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Lars Eicholt

@lacholt.bsky.social
612 followers 1.6K following 25 posts

molecular evolution.

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Reposted by Lars Eicholt
Matthew Hahn @3rdreviewer.bsky.social · 08/09/2026
NSF Biology Postdoc Fellowships are back! Good news for everyone...great news for someone who wants to work in our group? Just reach out if interested. www.nsf.gov/funding/oppo...
nsf.gov
Postdoctoral Research Fellowships in Biology (PRFB)
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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 01/09/2026
Join us next Tuesday, 5PM CET for our first ProSE after the summer! Betül Kaçar @kacarlab.bsky.social will talk about the origin and early evolution of ancient proteins! 📜🧬 tinyurl.com/prose-seminar2
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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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Lars Eicholt @lacholt.bsky.social · 26/08/2026
Analysing the properties of those subsets we could see that they are different from the rest. To test your own proteins - designed, de novo emerged or randomized - for these predictor discordances, we provide a testsuit: github.com/ArsLeicholt/... 6/6
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Lars Eicholt @lacholt.bsky.social · 26/08/2026
When we remove the subset, the correlations fit again as expected 5/6
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Lars Eicholt @lacholt.bsky.social · 26/08/2026
Using a simple score defined by high disorder, high plddt, low disorder and beta-sheet content, we found a bifurcating subset of sequences in all sequence sets but largest in de novo emerged and randomized 4/6
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Lars Eicholt @lacholt.bsky.social · 26/08/2026
Using Alphafold3 and Punch2, the now best predictors, we see the same behaviour again. But now we wanted to know if all those proteins show the same behaviour or if there is a subset that drives those predictions. 3/6
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Lars Eicholt @lacholt.bsky.social · 26/08/2026
We found earlier that in randomized and de novo emerged proteins predicted disordered regions showed high pLDDT, while predicted beta-sheets actually showed low pLDDT. Using Alphafold2, fldpnn, Iupred3, ESMfold 2/6 onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com
Random, de novo, and conserved proteins: How structure and disorder predictors perform differently
Understanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination ...
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Lars Eicholt @lacholt.bsky.social · 26/08/2026
Two years ago @lassemiddendorf.bsky.social and I noticed that structure and disorder predictor are discordant for de novo emerged and randomized proteins. We now identified which sequences drive these discordant predictions and what properties they have. 1/6 www.biorxiv.org/content/10.6...
biorxiv.org
A discrete protein subset drives structure prediction discordance in orphan proteins
Structure and disorder predictors are increasingly used as decision-grade tools in protein engineering and in the analysis of newly emerged proteins, yet how the current state-of-the-art behaves on se...
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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 13/08/2026
ICYMI: New Online! Mechanisms of transcription termination across the coding and noncoding loci of the genome
dlvr.it
Mechanisms of transcription termination across the coding and noncoding loci of the genome
Nature Reviews Molecular Cell Biology, Published online: 10 August 2026; doi:10.1038/s41580-026-01005-8Transcription termination by RNA polymerase II is a tightly regulated process that involves RNA surveillance and the chromatin environment. This Review discusses the interactions between transcription termination, RNA processing, nuclear RNA decay and mRNP export, which together guide RNA fate.
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Reposted by Lars Eicholt
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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Reposted by Lars Eicholt
Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Anirvan Chatterjee @chatterjee.net · 02/08/2026
This distinction makes sense to me www.schneier.com/blog/archive...
schneier.com
Should You Use AI for a Task? Here’s a Simple Way to Decide - Schneier on Security
This essay originally appeared in The Guardian. I teach public policy at the Harvard Kennedy School and the Munk School at the University of Toronto. And it will come as no surprise to you that my…
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Reposted by Lars Eicholt
Stanisław Dunin-Horkawicz @staszekdh.bsky.social · 30/07/2026
If you are into plasmid research, try pLAST. By representing plasmids as ORF chains, it enables fast searches of 700k PlasmidScope sequences in global (find similar plasmids) or local (find recurring gene modules) mode. Available as server or local package. Feedback welcome! Links below ⬇️
Similarity map of hits for a single query plasmid, with the query and selected hit highlighted.Global alignment of a single query-target plasmid pair, showing corresponding ORFs and conserved gene blocks.
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Tobias Warnecke @tobiaswarnecke.bsky.social · 29/07/2026
Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...
biorxiv.org
Bacteriocins in archaea and archaeocins in bacteria
Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...
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Janina Rinke @jannelrinke.bsky.social · 02/07/2026
Excited to share that our paper on Horizontal Gene Transfer is now out in its final form in @gigascience.bsky.social! 🥳 By analysing 163 high-quality ant genomes, we show that HGT from bacteria is widespread across the ants and likely has adaptive functions! doi.org/10.1093/giga... 🐜📸: Alex Wild
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 24/07/2026
How are evolutionarily young and old proteins distributed in sequence space? www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 24/07/2026
How are evolutionarily young and old proteins distributed in sequence space? www.biorxiv.org/content/10.64898/20…
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
Ehm did not expect transparent backgrounds in figures to look that bad here...
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
With @tothpetroczylab.bsky.social, Richard Goldstein, @bornberglab.bsky.social and a lot of help, inspiration and advise from many other colleagues and friends - more comments welcome! 7/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
Constrained but accessible: de novo proteins occupy regions defined by residue order and biophysical constraints and are not simply natural "random" sequences. Transmembrane helices provide a bridging link between different areas of space. 6/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
