bioinformatics chat

The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.

The bioinformatics chat is produced by Roman Cheplyaka.

Want to promote your research on the podcast? Take part in the bioinformatics chat open mic!

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Generalized PCA for single-cell data with William Townes (#43)

March 27, 2020

Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not zero-inflated, Will has designed a PCA-like procedure inspired by generalized linear models (GLMs) that, unlike the standard PCA, takes into account statistical properties of the data and avoids spurious correlations (such as one or more of the top principal components being correlated with the number of non-zero gene counts).

Also check out Will’s paper for a feature selection algorithm based on deviance, which we didn’t get a chance to discuss on the podcast.

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Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda (#42)

February 28, 2020

In this episode we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same concept, called simplitigs or spectrum-preserving string sets. Simplitigs offer a way to efficiently store and query large sets of k-mers—or, equivalently, large de Bruijn graphs.

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Epidemic models with Kris Parag (#41)

January 27, 2020

Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal models, and how insights from information theory can help us predict where an epidemic is going.

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Previous episodes

Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch (#40)

Amplicon sequence variants and bias with Benjamin Callahan (#39)

Issues in legacy genomes with Luke Anderson-Trocmé (#38)

Causality and potential outcomes with Irineo Cabreros (#37)

scVI with Romain Lopez and Gabriel Misrachi (#36)

The role of the DNA shape in transcription factor binding with Hassan Samee (#35)

Power laws and T-cell receptors with Kristina Grigaityte (#34)

Genome assembly from long reads and Flye with Mikhail Kolmogorov (#33)

Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber (#32)

Bioinformatics Contest 2019 with Alexey Sergushichev and Gennady Korotkevich (#31)

Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens (#30)

Haplotype-aware genotyping from long reads with Trevor Pesout (#29)

Space-efficient variable-order Markov models with Fabio Cunial (#28)

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

Feature selection, Relief and STIR with Trang Lê (#26)

Transposons and repeats with Kaushik Panda and Keith Slotkin (#25)

Read correction and Bcool with Antoine Limasset (#24)

RNA design, EteRNA and NEMO with Fernando Portela (#23)

smCounter2: somatic variant calling and UMIs with Chang Xu (#22)

Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov (#21)

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

Genome fingerprints with Gustavo Glusman (#19)

Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi (#18)

Rarefaction, alpha diversity, and statistics with Amy Willis (#17)

Javier Quilez on what makes large sequencing projects successful (#16)

Optimal transport for single-cell expression data with Geoffrey Schiebinger (#15)

Generating functions for read mapping with Guillaume Filion (#14)

Bracken with Jennifer Lu (#13)

Modelling the immune system and C-ImmSim with Filippo Castiglione (#12)

Collective cell migration with Linus Schumacher (#11)

Spatially variable genes and SpatialDE with Valentine Svensson (#10)

Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing (#9)

Perfect k-mer hashing in Sailfish (#8)

Metagenomics and Kraken (#7)

Allele-specific expression (#6)

Relative data analysis and propr with Thom Quinn (#5)

ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur (#4)

miRNA target site prediction and seedVicious with Antonio Marco (#3)

Single-cell RNA sequencing with Aleksandra Kolodziejczyk (#2)

Transcriptome assembly and Scallop with Mingfu Shao (#1)