Lars Eicholt
lacholt.bsky.social
Lars Eicholt
@lacholt.bsky.social
molecular evolution.
Pinned
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...
Reposted by Lars Eicholt
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...
February 11, 2026 at 6:18 PM
Reposted by Lars Eicholt
Whale evolution makes me uncomfortable
February 9, 2026 at 7:48 PM
Reposted by Lars Eicholt
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...)
February 8, 2026 at 6:29 PM
Reposted by Lars Eicholt
🚨 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/...
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),
doi.org
February 9, 2026 at 8:21 AM
Reposted by Lars Eicholt
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...
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
doi.org
February 3, 2026 at 3:38 PM
Reposted by Lars Eicholt
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...
February 3, 2026 at 2:36 PM
Slava is next! Also, check out the past seminars on Youtube. Link in the post below.
Next up in our ProSE seminar series: Vyacheslav Tretyachenko on alternative translation in the human proteome
Register to join: tinyurl.com/prose-seminar2
Past seminars: tinyurl.com/ProSE-videos
February 3, 2026 at 4:09 PM
Reposted by Lars Eicholt
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.
February 3, 2026 at 2:40 PM
Reposted by Lars Eicholt
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...
February 2, 2026 at 2:25 PM
Reposted by Lars Eicholt
@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
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
doi.org
February 3, 2026 at 9:23 AM
Reposted by Lars Eicholt
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)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Reposted by Lars Eicholt
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
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...
tinyurl.com
November 3, 2025 at 4:48 PM
Reposted by Lars Eicholt
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!
January 29, 2026 at 10:54 AM
Reposted by Lars Eicholt
🧬 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...
Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis
Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, still very little is known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from the closely related species Arabidopsis halleri, A. lyrata and A. thaliana and characterized genome-wide patterns of translation across them. Synteny analysis revealed 211 Open Reading Frames (ORFs) that have emerged de novo within the Arabidopsis genus and already exhibit signs of active translation. Most of these de novo translated ORFs were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved Coding DNA Sequences (CDS), and their GC content increased with phylogenetic conservation. While most of them were located in intergenic regions and are thus newly discovered, 34 were previously annotated as CDS in at least one genome, and are promising putative genes. Our results demonstrate the abundance of translation events outside of conserved CDS, and their role as starting material for the emergence of novel genes in plants. ### Competing Interest Statement The authors have declared no competing interest. Université de Lille, https://ror.org/0546v5182
doi.org
January 20, 2026 at 10:58 AM
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...
January 28, 2026 at 6:23 PM
Reposted by Lars Eicholt
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
Directors
www.evolbio.mpg.de
January 18, 2026 at 9:27 AM
Reposted by Lars Eicholt
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
Fullfabric :: AITHYRA-CeMM PhD
apply.cemm.at
January 8, 2026 at 10:48 AM
Reposted by Lars Eicholt
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!
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
academic.oup.com
January 7, 2026 at 9:35 PM
Reposted by Lars Eicholt
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
December 12, 2025 at 10:43 AM
Reposted by Lars Eicholt
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...
December 13, 2025 at 8:09 AM
Reposted by Lars Eicholt
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
Open Positions – GEvol – DFG SPP 2349
Open Positions – GEvol – DFG SPP 2349
g-evol.uni-muenster.de
December 3, 2025 at 3:32 PM
Reposted by Lars Eicholt
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...
December 8, 2025 at 8:01 AM
Reposted by Lars Eicholt
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
November 19, 2025 at 11:48 AM
Reposted by Lars Eicholt
🚀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.
November 12, 2025 at 12:41 PM
Reposted by Lars Eicholt
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.
The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven)
🗓️ November 11th, 5pm CET

Registration is now open: tinyurl.com/prose-seminar2
Please share!
November 10, 2025 at 2:00 PM