The sequences that bridge classes are unusually often predicted to contain transmembrane helices. Short hydrophobic stretches look like a plausible route into the occupied regions of sequence space. 5/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
Each class has its own characteristic k-mers. Because the distance is built from k-mers weighted by physicochemical similarity, we can ask which local patterns drive the separation instead of only observing that it exists. 4/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
De novo proteins are not a random draw from sequence space. They sit apart from canonical proteins and from all randomized sets — nearer to intergenic than to canonical, but clearly separated from both. 3/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
Randomizing sequences shifts distance distributions towards what is expected by chance, in every class. But the natural classes stay distinct from each other and from their randomized versions. Short, intergenic regions are close to random. Residue order, not just composition, carries signal. 2/7
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Lars Eicholt @lacholt.bsky.social · 25/07/2026
New preprint: how are young and old proteins distributed in sequence space? 🌌 Comparing de novo, intergenic and canonical proteins from yeast and fly with length- and composition-matched randomized controls, using alignment-free k-mer distances. 1/7 doi.org/10.64898/202...
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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 04/06/2026
Join us the last time before the summer break! Cesar A. Ramirez-Sarmiento will talk about "Unveiling the fold-switching behavior of RfaH: echoes of the past, signals of the present". As always, Tue 5PM CET, follow the link to sign-up: tinyurl.com/prose-seminar2
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Molecular Biology and Evolution @molbioevol.bsky.social · 26/05/2026
Patel, @lacholt.bsky.social et al. perform cross-species gene swap assays in D. melanogaster testes, showing that several orthologs of orphan gene Gdrd have undergone lineage-specific evolutionary changes. 🔗 doi.org/10.1093/molbev/msag119 #evobio #molbio #drosophila
doi.org
Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster
Abstract. Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we inve
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Reposted by Lars Eicholt
Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026
Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 05/05/2026
Join ProSe next week Tuesday, when Noelia Ferruz @noeliaferruz.bsky.social is talking about "Controllable Protein Design with Protein Language Models and Reinforcment Learning", TUE, May 12, 5PM CET! Sign-up here: tinyurl.com/prose-seminar2
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Reposted by Lars Eicholt
Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 08/04/2026
Our next speaker will be Timothy Fuqua @timothyfuqua.bsky.social with "The Evolution and Emergence of Regulatory DNA", 14th April, 5PM CET. Sign-up here: tinyurl.com/prose-seminar2
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Hassan uz Zaman @hassanzaman.bsky.social · 20/03/2026
Happy to announce that our paper on orphan gene evolution in bacteria dropped in PNAS yesterday! This is a problem I've been thinking about since the start of my PhD. Very grateful for this journey, as well as All The Friends I Made Along the Way. Also, Eid Mubarak to those who celebrate!
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Protein Structure Evolution (ProSE) Seminar @proteinstructure.bsky.social · 03/03/2026
Our next Talk will be "Protein Origami and the Hidden Rules of Functional Innovations"! March 11th, 5PM CET. Sign-up here: tinyurl.com/prose-seminar2
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Genome Biology and Evolution @genomebiolevol.bsky.social · 25/02/2026
Jones et al. analyzed two high-quality genomes of the cockroach genus Cryptocercus, the sister group to all termites, revealing relaxed selection in both Cryptocercus and termites. 🔗 doi.org/10.1093/gbe/evag028 #genome #evolution #sociality
doi.org
Cryptocercus Genomes Expand Knowledge of Adaptations to Xylophagy and Termite Sociality
Abstract. Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites),
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Kaçar Lab at UW-Madison @kacarlab.bsky.social · 11/02/2026
Latest work! 🧬 We uncover how evolution of translation initiation factor 2 (IF2) extensions links translation to bacterial stress response. We map 7 structural architectures & show how terminal extensions are enriched in intrinsic disorder & phase-separation features. Link: doi.org/10.64898/202...
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Emi @kayamalie.bsky.social · 09/02/2026
Whale evolution makes me uncomfortable
A diagram of the evolution of whales, from land dwelling mammals to the ocean giants we know today.
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Hassan uz Zaman @hassanzaman.bsky.social · 08/02/2026
I can't believe this seminar's been running for a year now! Our YouTube channel is now live—you can watch the recordings of genuinely some of the best molecular evolution talks on the internet. tinyurl.com/ProSE-videos (Maybe we should do a tier list soon...)
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Bornberglab @bornberglab.bsky.social · 09/02/2026
🚨 New paper in GBE! 🚨 This study analyzes two high-quality Cryptocercus genomes, the sister group to all termites, to investigate the transition to subsociality and wood-feeding (xylophagy) in Blattodea. 🪳 Check it out here: doi.org/10.1093/gbe/...
doi.org
Cryptocercus genomes expand knowledge of adaptations to xylophagy and termite sociality
Abstract. Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites),
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Lars Eicholt @lacholt.bsky.social · 05/02/2026
Thank you!
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Professor Mary J O'Connell @evol-molly.bsky.social · 03/02/2026
Congratulations to Eilidh Ward (first author and PhD student co-supervised by co-authors Julie Aspden, David Westhead and yours truly) on this lovely contribution - a method to visually inspect reads from novel open reading frames: doi.org/10.1093/bioa...
doi.org
InspectorORF: a tool for visualising Ribo-Seq and additional genomic or transcriptomic data
AbstractMotivation. The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our u
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Liz Neeley @lizneeley.bsky.social · 03/02/2026
Reposting w/alt text. Iranians are experiencing collective trauma. Thousands have been killed/injured, the economy is crippled & the threat of a wider conflict is real. It’s especially difficult for those living in Iran, as many have lost (or fear losing) loved ones. www.nature.com/articles/d41...
Correspondence in NATURE - 03 February 2026
Calling all scientists: Support your Iranian colleagues
By Mohammad Hosseini 

