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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#11 Collective cell migration with Linus Schumacher

September 18, 2017 | show notes

In this episode Linus Schumacher joins me to discuss mathematical models of collective cell migration and multidisciplinary research.

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#10 Spatially variable genes and SpatialDE with Valentine Svensson

September 3, 2017 | show notes

Valentine Svensson explains how he analyzes spatially-annotated single cell gene expression data using Gaussian processes.

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

August 18, 2017 | show notes

Michael Tessler and Christopher Mason join me to talk about their comparison of 16S amplicon sequencing and shotgun sequencing for quantifying microbial diversity.

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#8 Perfect k-mer hashing in Sailfish

August 5, 2017 | show notes

The original version of Sailfish, an RNA-Seq quantification tool, used minimal perfect hash functions to replace k-mers with unique integers. (The current version appears to be using a Cuckoo hashmap instead.)

This is my attempt to explain how a minimal perfect hash function could be built. The algorithm described here is not exactly the same as the one Sailfish used, but it follows the same idea.

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#7 Metagenomics and Kraken

July 9, 2017 | show notes

What is metagenomics and how is it different from phylotyping?

What is Kraken and how can it be faster than BLAST?

I’ve got the answers!

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#6 Allele-specific expression

June 25, 2017 | show notes

I talk about allele-specific expression: why it arises and how it can be reliably detected.

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#5 Relative data analysis and propr with Thom Quinn

June 10, 2017 | show notes

In this episode, Thom Quinn and I explore different ways to transform and analyze relative data arising in genomics.

We also discuss propr, Thom’s R package to compute various proportionality measures.

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

May 29, 2017 | show notes

In this episode I meet with Georg Stricker and Julien Gagneur from the Technical University of Munich to discuss ChIP-seq data analysis and their tool, GenoGAM.

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#3 miRNA target site prediction and seedVicious with Antonio Marco

May 12, 2017 | show notes

In this episode Antonio Marco talks about miRNA target site prediction and his tool, seedVicious.

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#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk

April 29, 2017 | show notes

In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing.

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#1 Transcriptome assembly and Scallop with Mingfu Shao

April 16, 2017 | show notes

In this episode Mingfu Shao talks about Scallop, an accurate reference-based transcript assembler.

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