the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.

https://bioinformatics.chat

Eine durchschnittliche Folge dieses Podcasts dauert 1h3m. Bisher sind 63 Folge(n) erschienen. Dieser Podcast erscheint alle 4 Wochen.

Gesamtlänge aller Episoden: 2 days 20 hours 19 minutes

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episode 13: Bracken with Jennifer Lu


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

Links:

  • The Bracken paper
  • The Kraken paper
  • The preprint that applies Kallisto to metagenomics


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 2017-10-21  46m
 
 

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


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


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 2017-10-08  1h6m
 
 

episode 11: Collective cell migration with Linus Schumacher


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

Links:

  • Semblance of Heterogeneity in Collective Cell Migration and associated code
  • Multidisciplinary approaches to understanding collective cell migration in developmental biology
  • Linus’s homepage


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 2017-09-18  1h0m
 
 

episode 10: Spatially variable genes and SpatialDE with Valentine Svensson


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

Links:

  • Valentine’s preprint, “SpatialDE - Identification Of Spatially Variable Genes”
  • SpatialDE code on GitHub
  • Valentine’s personal page
  • The Integrative Biology & Medicine conference


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 2017-09-03  57m
 
 

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


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

Links:

  • The 2017 Nature paper that we discuss: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
  • Michael’s et al...


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 2017-08-18  45m
 
 

episode 8: Perfect k-mer hashing in Sailfish


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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 2017-08-05  22m
 
 

episode 7: Metagenomics and Kraken


What is metagenomics and how is it different from phylotyping?

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

Let’s try to sort this out...


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 2017-07-09  28m
 
 

episode 6: Allele-specific expression


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


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 2017-06-25  33m
 
 

episode 5: Relative data analysis and propr with Thom Quinn


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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 2017-06-10  55m
 
 

episode 4: ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur


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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 2017-05-29  55m