bioinformatics chat

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

The bioinformatics chat is produced by Roman Cheplyaka and hosted by Roman and Jacob Schreiber.

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Differential gene expression and DESeq2 with Michael Love (#60)

May 12, 2021

In this episode, Michael Love joins us to talk about the differential gene expression analysis from bulk RNA-Seq data.

We talk about the history of Mike’s own differential expression package, DESeq2, as well as other packages in this space, like edgeR and limma, and the theory they are based upon. Mike also shares his experience of being the author and maintainer of a popular bioninformatics package.

Proteomics calibration with Lindsay Pino (#59)

April 21, 2021

In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifically, she discusses the difficulties of comparing measurements across different samples, potentially acquired in different labs, as well as a method she has developed recently for calibrating these measurements without the need for expensive reagents. The discussion then turns more broadly to questions in genomics that can potentially be addressed using proteomic measurements.

B cell maturation and class switching with Hamish King (#58)

March 31, 2021

In this episode, we learn about B cell maturation and class switching from Hamish King. Hamish recently published a paper on this subject in Science Immunology, where he and his coauthors analyzed gene expression and antibody repertoire data from human tonsils. In the episode Hamish talks about some of the interesting B cell states he uncovered and shares his thoughts on questions such as «When does a B cell decide to class-switch?» and «Why is the antibody isotype correlated with its affinity?»

Previous episodes

Enhancers with Molly Gasperini (#57)

Polygenic risk scores in admixed populations with Bárbara Bitarello (#56)

Phylogenetics and the likelihood gradient with Xiang Ji (#55)

Seeding methods for read alignment with Markus Schmidt (#54)

Real-time quantitative proteomics with Devin Schweppe (#53)

How 23andMe finds identical-by-descent segments with William Freyman (#52)

Basset and Basenji with David Kelley (#51)

ENCODE3 with Jill Moore (#50)

Most Permissive Boolean Networks with Loïc Paulevé (#49)

Machine learning for drug development with Marinka Zitnik (#48)

Reproducible pipelines and NGLess with Luis Pedro Coelho (#47)

HiFi reads and HiCanu with Sergey Nurk and Sergey Koren (#46)

Genome assembly and Canu with Sergey Koren and Sergey Nurk (#45)

DNA tagging and Porcupine with Kathryn Doroschak (#44)

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

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

Epidemic models with Kris Parag (#41)

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)