the bioinformatics chat
Roman Cheplyaka
the bioinformatics chat
Roman Cheplyaka
Tuesday 09 November 2021 : In this episode, Jacob Schreiber interviews Žiga Avsec about a recently released model, Enformer. Their discussion begins with...
Monday 27 September 2021 : The Bioinformatics Contest is back this year, and we are back to discuss it! This year’s contest winners Maksym Kovalchuk (1st prize)...
Wednesday 28 July 2021 : In this episode, Apostolos Chalkis presents sampling steady states of metabolic networks as an alternative to the widely used flux...
Wednesday 23 June 2021 : In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about data and computational methods for making sense of 3D genome structure....
Wednesday 12 May 2021 : In this episode, Michael Love joins us to talk about the differential gene expression analysis from bulk RNA-Seq data. We talk about the...
Wednesday 21 April 2021 : In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifically, she...
Wednesday 31 March 2021 : In this episode, we learn about B cell maturation and class switching from Hamish King. Hamish recently published a paper on this subject in...
Wednesday 10 March 2021 : In this episode, Jacob Schreiber interviews Molly Gasperini about enhancer elements. They begin their discussion by talking about Octant...
Wednesday 17 February 2021 : Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. However, the...
Wednesday 13 January 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...
Wednesday 16 December 2020 : In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs, SMEMs, and...
Wednesday 18 November 2020 : In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mass spectrometry data in the field of proteomics. They...
Tuesday 27 October 2020 : In this episode, Will Freyman talks about identity-by-descent (IBD): how it’s used at 23andMe, and how the templated positional...
Wednesday 07 October 2020 : In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight into the consequences...
Thursday 10 September 2020 : In this episode, Jacob Schreiber interviews Jill Moore about recent research from the ENCODE Project. They begin their discussion with an...
Wednesday 19 August 2020 : In systems biology, Boolean networks are a way to model interactions such as gene regulation or cell signaling. The standard interpretations...
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...
the bioinformatics chat
Roman Cheplyaka
#64 Enformer: predicting gene expression from sequence with Žiga Avsec
In this episode, Jacob Schreiber interviews Žiga Avsec about a recently released model, Enformer. Their discussion begins with...
#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt
The Bioinformatics Contest is back this year, and we are back to discuss it! This year’s contest winners Maksym Kovalchuk (1st prize)...
#62 Steady states of metabolic networks and Dingo with Apostolos Chalkis
In this episode, Apostolos Chalkis presents sampling steady states of metabolic networks as an alternative to the widely used flux...
#61 3D genome organization and GRiNCH with Da-Inn Erika Lee
In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about data and computational methods for making sense of 3D genome structure....
#60 Differential gene expression and DESeq2 with Michael Love
In this episode, Michael Love joins us to talk about the differential gene expression analysis from bulk RNA-Seq data. We talk about the...
#59 Proteomics calibration with Lindsay Pino
In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifically, she...
#58 B cell maturation and class switching with Hamish King
In this episode, we learn about B cell maturation and class switching from Hamish King. Hamish recently published a paper on this subject in...
#57 Enhancers with Molly Gasperini
In this episode, Jacob Schreiber interviews Molly Gasperini about enhancer elements. They begin their discussion by talking about Octant...
#56 Polygenic risk scores in admixed populations with Bárbara Bitarello
Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. However, the...
#55 Phylogenetics and the likelihood gradient with Xiang Ji
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...
#54 Seeding methods for read alignment with Markus Schmidt
In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs, SMEMs, and...
#53 Real-time quantitative proteomics with Devin Schweppe
In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mass spectrometry data in the field of proteomics. They...
#52 How 23andMe finds identical-by-descent segments with William Freyman
In this episode, Will Freyman talks about identity-by-descent (IBD): how it’s used at 23andMe, and how the templated positional...
#51 Basset and Basenji with David Kelley
In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight into the consequences...
#50 ENCODE3 with Jill Moore
In this episode, Jacob Schreiber interviews Jill Moore about recent research from the ENCODE Project. They begin their discussion with an...
#49 Most Permissive Boolean Networks with Loïc Paulevé
In systems biology, Boolean networks are a way to model interactions such as gene regulation or cell signaling. The standard interpretations...
#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...
