Timothy Fuqua 🏳‍🌈

Come be my colleague!

I’m looking forward to these next steps, and if you’re in Bern (or Stockholm), please get in touch!

…Starting in January, I’ll be working as a postdoc with Claudia Bank @cbank.bsky.social at the University of Bern, and collaborating with RIke Stelkens @stelkens.bsky.social on some exciting experimental evolution in yeast…

A photo of a smiling man (me) pointing at an image on a screen of a DNA gel. The image on the screen displays “TF”.

A bittersweet gift from the Wagner lab commemorating my last official day in the group: a gel that either stands for Tim Fuqua or Transcription Factor.

I’ve had some great memories here, sorting cells, and looking at promoters. I think it’s also time to announce where I’m off to next…

50 years ago, King & Wilson published a foundational paper that underlies the cis-regulatory paradigm (CRP) of #DevoEvo #EvoDevo, i.e., that *almost* all morphological evolution is driven by mutations in regulatory elements, rather than proteins, and it all arose from simple misunderstanding 🧪 🧵

We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887

We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩‍💻🎓: banklab.github.io/positions/

Please share widely!

#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED

Forgot to add the graphical abstract :)

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.

www.biorxiv.org/content/10.1...

Cauã is a great person with amazing ideas. I would highly recommend working in his new group!

I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...

...(Hot take) Because there is a correlation between promoter strength and robustness, I don't think we can rule out the counterintuitive possibility that some promoters are actually selected for their robustness, and not necessarily their strength.

Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...

Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...

...(Hot take) Because there is a correlation between promoter strength and robustness, I don't think we can rule out the counterintuitive possibility that some promoters are actually selected for their robustness, and not necessarily their strength.

...that in general, robustness increases with promoter strength. However, differences in spacer lengths, -10/-35 box composition, and overlapping -10/-35 boxes overlap can further increase robustness...

Predicting bacterial promoter function and evolution from random sequences An inferred mechanistic model that connects sequence (genotype) to function (constitutive gene expression phenotype) for any random sequence in Escherichia coli reveals the structure of constitutive p...

...we use a thermodynamic promoter model (elifesciences.org/articles/64543) to identify different sequence features associated with promoter mutational robustness. We find...

Strong promoters are mutationally robust Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...

A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...

www.biorxiv.org/content/10.1...

Did transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models!
www.biorxiv.org/content/10.1...

Congrats!!

Editor’s choice 😎 and it‘s a short read 😉.

We show evidence of de novo genes emerging from the Nucleosome Depleted Regions (NDRs) of yeast genomes. They are biased towards encoding transmembrane domains because of the NDRs too!

Bioimage Analysis Specialist | King's College London

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

A subset of transposable elements as mechano-response enhancer elements in controlling human embryonic stem cell fate - Nature Cell Biology Sun et al. identify a subset of transposable elements that serve as mechano-response enhancer elements that control gene expression and human stem cell fate.

Transposons turning into enhancers again! #TEsky

Call for Applications / Ausschreibung

Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer

Multiple overlapping binding sites determine transcription factor occupancy - Nature A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites."

www.nature.com/articles/s41...

What's the difference between dominance and epistasis? Two physically distinct mutations in a gene interact such that the het is identical to one of the homozygotes. If I define the gene as a locus, we call this dominance. If I define each bp as a locus, we call this epistasis.

Dissecting the cis-regulatory syntax of transcription initiation with deep learning Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understoo...

Here's the preprint if interested

www.biorxiv.org/content/10.1...

That’s very exciting! I look forward to reading that!

But my gut tells me you’re right. The drift barrier probably determines the extent by which promoter emergence differs between genomic and random DNA in different species.

Different for sure, but more complex? I.e. what percent of random sequences have eukaryotic promoter activity? A TATA box has a similar amount of info as a -10 box, right?

Selection plays a larger role in prokaryotes. The question =what selective forces removed the promoter-like sequences in proks?

Thanks! And fair points. I used the word “simple” to avoid unpacking the term “low information content” in the intro. But now I see that this is also problematic. Promoters, prokaryotic or eukaryotic, are obviously very exciting and mysterious, and far from simple to understand ☺️