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

November 18, 2020

In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mass spectrometry data in the field of proteomics. They begin by delving into the different types of mass spectrometry methods, including MS1, MS2, and, MS3, and the reasons for using each. They then discuss a recent paper from Devin, Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics that involved building a real-time system for quantifying proteomic samples from MS3, and the types of analyses that this system allows one to do.

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

October 27, 2020

In this episode Will Freyman talks about identity-by-descent (IBD): how it’s used at 23andMe, and how the templated positional Burrows-Wheeler transform can find IBD segments in the presence of genotyping and phasing errors.

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Basset and Basenji with David Kelley (#51)

October 7, 2020

In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight into the consequences of mutations on the genome. They begin their discussion by talking about Calico Labs, and then delve into a series of papers that David has written about using models, named Basset and Basenji, that connect genome sequence to functional activity and so can be used to quantify the effect of any mutation.

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Previous episodes

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)