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Reposted by Carl M. Kobel

Javier Santoyo @jsantoyo.bsky.social · 24d

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

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Carl M. Kobel @cmkobel.bsky.social · 2d

Finally got my tool published!

Tominaga K. (tomiken) @pacyc184.bsky.social · 26d

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes | Bioinformatics | Oxford Academic https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf517/8254279?rss=1&login=true

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

AbstractSummary. Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates

dx.doi.org

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Reposted by Carl M. Kobel

Cameron Thrash @jcamthrash.bsky.social · Jul 17

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... #jcampubs

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Reposted by Carl M. Kobel

Cameron Thrash @jcamthrash.bsky.social · 26d

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes academic.oup.com/bioinformati... #jcampubs

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Reposted by Carl M. Kobel

Stephen Turner @stephenturner.us · Jul 19

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... 🧬🖥️ github.com/cmkobel/comp...

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

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

www.biorxiv.org

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Reposted by Carl M. Kobel

Center for Evolutionary Hologenomics @hologenomics.bsky.social · Dec 4

👏Today our new Section Head Thomas Pontén officially takes over after Head of Section Morten Limborg!

Thanks to Morten for all his work and welcome Thomas in your new important role!🤩

At today’s meeting Ostaizka introduces @hologen.bsky.social and Carl his #hologenomics tool CompareM2! 🦠💡
@dg.dk

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Reposted by Carl M. Kobel

Maciek Wiatrak @macwiatrak.bsky.social · Jul 21

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

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Reposted by Carl M. Kobel

Jennifer Goff, PhD @jlgoff.bsky.social · Feb 2

I want to expand on the extent to which IDEAA materials have been purged: I wrote an article last year for women’s history month on the history of women in antimicrobial development….DELETED.

Jennifer Goff, PhD @jlgoff.bsky.social · Feb 2

I’m on one of ASMs IDEAA committees and we have received 0 communication from ASM staff on why this is happening. I had to find out via social media. Extremely disappointing.

Cecilia Noecker @cecilianoecker.bsky.social · Feb 2

ASM website screenshots from the wayback machine in December '24 (web.archive.org/web/20241211...) vs today. Pretty disappointing!! 🧪

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Reposted by Carl M. Kobel

Phil B. Pope @microbesrule.bsky.social · Jan 20

Congratulations DR @cmkobel.bsky.social on the successful defense of your thesis 🙌🏼 Massive thanks to @hairyllama.bsky.social and @manuelkleiner.bsky.social for the time and your style which made the day all the more entertaining.

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Carl M. Kobel @cmkobel.bsky.social · Dec 8

Coining the term "rumen community types" (RCT)

Ove Øyås 🇺🇦 @oveoyas.bsky.social · Dec 8

New preprint out from @cmkobel.bsky.social, @velma-te-a.bsky.social, @microbesrule.bsky.social and many others! 📄

It's been very cool to follow and play a small part in this story: Carl and Velma found two distinct community types across omics layers in the cow rumen that are driven by protozoa 🐮👾

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 7

Protozoal populations drive system-wide variation in the rumen microbiome https://www.biorxiv.org/content/10.1101/2024.12.05.626740v1

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Reposted by Carl M. Kobel

Ove Øyås 🇺🇦 @oveoyas.bsky.social · Dec 8

New preprint out from @cmkobel.bsky.social, @velma-te-a.bsky.social, @microbesrule.bsky.social and many others! 📄

It's been very cool to follow and play a small part in this story: Carl and Velma found two distinct community types across omics layers in the cow rumen that are driven by protozoa 🐮👾

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Dec 7

Protozoal populations drive system-wide variation in the rumen microbiome https://www.biorxiv.org/content/10.1101/2024.12.05.626740v1

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Reposted by Carl M. Kobel

Ove Øyås 🇺🇦 @oveoyas.bsky.social · Oct 29

Hi Bluesky! 🦋

I am transitioning to this platform and will start posting here about my own and others' cool science! 🤩

Sad to say goodbye to science Twitter, but I can't keep using a platform that is being used to destroy democracy...

