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Timothy Fuqua

@timothyfuqua.bsky.social
816 followers 991 following 211 posts

Postdoc in Claudia Bank’s group at the University of Bern. Editor for the Journal of Molecular Evolution (JME). How do novel traits and functions emerge and evolve? He/him 🏳‍🌈 timothyfuqua.com

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Timothy Fuqua @timothyfuqua.bsky.social · 20h
It’s all drift.
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Nature @nature.com · 23/09/2026
Nature research paper: The gene-regulatory evolution of the human skeleton go.nature.com/46GUxG8
go.nature.com
The gene-regulatory evolution of the human skeleton - Nature
Massively parallel reporter assays and human–ape hybrid skeletal cells are used to study the evolution of human cis-regulatory elements (CREs), revealing how differences in CREs have shaped the composition of human skeletal tissue.
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Proceedings of the National Academy of Sciences @pnas.org · 18/09/2026
How local is local adaptation? Researchers transplanted more than 700 lab-raised stickleback fish among lake and stream environments, finding that adaptation to specific sites can outweigh adaptation to broader habitat differences. In PNAS: ow.ly/yTOk50ZP97o
Two threespine stickleback fish. Image credit: Marius Roesti.
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Snorre Sulheim @sulheim.bsky.social · 18/09/2026
Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microsky
pnas.org
Cross-feeding enables robust coexistence between four bacterial species | PNAS
Resource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether...
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Timothy Fuqua @timothyfuqua.bsky.social · 18/09/2026
My PI is awesome. Congrats, Claudia!
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Nature Ecology & Evolution @natecoevo.nature.com · 11/09/2026
Read the accompanying News & Views commentary 👇 Ancient vocabulary for evolving cells: www.nature.com/articles/s41... Free to read: rdcu.be/XUoSoE9LiQ2a
nature.com
Ancient vocabulary for evolving cells - Nature Ecology & Evolution
A comparative multi-omic study finds that family-biased repertoires of short regulatory DNA motifs remain conserved over greater evolutionary distances than do the motif sets and co-occurring motif pa...
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IRB Barcelona @irbbarcelona.org · 10/09/2026
An international consortium led by #IRBBarcelona has produced the first comprehensive atlas showing how the #DNA sequence determines its shape, flexibility, and movements at the hexamer level. 📌 @natcomms.nature.com: DOI 10.1038/s41467-026-74390-5 #IRBScience
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Timothy Fuqua @timothyfuqua.bsky.social · 09/09/2026
Nice! 👍
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Wendy Bickmore @wbickmor.bsky.social · 08/09/2026
It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...
nature.com
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
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Flora Gaudillière-Jami @fgaudilliere.bsky.social · 07/09/2026
Our paper is now out in the @isme-microbes.bsky.social Journal (and selected as editor's choice)! We use an ecological framework to analyze the distribution of small transposable elements in over 30,000 prokaryotic genomes, characterizing their genomic niche doi.org/10.1093/isme...
doi.org
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Hanna Kokko @kokkonut.bsky.social · 04/09/2026
Are you into mathematical modelling of ecological and evolutionary systems? Look at this job ad for a senior lecturer in Lund. I've visited many times, splendid compact city, splendid department! lu.varbi.com/en/what:job/...
lu.varbi.com
Senior Lecturer in Computational Biology
Lund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit
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Pedro Beltrao @pedrobeltrao.bsky.social · 03/09/2026
8.8% success rate for the ERC Starting Grant is not acceptable. It is a lottery at this point with so many great scientists and ideas left to be funded. We keep talking about the competitiveness of Europe and we can't agree to properly fund our best instrument for scientific innovation.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 24/08/2026
@timothyfuqua.bsky.social & @vakirlis.bsky.social formalize “emergence bias” as the molecular predisposition that, upon mutation, biases a genetic sequence toward or against manifesting new or latent functions or phenotypes 🔗 academic.oup.com/gbe/article/... #societyjournal #genome #evolution
academic.oup.com
Emergence Biases in Molecular Evolution
Abstract. Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts, such as d
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Timothy Fuqua @timothyfuqua.bsky.social · 19/08/2026
@vakirlis.bsky.social and I are proposing a new term in the de-novo genes / molecular evolution cinematic universe. The term is: "Emergence Bias" and our perspective piece describing it was published in @genomebiolevol.bsky.social today! So, what is an emergence bias? (1/7)
academic.oup.com
Emergence Biases in Molecular Evolution
Abstract. Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts, such as d
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Jesse Veenvliet @jesseveenvliet.bsky.social · 17/08/2026
Looking forward to reading it in detail! You might find our piece interesting that deals with some similar ideas and how embryo models may be a useful testbed: royalsocietypublishing.org/rsfs/article...
