Carl M. Kobel
@cmkobel.bsky.social
Personal webpage: cmkobel.github.io/
Current flagship: github.com/cmkobel/comparem2/
Current flagship: github.com/cmkobel/comparem2/
Reposted by Carl M. Kobel
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
September 18, 2025 at 11:15 AM
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Finally got my tool published!
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
October 9, 2025 at 6:22 PM
Finally got my tool published!
Reposted by Carl M. Kobel
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... #jcampubs
July 17, 2024 at 8:23 PM
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... #jcampubs
Reposted by Carl M. Kobel
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes academic.oup.com/bioinformati... #jcampubs
September 15, 2025 at 4:27 PM
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes academic.oup.com/bioinformati... #jcampubs
Reposted by Carl M. Kobel
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
July 19, 2024 at 9:30 AM
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes www.biorxiv.org/content/10.1... 🧬🖥️ github.com/cmkobel/comp...
Reposted by Carl M. Kobel
👏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
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
December 4, 2024 at 10:53 AM
👏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
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
Reposted by Carl M. Kobel
💥 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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
July 21, 2025 at 9:56 AM
💥 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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
Reposted by Carl M. Kobel
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.
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.
ASM website screenshots from the wayback machine in December '24 (web.archive.org/web/20241211...) vs today. Pretty disappointing!! 🧪
February 2, 2025 at 9:16 PM
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.
Reposted by Carl M. Kobel
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.
January 20, 2025 at 11:43 AM
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.
Coining the term "rumen community types" (RCT)
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 🐮👾
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 🐮👾
Protozoal populations drive system-wide variation in the rumen microbiome https://www.biorxiv.org/content/10.1101/2024.12.05.626740v1
December 8, 2024 at 9:39 AM
Coining the term "rumen community types" (RCT)
Reposted by Carl M. Kobel
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 🐮👾
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 🐮👾
Protozoal populations drive system-wide variation in the rumen microbiome https://www.biorxiv.org/content/10.1101/2024.12.05.626740v1
December 8, 2024 at 8:14 AM
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 🐮👾
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 🐮👾
Reposted by Carl M. Kobel
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.
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.
October 29, 2024 at 9:53 AM
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.
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.
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...
Check out her talk on ciliate multi-omics, taking you through a history of science.
jams.org.au/index.php/ja...
October 2, 2024 at 12:25 PM
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...
Check out her talk on ciliate multi-omics, taking you through a history of science.
jams.org.au/index.php/ja...
Wow what a cool preprint!
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1
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
July 18, 2024 at 7:25 AM
Wow what a cool preprint!
Reposted by Carl M. Kobel
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1
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
July 17, 2024 at 12:47 AM
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes https://www.biorxiv.org/content/10.1101/2024.07.12.603264v1
Reposted by Carl M. Kobel
Dreaming of a one-stop-shop for analysing microbial genomes using all your favorite tools? Look no further, CompareM2 is out 🤩
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
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
July 17, 2024 at 11:57 AM
Dreaming of a one-stop-shop for analysing microbial genomes using all your favorite tools? Look no further, CompareM2 is out 🤩
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
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
July 16, 2024 at 11:54 AM
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
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
Reposted by Carl M. Kobel
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...
10,686 shotgun metagenomes from a variety of environments across Denmark
www.biorxiv.org/content/10.1...
June 28, 2024 at 2:28 PM
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...
10,686 shotgun metagenomes from a variety of environments across Denmark
www.biorxiv.org/content/10.1...
Reposted by Carl M. Kobel
So strange this doesn't get any attention. Anyhow, maybe adding an illustration works. This is the exact same model
July 11, 2024 at 10:54 AM
So strange this doesn't get any attention. Anyhow, maybe adding an illustration works. This is the exact same model
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
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
July 11, 2024 at 2:12 PM
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
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
Reposted by Carl M. Kobel
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...
1x postdoc
3x PhD
1x RA
More info @ rinkelab.org/index.php/op...
December 15, 2023 at 6:27 AM
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...
1x postdoc
3x PhD
1x RA
More info @ rinkelab.org/index.php/op...
Which style is better?
data %>%
mutate(type = "significant")
or
data %>%
mutate(type = "significant")
data %>%
mutate(type = "significant")
or
data %>%
mutate(type = "significant")
December 6, 2023 at 12:29 PM
Which style is better?
data %>%
mutate(type = "significant")
or
data %>%
mutate(type = "significant")
data %>%
mutate(type = "significant")
or
data %>%
mutate(type = "significant")
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?
December 5, 2023 at 3:07 PM
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?
Data science:
Is it bad if I have more comments than code?
Is it bad if I have more comments than code?
December 5, 2023 at 2:27 PM
Data science:
Is it bad if I have more comments than code?
Is it bad if I have more comments than code?
Reposted by Carl M. Kobel
Our latest episode is with the amazing @carlbergstrom.com talking all things science studies and 'Calling Bullshit' on mis- and disinformation.
Thanks so much to Carl for joining us on the podcast while he was in Melbourne!
#STS #MetasSci #HistSTM #PhilSci #SciComm #SocialPsyc🧪
Thanks so much to Carl for joining us on the podcast while he was in Melbourne!
#STS #MetasSci #HistSTM #PhilSci #SciComm #SocialPsyc🧪
S2 Ep 9 - Carl Bergstrom on Science and Disinformation - The HPS Podcast - Conversations from Histor...
Today's guest is Professor Carl Bergstrom from the University of Washington. Carl has been touring Australia over the last few weeks and we were delighted when he agreed to join us while he was in Mel...
thehpspodcast.buzzsprout.com
December 4, 2023 at 9:17 PM
Our latest episode is with the amazing @carlbergstrom.com talking all things science studies and 'Calling Bullshit' on mis- and disinformation.
Thanks so much to Carl for joining us on the podcast while he was in Melbourne!
#STS #MetasSci #HistSTM #PhilSci #SciComm #SocialPsyc🧪
Thanks so much to Carl for joining us on the podcast while he was in Melbourne!
#STS #MetasSci #HistSTM #PhilSci #SciComm #SocialPsyc🧪