Podcasts by the bioinformatics chat

the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.

Further podcasts by Roman Cheplyaka

Podcast on the topic Biowissenschaften

All episodes

the bioinformatics chat
#69 Suffix arrays in optimal compressed space and δ-SA with Tomasz Kociumaka and Dominik Kempa from 2023-09-29T19:00

Today on the podcast we have Tomasz Kociumaka and Dominik Kempa, the authors of the preprin...

Listen
the bioinformatics chat
#67 AlphaFold and variant effect prediction with Amelie Stein from 2023-07-29T19:00

This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022, with Amelie Stein Listen

the bioinformatics chat
#66 AlphaFold and shape-mers with Janani Durairaj from 2023-07-10T19:00

This is the second episode in the AlphaFold series, originally recorded on February 14, 2022, with Janani Durairaj, a postdoctoral researcher at the Univ...

Listen
the bioinformatics chat
#65 AlphaFold and protein interactions with Pedro Beltrao from 2023-06-21T19:00

In this episode, originally recorded on February 9, 2022, Roman talks to Pedro Beltrao about AlphaFold, the software developed by DeepMind that pre...

Listen
the bioinformatics chat
#64 Enformer: predicting gene expression from sequence with Žiga Avsec from 2021-11-09T19:00

In this episode, Jacob Schreiber interviews Žiga Avsec about a recently released model, Listen

the bioinformatics chat
#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt from 2021-09-27T19:00

The Bioinformatics Contest is back this year, and we are back to discuss it!

This year’s contest winners Listen

the bioinformatics chat
#62 Steady states of metabolic networks and Dingo with Apostolos Chalkis from 2021-07-28T19:00

In this episode, Apostolos Chalkis presents sampling steady states of metabolic networks as an alternative to the widely used flux balance analysis (FB...

Listen
the bioinformatics chat
#61 3D genome organization and GRiNCH with Da-Inn Erika Lee from 2021-06-23T19:00

In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about data and computational methods for making...

Listen
the bioinformatics chat
#60 Differential gene expression and DESeq2 with Michael Love from 2021-05-12T19:00

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...

Listen
the bioinformatics chat
#59 Proteomics calibration with Lindsay Pino from 2021-04-21T19:00

In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifically, she discusses the dif...

Listen
the bioinformatics chat
#58 B cell maturation and class switching with Hamish King from 2021-03-31T19:00

In this episode, we learn about B cell maturation and class switching from Hamish King. Hamish recently published a Listen

the bioinformatics chat
#57 Enhancers with Molly Gasperini from 2021-03-10T19:00

In this episode, Jacob Schreiber interviews Molly Gasperini about enhancer elements. They begin their discus...

Listen
the bioinformatics chat
#56 Polygenic risk scores in admixed populations with Bárbara Bitarello from 2021-02-17T19:00

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 populat...

Listen
the bioinformatics chat
#55 Phylogenetics and the likelihood gradient with Xiang Ji from 2021-01-13T19:00

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...

Listen
the bioinformatics chat
#54 Seeding methods for read alignment with Markus Schmidt from 2020-12-16T19:00

In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs...

Listen
the bioinformatics chat
#53 Real-time quantitative proteomics with Devin Schweppe from 2020-11-18T19:00

In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mas...

Listen
the bioinformatics chat
#52 How 23andMe finds identical-by-descent segments with William Freyman from 2020-10-27T19:00

In this episode, Will Freyman talks about identity-by-descent (IBD): how it’s used at 23andMe, and how the templat...

Listen
the bioinformatics chat
#51 Basset and Basenji with David Kelley from 2020-10-07T19:00

In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight...

Listen
the bioinformatics chat
#50 ENCODE3 with Jill Moore from 2020-09-10T19:00

In this episode, Jacob Schreiber interviews Jill Moore about recent research from the Listen

the bioinformatics chat
#49 Most Permissive Boolean Networks with Loïc Paulevé from 2020-08-19T19:00

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...

Listen
the bioinformatics chat
#48 Machine learning for drug development with Marinka Zitnik from 2020-07-29T19:00

In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to dr...

Listen
the bioinformatics chat
#47 Reproducible pipelines and NGLess with Luis Pedro Coelho from 2020-06-24T19:00

NGLess is a programming language specifically targeted at next generation sequencing (NGS) data processing. In this episode we chat with its main developer, ...

Listen
the bioinformatics chat
#46 HiFi reads and HiCanu with Sergey Nurk and Sergey Koren from 2020-05-27T19:00

In this episode, I continue to talk (but mostly listen) to Sergey Koren and Listen

the bioinformatics chat
#45 Genome assembly and Canu with Sergey Koren and Sergey Nurk from 2020-05-20T19:00

In this episode, Sergey Nurk and Sergey Koren from the NIH share th...

