the bioinformatics chat

In this episode Kristian Davidsen and Amrit Dhar present their project called SPURF. SPURF can predict the B cell receptor (BCR) substitution profile of a given clonal family based on a single representative sequence from that family. SPURF works by fitting a tensor regression model to publicly available Rep-seq data...

In this episode, Gustavo Glusman explains his method of reducing a VCF file to a small “fingerprint”, which could be then used to detect duplicate genomes, infer relatedness, map the population structure, and more...

The final round of Bioinformatics Contest 2018 was held on February 24-25th, and the qualification round took place two weeks earlier.

I invited the organizers of the contest, Alexey Sergushichev and Ekaterina Vyahhi, to discuss the problems and find out what it was like to organize the contest.

Timestamps for the problems:

• Qualification round
  • 0:41:38 Problem 1...

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

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...

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

Links:

• Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming...

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...

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

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