Lars Eicholt

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

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),

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

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...

A diagram of the evolution of whales, from land dwelling mammals to the ocean giants we know today.

Whale evolution makes me uncomfortable

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...)

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),

🚨 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/...

Thank you!

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

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...

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...

Slava is next! Also, check out the past seminars on Youtube. Link in the post below.

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.

Graphical abstract of pre-print

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...

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

@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

I will never be able to unsee it again!

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)

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...

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

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!

🧬 What does the starting material from which genes could emerge #denovo look like?
🌱 We used #RiboSeq to investigate the landscape of translated de novo ORFs in 3 #Arabidopsis species, and how they might be linked to gene birth!

📝 Check out our preprint here:
doi.org/10.1101/2025...

Read-only link here: rdcu.be/e09SM

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

Directors

The Max Planck Institute for Evolutionary Biology in Plön, Germany, seeks expressions of interest for open Max Planck Director positions. For details: http://www.evolbio.mpg.de/3856225/Directors. #job

I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning Abstract. Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. How

Alan's elegant work on evolutionary contrastive learning for understanding promoter regulatory logic out in @GeneticsGSA! academic.oup.com/genetics/art... Was really fun having him visit my lab for his sabbatical & work on this. New bucket list item: write a first-author paper as a PI!

Erich traveled to Berlin for the Schering Prize award ceremony, where he delivered the laudatio for Agnes Toth-Petroczy, this year’s recipient of the Schering Young Investigator Award. Warm congratulations to her!

Photo credits: Schering Stiftung/Michael Setzpfandt

Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉

In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria.

www.nature.com/articles/s41...

Postdoctoral Research Associates are sought for the GEvol project on evolutionary genomics. Candidates should have programming and data analysis skills. More info: https://g-evol.uni-muenster.de/open-positions/ #postdoc

Ending my PhD with a bang:
Face-to-face histones are important organizers of archaeal chromatin alongside classical histones.

www.biorxiv.org/content/10.6...

GBE | De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods

Grandchamp, @drdomain.bsky.social et al. publish a new Review on commonly used methods for de novo gene detection, address the limitations of nomenclature and detection methods, and establish a de novo gene annotation format to standardize reporting

🔗 doi.org/10.1093/gbe/evaf197

#genome #evolution

🚀We’re excited to share our new paper in Bioinformatics!

We introduce a user-friendly toolkit that implements our novel DeNoFo file-format for standardised annotation of de novo gene detection workflows — enabling reproducible methodology descriptions and easier dataset comparison across studies.

Join us tomorrow! Joana Pereira is talking about AI-powered classification and discovery across the protein universe. @joanampereira.bsky.social

5PM CET, link in the post and in our bio.