Key questions about the early evolution of archaea remain unanswered. Here, Huang et al. use improved methods of genome evolution to propose a euryarchaeal root for archaea, a methanogenic ancestor, a...

Most bacterial phyla have few or no representatives in pure culture. Here, Hedlund et al. isolate two new species within the phylum Atribacterota with unique cell biological features. In addition, the...

Abstract. Environmental genomics has led to the discovery of many new lineages of archaea, including “DPANN” (or Nanobdellati), comprising organisms with s

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

Long-read sequence assemblies from metagenomes contain frequent errors.

UNIVERSITY OF REGENSBURG   The Faculty of Biology and Pre-Clinical Medicine invites applications for a   Professurship (W2) in Microbiology   To be...

The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...

Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

The detectCores() function of the parallel package is probably one of the most used functions when it comes to setting the number of parallel workers to use in R. In this blog post, I’ll try to explai...

a blog for miscellaneous bioinformatics stuff

The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…

Wissenschaft/Forschung in Jena

Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

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Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered hallmarks of organelles necessary for stable integration...

Bioinformatician, Department of Organismal Biology, Uppsala University

Cultivation-independent techniques have facilitated the discovery of a diversity of thus far uncultivated organisms and led to the identification of new branches within the tree of life. This has resh...

In two recent community discussion sessions, we explored what mental model of machine learning/deep learning we could teach to learners already familiar with the basics of programming, to help them sa...

The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...

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In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…