Listen
the bioinformatics chat
#44 DNA tagging and Porcupine with Kathryn Doroschak from 2020-04-29T19:00

Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA called molecular bits, or molbits for short. These DNA tags then can be rapidly sequenc...

Listen
the bioinformatics chat
#43 Generalized PCA for single-cell data with William Townes from 2020-03-27T19:00

Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not zero-infla...

Listen
the bioinformatics chat
#42 Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda from 2020-02-28T19:00

In this episode, we hear from Amatur Rahman and Karel Břinda, who independently of one anothe...

Listen
the bioinformatics chat
#41 Epidemic models with Kris Parag from 2020-01-27T19:00

Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal mode...

Listen
the bioinformatics chat
#40 Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch from 2019-12-30T19:00

Does a given bacterial gene live on a plasmid or the chromosome? What other genes live on the same plasmid?

In this episode, we hear from Se...

Listen
the bioinformatics chat
#39 Amplicon sequence variants and bias with Benjamin Callahan from 2019-11-29T19:00

In this episode, Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and metagenomic studies. The t...

Listen
the bioinformatics chat
#38 Issues in legacy genomes with Luke Anderson-Trocmé from 2019-10-22T19:00

In this episode, Luke Anderson-Trocmé talks about his findings from the 1000 Genomes Project. Namely, the early sequenced genomes sometimes contai...

Listen
the bioinformatics chat
#37 Causality and potential outcomes with Irineo Cabreros from 2019-09-27T19:00

In this episode, I talk with Irineo Cabreros about causality. We discuss why causality matters, what does and does not imply causality, and two diffe...

Listen
the bioinformatics chat
#36 scVI with Romain Lopez and Gabriel Misrachi from 2019-08-30T19:00

In this episode, we hear from Romain Lopez and Gabriel Misrachi about sc...

Listen
the bioinformatics chat
#35 The role of the DNA shape in transcription factor binding with Hassan Samee from 2019-07-26T19:00

Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix depending on what exact nucleotides its made of at that position...

Listen
the bioinformatics chat
#34 Power laws and T-cell receptors with Kristina Grigaityte from 2019-06-29T19:00

An αβ T-cell receptor is composed of two highly variable protein chains, the α chain and the β chain. However, based only on bulk DNA or RNA sequencing it is impossible to determine which of the...

Listen
the bioinformatics chat
#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov from 2019-05-31T19:00

Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher error rate of the current long read sequencers, assemblers based...

Listen
the bioinformatics chat
#32 Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber from 2019-04-29T19:00

In this episode, we hear from Jacob Schreiber about his algorithm, Avocado.

Avocado uses deep tensor factorization to break a three...

Listen
the bioinformatics chat
#31 Bioinformatics Contest 2019 with Alexey Sergushichev and Gennady Korotkevich from 2019-03-24T19:00

The third Bioinformatics Contest took place in February 2019.

Alexey Sergushichev, one of the organizer...

Listen
the bioinformatics chat
#30 Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens from 2019-02-27T19:00

Hi-C is a sequencing-based assay that provides information about the 3-dimensional organization of the genome. In this episode, Simeon Carstens explains...

Listen
the bioinformatics chat
#29 Haplotype-aware genotyping from long reads with Trevor Pesout from 2019-01-27T19:00

Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at the cost of the increased error rate. Listen

the bioinformatics chat
#28 Space-efficient variable-order Markov models with Fabio Cunial from 2018-12-28T19:00

This time you’ll hear from Fabio Cunial on the topic of Markov models and space-efficient data structures. First we recall what a M...

Listen
the bioinformatics chat
#27 Classification of CRISPR-induced mutations and CRISPRpic with HoJoon Lee and Seung Woo Cho from 2018-11-29T19:00

In this episode, HoJoon Lee and Seung Woo Cho explain how to perform a CRISP...

Listen
the bioinformatics chat
#26 Feature selection, Relief and STIR with Trang Lê from 2018-10-27T19:00

Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate with a trait or genes whose expression correlate with a condition...

Listen
the bioinformatics chat
#25 Transposons and repeats with Kaushik Panda and Keith Slotkin from 2018-09-24T19:00

Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and ...

Listen
the bioinformatics chat
#24 Read correction and Bcool with Antoine Limasset from 2018-08-31T19:00

Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool based on the de Bruijn graph...

Listen
the bioinformatics chat
#23 RNA design, EteRNA and NEMO with Fernando Portela from 2018-07-27T19:00

In this episode, I talk to Fernando Portela, a software engineer and amateur scientist who works on RNA design — the problem ...

