the bioinformatics chat
Activity Overview
Episode publication activity over the past year
Episodes
#70 Prioritizing drug target genes with Marie Sadler
21 Dec 2023
Contributed by Lukas
In this episode, Marie Sadler talks about her recent Cell Genomics paper, Multi-layered genetic approaches to identify approved d...
#69 Suffix arrays in optimal compressed space and δ-SA with Tomasz Kociumaka and Dominik Kempa
29 Sep 2023
Contributed by Lukas
Today on the podcast we have Tomasz Kociumaka and Dominik Kempa, the authors of the preprint Collapsing the Hierarchy of Compress...
#68 Phylogenetic inference from raw reads and Read2Tree with David Dylus
28 Aug 2023
Contributed by Lukas
In this episode, David Dylus talks about Read2Tree, a tool that builds alignment matrices and phylogenetic trees from raw sequenc...
#67 AlphaFold and variant effect prediction with Amelie Stein
29 Jul 2023
Contributed by Lukas
This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022, with Amelie Stein, now an ...
#66 AlphaFold and shape-mers with Janani Durairaj
10 Jul 2023
Contributed by Lukas
This is the second episode in the AlphaFold series, originally recorded on February 14, 2022, with Janani Durairaj, a postdoctora...
#65 AlphaFold and protein interactions with Pedro Beltrao
21 Jun 2023
Contributed by Lukas
In this episode, originally recorded on February 9, 2022, Roman talks to Pedro Beltrao about AlphaFold, the software developed by...
#64 Enformer: predicting gene expression from sequence with Žiga Avsec
09 Nov 2021
Contributed by Lukas
In this episode, Jacob Schreiber interviews Žiga Avsec about a recently released model, Enformer. Their discussion begins with l...
#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt
27 Sep 2021
Contributed by Lukas
The Bioinformatics Contest is back this year, and we are back to discuss it! This year’s contest winners Maksym Kovalchuk (1st...
#62 Steady states of metabolic networks and Dingo with Apostolos Chalkis
28 Jul 2021
Contributed by Lukas
In this episode, Apostolos Chalkis presents sampling steady states of metabolic networks as an alternative to the widely used flu...
#61 3D genome organization and GRiNCH with Da-Inn Erika Lee
23 Jun 2021
Contributed by Lukas
In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about data and computational methods for making sense of 3D genome s...
#60 Differential gene expression and DESeq2 with Michael Love
12 May 2021
Contributed by Lukas
In this episode, Michael Love joins us to talk about the differential gene expression analysis from bulk RNA-Seq data. We talk a...
#59 Proteomics calibration with Lindsay Pino
21 Apr 2021
Contributed by Lukas
In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifical...
#58 B cell maturation and class switching with Hamish King
31 Mar 2021
Contributed by Lukas
In this episode, we learn about B cell maturation and class switching from Hamish King. Hamish recently published a paper on this...
#57 Enhancers with Molly Gasperini
10 Mar 2021
Contributed by Lukas
In this episode, Jacob Schreiber interviews Molly Gasperini about enhancer elements. They begin their discussion by talking about...
#56 Polygenic risk scores in admixed populations with Bárbara Bitarello
17 Feb 2021
Contributed by Lukas
Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. Ho...
#55 Phylogenetics and the likelihood gradient with Xiang Ji
13 Jan 2021
Contributed by Lukas
In this episode, we chat about phylogenetics with Xiang Ji. We start with a general introduction to the field and then go deeper ...
#54 Seeding methods for read alignment with Markus Schmidt
16 Dec 2020
Contributed by Lukas
In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs, SME...
#53 Real-time quantitative proteomics with Devin Schweppe
18 Nov 2020
Contributed by Lukas
In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mass spectrometry data in the field of proteomic...
#52 How 23andMe finds identical-by-descent segments with William Freyman
27 Oct 2020
Contributed by Lukas
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
07 Oct 2020
Contributed by Lukas
In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight into the consequenc...
#50 ENCODE3 with Jill Moore
10 Sep 2020
Contributed by Lukas
In this episode, Jacob Schreiber interviews Jill Moore about recent research from the ENCODE Project. They begin their discussion...
