Timothy Fuqua

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...

Amazing, thank you! 🙏

Posting into the void again :P Any ideas?

Looks like it could be a dyer’s polypore?

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!

Ancient co-option of LTR retrotransposons as yeast centromeres - Nature Evolutionarily related ‘proto-point’ centromeres providing resolution to the evolutionary origins of point centromeres are identified in yeast, and comparison shows they evolved in an ancestor with re...

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

Amazing work, Edoardo!

The replicase???

Figure 1. The genome is enriched with active promoters relative to random DNA. (A) We cloned the random library of 150 bp N-mer sequences (n=17,129, purple), and the genomic library of 100-300 bp sequences (n=91,866, magenta) into the dual-reporter plasmid MR1 (pMR1), which drives the expression of green fluorescent protein (GFP, teal) from inserts on the top DNA strand, and that of red fluorescent protein (RFP, orange) on the bottom strand. We transformed E. coli cells with the plasmid libraries. (B) We sorted the bacterial libraries into fluorescence bins at four fluorescence strengths: none, weak, moderate, and strong for both GFP and RFP (eight bins total) with a cell-sorter. We bulk-sequenced the library inserts from each bin and calculated fluorescence scores in arbitrary units (a.u.) ranging between one (none) and four (strongest) (Methods). (C) The probability that a DNA sequence in the random (purple) and genomic (magenta) libraries is a promoter relative to its AT-content. (D) For 102 position-weight matrices (PWMs) for transcription factors and sigma (σ) factors, we plot the percentage of sequences in each library (purple: random, magenta: genome) that encode at least one putative factor binding site (vertical axis) against the respective PWM’s information content in bits. We test for equality of the frequency distributions between the random and genome libraries with a paired t-test (p=7.48×10−12).

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?

Emergence and evolution of protein-coding de novo genes Nature Reviews Genetics, Published online: 28 January 2026; doi:10.1038/s41576-025-00929-9De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanistic and evolutionary processes underlying their emergence and evolution, and the patterns in their encoded protein structures.

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 😀

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

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

Schematic representation of fitness landscapes. (A) Orange lines show maximum (dashed) and average (dotted) fitness of a population on a narrower peak (yellow circles), blue lines show the same for a wider peak (blue circles). (B) Trajectory of a population in a periodically changing environment with respect to a given fitness landscape (solid arrow) and with respect to an unseen other fitness landscape (dashed arrow). (C) Hypothetical “trapping” of the population in variable environments.

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!

Come to my talk today :)

The biases and mechanisms of regulatory DNA evolution and emergence Welcome to a seminar with Dr Timothy Fuqua from the University of Bern.

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!

An expanded registry of candidate cis-regulatory elements - Nature The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types...

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 👀

The biases and mechanisms of regulatory DNA evolution and emergence Welcome to a seminar with Dr Timothy Fuqua from the University of Bern.

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: