bioinformatics chat

the bioinformatics chat

The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.

The bioinformatics chat is produced by Roman Cheplyaka.

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#23 RNA design, EteRNA and NEMO with Fernando Portela

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.

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#22 smCounter2: somatic variant calling and UMIs with Chang Xu

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.

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#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov

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.

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Previous episodes

#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar

#19 Genome fingerprints with Gustavo Glusman

#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi

#17 Rarefaction, alpha diversity, and statistics with Amy Willis

#16 Javier Quilez on what makes large sequencing projects successful

#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger

#14 Generating functions for read mapping with Guillaume Filion

#13 Bracken with Jennifer Lu

#12 Modelling the immune system and C-ImmSim with Filippo Castiglione

#11 Collective cell migration with Linus Schumacher

#10 Spatially variable genes and SpatialDE with Valentine Svensson

#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing

#8 Perfect k-mer hashing in Sailfish

#7 Metagenomics and Kraken

#6 Allele-specific expression

#5 Relative data analysis and propr with Thom Quinn

#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur

#3 miRNA target site prediction and seedVicious with Antonio Marco

#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk

#1 Transcriptome assembly and Scallop with Mingfu Shao