. How to prevent it? Which tricks do you use to integrate AI in training responsibly?

100

Teif lab @teiflab.bsky.social · 19/06/2026

Yes, absolutely, writing is an essential skill. I think both writing and calculating are probably important for brain training. So this deskilling has the potential to weaken general cognitive thinking

010

Teif lab @teiflab.bsky.social · 18/06/2026

Deskilling definitely. In a similar way, as many people will struggle to do simple math like 11×12 (and division is more difficult) since it's possible to do it with a calculator.

101

Teif lab @teiflab.bsky.social · 12/06/2026

Great preprint by @vram142.bsky.social & Co www.biorxiv.org/content/10.6... "fiber homotypy," where chromatin fibers with similar nucleosome spacing interact more frequently in 3D --> Related to our previous "nucleosome homology recognition" in chromatin royalsocietypublishing.org/rsif/article...

0165

Teif lab @teiflab.bsky.social · 10/06/2026

Come celebrate Professor Leo Schalkwyk with us! We’re holding a one-day symposium to mark Leo's remarkable career and many contributions to genomics. 📆26 June 2026 📍University of Essex, Colchester Details and registration: schalkwykfest.essex.ac.uk There will be a BBQ as well!

252

Teif lab @teiflab.bsky.social · 04/06/2026

Sun et al, 2026. NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture www.cell.com/molecular-ce...

084

Teif lab @teiflab.bsky.social · 26/05/2026

Good that the heatwave is over 😀

000

Teif lab @teiflab.bsky.social · 26/05/2026

"The model is based on the biology of widow spiders"

100

Teif lab @teiflab.bsky.social · 15/05/2026

The +1 nucleosome functions in Pol II transcription initiation and the transition to elongation www.biorxiv.org/content/10.6... [Yumeng Zhan, Julio Abril-Garrido, Frauke Grabbe, Paulina Seweryn, Ute Neef, Christian Dienemann, Patrick Cramer]

051

Reposted by Teif lab

Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 08/05/2026

Did you know that Pierre Chambon's laboratory was the first to use the term "nucleosome" in 1975 ? www.cell.com/cell/fulltex...

17630

Teif lab @teiflab.bsky.social · 03/05/2026

I meant visual resemblance of multimer "flowers" to micelles. It follows from the classical lambda switch, but unlike classical lambda switch, which is about individual TFs competing or cooperating, in the enhanceosone/micelle view, the focus is on the event of assembly of the whole complex