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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ENCODE3 with Jill Moore (#50)

September 10, 2020

In this episode, Jacob Schreiber interviews Jill Moore about recent research from the ENCODE Project. They begin their discussion with an overview and goals of the ENCODE Project, and then discuss a bundle of papers that were recently published in various Nature journals and the flagship paper, Expanded encyclopaedias of DNA elements in the human and mouse genomes. They conclude their discussion by talking about the challenges with managing a large project as a trainee in a consortium setting.

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Most Permissive Boolean Networks with Loïc Paulevé (#49)

August 19, 2020

In systems biology, Boolean networks are a way to model interactions such as gene regulation or cell signaling. The standard interpretations of Boolean networks are the synchronous, asynchronous, and fully asynchronous semantics.

In this episode Loïc Paulevé explains how the same Boolean networks can be interpreted in a new, “most permissive” way. Loïc proved mathematically that his semantics can reproduce all behaviors achievable by a compatible quantitative model, whereas the traditional interpretations in general cannot. Furthermore, it turns out that deciding whether a certain state in a Boolean network is reachable can be done much more efficiently in MPBNs than in the traditional interpretations.

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

July 29, 2020

In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to drug development. They begin their discussion with an overview of open research questions in the field, including limiting the search space of high-throughput testing methods, designing drugs entirely from scratch, predicting ways that existing drugs can be repurposed, and identifying likely side-effects of combining existing drugs in novel ways. Focusing on the last of these areas, they then discuss one of Marinka’s recent papers, Modeling polypharmacy side effects with graph convolutional networks.

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Previous episodes

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)