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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January 27, 2019
Long read sequencing technologies, such as Oxford Nanopore and PacBio,
produce reads from thousands to a million base pairs in length,
at the cost of the increased error rate. Trevor Pesout
describes how he and his colleagues leverage long reads for simultaneous
variant calling/genotyping and phasing. This is possible thanks to a clever
use of a hidden Markov model, and two different algorithms based on this model
are now implemented in
the MarginPhase and WhatsHap tools.
December 28, 2018
This time you’ll hear from Fabio Cunial on the topic of Markov models and
space-efficient data structures. First we recall what a Markov model is and
why variable-order Markov models are an improvement over the standard,
fixed-order models. Next we discuss the various data structures and indexes
that allowed Fabio and his collaborators to represent these models in a very
small space while still keeping the queries efficient. Burrows-Wheeler
transform, suffix trees and arrays, tries and suffix link trees, and more!
November 29, 2018
In this episode HoJoon Lee and Seung Woo Cho explain how to perform a CRISPR
experiment and how to analyze its results. HoJoon and Seung Woo developed an
algorithm that analyzes sequenced amplicons containing the CRISPR-induced
double-strand break site and figures out what exactly happened there (e.g.
a deletion, insertion, substitution etc.)
#26 Feature selection, Relief and STIR with Trang Lê
#25 Transposons and repeats with Kaushik Panda and Keith Slotkin
#24 Read correction and Bcool with Antoine Limasset
#23 RNA design, EteRNA and NEMO with Fernando Portela
#22 smCounter2: somatic variant calling and UMIs with Chang Xu
#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar
#19 Genome fingerprints with Gustavo Glusman
#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi
#17 Rarefaction, alpha diversity, and statistics with Amy Willis
#16 Javier Quilez on what makes large sequencing projects successful
#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger
#14 Generating functions for read mapping with Guillaume Filion
#13 Bracken with Jennifer Lu
#12 Modelling the immune system and C-ImmSim with Filippo Castiglione
#11 Collective cell migration with Linus Schumacher
#10 Spatially variable genes and SpatialDE with Valentine Svensson
#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing
#8 Perfect k-mer hashing in Sailfish
#7 Metagenomics and Kraken
#6 Allele-specific expression
#5 Relative data analysis and propr with Thom Quinn
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
#3 miRNA target site prediction and seedVicious with Antonio Marco
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk
#1 Transcriptome assembly and Scallop with Mingfu Shao