Sifting through my website stats, I realised that bioinformaticians are reading more posts discussing "how to do bioinformatics" than the ones with a strict scientific content. Is this a feature of this blog, or does it reflect a common problem with working habits? Drawing some conclusions after two years of atcgeek After almost a couple … Continue reading Is "how to do bioinformatics" the major topic in bioinformaticians online reading habits?
It was a cold November morning, year 2011. Sapienza University has a huge campus next to the city centre of Rome, where the main faculties are stored in huge buildings in the rationalist style. Yet, the faculty of Biochemistry has a detached site in the neighboured flanking the campus, San Lorenzo. I was crossing the streets of … Continue reading The four most stupid things I have ever done in bioinformatics.
To anyone having to do something with immunity studies, the nuclear factor kappa-light-chain-enhancer of activated B cells, will sound really familiar. The NF-kB is a protein complex deputed to initiate the transcriptional response to external stimuli, such as stress, citokines, antigens, bacteria, free radicals or UV light irradiation. Expressed in active B cells, it is … Continue reading Applying phylogenetics and bioinformatics to NF-kB studies
Even if the affirmation of RNAseq as "tool of choice" to explore the transcriptome is a fact, the challenges to improve the reliability and reproducibility of this method are still quite a lot. On the statistical side, the choice between parametric and non-parametric tests is a point of controversy. In 2011, Robert Tibshiran argued that even though parametric tests … Continue reading Let's explore rSeqNP, a non-parametric approach to detect differential expression from RNA-Seq data
We could agree that a bioinformatician is basically a naked, starving castaway who's trying to survive in a desert island. As in one of those realities that run on tv, or in the movie starring Tom Hanks, he is provided with a knife, quite a few clothes, and a good dose of motivation. In this allegory, … Continue reading Project Rosalind: learn bioinformatics and programming through problem solving
I return on pipeline creation tools because I was warned about Nextflow project, a DSL for parallel and scalable computational pipeline creation. As already discussed in a recent post, we can sort pipeline solutions according to how they deal with your code. Some of them are able to connect functions, some of them require dedicated modules, and others … Continue reading Nextflow: a DSL for parallel and scalable computational pipelines.
The paper I am going to explore today introduces MethylMix, an R package designed to identify DNA methylation-driven genes. DNA methylation is one of the processes that are more extensively studied in biomedicine, since it has been found as a principal mechanism of gene regulation in many diseases. Although high-throughput methods are able to produce … Continue reading MethylMix: an R package for identifying DNA methylation-driven genes