Listen
the bioinformatics chat
#22 smCounter2: somatic variant calling and UMIs with Chang Xu from 2018-06-29T19:00

In this episode I’m joined by Chang Xu. Chang is a senior biostatistician at QIAGEN and an author of smCounter2, a low-frequency soma...

Listen
the bioinformatics chat
#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov from 2018-05-31T19:00

Linear mixed models are used to analyze GWAS data and detect QTLs. Listen

the bioinformatics chat
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar from 2018-04-30T19:00

In this episode Kristian Davidsen and Amrit Dhar present their project called SPURF. SPURF can predict the B c...

Listen
the bioinformatics chat
#19 Genome fingerprints with Gustavo Glusman from 2018-04-07T19:00

In this episode, Gustavo Glusman explains his method of reducing a VCF file to a small “fingerprint”, which could be then us...

Listen
the bioinformatics chat
#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi from 2018-03-03T19:00

The final round of Bioinformatics Contest 2018 was held on February 24-25th, and the qualification round took place two weeks earlier.

I invited t...

Listen
the bioinformatics chat
#17 Rarefaction, alpha diversity, and statistics with Amy Willis from 2018-01-22T19:00

In this episode, Amy Willis joins me to talk about good and bad ways to estimate taxonomic richness in microbial ecology studies.

...

Listen
the bioinformatics chat
#16 Javier Quilez on what makes large sequencing projects successful from 2017-12-24T19:00

Javier Quilez and I discuss what it’s like to be a bioinformatician, how to improve communication between the wet and dry labs and make the research more...

Listen
the bioinformatics chat
#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger from 2017-11-26T19:00

Geoffrey Schiebinger explains how reconstructing developmental trajectories from single-cell RNA-seq data can be reduced to the mathemati...

Listen
the bioinformatics chat
#14 Generating functions for read mapping with Guillaume Filion from 2017-11-13T19:00

Guillaume Filion recently published a preprint in which he applies generati...

Listen
the bioinformatics chat
#13 Bracken with Jennifer Lu from 2017-10-21T19:00

Jennifer Lu joins me to discuss species abundance estimation from metagenomic sequencing data.

Links:

<...

Listen
the bioinformatics chat
#12 Modelling the immune system and C-ImmSim with Filippo Castiglione from 2017-10-08T19:00

In this episode, Filippo Castiglione and I discuss different ways to model the immune system.

Links:

...

Listen
the bioinformatics chat
#11 Collective cell migration with Linus Schumacher from 2017-09-18T19:00

In this episode, Linus Schumacher joins me to discuss mathematical models of collective cell migration and multidisciplinary research.

...

Listen
the bioinformatics chat
#10 Spatially variable genes and SpatialDE with Valentine Svensson from 2017-09-03T19:00

Valentine Svensson explains how he analyzes spatially-annotated single cell gene expression data using Gaussian processes.

...

Listen
the bioinformatics chat
#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing from 2017-08-18T19:00

Michael Tessler and Christopher Mason join me to talk about their comparison of 16S amplicon sequenci...

Listen
the bioinformatics chat
#8 Perfect k-mer hashing in Sailfish from 2017-08-05T19:00

The original version of Sailfish, an RNA-Seq quantification tool, used minimal perfect hash functions to replace k-mers...

Listen
the bioinformatics chat
#7 Metagenomics and Kraken from 2017-07-09T19:00

What is metagenomics and how is it different from phylotyping?

What is Kraken and how can it be faster than BLAST?

Let’s try to sort this out.

Sectio...

Listen
the bioinformatics chat
#6 Allele-specific expression from 2017-06-25T19:00

I talk about allele-specific expression: why it arises and how it can be reliably detected.

Sections:

  • The biology of allele-specific expression (2:17...

    Listen
the bioinformatics chat
#5 Relative data analysis and propr with Thom Quinn from 2017-06-10T19:00

In this episode, Thom Quinn and I explore different ways to transform and analyze relative data arising in genomics.

We also discuss Listen

the bioinformatics chat
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur from 2017-05-29T19:00

In this episode, I meet with Georg Stricker and Julien Gagneur from the Technical University of Munich to discuss ChIP-seq data analysis and their tool, Listen

the bioinformatics chat
#3 miRNA target site prediction and seedVicious with Antonio Marco from 2017-05-12T19:00

In this episode Antonio Marco talks about miRNA target site prediction and his tool, seedVicious.

...

Listen
the bioinformatics chat
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk from 2017-04-29T19:00

In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing.

Links:...

Listen
the bioinformatics chat
#1 Transcriptome assembly and Scallop with Mingfu Shao from 2017-04-16T19:00

In this episode, Mingfu Shao talks about Scallop, an accurate reference-based transcript a...

Listen