bioinformatics chat

the bioinformatics chat

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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#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar

April 30, 2018

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.

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#19 Genome fingerprints with Gustavo Glusman

April 7, 2018

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.

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#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi

March 3, 2018

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.

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Previous episodes

#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