Reposted by Timothy FuquaNature @nature.com · 23/09/2026Nature research paper: The gene-regulatory evolution of the human skeleton go.nature.com/46GUxG8go.nature.comThe gene-regulatory evolution of the human skeleton - NatureMassively 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. 0198
Reposted by Timothy FuquaProceedings of the National Academy of Sciences @pnas.org · 18/09/2026How 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 15822
Reposted by Timothy FuquaSnorre Sulheim @sulheim.bsky.social · 18/09/2026Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microskypnas.orgCross-feeding enables robust coexistence between four bacterial species | PNASResource supply is generally considered a dominant driver of microbial diversity. Here, using a four-species bacterial consortium, we asked whether... 15223
Reposted by Timothy FuquaNature Ecology & Evolution @natecoevo.nature.com · 11/09/2026Read the accompanying News & Views commentary 👇 Ancient vocabulary for evolving cells: www.nature.com/articles/s41... Free to read: rdcu.be/XUoSoE9LiQ2anature.comAncient vocabulary for evolving cells - Nature Ecology & EvolutionA 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 FuquaIRB Barcelona @irbbarcelona.org · 10/09/2026An 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
Reposted by Timothy FuquaWendy Bickmore @wbickmor.bsky.social · 08/09/2026It 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.comMechanisms underlying disease-causing variants in promoters and enhancers - Nature GeneticsThis 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... 16424
Reposted by Timothy FuquaFlora Gaudillière-Jami @fgaudilliere.bsky.social · 07/09/2026Our 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.orgCharacterizing the ecological niche of insertion sequences within prokaryotic genomesAbstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious 34930
Reposted by Timothy FuquaHanna Kokko @kokkonut.bsky.social · 04/09/2026Are 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.comSenior Lecturer in Computational BiologyLund 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 FuquaPedro Beltrao @pedrobeltrao.bsky.social · 03/09/20268.8% 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 FuquaGenome 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 #evolutionacademic.oup.comEmergence Biases in Molecular EvolutionAbstract. 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 FuquaErik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026Remember 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/nnature.comBonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature BiotechnologyHigh-dimensional data are visualized through representation on tree structures. 110545
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.comEmergence Biases in Molecular EvolutionAbstract. Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts, such as d 14518
Reposted by Timothy FuquaJesse Veenvliet @jesseveenvliet.bsky.social · 17/08/2026Looking 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.orgThe logic of monsters: development and morphological diversity in stem-cell-based embryo modelsAbstract. Organoids and stem-cell-based embryo models (SEMs) are imperfect organ or embryo representations that explore a much larger space of possible for 141
Reposted by Timothy FuquaArnaud Krebs @arnaudkr.bsky.social · 12/08/2026How 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 FuquaJulio Ayala-López @ayalopjulio.bsky.social · 10/08/2026Happy 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 1165
Reposted by Timothy FuquaEvgeny Kvon @evgenykvon.bsky.social · 05/08/2026A 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.orgEnhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitionsHousekeeping 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 FuquaTeif lab @teiflab.bsky.social · 26/07/2026Woolfe 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 FuquaBryan Gitschlag @bryangitschlag.bsky.social · 20/07/2026Excited 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 FuquaGavin Sherlock @gsherloc.bsky.social · 16/07/2026Jana 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
Reposted by Timothy FuquaLuca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026Our 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.orgEnhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature GeneticsTünnermann 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 FuquaAndreas Gschwind @argschwind.bsky.social · 15/07/2026Thrilled 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.comAn encyclopedia of human enhancer–gene regulatory interactions - NatureAn 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 FuquaTheoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 14/07/2026The @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) 173
Reposted by Timothy FuquaTim @timisstuck.bsky.social · 13/07/2026Composing 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
Reposted by Timothy FuquaCIBSS – 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 22331
Reposted by Timothy FuquabioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10/07/2026Repetitive sequence material shapes the earliest stages of de novo gene evolution in insects www.biorxiv.org/content/10.64898/20… 074
Reposted by Timothy FuquaGopinath Chattopadhyay @gopinath21.bsky.social · 07/07/2026My 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.orgNegative Autoregulation Promotes the Evolution of Strong Environmental SwitchingLiving 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... 182
Reposted by Timothy FuquaCian O'Donnell @cianodonnell.bsky.social · 28/06/2026During 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 16811
Reposted by Timothy FuquaCharles Mullon @charlesmullon.bsky.social · 26/06/2026Last chance to apply ! 037
Reposted by Timothy FuquaTheoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 25/06/2026Bacteria 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). 162
Reposted by Timothy FuquaTheoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 25/06/2026PhD 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. 193
Reposted by Timothy FuquaHarmit Singh Malik @harmitmalik.bsky.social · 24/06/2026I 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. 1229264
Timothy Fuqua @timothyfuqua.bsky.social · 23/06/2026Congrats @zacharybailey.bsky.social and all co-authors involved! 041
Reposted by Timothy FuquaMikey P @polyploid.party · 11/06/2026Can 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 2487
Reposted by Timothy FuquaLara 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. 19698
Reposted by Timothy FuquaTheoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 10/06/2026The 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.chDie Schatztruhe macht Statistik lebendigDas Programm «IMPULS: LEHRE» fördert innovative Lehrprojekte an der Uni Bern. Eines davon ist die «Schatztruhe». 064
Reposted by Timothy FuquaChloé Haberkorn @chloehbk.bsky.social · 06/06/2026New 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.orgAdaptive Benefits of Hybridization in Saccharomyces Yeast are Constrained by Genomic Background and Depend on TemperatureAbstract. Climate change urges us to better understand and predict evolutionary responses to temperature shifts. Hybridization, by increasing genetic varia 1249
Reposted by Timothy FuquaTom 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— 332109632
Reposted by Timothy FuquaJosé 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... 13917
Reposted by Timothy FuquaTheoretical Ecology and Evolution (THEE) Group @thee-bank-lab.bsky.social · 02/06/2026Happy 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»6.48 141
Reposted by Timothy FuquaBen 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: 171
Reposted by Timothy FuquaTimothy Fuqua @timothyfuqua.bsky.social · 29/05/2026Our 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.orgDe novo promoters emerge more readily from random DNA than from genomic DNAPromoters emerge three times more readily from random DNA than from genomic DNA. 39024
Timothy Fuqua @timothyfuqua.bsky.social · 29/05/2026Our 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.orgDe novo promoters emerge more readily from random DNA than from genomic DNAPromoters emerge three times more readily from random DNA than from genomic DNA. 39024
Reposted by Timothy FuquaCauã Westmann @cauawest.bsky.social · 29/05/2026Happy 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.orgSynthetic biology as an empirical tool for evolutionary theory 052