The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.
The bioinformatics chat is produced by Roman Cheplyaka.
July 27, 2018
In this episode I talk to Fernando Portela, a software engineer and amateur scientist who works on RNA design — the problem of composing an RNA sequence that has a specific secondary structure.
We talk about how Fernando and others compete and collaborate in designing RNA molecules in the online game EteRNA and about Fernando’s new RNA design algorithm, NEMO, which outperforms all prior published methods by a wide margin.
June 29, 2018
In this episode I’m joined by Chang Xu. Chang is a senior biostatistician at QIAGEN and an author of smCounter2, a low-frequency somatic variant caller. To distinguish rare somatic mutations from sequencing errors, smCounter2 relies on unique molecular identifiers, or UMIs, which help identify multiple reads resulting from the same physical DNA fragment.
Chang explains what UMIs are, why they are useful, and how smCounter2 and other tools in this space use UMIs to detect low-frequency variants.
May 31, 2018
Linear mixed models are used to analyze GWAS data and detect QTLs. Andrey Ziyatdinov recently released an R package, lme4qtl, that can be used to formulate and fit these models. In this episode Andrey and I discuss linear mixed models, genome-wide association studies, and strengths and weaknesses of lme4qtl.