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

February 17, 2021

Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. However, the prediction accuracy suffers when GWAS from one population are used to calculate PRS within a different population, which is a problem because the majority of the GWAS are done on cohorts of European ancestry.

In this episode, Bárbara Bitarello helps us understand how PRS work and why they don’t transfer well across populations.

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

January 13, 2021

In this episode, we chat about phylogenetics with Xiang Ji. We start with a general introduction to the field and then go deeper into the likelihood-based methods (maximum likelihood and Bayesian inference). In particular, we talk about the different ways to calculate the likelihood gradient, including a linear-time exact gradient algorithm recently published by Xiang and his colleagues.

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

December 16, 2020

In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs, SMEMs, and maximal spanning seeds. Markus also presents his recent work on computing variable-sized seeds (MEMs, SMEMs, and maximal spanning seeds) from fixed-sized seeds (k-mers and minimizers) and his Modular Aligner.

Previous episodes

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)