Iranian researchers are in a difficult situation. Those in Iran face low wages, high inflation, sociopolitical instability, resource mismanagement, oppression by the authorities and longstanding international sanctions. High prices hinder conference attendance, as do difficulties obtaining visas. Unstable Internet connections, frequent power outages and lack of access to scholarly sources jeopardize collaborations. Scholars also have to contend with isolation, and sometimes biases, from the international community. And for those who work abroad, travelling to and from Iran is risky, even with visas and double citizenship.

Recent tensions have further exacerbated the situation. Scientists, in shock and distress, have condemned violence against civilians. Research requires focus, concentration and a calm state of mind - rare commodities in these times.

The international research community can support Iranian colleagues: send a message, show them that they are not forgotten. If your institutional policies allow it, try to work with researchers in Iran. International collaborations will help to build capacity there, strengthening civil society and enabling it to tackle systemic challenges.

There is no need to be a politician to engage in science diplomacy. Do not wait for big initiatives to build bridges. At this moment, Iranian researchers can benefit from kind gestures. Show solidarity.
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Lars Eicholt @lacholt.bsky.social · 03/02/2026
Slava is next! Also, check out the past seminars on Youtube. Link in the post below.
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Hassan uz Zaman @hassanzaman.bsky.social · 03/02/2026
Come one, come all to the first Protein Structure Evolution talk of the year (Feb 10)! Click here to register if you like cool science: tinyurl.com/prose-seminar2 Jointly organized by @lacholt.bsky.social, @caro-rocha.bsky.social, @claudiaalcar.bsky.social, @zachary-ardern.bsky.social and myself.
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Magnus Kjærgaard @proteinmagnus.bsky.social · 02/02/2026
Does targeting enzymes and substrates in a condensate lead to rate enhancement? No. Here, we investigate how the condensate environment can inhibit an enzyme reaction. Spoiler: Mass-transport limitations. We find a strong correlation between diffusion and reaction rates. doi.org/10.64898/202...
Graphical abstract of pre-print
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Genome Biology and Evolution @genomebiolevol.bsky.social · 03/02/2026
@ccasola.bsky.social, A. Owoyemi and @vakirlis.bsky.social test the hypothesis that many noncanonical proteins possess low stability in the cellular environment, finding that noncanonical proteins were enriched for degradation-related features. 🔗 doi.org/10.1093/gbe/evag009 #genome #evolution
doi.org
Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms
Abstract. The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of t
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Lars Eicholt @lacholt.bsky.social · 03/02/2026
I will never be able to unsee it again!
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Laurie Belcher @lauriebelch.bsky.social · 29/01/2026
Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)
biorxiv.org
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Klara Hlouchova lab @hlouchova-lab.bsky.social · 03/11/2025
Can proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v #ProteinDesign #OriginsOfLife
tinyurl.com
Ancient amino acid sets enable stable protein folds
Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...
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Nature Reviews Genetics @natrevgenet.nature.com · 29/01/2026
De novo genes arise from previously non-coding sequences. This evolutionary path — when randomly expressed sequences become folded and active proteins — challenges our understanding of genetic innovation. New Review by @bornberglab.bsky.social and @lacholt.bsky.social out now!
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