I always spend as much time formatting and trying out new writing tools as I do writing itself. “What is there to try out? Simply use Word, right?” Word is really fine if you want to print out a letter, but once you want to do anything more complex—like writing a scientific report with figures, tables, citations, and cross-references—it quickly becomes a nightmare.

Semantic Line Breaking for Markdown Semantic Line Breaking for Markdown A feature of markdown (Quarto) is that it ignores line breaks. A line break is just a space. (A double line break is a new paragraph).

From Code to Presentation: Solving SVG Image Conversion in Quarto From Code to Presentation: Solving SVG Image Conversion in Quarto Recently, I decided to switch from traditional PowerPoint presentations to Quarto-based presentations (mainly Reveal.

Why we need Snakemake? Snakemake There is more! Tips and Tricks Why we need Snakemake? Running Jobs on a HPC the old way Imagine you have to run a job on a HPC cluster for many samples.

Connecting to a high-performance computing (HPC) server might seem daunting at first. However, with the right tools and guidance, it can be a straightforward process. This blog post aims to demystify the connection process, making it accessible to both novices and seasoned users.

Speaking at the ESA Planetary Protection Workshop on Assessing metagenomic methods for their inclusion in ESA standards.

A Tutorial about Metagenome-Atlas at the ISMB/ECCB conference

Talk title: Decoding the Microbial Universe: Large-Scale Metagenomics at the Sub-Species Level

Content In preparation. Already have a look at the course from last year

Prof. Samuel Flores, dean of Students for MedBioInfo, the Swedish National Research School in Medical Bioinformatics, invited me to give a talk on metagenomics. This was a fantastic opportunity to discuss how metagenomics can be used in a variety of research projects.

Tričković et al. develop a comprehensive genomic human gut microbiota subspecies catalog by defining operational subspecies units (OSUs) in an unbiased, cohort-independent manner. Panhashome, a sketching-based method, enables rapid OSU quantification and identification of genes driving intraspecies variations. A subspecies-based machine-learning CRC diagnostic algorithm outperforms species-level methods by leveraging subspecies-level information.

Mouse is the most used model for studying the impact of microbiota on its host, but the rep- ertoire of species from the mouse gut …

Warmth exposure (34°C) protects against ovariectomy-induced bone loss in adult female, as well as in young male mice. Transplantation of the warm-adapted microbiota phenocopies the warmth-induced bone effects.

Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; …

We report streptococcal dysbiosis in acute diarrhoea irrespective of aetiology. Compared with 20 healthy local controls, 71 Bangladeshi …

Malnutrition predisposes to diarrhea and diarrhea adversely affects the nutritional status creating a vicious cycle. The role of the …