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.
#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.
#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.
#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.
#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!
#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.
#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.
#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.
#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.
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk
April 29, 2017 | show notes
In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing.
#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.