Sign in

Timothy Fuqua 🏳️‍🌈

@timothyfuqua.bsky.social
823 followers 996 following 212 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

PostsRepliesMedia
Reposted by Timothy Fuqua 🏳️‍🌈
Harmit Singh Malik @harmitmalik.bsky.social · 10/10/2026
Most animal species pack sperm DNA with protamines instead of histones. Protamines are essential for male fertility. They are among the fastest-evolving genes in animals. That makes little sense. We think we know why, in a new paper led by @ching-hochang.bsky.social. www.science.org/doi/10.1126/...
science.org
Rapid protamine evolution suppresses meiotic drive in Drosophila
Many animal species replace histones with protamines during spermatogenesis. Although essential for sperm function, protamines evolve rapidly for reasons that remain unknown. Using in vivo gene replac...
323180
Reposted by Timothy Fuqua 🏳️‍🌈
Mir Lab @mirlab.bsky.social · 09/10/2026
1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348
tinyurl.com
Enhancer binding kinetics explain transcription factor hub formation
Transcription factors (TFs) form dynamic, high-concentration clusters, condensates, or hubs, proposed to increase TF binding frequency at target enhancers. However, how enhancer sequence shapes hub pr...
58541
Reposted by Timothy Fuqua 🏳️‍🌈
Ann T. Tate @annttate.bsky.social · 09/10/2026
Please RT: Do you use math to address interesting biological problems? Join us at Vanderbilt BioSci! We are conducting an open-rank TT search in Theoretical Biology: apply.interfolio.com/194619. We are a friendly and collaborative department with interests spanning a range of biological disciplines!
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
04558
Reposted by Timothy Fuqua 🏳️‍🌈
Jana Helsen @helsenjana.bsky.social · 08/10/2026
Looking to do a PhD in evolutionary cell biology, chromosomes & centromeres? 🧬🔬 The winter call for the UNIGE PhD recruitment is open, and my lab is among those recruiting through the Molecular Biosciences program! 🗓️ Apply by Nov 1st: lifesciencesphd.unige.ch
lifesciencesphd.unige.ch
University of Geneva - PhD School of Life Sciences | Welcome to the PhD School in Life Sciences at the Faculties of Medicine and Science
The University of Geneva Faculties of Medicine and Science join their forces to offer an outstanding study and research environment in Life Sciences. Highly motivated students with a Master’s degree o...
02327
Reposted by Timothy Fuqua 🏳️‍🌈
Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
179105
Reposted by Timothy Fuqua 🏳️‍🌈
Blake Matthews @ebmatthews.bsky.social · 02/10/2026
Three new evolutionary ecology PhD positions are open in Switzerland (Eawag, and Uni. Bern) to work on Greenland lake ecosystems. We are interested in how stickleback and copepods evolve, and how their evolution affects the trajectories of lake ecosystem development. apply.refline.ch/673277/1403/...
apply.refline.ch
3 PhD positions in the fields of Evolutionary Ecology, Evolutionary Genomics, and Ecosystem Science
The Department of Fish Ecology & Evolution (FishEc) has vacancies for
02938
Reposted by Timothy Fuqua 🏳️‍🌈
Theoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 08/10/2026
A great opportunity!
021
Reposted by Timothy Fuqua 🏳️‍🌈
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 06/10/2026
Let's talk about enhancer evolution at my poster (no. 61), discuss the automated yeast evolution we're doing in @thee-bank-lab.bsky.social (video below), or chat about hosting opportunities for the ERC StG next cycle ;) #EMBOEvoEco
072
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 06/10/2026
Let's talk about enhancer evolution at my poster (no. 61), discuss the automated yeast evolution we're doing in @thee-bank-lab.bsky.social (video below), or chat about hosting opportunities for the ERC StG next cycle ;) #EMBOEvoEco
072
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 02/10/2026
It’s all drift.
020
Reposted by Timothy Fuqua 🏳️‍🌈
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.
0187
Reposted by Timothy Fuqua 🏳️‍🌈
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.
15822
Reposted by Timothy Fuqua 🏳️‍🌈
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...
15223
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 18/09/2026
My PI is awesome. Congrats, Claudia!
071
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 18/09/2026
(4/4) Interested in the program? More info can be found here:
unibe.ch
CAS Hochschullehre
Der modular aufgebaute Studiengang führt zu einer umfassenden Lehr- und Lernförderungs-Qualifikation. Die Teilnehmenden erlangen die methodische Kompetenz zur Planung, Durchführung und Qualitätssicher...
000
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 18/09/2026
(3/4) The Department of Biology is now implementing a project from Claudia’s studies for a new quantitative biology curriculum with support of a Uni Bern grant:
teachinghub.unibe.ch
QUBI – Quantitative Biologie
Methodenkompetenz biologisch verankern: ein Brückenkurs verbindet Statistik und Programmierung mit realer Forschung
100
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 18/09/2026
(2/4) This 15 ECTS program focuses on evidence-based teaching practices, including course design, teaching methods, student assessment, supervision, and methods to continuously improve teaching.
100
Reposted by Timothy Fuqua 🏳️‍🌈
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...
