Really excited that our DFG grant on the Speciation Genomics of Eye Size variation in *Heliconius* has been funded :) In the next weeks, I will post an advert for a PhD, but if you know of good students, please suggest they get in touch. Please repost.

#ERGAReads | Thinking of sequencing a genome in your lab? 🧬 This review offers practical guidance on how to start a #genome project for non-model species - covering DNA extraction, sequencing tech, costs, and more! 🔗 rdcu.be/eiHRG @sgn.one @leibnizlib.bsky.social #biodiversity #genomics

Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...

Here we describe the motivations and methods behind our #A3Cat resource - Arthropoda Assembly Assessment Catalogue (website here: a3cat.unil.ch) academic.oup.com/gigascience/... currently with 7'321 #arthropod #genome assemblies

Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.

if you are trying to get HMW DNA out of any species, have a look at the stellar progress from Sanger Tree of Life core lab who have now extracted DNA from 1000s of species. Paper showcasing things learned along the way now up on bioRxiv at www.biorxiv.org/content/10.1...

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. #TelomericRepeats #AssembledGenomces #LongReads #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1

To support genome structure studies in non-model systems, we developed SyntenyFinder, a synteny analysis pipeline combining OrthoFinder and RIdeogram. Learn more on our GitHub: github.com/symgenoevola...

De novo genes research community 🧬 - please consider using for your future or past work our new methodology annotation format for better comparability of studies and higher reproducibility. (1/3)

Still no reading material for the Easter break🌞🌻🐰? Then I have a suggestion: "Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide" (lnkd.in/dsRmSBDE). It was a pleasure to work on this new publication with TilmanSchell & @lpodsiadlowski.bsky.social🙏!

Gonna write a paper on this. PLEASE DON'T USE VCFTOOLS TO CALCULATE π. It is a random number generator, as the software assumes all bp that aren't SNPs are invariant (i.e. ignores missing data). This is especially bad in plant genomes, with abundant TEs where you can't map reads.

You need to use PIXY with a gvcf, ANGSD with genotype likelihoods, or MOP to estimate the number of bp with data in each window to use as a denominator. pixy.readthedocs.io www.popgen.dk/angsd/index.... github.com/RILAB/mop

Transmissible cancer in marine mussels. On depth study this week on the cover of @NatureCancer

Discover what it's like to be a #bee from author Lars Chittka in today's Ideas post. press.princeton.edu/ideas/what-i... #Science #Nature #bees #AnimalBehavior

Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells https://www.biorxiv.org/content/10.1101/2023.11.21.567988v1

Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads https://www.biorxiv.org/content/10.1101/2023.11.21.568046v1

Cool journals.plos.org/plosbiology/...

A large-scale assessment of sequence database search tools for homology-based protein function prediction https://www.biorxiv.org/content/10.1101/2023.11.14.567021v1

In my latest newsletter, I'm excited to announce my 3rd book! THE INFINITE EXTENT. A book about life at different scales--of size, time, geography, longevity, connectivity, individuality, & more. I see it as the conclusion of a trilogy of books. More details: buttondown.email/edyong209/ar...

The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education onlinelibrary.wiley.com/doi/10.1002/...

A major change in the BRAKER genome annotation world: The GeneMark-Team changed the license of GeneMark (thank you so much!!!). There is no more need to install a license key file. Also GeneMark-ETP has improved stability due to their efforts. github.com/Gaius-August...

Call for Papers! Genome Research is now encouraging submissions for a Special Issue on Long-read DNA Sequencing Applications in Biology and Medicine, Guest Edited by Ana Conesa, Alexander Hoischen, and Fritz Sedlazeck @sedlazeck.bsky.social. bit.ly/grcallforpapers #longreads #T2T #ASHG23

Today we publish a new paper on a molecular phylogeny of true crabs. We find crabs transitioned from marine to non-marine environments 7-17x over 100+ myr! This culminates 15+ years(!) of effort from an international team! 1/4 (thread in replies) academic.oup.com/sysbio/advan... 🧪🦀🦑#evosky

Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution https://www.biorxiv.org/content/10.1101/2023.11.01.564642v1

We are happy to host Dario Valenzano @valenzanolab from @LeibnizFLI for our next #MeeGene @Leibniz_LIB seminar on Tuesday 07.11.2023 15h CET. He will talk about "Evolutionary ecology of aging". If you like to join, drop us an email: [email protected] for the zoom link.

Influence of social lifestyles on host–microbe symbioses in the bees 🦠 onlinelibrary.wiley.com/doi/10.1002/...

Back to sequences: find the origin of kmers https://www.biorxiv.org/content/10.1101/2023.10.26.564040v1

Juchu! Forschungsteam mit Senckenberg-Genomiker Prof. Michael Hiller erhält ERC Synergy Grant 2023 in Höhe von 12 Mio €! 🥳💐 Das Projekt „BATPROTECT“ erforscht Langlebigkeit und Krankheitsresistenz von Fledermäusen.🦇🧬 Ziel: Grundlagen für künftige Therapeutika.💊 👉 sgn.one/sxv 📷 San Martin/Wikimedia

Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...

The hacked the @nanopore sequencer to read amino acids and PTMs along protein strands. This opens up the possibility for barcode sequencing at the protein level for highly multiplexed assays, PTM monitoring, and protein identification 🧬🧪🤯 www.biorxiv.org/content/10.1...

We can end all of this. It's time for a completely open publication system. Like a preprint server, but with reviews. A system supporting these two things at once is a journal. At least, it replaces a journal with something better.

More crab evolution myth busting even though I got ratioed on my own research last time. 🧪🦀 Carcinization is not inevitable! Crab bodies have been LOST multiple times going back to elongated forms! Best illustrated by triangles in this figure by my colleague Javier Luque (paper link in next post)

Skimming genomes for systematics and DNA barcodes of corals https://www.biorxiv.org/content/10.1101/2023.10.17.562770v1

MOAL: Multi-Omic Analysis at Lab.A simplified methodology workflow to make reproducible omic bioanalysis. https://www.biorxiv.org/content/10.1101/2023.10.17.562686v1

Hello everyone! I'm Ellen Martinson! I'm an assist prof at University of New Mexico. I study parasitoid wasp venom and galling insects trying to unravel the molecular mechanisms behind species interactions. I'm looking for grad students and a postdoc, so please RT (or whatever the phrase is here)

Rapid adaptation - how fast and how parallel? Really cool @markcbitter.bsky.social @petrovadmitri.bsky.social & co !

One more week until our first #MeeGene seminar of this fall semester: come and join us on zoom next Tuesday (October 24, 3pm CEST) and listen to Marilou Bodde from the Sanger Institute talking about #Anopheles #genomic #monitoring. Drop us an email at [email protected] to get the login details.

BTR: A Bioinformatics Tool Recommendation System www.biorxiv.org/content/10.1... github.com/ryangreenj/b...