xabivc.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Awesome GUI for ClipKit. Use this application to get rid of your ambiguous regions when setting up Phylogenetic analysis! academic.oup.com/nar/advance-...

submitted 8 days ago • 1 comment

Excited to share new research led by our very own @lingdong-shi.bsky.social showing that many archaeal 23S rRNAs are circularized in active ribosomes. Check out the preprint below.

submitted 5 days ago • 0 comments

Effects of soluble electron shuttles on microbial iron reduction and methanogenesis journals.asm.org/doi/full/10.... #jcampubs

submitted 6 days ago • 0 comments

As I might have said 27 years ago if there was social media: ANNOUNCING GCUA: General Codon Usage Analysis. I published first version in 1999 & I wrote it in C. The current version is written in python and has a few more bells and whistles, particularly plotly visualizations github.com/mol-evol/gcua

submitted 6 days ago • 3 comments

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

submitted 6 days ago • 5 comments

Virus species names have been standardized; virus names remain unchanged journals.asm.org/doi/full/10.... #jcampubs

submitted 10 days ago • 0 comments

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

submitted 8 days ago • 4 comments

Feliç #SantJordi! In Catalunya, today we celebrate love, literature and dragons, exchanging books and roses🐉 🌹 📖 . Honoring the dragon of the legend of Sant Jordi, today’s #Midweekmicrobe is Dracomyxa pallida, a giant ameboid freshwater foraminifer #ProtistsOnSky 📷 Wylezich et al. 2014

submitted 11 days ago • 1 comment

Engineering bacteriophages through deep mining of metagenomic motifs www.science.org/doi/full/10.... #jcampubs

submitted 13 days ago • 0 comments

GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.

submitted 16 days ago • 0 comments

Resuscitation-promoting factor (Rpf) terminates dormancy among diverse soil bacteria #mSystems by @jaytlennon.bsky.social et al journals.asm.org/doi/10.1128/...

submitted 17 days ago • 0 comments

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2

submitted 17 days ago • 3 comments

Release 10-RS226 (16th April 2025) GTDB - Genome Taxonomy Database https://gtdb.ecogenomic.org/

submitted 18 days ago • 0 comments

Microbial oxidation of short-chain gaseous alkanes www.nature.com/articles/s41... #jcampubs

submitted 19 days ago • 0 comments

Bacterial operons may persist in eukaryotes (e.g. fungi) after horizontal gene transfer, according to Kogay et al. Operon-derived gene pairs suggest initial neutral retention and later functional integration or degeneration. 🔗 doi.org/10.1093/gbe/... #NewPaperAlert #genome #evolution #fungi

submitted 19 days ago • 0 comments

#GenomeWatch: Cellular souvenirs in viral luggage by Yumary Vasquez Recent findings of cellular-like genes in giant viruses show how these viruses acquire and repurpose host cellular machinery, in @naturerevmicro.bsky.social: rdcu.be/ehIdE 🖥️🧬🦠🧪

submitted 20 days ago • 0 comments

New preprint! We developed a fast method that allows the use of hybridization capture workflows with @nanoporetech.com without additional ligation-based steps! We validated our method using targeted viral metagenomics @twistbioscience.com and Viral WGS @Agilent www.medrxiv.org/content/10.1...

submitted 23 days ago • 0 comments

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data journals.asm.org/doi/full/10.... #jcampubs

submitted 23 days ago • 0 comments

wgatools: an ultrafast toolkit for manipulating whole-genome alignments academic.oup.com/bioinformati... 🧬🖥️🧪 written in Rust github.com/wjwei-handso...

submitted 21 days ago • 0 comments

Shaken not stirred: Effect of different mixing modes during the cultivation of methanogenic pure cultures www.sciencedirect.com/science/arti... #OpenAccess #archaea #MicroSky

submitted 24 days ago • 0 comments

If you use Kraken for profiling microbial / environmental / ancient metagenomic data, please check this preprint where I benchmark filtering strategies of Kraken outputs on simulated microbial and environmental metagenomic samples, and provide recommendations for optimal filtering thresholds

submitted 24 days ago • 4 comments

Fast protein structure searching using structure graph embeddings academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/greener-grou... "accuracy comparable to the best current methods and can search the AlphaFold database TED domains in a 10th of a second per query on CPU"

submitted 24 days ago • 1 comment

We present MetaFlowTrain, an easy-to-build, highly parallelized, and cost-effective fluidic system for studying microbial exometabolites and their roles in modulating microbe–microbe–host interactions. Kudos to @chesneau-g.bsky.social @mpipz.bsky.social Give it a try: www.nature.com/articles/s41...

submitted 24 days ago • 7 comments

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

submitted 24 days ago • 2 comments

Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.microbiologyresearch.org/content/jour... #jcampubs

submitted 25 days ago • 1 comment

CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/wwood/coverm

submitted 25 days ago • 0 comments

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

submitted 25 days ago • 11 comments

Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) from Archaea onlinelibrary.wiley.com/doi/abs/10.1...

submitted 28 days ago • 0 comments

How #genome-wide sequence divergence maps to species status www.pnas.org/doi/10.1073/... #biodiversity #genomics

submitted 28 days ago • 1 comment

AI for research: the ultimate guide to choosing the right tool www.nature.com/articles/d41...

submitted 27 days ago • 0 comments

Biological molybdenum usage stems back to 3.4 billion years ago https://www.biorxiv.org/content/10.1101/2025.04.02.646658v1

submitted 28 days ago • 0 comments

"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...

submitted 87 days ago • 9 comments

Anaerobic degradation of polycyclic aromatic hydrocarbons journals.asm.org/doi/full/10.... #jcampubs

submitted 31 days ago • 1 comment

Sketch, capture and layout phylogenies www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/husonlab/phy...

submitted 31 days ago • 0 comments

A database of structures for ecologically relevant microbial traits - Looks cool - here's the github: github.com/timghaly/Eco...

submitted 31 days ago • 1 comment

Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons @shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...

submitted 32 days ago • 6 comments

We've identified a group of nucleases that can target multiple phages with hypermodified DNA, using a sensor domain present across many domains of life. We’ve even used this as a tool to find phages with hypermodified DNA! Really thankful to all the co-authors who have been such great help!

submitted 32 days ago • 1 comment

Adding to my list of unusual collaborations.... www.nature.com/articles/s41...

submitted 34 days ago • 0 comments

Metabolic Diversity and Adaptation of Carbon-Fixing Microorganisms in Extreme Glacial Cryoconite academic.oup.com/ismecommun/a... #jcampubs

submitted 34 days ago • 0 comments

Current trends in electromicrobiology of methane oxidation www.cell.com/trends/micro... #jcampubs

submitted 34 days ago • 1 comment

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

submitted 34 days ago • 2 comments

wow, telomeric transposons in bacteria with linear chromosomes! (of course this was first figured out in flies, inc by Bob Levis, who i was happy to see few days ago at the fly meeting). 🪰 www.science.org/doi/10.1126/... www.sciencedirect.com/science/arti... www.sciencedirect.com/science/arti...

submitted 38 days ago • 0 comments

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them? If so, you might this little project: github.com/rrwick/conda...

submitted 38 days ago • 1 comment