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

After two weeks, I'm finally done! In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches. thomvolker.github.io/blog/2506_re...

submitted 3 days ago • 7 comments

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI doi.org/10.1080/1949...

submitted 4 days ago • 0 comments

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

submitted 8 days ago • 5 comments

Suomi noussut OECD:n työttömyystilastoissa toiseksi. Ei tätä suhdanteella niin vain selitetä vaan kyseessä myös hallituksen talouspolitiikan epäonnistuminen (joka vielä pahentanut suhdannetta).

submitted 8 days ago • 4 comments

The rehabilitation room from clockwork orange but with 2025 science funding levels and PR teams

submitted 8 days ago • 0 comments

One simple way for people who are not well-versed in machine learning to evaluate the use of ML in clinical research: Replace "ML" with "logistic regression." If your reaction is: 1. Oh, that's confounded -> it's still confounded 2. Wow, how can you do that with logistic regression? -> keep reading

submitted 9 days ago • 1 comment

Laypeople often learn about science from expert explanations & those explanations often contain JARGON. Does jargon make explanations better or worse? In a paper out today in Nature Human Behaviour, @cruzf.bsky.social and I find that jargon can support illusions of understanding...

submitted 9 days ago • 12 comments

tää oli kunnon hv -haku, deadline välittömästi joululomien jälkeen ja hylsyt pari päivää ennen juhannusta. Tsemiä kaikille rannalle jääville.

submitted 9 days ago • 0 comments

Excellent paper in #MGen by Theo Ross, Kristin Hegstad and collaborators 'Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium' www.microbiologyresearch.org/content/jour...

submitted 9 days ago • 2 comments

Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster www.cell.com/cell-host-mi...

submitted 10 days ago • 1 comment

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

submitted 10 days ago • 3 comments

dude this party is such an echo chamber. it's just friends hanging out and chilling and having a good time. you need to invite some people over who want to kill you with hammers

submitted 10 days ago • 393 comments

"If SUVs were a country, they would rank as the fifth most polluting in the world" www.theguardian.com/world/2025/j...

submitted 10 days ago • 0 comments

"simulation of up to 44 qubits using [...] 4096 GPGPUs across 1024 nodes" don't have a quantum computer? np just brute force algorithm fiqci.fi/_posts/2025-...

submitted 10 days ago • 0 comments

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

submitted 11 days ago • 3 comments

A monumental collaborative effort with many incredible people ☺️ Proud to be part of this!

submitted 11 days ago • 0 comments

ish is a grep-like CLI tool that uses optimal alignment instead of exact matching. It’s record-type aware, supporting line, FASTA, and FASTQ records. Built in Mojo as a proof of concept for bioinformatics. 🧵1/5

submitted 12 days ago • 1 comment

Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field. rdcu.be/epoRR @blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.

submitted 17 days ago • 3 comments

"Relatively little attention is given to critical LMIC issues, such as reducing infection burden, antibiotic overuse in livestock farming, prescribing practices among primary care providers, and developing affordable, rapid diagnostic tests for detecting #AMR" www.cell.com/trends/micro...

submitted 17 days ago • 0 comments

Today is #WorldBicycleDay 🚲 Did you know❓ Cycle lanes count for just 0.2% of the current road infrastructure. It’s time to demand safer streets that put the health & safety of pedestrians and cyclists first 👉bit.ly/4jPzXsa

submitted 18 days ago • 9 comments

🚨 Very excited to finally say… 🚨 The story of Noodlococcus - the contaminant that started ContamClub - is available to read 📖🍜🦠 Check it out ➡️ doi.org/10.1101/2025... 1/15 🧵

submitted 19 days ago • 1 comment

Hälyttävää, että Suomi on Euroopan suurin nousija lasten köyhyys- ja syrjäytymisriskissä. Indikaattori perustuu kolmeen tekijään: pienituloisuus, vajaatyöllisyys, aineellinen puute. Suomen kehitystä ajaa erityisesti vajaatyöllisyys ja aineellinen puute. (1/3) ec.europa.eu/eurostat/en/...

submitted 19 days ago • 7 comments

'Incidence, case-fatality rates and risk factors of bloodstream infections caused by Escherichia coli, Klebsiella species and Pseudomonas aeruginosa, England, April 2017 to March 2022' pmc.ncbi.nlm.nih.gov/articles/PMC...

submitted 21 days ago • 0 comments

"favorably altered stool microbiome" What can favorably altered even mean, if not stated in terms of benefit to patient focused outcomes? This entire field of full this kind of conguring of "benefit"

submitted 21 days ago • 5 comments

“A program is a shared mental construct that lives in the minds of the people who work on it. If you lose the people, you lose the program. The code is merely a written representation of the program, and it's lossy, so you can't reconstruct a program from its code.” gist.github.com/onlurking/fc...

submitted 21 days ago • 1 comment

New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found… → 800+ MAGs → 11,000+ BGCs → and still nowhere near saturation. Soil is wild. Preprint here: www.biorxiv.org/content/10.1... #microbiome #metagenomics #BGCs #naturalproducts #secmet

submitted 22 days ago • 2 comments

why, yes, of course I want to buy 7000 kg of antibiotics

submitted 22 days ago • 0 comments

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO gbintk.readthedocs.io/en/latest/

submitted 22 days ago • 1 comment

🚨 Out now! Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻 @travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org #MicroSky 🦠 #MicrobiomeSky www.nature.com/articles/s41...

submitted 46 days ago • 0 comments

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

submitted 24 days ago • 5 comments

HMMER is the bedrock of genomic annotation globally, and now its funding is terminated for no reason. @cryptogenomicon.bsky.social is now on bsky:

submitted 24 days ago • 2 comments

I started tgv to learn Rust and building it has been unbelievably fun! If you wanna pick up a super fast and fun programming language, tgv is open for contribution! There aren't many bioinformatics tools built entirely by the community. If tgv can become one, I'll be so psyched

submitted 24 days ago • 1 comment

JOBS ALERT! PhD position & 3-y postdoc position in statistics within my research group at @ocbe.bsky.social @uio.no Both are linked to a project funded from the Research Council of Norway on Integrative Bayesian clustering for high-dim data in omics Deadline: 13 June 2025 More info & links below!

submitted 24 days ago • 1 comment

they found the pet café E. coli (wonder whether these are just common STs in the area rather than preferential pet café regular colonizers) www.microbiologyresearch.org/content/jour...

submitted 24 days ago • 0 comments

(1/6) 🌟 Excited to share our new paper! Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠 This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024. 🔗 www.microbiologyresearch.org/content/jour...

submitted 25 days ago • 2 comments

Movi Color: fast and accurate long-read classification with the move structure https://www.biorxiv.org/content/10.1101/2025.05.22.655637v1

submitted 25 days ago • 0 comments

📢 Attention all phage-interested: the WHO has just release its first report on phages! This report highlights key insights from expert consultations, webinars, and a dedicated workshop in Tbilisi, Georgia. Read report here ➡️ www.who.int/europe/publi...

submitted 25 days ago • 1 comment

Academia in 2025: For weeks I’ve been working through botched copy-edits of my monograph, outsourced by the publisher to a company I’d never heard of, until it finally dawned on me the terrible job might be AI. A quick search confirmed the company recently launched new AI software, which now means..

submitted 25 days ago • 80 comments

Hankehakemus ja paperi lähetetty & ulkona +10 ja sataa, juhannusfiilis tuli kuukauden etuajassa

submitted 25 days ago • 0 comments

📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8

submitted 25 days ago • 1 comment

New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo. We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries. www.biorxiv.org/content/10.1...

submitted 26 days ago • 2 comments