I'll be moving my old Twitter posts here in the coming days.

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Carl M. Kobel @cmkobel.bsky.social · Oct 2

My supervisor, @velma-te-a.bsky.social, is so cool!!!

Check out her talk on ciliate multi-omics, taking you through a history of science.

jams.org.au/index.php/ja...

Carl M. Kobel @cmkobel.bsky.social · Jul 18

Wow what a cool preprint!

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 17

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1

Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and a

www.biorxiv.org

Reposted by Carl M. Kobel

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 17

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1

Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and a

www.biorxiv.org

1

Reposted by Carl M. Kobel

Thea Os Andersen @theaosandersen.bsky.social · Jul 17

Dreaming of a one-stop-shop for analysing microbial genomes using all your favorite tools? Look no further, CompareM2 is out 🤩

Carl M. Kobel @cmkobel.bsky.social · Jul 16

Yay new version of CompareM2 (v2.8.2)
github.com/cmkobel/Comp...

- New "passthrough argument" feature to address any command line argument to any rule in the workflow.

#microbiology #bioinformatics #opensource #science #genomics

Release v2.8.2 · cmkobel/CompareM2

What's Changed Update README.md by @wwood in #102 New Contributors @wwood made their first contribution in #102 Full Changelog: v2.8.1...v2.8.2 2.8.2 Add --cite parameter to executable. New mo...

github.com

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Carl M. Kobel @cmkobel.bsky.social · Jul 17

And now the preprint is out!

www.biorxiv.org/content/10.1...

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

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

www.biorxiv.org

Carl M. Kobel @cmkobel.bsky.social · Jul 16

Yay new version of CompareM2 (v2.8.2)
github.com/cmkobel/Comp...

- New "passthrough argument" feature to address any command line argument to any rule in the workflow.

#microbiology #bioinformatics #opensource #science #genomics

Release v2.8.2 · cmkobel/CompareM2

What's Changed Update README.md by @wwood in #102 New Contributors @wwood made their first contribution in #102 Full Changelog: v2.8.1...v2.8.2 2.8.2 Add --cite parameter to executable. New mo...

github.com

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Reposted by Carl M. Kobel

Alex Crits-Christoph @acritschristoph.bsky.social · Jun 28

Microflora Danica: the atlas of Danish environmental microbiomes

10,686 shotgun metagenomes from a variety of environments across Denmark

www.biorxiv.org/content/10.1...

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Reposted by Carl M. Kobel

Mieke Roth 🟥 @miekeroth.com · Jul 11

So strange this doesn't get any attention. Anyhow, maybe adding an illustration works. This is the exact same model

A rendered model of a daphnia, seen diagonally from the side

A render of the model of the daphnia, seen head on

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Carl M. Kobel @cmkobel.bsky.social · Jul 11

Holo-omics review is out!

There are no animals - Only holobionts.

link: doi.org/10.1039/D4MO...

@oveoyas.bsky.social @microbesrule.bsky.social @jennymerkesvik.bsky.social @velma-te-a.bsky.social
#symbiosis #microbiology #holoomics #bioinformatics #science #openaccess

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Reposted by Carl M. Kobel

Chris Rinke @chrisrinke.bsky.social · Dec 15

Currently, we have the following open positions in the Rinke Group for Microbial MultiOmics and Biorecycling (MMOB) @ the University of Innsbruck, Austria:

1x postdoc
3x PhD
1x RA

More info @ rinkelab.org/index.php/op...

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Carl M. Kobel @cmkobel.bsky.social · Dec 6

Which style is better?

data %>%
mutate(type = "significant")

or

data %>%
mutate(type = "significant")

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Carl M. Kobel @cmkobel.bsky.social · Dec 5

Wouldn't it be better if R had a non-vector data type, then there would be no doubt distinguishing vectorized and non-vectorized functions?

Carl M. Kobel @cmkobel.bsky.social · Dec 5

Data science:
Is it bad if I have more comments than code?