#49 Most Permissive Boolean Networks with Loïc Paulevé
19 Aug 2020
Contributed by Lukas
In systems biology, Boolean networks are a way to model interactions such as gene regulation or cell signaling. The standard inte...
#48 Machine learning for drug development with Marinka Zitnik
29 Jul 2020
Contributed by Lukas
In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to drug development. They begin...
#47 Reproducible pipelines and NGLess with Luis Pedro Coelho
24 Jun 2020
Contributed by Lukas
NGLess is a programming language specifically targeted at next generation sequencing (NGS) data processing. In this episode we ch...
#46 HiFi reads and HiCanu with Sergey Nurk and Sergey Koren
27 May 2020
Contributed by Lukas
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk. If you missed the previous episode, you ...
#45 Genome assembly and Canu with Sergey Koren and Sergey Nurk
20 May 2020
Contributed by Lukas
In this episode, Sergey Nurk and Sergey Koren from the NIH share their thoughts on genome assembly. The two Sergeys tell the stor...
#44 DNA tagging and Porcupine with Kathryn Doroschak
29 Apr 2020
Contributed by Lukas
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
27 Mar 2020
Contributed by Lukas
Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such d...
#42 Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda
28 Feb 2020
Contributed by Lukas
In this episode, we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same co...
#41 Epidemic models with Kris Parag
27 Jan 2020
Contributed by Lukas
Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the ren...
#40 Plasmid classification and binning with Sergio Arredondo-Alonso and Anita Schürch
30 Dec 2019
Contributed by Lukas
Does a given bacterial gene live on a plasmid or the chromosome? What other genes live on the same plasmid? In this episode, we ...
#39 Amplicon sequence variants and bias with Benjamin Callahan
29 Nov 2019
Contributed by Lukas
In this episode, Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing an...
#38 Issues in legacy genomes with Luke Anderson-Trocmé
22 Oct 2019
Contributed by Lukas
In this episode, Luke Anderson-Trocmé talks about his findings from the 1000 Genomes Project. Namely, the early sequenced genome...
#37 Causality and potential outcomes with Irineo Cabreros
27 Sep 2019
Contributed by Lukas
In this episode, I talk with Irineo Cabreros about causality. We discuss why causality matters, what does and does not imply caus...
#36 scVI with Romain Lopez and Gabriel Misrachi
30 Aug 2019
Contributed by Lukas
In this episode, we hear from Romain Lopez and Gabriel Misrachi about scVI—Single-cell Variational Inference. scVI is a probabi...
#35 The role of the DNA shape in transcription factor binding with Hassan Samee
26 Jul 2019
Contributed by Lukas
Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix...
#34 Power laws and T-cell receptors with Kristina Grigaityte
29 Jun 2019
Contributed by Lukas
An αβ T-cell receptor is composed of two highly variable protein chains, the α chain and the β chain. However, based only on ...
#33 Genome assembly from long reads and Flye with Mikhail Kolmogorov
31 May 2019
Contributed by Lukas
Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher...
#32 Deep tensor factorization and a pitfall for machine learning methods with Jacob Schreiber
29 Apr 2019
Contributed by Lukas
In this episode, we hear from Jacob Schreiber about his algorithm, Avocado. Avocado uses deep tensor factorization to break a th...
#31 Bioinformatics Contest 2019 with Alexey Sergushichev and Gennady Korotkevich
24 Mar 2019
Contributed by Lukas
The third Bioinformatics Contest took place in February 2019. Alexey Sergushichev, one of the organizers of the contest, and Gen...
#30 Bayesian inference of chromatin structure from Hi-C data with Simeon Carstens
27 Feb 2019
Contributed by Lukas
Hi-C is a sequencing-based assay that provides information about the 3-dimensional organization of the genome. In this episode, S...
#29 Haplotype-aware genotyping from long reads with Trevor Pesout
27 Jan 2019
Contributed by Lukas
Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in le...
#28 Space-efficient variable-order Markov models with Fabio Cunial
28 Dec 2018
Contributed by Lukas
This time you’ll hear from Fabio Cunial on the topic of Markov models and space-efficient data structures. First we recall what...
