Oh my god, look at this!

elifesciences.org/articles/986... I'm super excited to announce that we have published the official "Version of Record" for our work on promoter emergence and evolution! A thread below for those who want to know more:

Genome modelling and design across all domains of life - Evo2 A biological foundation model trained on 9 trillion DNA base pairs to predict the functional impacts of genetic variation www.nature.com/articles/s41...

Really nice to see @marstonlab.bsky.social's News & Views piece cover the evolution of budding yeast centromeres in @nature.com. Check it out for a clear and concise breakdown of @maxhaase.bsky.social’s new paper and ours! 🧬

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...

Posting into the void again :P Any ideas?

I'm looking for a textbook / workbook for using Bash and other things bioinformatics-related in the command line (e.g. making phylogenic trees, genome alignments, SNP calling, etc.). Thanks in advance!

Our paper is now out in Nature: “Ancient co-option of LTR retrotransposons as yeast centromeres” www.nature.com/articles/s41... A short thread on how retrotransposons helped give rise to yeast point centromeres. 1/14

The replicase???

De-novo promoters emerge more readily from random DNA than from genomic DNA www.biorxiv.org/content/10.1...

I'm looking for a Swiss department to host me for an SNSF Starting Grant. I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com If your department might be a match, let’s chat!

Can you infer cause and effect between genes without disturbing the cell? 🧬 This study shows how natural “noise” in gene expression can reveal directed gene–gene interactions. buff.ly/mruUeLZ

Now published in @science.org www.science.org/doi/10.1126/...

Wanna read about yeasts and heat waves? 🥵 Check out our new preprint with @jennifermolinet.bsky.social and @stelkens.bsky.social! doi.org/10.64898/202...

New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos. www.biorxiv.org/content/10.6...

I just did my first tetrad dissection! 🍞🧫 Am I a yeast person now?

New online! Emergence and evolution of protein-coding de novo genes

2026 has just begun and we are looking forward to welcoming you to EMBL for another year of groundbreaking science. Our programme now features even more events, check it out ➡️ s.embl.org/2026-poster

Claudia Bank's (@cbank.bsky.social) research group, Theoretical Ecology and Evolution (THEE) is now on Bluesky! I posted a thread showing some of the group's publications from 2025 to get the account going. Please consider following the group for updates related to ecology and evolution 😀

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!