royalsocietypublishing.org
The logic of monsters: development and morphological diversity in stem-cell-based embryo models
Abstract. Organoids and stem-cell-based embryo models (SEMs) are imperfect organ or embryo representations that explore a much larger space of possible for
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Timothy Fuqua @timothyfuqua.bsky.social · 17/08/2026
See you there :)
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Arnaud Krebs @arnaudkr.bsky.social · 12/08/2026
How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org
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Julio Ayala-López @ayalopjulio.bsky.social · 10/08/2026
Happy to share this preprint of one of my PhD chapters with @cbank.bsky.social and @spei.bsky.social! We use a population genetics model and find the conditions under which hybrid incompatibilities can be maintained in an isolated population when BDMI loci are overdominant. 1/3
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Timothy Fuqua @timothyfuqua.bsky.social · 06/08/2026
Amazing work!
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Evgeny Kvon @evgenykvon.bsky.social · 05/08/2026
A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...
biorxiv.org
Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions
Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...
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Teif lab @teiflab.bsky.social · 26/07/2026
Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders
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Bryan Gitschlag @bryangitschlag.bsky.social · 20/07/2026
Excited to announce that this fall I'm starting my lab at the University of South Carolina! Our hybrid wet/dry lab will explore fundamental topics in animal evolution, looking at how different evolutionary processes combine quantitatively [pleiotropic conflicts, mutation bias, etc.].
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Gavin Sherlock @gsherloc.bsky.social · 16/07/2026
Jana is an incredible scientist and mentor. I’m excited to see her lab’s work in the coming years, and it has been an absolute privilege to work with her. I highly encourage you to check out her lab!
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Timothy Fuqua @timothyfuqua.bsky.social · 16/07/2026
Jana is great. Join her group!
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Andreas Gschwind @argschwind.bsky.social · 15/07/2026
Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/
nature.com
An encyclopedia of human enhancer–gene regulatory interactions - Nature
An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...
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Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 14/07/2026
The @cbank.bsky.social lab is going 🚄 to #MMEE2026 in Cork next week! @ayalopjulio.bsky.social will present Thursday afternoon on hybrid incompatibilities, and @lorhab.bsky.social will present Wednesday afternoon on the repeatability of adaptation (1/3)
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Tim @timisstuck.bsky.social · 13/07/2026
Composing a decision letter and deciding on reviewer comments to be addressed/overruled is THE single most important task for which we have editors, IMO. If you get a decision from a journal with zero guidance and a laundry list of unreasonable reviewer demands, the journal editor has FAILED.
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CIBSS – Centre for Integrative Biological Signalling Studies @cibss.bsky.social · 13/07/2026
📣 #JobAlert The Faculty of Biology of @uni-freiburg.de invites applications for a Professorship (W3) for Bioinformatics and Molecular Genetics. ❗ Application Deadline: 15 August, 2026 🔗 kurzlinks.de/roi8 #Biology #Bioinformatics #MolecularGenetics
Job alert text with logo of University of Freiburg.
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10/07/2026
Repetitive sequence material shapes the earliest stages of de novo gene evolution in insects www.biorxiv.org/content/10.64898/20…
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Gopinath Chattopadhyay @gopinath21.bsky.social · 07/07/2026
My first work from my postdoctoral research in Andreas Wagner’s lab at the Institute of Evolutionary Biology and Environmental Studies, University of Zurich, is now available as a preprint. Link: www.biorxiv.org/content/10.6...
biorxiv.org
Negative Autoregulation Promotes the Evolution of Strong Environmental Switching
Living systems rely on gene regulatory circuits to respond to environmental change. Such circuits often act as molecular switches: OFF in the absence of a cue, and ON in its presence. We do not know h...
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Cian O'Donnell @cianodonnell.bsky.social · 28/06/2026
During my postdoc I was trying to move to a new area, my supervisor said: you have to go to a conference, it's the only way to learn what they are thinking and what the key questions are. He was completely right. Science is a collective and social human pursuit, not a bunch of pdfs online
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Charles Mullon @charlesmullon.bsky.social · 26/06/2026
Last chance to apply !
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Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 25/06/2026
Bacteria that evolve antibiotic resistance epigenetically in cows 🐮?!!? If you're at #SMBE2026 , listen to group member Adamandia (Mado) Kapopoulou's ✨flash talk ✨ at 14:20 on Tue (30th) in Session 3 (Lumbye room).
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Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 25/06/2026
PhD candidate @wachalak.bsky.social from our department will be presenting at #SMBE2026 in Session 15: "Detecting selection and local adaptation on (im)possible systems". Listen to her ✨flash talk✨ "Detecting local adaptation within chromosomal inversions" on Wed the 1st of July at 11:10.
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Harmit Singh Malik @harmitmalik.bsky.social · 24/06/2026
I know it seems like a heretical idea, but one way to figure out if a preprint is really interesting (to you) is... to read the preprint. Then, in the spirit of sharing, send a note to authors: a simple kudos or a more detailed question. I do this a dozen times a year. It's awesome. Try it.
