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

Come see my poster tomorrow at #ESEB2025 P01.124 "The latent cis-regulatory potential of mobile DNA in Escherichia coli" or just read it here :)

Dierks et al. engineered an replisome that replicates only target plasmids at mutation rates 100,000 times higher than normal but leaving the rest of the genome unchanged. They evolved TEM-1 β-lactamase to gain strong resistance to several antibiotics in under a week. www.science.org/doi/10.1126/...

Going to #ESEB2025 ? We should connect! I'll be talking about some unpublished work on promoter emergence in random vs genomic DNA (preprint coming very soon???) and presenting a poster about our recent work turning transposons into promoters (P01.124, see thread).

Babe, wake up, EMBL courses and conferences just dropped for 2026! www.embl.org/about/info/c...

Some exciting work from our group on the evolution of transcription factor binding sites! Also, please consider following @gopinath21.bsky.social who just made a Bluesky account :)

Some exciting work from our group on the evolution of transcription factor binding sites! Also, please consider following @gopinath21.bsky.social who just made a Bluesky account :)

📢 We are recruiting! Several projects are available and can be tailored to the candidate's profile. Most include confocal imaging/spatial OMICs technologies. Please share and RT 🙏

This is really interesting. De-novo genes are more likely to be regulated by certain TFs over others!

Intragenic regions in yeast have a "neofunctional bias" towards encoding transmembrane domains (if translated). @vakirlis.bsky.social and I figured out this is b/c these regions are enriched with polyA, polyT, and TATA-like motifs. Read the short report here:

Hey y'all, grant-pending, I may be unemployed starting from October. If you have any leads on biotech / postdoc positions in the German-speaking part of Switzerland, I'd greatly appreciate a message. I'm great with Data Analysis, Molecular Biology, and Teaching. (Plz RT!) More at timothyfuqua.com

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

This was kind of what I planned on doing on my postdoc, but in the intestine So cool to study the evolution of gene expression! www.science.org/doi/10.1126/...

Nature research paper: In vivo mapping of mutagenesis sensitivity of human enhancers https://go.nature.com/3I53Fes

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

In vivo mapping of mutagenesis sensitivity of human enhancers www.nature.com/articles/s41...

Congrats @pamferretti.bsky.social !!!!

Today I'm finally sitting down and reading all of those papers that I re-tweeted (skeeted?) this year that I said I would read eventually. Wish me luck!

#drosophila @flybase.bsky.social request emergency funding: "As it stands, by the end of July, 2025, there will be no future updates to FlyBase, and in the worst case scenario access to the website will also be lost" => please donate! www.philanthropy.cam.ac.uk/give-to-camb...

Self-replicating RNAs!

I love the concept of domesticated transposable elements. I like that my genome has its little viral pets to feed nucleic acids and take out for transcriptional walkies. 🧬

Happy to announce that our study on the latent cis-regulatory potential of mobile DNA is officially published! TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.

Happy to announce that our study on the latent cis-regulatory potential of mobile DNA is officially published! TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.

The regulatory potential of transposable elements in maize ->Nature | More info from EcoSearch

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

An interesting alternative perspective on the Colossal "dire wolves."

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Non-model Bioeng Custom Lab Hardware Turn Key Genetic Design Please repost for reach 💚

Hey #TEsky hivemind, a student today asked me what percentage of human Transposable Elements (TEs) are autonomous vs non-autonomous (i.e. require a "helper"TE for transposition). Any ideas? Please RT!

Hey #TEsky hivemind, a student today asked me what percentage of human Transposable Elements (TEs) are autonomous vs non-autonomous (i.e. require a "helper"TE for transposition). Any ideas? Please RT!

Celebrating a small win today: thanks to some naive/lucky $NVDA investments and the crashing USD, I have finally finished paying off my US student loans! One probably shouldn't have to leverage the stock market and a recession to pay off government-provided education loans...

Switzerland has been kind to me. Having come from the US and living there now, I’m happy to talk to people thinking about leaving (I’m not in this lab, but hear good things!)

Excited to do a postdoc in beautiful Neuchatel / Switzerland🇨🇭? We have several postdoc positions open at the moment! Check our website for the full ads here: pathogen-genomics.org/jobs Happy to answer any question and please spread the word to anyone who might be interested!

Some of you think having a first-author Nature paper will cure your academic stress. Spoiler: it’s not. Anxiety is Reviewer 2 and will never be satisfied. It’s not going away on its own. Talk to a therapist and make lifestyle changes.

👇🏾👌🏾

To the top of the "to-read" list. Looks like a heroic amount of work from the Hahn lab (large-scale ChEC-seq compendium!) www.nature.com/articles/s41...

This is the publishing ecology that I sought to respectfully address in journals.biologists.com/dev/article/... And now I'm just frankly annoyed.

An excellent overview of mutual information: medium.com/swlh/a-deep-...