Teif lab

Teif lab

@teiflab.bsky.social

Teif lab at the University of Essex. We work on gene regulation in chromatin and applications to liquid biopsies, using approaches of genomics, biophysics, bioinformatics & AI. Our focus is nucleosomics, TF binding, CTCF, cfDNA. https://generegulation.org

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Teif lab
@teiflab.bsky.social

Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"

Teif lab
@teiflab.bsky.social

AlBawardi et al, 2026. Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility www.biorxiv.org/content/10.6... ▶️heterochromatin-like sequences produce compact fibres ▶️positional irregularity (>2-3 bp) triggers a state transition

Teif lab
@teiflab.bsky.social

Molecular Acrobats: How CHD Remodelers Shape the Genetic Playground to License Cell Identity [review by İsa Özdemir and Sarah Hainer] onlinelibrary.wiley.com/doi/10.1002/...

onlinelibrary.wiley.comMolecular Acrobats: How CHD Remodelers Shape the Genetic Playground to License Cell IdentityIn eukaryotes, DNA is not a naked repository of genetic information but is tightly wound around histone octamers to form nucleosomes. While this packaging solves the spatial problem of fitting 2 mete...
Teif lab
@teiflab.bsky.social

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

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Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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.orgSingle molecule footprinting measures low nucleosome occupancy in mature spermatozoa of mice and menNucleosomes 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...
Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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

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 🧵

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Teif lab
@teiflab.bsky.social

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.

Teif lab
@teiflab.bsky.social

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

Teif lab
@teiflab.bsky.social

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 🧵

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Teif lab
@teiflab.bsky.social

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.

Teif lab
@teiflab.bsky.social

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.

Teif lab
@teiflab.bsky.social

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 🧵

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Teif lab
@teiflab.bsky.social

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.

Teif lab
@teiflab.bsky.social

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.

Teif lab
@teiflab.bsky.social

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 🧵

Teif lab
@teiflab.bsky.social

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

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.

Teif lab
@teiflab.bsky.social

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?

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Teif lab
@teiflab.bsky.social

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!

Teif lab
@teiflab.bsky.social

Tested LinkedIn for a paper announcement, and it worked perfectly. About 3x more engagements than on Bluesky. Obviously, LinkedIn is a different culture, more formal and less chatty, but for professional things it works just fine. Can't believe it was there all the time, and we just did not use it

Teif lab
@teiflab.bsky.social

Preparing a lecture about cancer genomics. Looking for a 3D map of human chromatin to show chromosomes 22 and 9 close to each other to demonstrate Philadelphia chromosome translocation. Chromosome territories like the one below don't show them together. Any other visualisations in this style?

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Teif lab
@teiflab.bsky.social

Preparing a lecture about cancer genomics. Looking for a 3D map of human chromatin to show chromosomes 22 and 9 close to each other to demonstrate Philadelphia chromosome translocation. Chromosome territories like the one below don't show them together. Any other visualisations in this style?