Mastodawn

Falk Hildebrand Feb 19, 2023

Finally got around to documenting "custom reference databases" when assigning tax to your ASVs/OTUs in LotuS2: https://github.com/hildebra/lotus2
Hope over the next weeks I can extend a bit the different extra functions that LotuS2 has (few documented so far)

GitHub - hildebra/lotus2: Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS. - GitHub - hildebra/lotus2: Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

GitHub

Falk Hildebrand Dec 19, 2022

Dan Dec 18, 2022

The most comfortable way to connect with your #Twitter friends on #Mastodon:
https://movetodon.org
It only takes a click and you follow them on Mastodon. #twittermigration made easy!

Movetodon: Finds your Twitter Friends on Mastodon

Falk Hildebrand Dec 19, 2022

Zach Reitz Dec 19, 2022

I'm pleased to announce that antiSMASH can now predict if an NRPS BGC produces a metallophore!

Check out our new preprint for all the details:
https://www.biorxiv.org/content/10.1101/2022.12.14.519525v1

I tested the new algorithm on 15k bacterial genomes. NRP metallophores make up an astounding 25% of all NRPS BGCs! This thread will have some more highlights.

Test it out on the antiSMASH website and let me know what you think!
https://antismash.secondarymetabolites.org/#!/start
(You may have to clear your cache for "Enable antiSMASH beta" to appear)

Falk Hildebrand Dec 2, 2022

PLOS Biology Dec 2, 2022

.@RalserLab identifies a new H2S utilizing enzyme, Hsu1p, that recycles hydrosulfide & helps growth under #sulfur limitation, allowing #yeast to overcome Met17 #auxotrophy when grown in high density, revealing cell-cell metabolic interactions #PLOSBiology https://plos.io/3B2vWvY

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

In yeast, Met17p deletion induces the overflow of hydrosulfide ions due to methionine auxotrophy. This study identifies a new H2S utilizing enzyme, Hsu1p, that recycles hydrosulfide and confers a growth advantage under sulfur limitation; Hsu1p allows the cells to overcome methionine auxotrophy when grown in high density, underscoring the importance of cell-cell metabolic interactions.

Falk Hildebrand Nov 19, 2022

Stephen Fry Nov 18, 2022

Do watch this to the end

#Qatar #LGBTQ #football #worldcup

Falk Hildebrand Nov 11, 2022

Peter Sunde Kolmisoppi Nov 7, 2022

One lesson from moving between social networks is that we should maybe stop using phrases that are part of a brand. "Tweeting" or for that matter "Tooting". How about "writing" or something else non-brand related?

Falk Hildebrand Nov 9, 2022

I wanted to advertise a postdoc position in beautiful Norwich, that is for 3+2 years.
We are looking for a bioinformatician, or someone who wants to become one. In the post we will investigate gut metagenomes using 3rd gen sequencing, deep learning, to investigate pan genomes and microbial adaptation, mostly using human gut time series of various host ailments.

Please retoot or send to interested parties, thanks!
https://www.earlham.ac.uk/vacancy/postdoctoral-research-scientist-bioinformatics-hildebrand?utm_campaign=Oktopost-Vacancy%3A+Postdoctoral+Research+Scientist+%28Bioinformatics%29&utm_content=Oktopost-004p8kfdl68ecc6&utm_medium=social&utm_source=twitter

Postdoctoral Research Scientist (Bioinformatics)

Earlham Institute

Falk Hildebrand Nov 8, 2022

Hey, I am a group leader at the Quadram & Earlham Institutes in Norwich, UK. My interests are developing metagenomic bioinformatics, human gut microbiome, how we can better dissect strains of bacteria in these and how they evolve with their maturing host. Just text me for any further questions! Oh and this is my group's webpage: www.falk.science

Falk Hildebrand Nov 3, 2022

We have funding for two exciting PhD projects, apply if this sounds like your project (by 21st Nov `22):
"Too rare to see? Investigating microbes overlooked by metagenomics"
https://biodtp.norwichresearchpark.ac.uk/projects/too-rare-to-see-investigating-microbes-overlooked-by-metagenomics/?utm_content=buffer3565e&utm_medium=social&utm_source=facebook.com&utm_campaign=buffer

AND
"Deep learning assisted metagenomics to explore microbiomes"
https://biodtp.norwichresearchpark.ac.uk/projects/deep-learning-assisted-metagenomics-to-explore-microbiomes/?utm_content=buffer1d5d9&utm_medium=social&utm_source=linkedin.com&utm_campaign=buffer

Too rare to see? Investigating microbes overlooked by metagenomics | Doctoral Training Partnership

Microbial communities consist of thousands of species, some abundant but most actually very rare.

Doctoral Training Partnership