054
Reposted by Timothy Fuqua 🏳️‍🌈
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
012
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 09/09/2026
I agree, “verification” connotates with “validates” or “supports.” The paper IMO supports the Expansion Hypothesis more than the Mutational Robustness hypothesis.
010
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 09/09/2026
Read it yesterday on the train. It’s very succinct and the figures are beautiful. Nice work everyone!
010
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 09/09/2026
Nice! 👍
120
Reposted by Timothy Fuqua 🏳️‍🌈
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...
16524
Reposted by Timothy Fuqua 🏳️‍🌈
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
34930
Reposted by Timothy Fuqua 🏳️‍🌈
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
04157
Reposted by Timothy Fuqua 🏳️‍🌈
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.
37722
Reposted by Timothy Fuqua 🏳️‍🌈
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
0167
Reposted by Timothy Fuqua 🏳️‍🌈
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.
110545
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
Thanks, Nikos. Congrats on the great collaboration!
010
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
So here we are, inventing new terms. In our defense, Gould and Vrba said, "Terms in themselves are trivial, but … they reflect (or even create) different theories about the structure of the world” (Gould and Vrba, Paleobiology 1982)". If you think the term is useful, please consider using it! (7/7)
100
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
Thus a great collaboration was born! (*Avengers theme in background*) While trying to write the Emergence Bias piece, we "accidently" wrote another paper (last plug!). Turns out, polyA/T tracts in nucleosome depleted regions explain why de novo proteins in yeast make transmembrane domains... (6/7)
academic.oup.com
Intergenic polyA/T tracts explain the propensity of yeast de novo genes to encode transmembrane domains
Abstract. New genes can emerge de novo from non-genic genomic regions. In budding yeast, computational predictions have shown that intergenic regions harbo
110
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
Nikos was explaining to me that yeast genomes are biased towards making de novo proteins with transmembrane domains (another shameless plug)! (5/7)...
nature.com
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences - Nature Communications
There is increasing evidence that protein-coding genes can emerge de novo from noncoding genomic regions. Vakirlis et al. propose that sequences encoding transmembrane polypeptides can emerge de novo ...
100
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
We realized that the term was missing ~3 years ago at an EMBO conference, where @vakirlis.bsky.social and I met having dinner together. I was blabbering to Nikos that there are biases underlying prokaryotic promoter emergence (shameless plug below) and... (4/7)
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.
120
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
An emergence bias is the molecular predisposition that, upon mutation, biases a genetic sequence towards or against manifesting new or latent functions or phenotypes. I.e. mutating different types of (non-functional) DNA sequences will not produce the same biological activities equally. (3/7)
A cartoon of different colored DNA sequences representing differnet types of DNA being mutated. These mutations create different distributions of new biological functions, shown with pie charts in the corresponding colors. Each pie chart has a different ratio of new biological functions.
100
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 19/08/2026
There are many described biases in molecular evolution, like developmental, mutational, and even phenotypic biases. But we feel that none of these appropriately describe the emergence of new biological functions. Think: de-novo proteins, promoters, and enhancers. (2/7)
100
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
14922
Reposted by Timothy Fuqua 🏳️‍🌈
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
141
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 17/08/2026
See you there :)
000
Reposted by Timothy Fuqua 🏳️‍🌈
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
17626
Reposted by Timothy Fuqua 🏳️‍🌈
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
1175
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 06/08/2026
Amazing work!
020
Reposted by Timothy Fuqua 🏳️‍🌈
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...
15721
Reposted by Timothy Fuqua 🏳️‍🌈
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
13412
Reposted by Timothy Fuqua 🏳️‍🌈
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.].
2266
Reposted by Timothy Fuqua 🏳️‍🌈
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!
093
Timothy Fuqua 🏳️‍🌈 @timothyfuqua.bsky.social · 16/07/2026
Jana is great. Join her group!
120
Reposted by Timothy Fuqua 🏳️‍🌈
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...
48345
Reposted by Timothy Fuqua 🏳️‍🌈
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...
18041
Reposted by Timothy Fuqua 🏳️‍🌈
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)
183
Reposted by Timothy Fuqua 🏳️‍🌈
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.
62514