the bioinformatics chat
Roman Cheplyaka
the bioinformatics chat
Roman Cheplyaka
Wednesday 29 July 2020 : In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to drug development. They begin their...
Wednesday 24 June 2020 : NGLess is a programming language specifically targeted at next generation sequencing (NGS) data processing. In this episode we chat with its...
Wednesday 27 May 2020 : In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk. If you missed the previous episode, you should...
Wednesday 20 May 2020 : In this episode Sergey Nurk and Sergey Koren from the NIH share their thoughts on genome assembly. The two Sergeys tell the stories behind...
Wednesday 29 April 2020 : Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA called molecular bits, or molbits for...
Friday 27 March 2020 : Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not...
Friday 28 February 2020 : In this episode we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same concept,...
Monday 27 January 2020 : Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal...
Monday 30 December 2019 : 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...
Friday 29 November 2019 : In this episode Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and...
Tuesday 22 October 2019 : In this episode Luke Anderson-Trocmé talks about his findings from the 1000 Genomes Project. Namely, the early sequenced genomes sometimes...
Friday 27 September 2019 : In this episode I talk with Irineo Cabreros about causality. We discuss why causality matters, what does and does not imply causality, and...
Friday 30 August 2019 : In this episode we hear from Romain Lopez and Gabriel Misrachi about scVI—Single-cell Variational Inference. scVI is a probabilistic model...
Friday 26 July 2019 : Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix depending...
Saturday 29 June 2019 : 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...
Friday 31 May 2019 : Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher error rate...
Monday 29 April 2019 : In this episode we hear from Jacob Schreiber about his algorithm, Avocado. Avocado uses deep tensor factorization to break a...
Sunday 24 March 2019 : The third Bioinformatics Contest took place in February 2019. Alexey Sergushichev, one of the organizers of the contest, and Gennady...
Wednesday 27 February 2019 : Hi-C is a sequencing-based assay that provides information about the 3-dimensional organization of the genome. In this episode Simeon...
Sunday 27 January 2019 : Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at...
Friday 28 December 2018 : This time you’ll hear from Fabio Cunial on the topic of Markov models and space-efficient data structures. First we recall what a Markov...
Thursday 29 November 2018 : In this episode HoJoon Lee and Seung Woo Cho explain how to perform a CRISPR experiment and how to analyze its results. HoJoon and Seung Woo...
Saturday 27 October 2018 : Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate with a...
Monday 24 September 2018 : Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and transposable elements. We talk LINEs, SINEs,...
Friday 31 August 2018 : Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool based on the de...
the bioinformatics chat
Roman Cheplyaka
#48 Machine learning for drug development with Marinka Zitnik
In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to drug development. They begin their...
#47 Reproducible pipelines and NGLess with Luis Pedro Coelho
NGLess is a programming language specifically targeted at next generation sequencing (NGS) data processing. In this episode we chat with its...
#46 HiFi reads and HiCanu with Sergey Nurk and Sergey Koren
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk. If you missed the previous episode, you should...
#45 Genome assembly and Canu with Sergey Koren and Sergey Nurk
In this episode Sergey Nurk and Sergey Koren from the NIH share their thoughts on genome assembly. The two Sergeys tell the stories behind...
#44 DNA tagging and Porcupine with Kathryn Doroschak
Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA called molecular bits, or molbits for...
#43 Generalized PCA for single-cell data with William Townes
Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not...
#42 Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda
In this episode we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same concept,...
#41 Epidemic models with Kris Parag
Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal...
#40 Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch
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...
#39 Amplicon sequence variants and bias with Benjamin Callahan
In this episode Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and...
#38 Issues in legacy genomes with Luke Anderson-Trocmé
In this episode Luke Anderson-Trocmé talks about his findings from the 1000 Genomes Project. Namely, the early sequenced genomes sometimes...
#37 Causality and potential outcomes with Irineo Cabreros
In this episode I talk with Irineo Cabreros about causality. We discuss why causality matters, what does and does not imply causality, and...
#36 scVI with Romain Lopez and Gabriel Misrachi
In this episode we hear from Romain Lopez and Gabriel Misrachi about scVI—Single-cell Variational Inference. scVI is a probabilistic model...
#35 The role of the DNA shape in transcription factor binding with Hassan Samee
Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix depending...
#34 Power laws and T-cell receptors with Kristina Grigaityte
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...
#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov
Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher error rate...
#32 Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber
In this episode we hear from Jacob Schreiber about his algorithm, Avocado. Avocado uses deep tensor factorization to break a...
#31 Bioinformatics Contest 2019 with Alexey Sergushichev and Gennady Korotkevich
The third Bioinformatics Contest took place in February 2019. Alexey Sergushichev, one of the organizers of the contest, and Gennady...
#30 Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens
Hi-C is a sequencing-based assay that provides information about the 3-dimensional organization of the genome. In this episode Simeon...
#29 Haplotype-aware genotyping from long reads with Trevor Pesout
Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at...
#28 Space-efficient variable-order Markov models with Fabio Cunial
This time you’ll hear from Fabio Cunial on the topic of Markov models and space-efficient data structures. First we recall what a Markov...
#27 Classification of CRISPR-induced mutations and CRISPRpic with HoJoon Lee and Seung Woo Cho
In this episode HoJoon Lee and Seung Woo Cho explain how to perform a CRISPR experiment and how to analyze its results. HoJoon and Seung Woo...
#26 Feature selection, Relief and STIR with Trang Lê
Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate with a...
#25 Transposons and repeats with Kaushik Panda and Keith Slotkin
Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and transposable elements. We talk LINEs, SINEs,...
#24 Read correction and Bcool with Antoine Limasset
Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool based on the de...