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Timothy Fuqua @timothyfuqua.bsky.social · 23/06/2026
Congrats @zacharybailey.bsky.social and all co-authors involved!
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Mikey P @polyploid.party · 11/06/2026
Can we take a moment to appreciate the rendering of transposable elements as mischievous little scamps in this Medeiros et al paper? acsess.onlinelibrary.wiley.com/doi/10.1002/... #PlantScience
Illustration of double helix DNA strand with a transposable element depicted as a single twist of double helix with arms and legs running along the strand.
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Lara Krüger @lara-kruger.bsky.social · 09/06/2026
📢 We are looking for a Junior Group Leader to join us at @institutcurie.bsky.social! Having joined the department just over a year ago, I can honestly say that it is an exceptionally stimulating and supportive scientific environment, filled with outstanding colleagues — all in the heart of Paris.
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Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 10/06/2026
The University of Bern's features the "Treasure Chest project", which uses real-world scenarios to teach stats to bio students. Our collaborator Stephan Peischl @spei.bsky.social connects genetics to epidemiology, bringing statistics to life! Article (in DE) in the link below:
uniaktuell.unibe.ch
Die Schatztruhe macht Statistik lebendig
Das Programm «IMPULS: LEHRE» fördert innovative Lehrprojekte an der Uni Bern. Eines davon ist die «Schatztruhe».
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Timothy Fuqua @timothyfuqua.bsky.social · 10/06/2026
Guys, it’s working!!!
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Chloé Haberkorn @chloehbk.bsky.social · 06/06/2026
New paper out in Evolution 🧫🧬 doi.org/10.1093/evol... with a pretty big crew & @stelkens.bsky.social ! Story started over 20 years ago, fun to jump in late and help wrap it up :)
doi.org
Adaptive Benefits of Hybridization in Saccharomyces Yeast are Constrained by Genomic Background and Depend on Temperature
Abstract. Climate change urges us to better understand and predict evolutionary responses to temperature shifts. Hybridization, by increasing genetic varia
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Tom Astle @tjalamont.bsky.social · 04/06/2026
#Bugsky 🐙🌿 Shared with me by a fof in SoCal - this is a gynandromorph (both male & female) valley carpenter bee (Xylocopa sonorina). Females are black, males orange, so the extreme color dimorphism really stands out. Per Doug Yanega at UC Riverside, bee gynandromorphs he’s seen are mosaic instead—
A photo looking down on an unusual bee clinging to a green shirt. The bee is a stout bee called a carpenter bee, but what’s unusual is that it is both male and female, known as a gynandromorph. In this particular species (Xylocopa sonorina), females are jet black and males are fuzzy orange. This one has an abdomen that is divided into four perfect quadrants, like a checkerboard, alternating orange and black. The thorax is mostly black but with some orange.
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José Cerca @naturalselection.bsky.social · 02/06/2026
🧨 New publication out (I think this one is 🌶️ ): Cerca & @stelkens.bsky.social - "The identity crisis of speciation genomics". academic.oup.com/evolinnean/a...
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Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 02/06/2026
Happy pride month 🏳️‍🌈 PhD candidate, @lorhab.bsky.social from the group was recently on the radio with Radio Bern (RABE) to talk about the network Queer UniBE, an LGBTQ+ organization for staff at the University of Bern (session starts ~19 minutes, German only): rabe.ch/beitrag/20-0... (post 1/2)
rabe.ch
«Wir Iraner*innen befinden uns hierzulande in der Schwebe»
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Ben Vezina @bananabenana.bsky.social · 30/05/2026
"intragenic promoters that we found occur more often on the antisense strands of these genes" Wow, cool. The compactness of bacterial genomes continues to amaze me. #MicroSky #Ecoli #microbiology Fig S2C:
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Timothy Fuqua @timothyfuqua.bsky.social · 29/05/2026
Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!! TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
science.org
De novo promoters emerge more readily from random DNA than from genomic DNA
Promoters emerge three times more readily from random DNA than from genomic DNA.
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Timothy Fuqua @timothyfuqua.bsky.social · 29/05/2026
Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!! TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)
science.org
De novo promoters emerge more readily from random DNA than from genomic DNA
Promoters emerge three times more readily from random DNA than from genomic DNA.
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Cauã Westmann @cauawest.bsky.social · 29/05/2026
Happy to share that our preprint is now out! We discuss how Synthetic Biology can be used as a powerful tool to answer questions in evolutionary biology. We hope it will be a useful resource for the community! With @3xueying.bsky.social and @hhydrochaerus.bsky.social ecoevorxiv.org/repository/v...
ecoevorxiv.org
Synthetic biology as an empirical tool for evolutionary theory
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