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

Roche Xpounds on New Sequencing Technology My deep dive on this exciting new entrant omicsomics.blogspot.com/2025/02/roch... 🧬🖥️

submitted 4 days ago • 1 comment

See our latest review about design trends, use, and limitations of Synthetic communities for plant health.

submitted 5 days ago • 0 comments

Landmark paper claxon! 'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting' www.medrxiv.org/content/10.1... Significant savings associated with proactive genomic epidemiology.

submitted 6 days ago • 4 comments

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

submitted 17 days ago • 2 comments

Dot plots are an effective (if old school!) way to visualise the pairwise comparison of genomes. For our recent pangenomics project (rdcu.be/d8PZ7), I wrote a small Python package to produce publication ready dot plots. Check it out! github.com/drboothtj/do... pypi.org/project/dotp... 🧪🧬🦠

submitted 18 days ago • 0 comments

See the numerous positions at Novonesis on bacterial and fungal strain development - in 🇩🇰 www.novonesis.com/en/careers/j...

submitted 28 days ago • 0 comments

Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal: www.jobs.ethz.ch/job/view/JOP... Closing date: 24th Feburary 🧪🧫🔬

submitted 29 days ago • 0 comments

Huge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀 Plus a whole bunch of updates for dorado polish and the odd misc bug fix. github.com/nanoporetech...

submitted 34 days ago • 1 comment

getphylo is finally official! Build phylogenetic trees directly from genbank files - at breakneck speed! I'd like to thank everyone who provided feedback and encourage you to continue. Improving getphylo doesn't stop now the paper is out! 1/5 🧪 bmcbioinformatics.biomedcentral.com/articles/10....

submitted 33 days ago • 2 comments

Have a look at @thombooth.bsky.social's #getphylo tool to build phylogenies! Thanks to @thombooth.bsky.social, Simon Shaw, @wemakemolecules.bsky.social (Pablo Cruz Morales) for the great collaboration @dtu.dk!

submitted 33 days ago • 0 comments

Has anyone seen this pattern before? @nanoporetech.com 10.4.1 flowcell (severely over warrenty..) on new #Mk1D. Pores get zapped at the first mux scan, and the remaining pores sequence at 200bps instead of 400bps, despite target temp? (also how can there be more failed reads than total reads?)

submitted 34 days ago • 1 comment

"Institut Pasteur has decided to leave X because of serious abuses observed on the platform... oppose[s] the campaign by Musk to weaken democracies and destabilize Europe's institutional foundations" www.pasteur.fr/en/home/pres...

submitted 39 days ago • 2 comments

Feeding 9 billion people will take lots of creativity and the best scientists. Check how Dr. Loes van Dam is working on new fungal foods are DTU biosustain. #DTU_BRIGHT www.euronews.com/health/2025/...

submitted 46 days ago • 0 comments

Have a look at our latest study on large-scale #Streptomyces BGC mining / pangenome analysis: genomebiology.biomedcentral.com/articles/10....

submitted 40 days ago • 1 comment

New pangenome of Streptomyces study out! I found the BGC synteny within species particularly interesting as it changes my view of what I thought was hybermobile chromosome ends: they don't seem to be changing that much or fast, mostly just certain groups picking up a few BGCs here and there.

submitted 40 days ago • 1 comment

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

submitted 45 days ago • 27 comments

Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans. With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!

submitted 48 days ago • 9 comments

I just made a first release of TNA - new tool to compare 2 bacterial genomes. Is shamelessly inspired by ACT, but should be simpler to use. Drag-n-drop two genomes: it runs BLAST for you and then you can visualize. For Mac, Windows 11, Linux tna.readthedocs.io

submitted 87 days ago • 9 comments

new lab member and a bunch of workhorses (on their makeshift heat sink) @nanoporetech.com

submitted 47 days ago • 1 comment

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

submitted 54 days ago • 2 comments

Christmas @CeMiSt: Streptomyces lonegramiae arrived! A picky strain substratewise, 11½ Mbp genome & 45 biosynthetic gene clusters (antiSMASH). Excited to discover more! Thanks @leibniz-dsmz.bsky.social @matissmaleckis.bsky.social @lingding.bsky.social @tuesparholt.bsky.social @Tilmann Weber @dg.dk

submitted 61 days ago • 0 comments

🎄 New Dorado release (v0.9.0) – and it's big! 🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka ⚡ Faster modified base calling models 🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling github.com/nanoporetech...

