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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#25 Transposons and repeats with Kaushik Panda and Keith Slotkin

September 24, 2018

Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and transposable elements. We talk LINEs, SINEs, LTRs, and even Sleeping Beauty transposons! Kaushik and Keith explain why repeats matter for your whole-genome analysis and answer listeners’ questions.

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#24 Read correction and Bcool with Antoine Limasset

August 31, 2018

Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool based on the de Bruijn graph, and it corrects reads far better than any of the current methods like Bloocoo, Musket, and Lighter.

We discuss why and when read correction is needed, how Bcool works, and why it performs better but slower than k-mer spectrum methods.

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#23 RNA design, EteRNA and NEMO with Fernando Portela

July 27, 2018

In this episode I talk to Fernando Portela, a software engineer and amateur scientist who works on RNA design — the problem of composing an RNA sequence that has a specific secondary structure.

We talk about how Fernando and others compete and collaborate in designing RNA molecules in the online game EteRNA and about Fernando’s new RNA design algorithm, NEMO, which outperforms all prior published methods by a wide margin.

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Previous episodes

#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