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. Links: Preprint: Predicting B Cell Receptor Substitution Profiles Using Public R...

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. Links: The genome fingerprints paper The genotype fingerprints preprint The data fingerprints preprint The blog post about time series visualization

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. Synthesis of ATP 0:48:46 Problem 2....

In this episode, Amy Willis joins me to talk about good and bad ways to estimate taxonomic richness in microbial ecology studies. Links: Rarefaction, alpha diversity, and statistics Estimating Diversity via Frequency Ratios Estimating the Number of Species in Microbial Diversity Studies Summer Institutes 2018 at the University of Washington STAMPS: Strategies and Techniques for Analyzing Microbial...

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 . Links: Parallel sequencing...

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. Talk by Geoffrey and Lénaïc Chizat

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. Links: Guillaume’s preprint: Analytic combinatorics for bioinformatic...

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

In this episode, Filippo Castiglione and I discuss different ways to model the immune system. Links: Celada’s and Seiden’s 1992 paper, “A computer model of cellular interactions in the immune system” Filippo’s 2001 paper, “Design and implementation of an immune system simulator” PLOS One paper, “Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the...

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

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

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. 2016 paper that describes their original 16S study: A Global eDNA Com...

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...

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. Sections: Culturing and its limitation (00:18) Metagenomics vs phylotyping (1:43) BLAST (5:53) The idea behind Kraken (8:14) How Kraken organizes its database (18:08) Links: The paper about Kraken A freely accessible (though a bit dated) book on metagenomic...

I talk about allele-specific expression: why it arises and how it can be reliably detected. Sections: The biology of allele-specific expression (2:17) Detecting allele-specific expression with RNA-seq (7:46) Mapping and sequencing biases (16:39) The experiment in yeast (19:47) Statistical models (21:44) Links: A powerful and flexible statistical framework for testing hypotheses of allele-specific...

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. Links: Thom’s preprint about propr — take a look if you feel lost in all the quantities that we discuss :) David Lovell original paper introducing proportionality for relative data and a very detai...

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 . Links: Preprint about GenoGAM Georg on GitHub Julien’s lab on Twitter [BC] 2 — The Basel Computational Biology Conference (Basel, September 2017), where you can meet Georg The European Human Genetics Conference (Copenhagen, May 2017), wh...

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

In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing. Links: A review paper by Aleksandra Comparative analysis of single-cell RNA sequencing methods, including the cost table Power Analysis of Single Cell RNA‐Sequencing Experiments Monocle: a toolkit for analyzing single-cell gene expression experiments Questions from listeners on bioinformatics.chat and reddit

In this episode, Mingfu Shao talks about Scallop , an accurate reference-based transcript assembler. Links: The preprint about Scallop The preprint about flow decomposition The video of a talk by Ben Langmead about Rail-RNA The preprint about Rail-RNA