very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

We lost a legend…

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

One of the most-viewed PNAS articles in the last week is “The variability of evolvability: Properties of dynamic fitness landscapes determine how phenotypic variability evolves.” Explore now: https://ow.ly/XouU50XWiiV For more trending articles, visit https://ow.ly/AiXL50XWi81.

📣 #EMBOEvoEco returns in 2026 to uncover the mechanistic foundations of ecological and evolutionary change! Keynote lectures will spotlight the ecology and evolution of symbiosis. Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl#EMBOEvoEco

Come to my talk today :)

If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers! More info here: news.ki.se/calendar/the...

New year, new conferences! Consider submitting to the symposium on Fitness landscapes and Genotype-phenotype maps, linking computational and experimental approaches (organising with @n-martin.bsky.social; @dbajic.bsky.social invited spreaker) at SMBE (28/6-2/7)! Abstract deadline February 3rd!

Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬 Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort! A "meme-torial" of the science is coming soon 👀

If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers! More info here: news.ki.se/calendar/the...

Thanks @bryangitschlag.bsky.social for answering my question about mitochondrial genes! Nice little thread below:

Question for #mitochondria people: Many mitochondrial genes are encoded in the nuclear genome. How? Did these genes originate in ancestral mitochondria and horizontally transfer to the nucleus, or did they emerge de novo in the nuclear genome and replace their mitochondrial counterparts? Plz RT.

“this structure has been resolved!! your image is in the database!!” the image in the database:

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

this is amazing they show some compelling evidence for 3' to 5' translation #RNASky #RNABiology 🧪 www.biorxiv.org/content/10.6...

What if complex life began when evolution hit a search bottleneck? Across 6,500+ species, 🧬 length follow a scale-invariant law. At eukaryote origins, proteins plateau while 🧬 keep growing as noncoding regulatory DNA. Phase transition? www.pnas.org/doi/10.1073/... 👉 manlius.substack.com

JASPAR 2026 is out 🎉 The new release massively expands the TF motif collections and adds a dedicated DeepLearning collection of motifs learned from deep learning models. Database: jaspar.elixir.no Paper (NAR): doi.org/10.1093/nar/... 🧵1/2

I am pleased to announce that from Jan 1 2026 I take over as Editor-in-Chief of the journal Biological Theory. My first act, with the support of the editorial team, is to bring the journal to BlueSky from X. Please follow us @biologicaltheory.bsky.social. We will be posting about all our articles.

Now online! An archaeal transcription factor bridges prokaryotic and eukaryotic regulatory paradigms

Exactly. Figures (outline)> Methods > Results > Discussion > Introduction > Abstract > Title

This is probably my favorite paper of 2025. Beautiful work by @elphegenoralab.bsky.social and @karissalhansen.bsky.social that should be on the top of the reading list for everyone with even a slight interest in gene expression!

My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up! tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs. Check it out! academic.oup.com/bioinformati...

Brückner, D. B., & Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences, #EpithelialMechanics www.pnas.org/doi/10.1073/...

Come be my colleague!

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 :)

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.

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...

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...

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 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-...

Transposons turning into enhancers again! #TEsky

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

"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.

Here's the preprint if interested www.biorxiv.org/content/10.1...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

If a wasp visits your picnic this wknd, what’s she after? #HamOrJam? Worker wasps hunt protein for the larvae but need sugar themselves. Help us learn about their food preferences-tell us what wasps want at your picnic. #CitizenScience #WaspPicnicSurvey docs.google.com/forms/d/e/1F...

Nice talk from @timothyfuqua.bsky.social on the capacity of bacterial genomes to evolve promoters 'de novo'. One impt number: what % of genomic sequence is, or is mutationally close to, being a promoter? Another, more overlooked: how does this compare to the # in random sequence? #ESEB2025

The day finished off strong with loads of great talks in the Genomics of Evolutionary Innovations symposium! I'm pleased to report that my talk went well ☺️ 🎨🖌️ #eseb2025 #eseb #esebconference @eseb2025.bsky.social @jfenn.bsky.social @timothyfuqua.bsky.social

Come in half an hour!

How do new promoters emerge from genomic DNA vs randomly synthesized DNA? Come see my talk at 15:30 in room 113 (Genomic basis of evolutionary innovations) at #ESEB2025 to find out!

Come say hi #ESEB2025