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

January 22, 2018

In this episode Amy Willis joins me to talk about good and bad ways to estimate taxonomic richness in microbial ecology studies.

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#16 Javier Quilez on what makes large sequencing projects successful

December 24, 2017

Javier Quilez and I discuss what it’s like to be a bioinformatician, how to improve communication between the wet and dry labs and make the research more reproducible.

Make sure to read Javier’s paper we are discussing; it’s a light and entertaining read. The last author on this paper is Guillaume Filion, whom you may remember from the episode on generating functions.

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

November 26, 2017

Geoffrey Schiebinger explains how reconstructing developmental trajectories from single-cell RNA-seq data can be reduced to the mathematical problem called optimal transport.

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Previous episodes

#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