submitted 69 days ago • 2 comments

www.biorxiv.org/content/10.1... 🖥️🧬

submitted 69 days ago • 0 comments

To honour Lone Gram’s significant contributions to microbial secondary metabolite research, DSMZ researchers named the strain Streptomyces lonegramiae (DSM 41529) after her. Fun Fact: Gram's great-grandfather developed the Gram stain 😉 #herstory #HonoringWomenInSTEM #WomenInScience #microbiology

submitted 73 days ago • 2 comments

Excited to join the #Nanopore Community on BlueSky. Follow us for the latest updates and discussions about Oxford Nanopore and Nanopore Community. #WYMM

submitted 94 days ago • 2 comments

Check out this bombshell publication by Michael Fischbach @mfgrp.bsky.social and coworkers @stanford-chemh.bsky.social @stanfordmedicine.bsky.social, imagine a cancer immune therapy/vaccine where treatment begins and ends with a painless topical skin treatment! 🤯 www.nature.com/articles/s41...

submitted 75 days ago • 6 comments

Benchtop HiFi: PacBio Unveils Vega 🧬🖥️ omicsomics.blogspot.com/2024/11/benc...

submitted 109 days ago • 1 comment

Want to make beautiful scientific figures? Easy! The NIH released a library of 2000+ free scientific illustrations called BioArt. Check it out! bioart.niaid.nih.gov #AcademicSky #PsychSciSky 🧠🟦 🧪

submitted 117 days ago • 30 comments

Biotechnological & pharmaceutical potential of 28 novel type strains of Actinomycetes (incl. 23 Streptomyces species) from different environments worldwide. Proposed species names in honour of female scientists 👏 incl Lone Gram & Liz Wellington doi.org/10.1016/j.cr...

submitted 120 days ago • 0 comments

Belatedly checking out rrwick's take on the latest medaka release. I agree with the takes - hybracter by @gbouras13.bsky.social is fantastic. For post-assembly, I also just check the structures (plasmids etc) and use short reads for polish. rrwick.github.io/2024/10/17/m... 💻🧬

submitted 128 days ago • 1 comment

If you want to know why research.com rankings are completely insane, look no further than Microbiology

submitted 271 days ago • 0 comments

There's a ~1000nt sub-viral RNA that shows up on every continent, and in humans, and it seems to have gone unnoticed! It has no sequence similarity to any database and codes for a wacky protein Super happy to finally share my thesis work on "Obelisks" tinyurl.com/yc54fzj9 #MicroSky #microbiomesky

submitted 400 days ago • 2 comments

Have a look at our newest preprint: biorxiv.org/content/10.1.... We generated >1000 (mostly) actinomycetes high-quality genomes from our DTUBiosustain strain collection. Many thanks to everyone involved!

submitted 403 days ago • 0 comments

New manuscript is out on a scale new to me: We sequenced >1000 genomes, mostly complete, of filamentous Actinobacteria. With these, we can start asking questions like "How long are Streptomyces terminal inverted repeats" and get answers like this 🧬🖥️ #secmet.

submitted 404 days ago • 6 comments

First post on bluesky. Inevitably Streptomyces coelicolor, literally blue as the sky @stcmicrobeblog.bsky.social

submitted 453 days ago • 0 comments

Here is some recent work we've been doing at Cultivarium on detecting methylation patterns with nanpore. We find that nanopore's modified basecalling models works well - if you have recently sequenced a prokaryotic isolate you can use MicrobeMod to ID methylation: www.biorxiv.org/content/10.1...

submitted 467 days ago • 2 comments