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The Stupidest Machine Learning Mistakes in Bioinformatics

bioinformatics

machine-learning

reproducibility

Ten ways to build an impressive model that answers the wrong question—and how to catch them.

Matrix Operations and Linear Algebra

bioinformatics

linear-algebra

deep-learning

From expression tables to Transformer attention, with a little wordplay and runnable NumPy examples.

The Stupidest Mistakes in Machine Learning

machine-learning

deep-learning

reproducibility

Ten mistakes that survive a successful training run: lessons from researchers, engineers, and a few lines of arithmetic.

Small Mistakes, Big Consequences: Notes on Common Errors in Bioinformatics

bioinformatics

command-line

Most bioinformatics errors are not exotic. They are an index that starts at the wrong number, a genome build nobody wrote down, or a stray space in a shell command. They are…

nf-core/atacseq: Mapping Accessible Chromatin with “Molecular Scissors”

bioinformatics

nextflow

atac-seq

Most nucleated cells in the human body share essentially the same DNA, yet perform different functions. Think of the genome as an instruction manual: different cells make…

nf-core/sarek: From DNA Reads to Variant Discovery

bioinformatics

nextflow

Sarek shares its name with a national park in northern Sweden. Early releases used names such as Ruotes and Skårki, giving the project a distinctive geographic identity. The…

scRNA-seq: Tracing the Barcode Disagreement Between Cell Ranger and Simpleaf

bioinformatics

scrna-seq

Genome plots by R

bioinformatics

r

Need a circos plot, a chromosome map, and a zoomed-in regional view, and you’d rather not spend an afternoon fighting circlize margins again? Same idea as last time, same…

Nextflow: Local Server, Cluster, or Cloud computation?

bioinformatics

cloud

nextflow

Nextflow shines when it comes to resource management, natively supporting everything from your local machine and local HPC clusters to top-tier cloud platforms. You can…

RNA-seq plots by R

bioinformatics

r

Making the same five RNA-seq figures from scratch, every single project, for the hundredth time? Yeah, me too. So I finally sat down and turned the whole mess into one R…

What If You want Customize an nf-core Pipeline?

bioinformatics

nextflow

nf-core

Take nf-core/rnaseq as an example: if your research question calls for a different analysis path, where should you make the change?

Nextflow: Reproducible Bioinformatics at Scale

bioinformatics

workflow

nextflow

In modern computational biology, reproducibility is no longer a bonus. It is the standard.

Workflow Management in Bioinformatics and Deep Learning

bioinformatics

deep-learning

workflow

Bioinformatics stitches together a dozen independent tools per sample; deep learning trains end-to-end in one script. Why the two fields standardize so differently – and what that says about a good workflow framework.

My Story

reflections

career

From a village shop counter to bioinformatics to AI – three hurdles, and why curiosity is the one thing age doesn’t have to take.