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Daan Speth

@daanspeth.bsky.social

1.8K followers 1.8K following 264 posts

Computational microbiologist. Senior scientist at @cemess.bsky.social, @univie.ac.at. Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology. Maintainer of the GlobDB genome database globdb.org

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Daan Speth @daanspeth.bsky.social · 25/03/2026

We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵

Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories

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Daan Speth @daanspeth.bsky.social · 02/03/2026

CUGO (colocated unidirectional gene organization) can be used to investigate and visualize consensus genomic context of protein sequences in a dataset. The CUGO plots can capture consensus genomic context of tens of thousands of sequences in one go. 4/

Example CUGO plot. See AASTK documentation (https://globdb.org/aastk) for details

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Daan Speth @daanspeth.bsky.social · 02/03/2026

PASR (Protein alignment score ratio) can be used to find sequences of interest in a dataset, or create a reference database of a protein of interest. 3/

Example PASR plot. See AASTK documentation (https://globdb.org/aastk) for details

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Daan Speth @daanspeth.bsky.social · 02/03/2026

CASM (clustering alignment score matrix) is a tool designed to find structure in large protein datasets (eg >100k sequences of a complex superfamily). It can be used to cluster such datasets, visualize them in 2D, and annotate with available metadata (see below). 2/

Example CASM plot. See AASTK documentation (https://globdb.org/aastk) for details

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Daan Speth @daanspeth.bsky.social · 10/09/2025

Congrats to Nils Ganzwohl and Carolin Otersen for winning the Poster prizes at the 28th European Nitrogen Cycle meeting #ENC28

prize winner Nils Ganzwohl with the ENC28 organizing committee

prize winner Carolin Otersen with the ENC28 organizing committee

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Daan Speth @daanspeth.bsky.social · 08/03/2025

joined the march for science in vienna yesterday, in support of and in solidarity with the many colleagues in the US

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Daan Speth @daanspeth.bsky.social · 24/09/2023

On point, and it also shows that methods I've used don't make it into abstracts much. from here: shiny.rcg.sfu.ca/u/r... by @morinryan.bsky.social 🧬🖥️🦠

word cloud of pubmed abstracts with Daan Speth as a co-author. The words "bacteria", "anammox", and "methane" feature most prominently

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