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.

Don't miss the next episode! Subscribe on iTunes, Google Podcasts, or via an RSS feed link.

#27 Classification of CRISPR-induced mutations and CRISPRpic with HoJoon Lee and Seung Woo Cho

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.)

Download MP3

#26 Feature selection, Relief and STIR with Trang Lê

October 27, 2018

Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate with a trait or genes whose expression correlate with a condition. Relief can also be made sensitive to interaction effects (known in genetics as epistasis).

In this episode Trang Lê joins me to talk about Relief and her version of Relief called STIR (STatistical Inference Relief). While traditional Relief algorithms could only rank features and needed a user-supplied threshold to decide which features to select, Trang’s reformulation of Relief allowed her to compute p-values and make the selection process less arbitrary.

Download MP3

#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.

Download MP3

Previous episodes

#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