🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

My ANDV #Hantavirus @nextstrain.org phylogenies now pull directly from @pathoplexus.org to incorporate all seqs I'll continue to improve them, & will keep them updated Change the Tip Labels in the left-hand menu. You can see links to all builds, plus tanglegrams at: nextstrain.org/groups/hodcr...

I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray). The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

Researchers Uncover Hidden Genetic World in Antarctic Waters "at least a third of the genes identified are missing from existing marine gene catalogs" @loimai.bsky.social #microbiome #oceans

Exciting new methane research: Huge credit to @annajwallenius.bsky.social & Andy Leu for using nifty bioinformatics to disentangle 8 novel MAGs of 'Candidatus Methanoborealis' This is version 1 of our #bioRxiv preprint. Aanalysis is ongoing & we welcome your feedback! doi.org/10.64898/202...

Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper: doi.org/10.1128/mbio...

New paper from my 2nd PostDoc is now published in The ISME Journal by @isme-microbes.bsky.social! #Sulfur disproportionation occurs globally across anoxic habitats & has multiple mechanisms of independent evolutionary origin academic.oup.com/ismej/advanc... #Bacteria #Microbes #Evolution #DeepSea

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/ Bonus: beautiful seascape and friendly spirit!

Antarctica InSync will host two webinars, bringing together the science community to discuss the draft White Papers currently available on our website. · 20 January, 17:00–19:00 (CET) · 21 January, 09:00–11:00 (CET) 📌 Register: lnkd.in/epX4_JiA 📝 Provide input to the draft papers: lnkd.in/eYfJgTUV

Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below

1/ The overturning circulation is a network of ocean currents transporting heat, carbon, oxygen and nutrients around the world. At the heart of this circulatory system is the global pumphouse of #Antarctica and the Southern Ocean. Animation: NASA-SVS

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....

www.nature.com/articles/s41... Thrilled to share our new study! We show that mirusviruses include lineages packed with spliceosomal introns and likely replicating in the nucleus of unicellular eukaryotes—a sharp contrast to most large and giant eukaryotic viruses that replicate in the cytoplasm.

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF

New GEOTRACES Science Highlight! 🌊 Long-range transport of iron via the #Agulhas Current and counter-current: a boon for the phytoplankton www.geotraces.org/long-range-t... Paper first authors: Eva Bucciarelli & Pierrick Penven, LEMAR #oceanscience #traceelements @scor-int.bsky.social

Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6

This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...

Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely. mcgill.wd3.myworkdayjobs.com/en-US/McGill...

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience