Timothy Fuqua 🏳🌈
@timothyfuqua.bsky.social
Incoming postdoc in Claudia Bank’s lab. Promoters, emergence, fitness landscapes, dogs 🐶 and triathlon 🏊 🚲 🏃. He/him 🏳🌈.
timothyfuqua.com
timothyfuqua.com
Pinned
The latent cis-regulatory potential of mobile DNA in Escherichia coli - Nature Communications
The mechanism and extent to which transposons can alter the gene expression of their hosts is not well understood. This study finds that in the IS3 family of transposable elements in E.coli, de-novo p...
www.nature.com
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.
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.
Reposted by Timothy Fuqua 🏳🌈
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/...
November 10, 2025 at 8:00 AM
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!
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
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
October 30, 2025 at 5:59 PM
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…
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…
October 30, 2025 at 5:57 PM
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…
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…
Reposted by Timothy Fuqua 🏳🌈
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 🧪 🧵
October 29, 2025 at 12:35 AM
Reposted by Timothy Fuqua 🏳🌈
We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887
October 28, 2025 at 6:43 PM
We are hiring an Imaging Scientis. Apply here: go.mbl.edu/AS1887
Reposted by Timothy Fuqua 🏳🌈
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
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
October 28, 2025 at 4:22 PM
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
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Forgot to add the graphical abstract :)
October 23, 2025 at 11:19 AM
Forgot to add the graphical abstract :)
Reposted by Timothy Fuqua 🏳🌈
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 22, 2025 at 5:46 PM
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...
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...
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...
October 21, 2025 at 2:59 PM
Cauã is a great person with amazing ideas. I would highly recommend working in his new group!
Reposted by Timothy Fuqua 🏳🌈
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...
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...
October 20, 2025 at 6:14 PM
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...
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...
Reposted by Timothy Fuqua 🏳🌈
...(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.
October 21, 2025 at 8:02 AM
...(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.
Reposted by Timothy Fuqua 🏳🌈
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...
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...
www.nature.com
October 21, 2025 at 9:43 AM
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 21, 2025 at 8:02 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Timothy Fuqua 🏳🌈
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...
www.biorxiv.org/content/10.1...
October 16, 2025 at 10:01 PM
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...
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!
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!
SEPTEMBER's EDITOR's CHOICE:
Intergenic, repetitive motifs that act as nucleosome repleted regions in the budding yeast genome, have evolved de novo into novel protein-coding genes:
doi.org/10.1093/jeb/...
@vakirlis.bsky.social
@timothyfuqua.bsky.social
Intergenic, repetitive motifs that act as nucleosome repleted regions in the budding yeast genome, have evolved de novo into novel protein-coding genes:
doi.org/10.1093/jeb/...
@vakirlis.bsky.social
@timothyfuqua.bsky.social
September 30, 2025 at 8:26 PM
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!
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!
Reposted by Timothy Fuqua 🏳🌈
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-...
Bioimage Analysis Specialist | King's College London
www.kcl.ac.uk
September 29, 2025 at 9:48 AM
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
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.
www.nature.com
September 18, 2025 at 6:13 AM
Transposons turning into enhancers again! #TEsky
Reposted by Timothy Fuqua 🏳🌈
Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer
September 9, 2025 at 12:10 PM
Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer
Reposted by Timothy Fuqua 🏳🌈
"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...
www.nature.com/articles/s41...
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...
www.nature.com
September 3, 2025 at 8:57 PM
"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...
www.nature.com/articles/s41...
Reposted by Timothy Fuqua 🏳🌈
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.
September 1, 2025 at 8:06 PM
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.
Reposted by Timothy Fuqua 🏳🌈
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)
"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)
De-novo promoters emerge more readily from random DNA than from genomic DNA
Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...
www.biorxiv.org
August 28, 2025 at 6:37 AM
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)
"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)
Reposted by Timothy Fuqua 🏳🌈
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...
#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...
August 23, 2025 at 9:51 AM
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...
#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...
Reposted by Timothy Fuqua 🏳🌈
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
August 20, 2025 at 5:21 AM
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
Reposted by Timothy Fuqua 🏳🌈
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
I'm pleased to report that my talk went well ☺️ 🎨🖌️
#eseb2025 #eseb #esebconference
@eseb2025.bsky.social @jfenn.bsky.social @timothyfuqua.bsky.social
August 19, 2025 at 6:37 PM
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
I'm pleased to report that my talk went well ☺️ 🎨🖌️
#eseb2025 #eseb #esebconference
@eseb2025.bsky.social @jfenn.bsky.social @timothyfuqua.bsky.social