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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#14 Generating functions for read mapping with Guillaume Filion

November 13, 2017

Guillaume Filion recently published a preprint in which he applies generating functions, a concept from analytic combinatorics, to estimating the optimal seed length for read mapping.

In this episode, Guillaume and I attempt to explain the core concepts from analytic combinatorics and why they are useful in modeling sequences.

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#13 Bracken with Jennifer Lu

October 21, 2017

Jennifer Lu joins me to discuss species abundance estimation from metagenomic sequencing data.

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

October 8, 2017

In this episode Filippo Castiglione and I discuss different ways to model the immune system.

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Older episodes

#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