iiinova — where your digital self keeps evolving

Reposted by Lars Podsiadlowski

Richard Merrill @dickmerrill.bsky.social · 22/04/2025

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.

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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 23/04/2025

#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

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Rob Waterhouse @rmwaterhouse.bsky.social · 20/04/2025

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

academic.oup.com

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

AbstractBackground. Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rap

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Joana Meier @joanameier.bsky.social · 24/02/2025

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.

docs.google.com

Darwin Tree of Life Impact Assessment

This form is used to share information within DToL about case studies, ongoing research, and funding awards that demonstrate the impact the Darwin Tree of Life consortium project has had on Global and...

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mara lawniczak @marakat.bsky.social · 14/04/2025

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...

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 18/04/2025

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads www.biorxiv.org/content/10.1101/202…

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Elias Dohmen @drdomain.bsky.social · 03/04/2025

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)

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Carola Greve @cgreve.bsky.social · 17/04/2025

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🙏!

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 01/02/2024

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.

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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 01/02/2024

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

github.com

GitHub - RILAB/mop: Simple tool for capturing alignment regions with sufficient quality for genotypi...

Simple tool for capturing alignment regions with sufficient quality for genotyping. - GitHub - RILAB/mop: Simple tool for capturing alignment regions with sufficient quality for genotyping.

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Princeton University Press @princetonupress.bsky.social · 27/11/2023

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

The Mind of a Bee
Lars Chittka
A rich and surprising exploration of the intelligence of bees

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Ed Yong is offline @edyong209.bsky.social · 15/11/2023

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...

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Christoph Bleidorn @cblei.bsky.social · 13/11/2023

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

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Katharina Hoff @katharinahoff.bsky.social · 07/11/2023

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...

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Genome Research @genomeresearch.bsky.social · 06/11/2023

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

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Jo Wolfe, PhD @jopabinia.bsky.social · 06/11/2023

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

circular timetree of 344 true crabs, colored by superfamily and with line drawings of representatives around the circle that makes it look like a zodiac/mandala

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Madlen Stange @mstange.bsky.social · 03/11/2023

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: meegene@leibniz-lib.de for the zoom link.

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Senckenberg Gesellschaft für Naturforschung @sgn.one · 26/10/2023

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

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Mikhail Kolmogorov @mishakolmogorov.bsky.social · 24/10/2023

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...

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Vaughn Cooper @vscooper.micropopbio.org · 21/10/2023

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...

biorxiv.org

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitiv...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Erik Garrison @thinks.lol · 23/10/2023

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.

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Jo Wolfe, PhD @jopabinia.bsky.social · 09/10/2023

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)

Phylogenetic relationships among the main families, superfamilies, and sections of “true” crabs or Brachyura.
Each color and letter (encircled) represents one of the nine major brachyuran evolutionary branches. Dromiacea (red) (A) and Homoloida (purple) (B) are first known from the Jurassic, while †Callichimaeroida section nov. (dark blue) (C), †Torynommoida (light blue) (D), †Etyoida (dark green) (E), Raninoida (light green) (F), †Dakoticancroida (yellow) (G), Cyclodorippoida (orange) (H), and Eubrachyura or “higher” brachyurans (brown) (I) are all first known from the Cretaceous. Thick solid lines represent the ages of the first and last occurrences of each family within the main lineages. Dotted lines and daggers indicate extinct taxa; solid lines indicate living taxa. Black triangles indicate that in Anomura, decarcinization has occurred twice (anomuran clades not illustrated). White triangles indicate the three Brachyura lineages where decarcinization has occurred

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Ellen O. Martinson @waspvenom.bsky.social · 18/10/2023

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)

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Jukka-Pekka Verta @jpverta.bsky.social · 19/10/2023

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

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Madlen Stange @mstange.bsky.social · 17/10/2023

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 meegene@leibniz-lib.de to get the login details.

Talk advertisement with a background picture of the savanna exposition of the Museum Koenig in Bonn Germany (Elephant to the right, Giraffe drinking from a well on the left, zebra on the left). Photo of Marilou Bodde on the right. Talk title: “Genomic monitoring of Anopheles mosquito populations". Via zoom on Tuesday October 24, 2023, 3pm CEST.

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Stephen Turner @stephenturner.us · 18/10/2023

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

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