Ranked #1
#6 Allele-specific expression
#6 Allele-specific expression
I talk about allele-specific expression: why it arises and how it can bereliably detected. Sections: The biology of all... Read more
25 Jun 2017
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33mins
Ranked #2
#39 Amplicon sequence variants and bias with Benjamin Callahan
#39 Amplicon sequence variants and bias with Benjamin Callahan
In this episode, Benjamin Callahan talks about some of the issues faced bymicrobiologists when conducting amplicon seque... Read more
29 Nov 2019
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1hr 1min
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Ranked #3
#35 The role of the DNA shape in transcription factor binding with Hassan Samee
#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 t... Read more
26 Jul 2019
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1hr 1min
Ranked #4
#30 Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens
#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 ep... Read more
27 Feb 2019
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1hr 5mins
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Ranked #5
#5 Relative data analysis and propr with Thom Quinn
#5 Relative data analysis and propr with Thom Quinn
In this episode, Thom Quinn and I explore different waysto transform and analyze relative data arising in genomics. We a... Read more
10 Jun 2017
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55mins
Ranked #6
#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov
#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov
Linear mixed models are used to analyze GWAS data and detect QTLs.Andrey Ziyatdinov recently released an R package, lme4... Read more
31 May 2018
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50mins
Ranked #7
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
In this episode, I meet with Georg Stricker and Julien Gagneur from the Technical University of Munichto discuss ChIP-se... Read more
29 May 2017
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55mins
Ranked #8
#3 miRNA target site prediction and seedVicious with Antonio Marco
#3 miRNA target site prediction and seedVicious with Antonio Marco
In this episodeAntonio Marcotalks about miRNA target site prediction and his tool, seedVicious. Links: seedVicious prep... Read more
12 May 2017
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56mins
Ranked #9
#19 Genome fingerprints with Gustavo Glusman
#19 Genome fingerprints with Gustavo Glusman
In this episode, Gustavo Glusman explains his method of reducing a VCF fileto a small “fingerprint”, which could be then... Read more
7 Apr 2018
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1hr 28mins
Ranked #10
#16 Javier Quilez on what makes large sequencing projects successful
#16 Javier Quilez on what makes large sequencing projects successful
Javier Quilez and I discuss what it’s like to bea bioinformatician, how to improve communication between the wet and dry... Read more
24 Dec 2017
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1hr 3mins
Ranked #11
#23 RNA design, EteRNA and NEMO with Fernando Portela
#23 RNA design, EteRNA and NEMO with Fernando Portela
In this episode, I talk to Fernando Portela,a software engineer andamateur scientistwho works on RNA design — the proble... Read more
27 Jul 2018
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1hr 31mins
Ranked #12
#13 Bracken with Jennifer Lu
#13 Bracken with Jennifer Lu
Jennifer Lu joins me to discuss species abundance estimation from metagenomic sequencing data. Links: The Bracken paper... Read more
21 Oct 2017
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46mins
Ranked #13
#38 Issues in legacy genomes with Luke Anderson-Trocmé
#38 Issues in legacy genomes with Luke Anderson-Trocmé
In this episode, Luke Anderson-Trocmétalks about his findings from the 1000 Genomes Project. Namely, the earlysequenced ... Read more
22 Oct 2019
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1hr 1min
Ranked #14
#22 smCounter2: somatic variant calling and UMIs with Chang Xu
#22 smCounter2: somatic variant calling and UMIs with Chang Xu
In this episode I’m joined by Chang Xu. Chang is a senior biostatisticianat QIAGEN and an author of smCounter2, a low-fr... Read more
29 Jun 2018
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1hr 4mins
Ranked #15
#36 scVI with Romain Lopez and Gabriel Misrachi
#36 scVI with Romain Lopez and Gabriel Misrachi
In this episode, we hear from Romain Lopez and Gabriel Misrachi aboutscVI—Single-cell Variational Inference.scVI is a pr... Read more
30 Aug 2019
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1hr 20mins
Ranked #16
#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov
#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov
Modern genome assembly projects are often based on long reads in an attempt tobridge longer repeats. However, due to th... Read more
31 May 2019
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1hr 12mins
Ranked #17
#40 Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch
#40 Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch
Does a given bacterial gene live on a plasmid or the chromosome? Whatother genes live on the same plasmid? In this episo... Read more
30 Dec 2019
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45mins
Ranked #18
#14 Generating functions for read mapping with Guillaume Filion
#14 Generating functions for read mapping with Guillaume Filion
Guillaume Filion recently published a preprint in which he appliesgenerating functions, a concept from analytic combinat... Read more
13 Nov 2017
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1hr 10mins
Ranked #19
#8 Perfect k-mer hashing in Sailfish
#8 Perfect k-mer hashing in Sailfish
The original version of Sailfish, an RNA-Seq quantification tool, used minimal perfect hash functions toreplace k-mers w... Read more
5 Aug 2017
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22mins
Ranked #20
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar
In this episodeKristian DavidsenandAmrit Dharpresent their project called SPURF.SPURF can predict the B cell receptor (B... Read more
30 Apr 2018
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2hr 1min