#27 Classification of CRISPR-induced mutations and CRISPRpic with HoJoon Lee and Seung Woo Cho
29 Nov 2018
Contributed by Lukas
In this episode, HoJoon Lee and Seung Woo Cho explain how to perform a CRISPR experiment and how to analyze its results. HoJoon a...
#26 Feature selection, Relief and STIR with Trang Lê
27 Oct 2018
Contributed by Lukas
Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate ...
#25 Transposons and repeats with Kaushik Panda and Keith Slotkin
24 Sep 2018
Contributed by Lukas
Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and transposable elements. We talk LINEs, ...
#24 Read correction and Bcool with Antoine Limasset
31 Aug 2018
Contributed by Lukas
Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool base...
#23 RNA design, EteRNA and NEMO with Fernando Portela
27 Jul 2018
Contributed by Lukas
In this episode, I talk to Fernando Portela, a software engineer and amateur scientist who works on RNA design — the problem of...
#22 smCounter2: somatic variant calling and UMIs with Chang Xu
29 Jun 2018
Contributed by Lukas
In this episode I’m joined by Chang Xu. Chang is a senior biostatistician at QIAGEN and an author of smCounter2, a low-frequenc...
#21 Linear mixed models, GWAS, and lme4qtl with Andrey Ziyatdinov
31 May 2018
Contributed by Lukas
Linear mixed models are used to analyze GWAS data and detect QTLs. Andrey Ziyatdinov recently released an R package, lme4qtl, tha...
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar
30 Apr 2018
Contributed by Lukas
In this episode Kristian Davidsen and Amrit Dhar present their project called SPURF. SPURF can predict the B cell receptor (BCR) ...
#19 Genome fingerprints with Gustavo Glusman
07 Apr 2018
Contributed by Lukas
In this episode, Gustavo Glusman explains his method of reducing a VCF file to a small “fingerprint”, which could be then use...
#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi
03 Mar 2018
Contributed by Lukas
The final round of Bioinformatics Contest 2018 was held on February 24-25th, and the qualification round took place two weeks ear...
#17 Rarefaction, alpha diversity, and statistics with Amy Willis
22 Jan 2018
Contributed by Lukas
In this episode, Amy Willis joins me to talk about good and bad ways to estimate taxonomic richness in microbial ecology studies....
#16 Javier Quilez on what makes large sequencing projects successful
24 Dec 2017
Contributed by Lukas
Javier Quilez and I discuss what it’s like to be a bioinformatician, how to improve communication between the wet and dry labs ...
#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger
26 Nov 2017
Contributed by Lukas
Geoffrey Schiebinger explains how reconstructing developmental trajectories from single-cell RNA-seq data can be reduced to the m...
#14 Generating functions for read mapping with Guillaume Filion
13 Nov 2017
Contributed by Lukas
Guillaume Filion recently published a preprint in which he applies generating functions, a concept from analytic combinatorics, t...
#13 Bracken with Jennifer Lu
21 Oct 2017
Contributed by Lukas
Jennifer Lu joins me to discuss species abundance estimation from metagenomic sequencing data. Links: T...
#12 Modelling the immune system and C-ImmSim with Filippo Castiglione
08 Oct 2017
Contributed by Lukas
In this episode, Filippo Castiglione and I discuss different ways to model the immune system. Links: Ce...
#11 Collective cell migration with Linus Schumacher
18 Sep 2017
Contributed by Lukas
In this episode, Linus Schumacher joins me to discuss mathematical models of collective cell migration and multidisciplinary rese...
#10 Spatially variable genes and SpatialDE with Valentine Svensson
03 Sep 2017
Contributed by Lukas
Valentine Svensson explains how he analyzes spatially-annotated single cell gene expression data using Gaussian processes. ...
#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing
18 Aug 2017
Contributed by Lukas
Michael Tessler and Christopher Mason join me to talk about their comparison of 16S amplicon sequencing and shotgun sequencing fo...
#8 Perfect k-mer hashing in Sailfish
05 Aug 2017
Contributed by Lukas
The original version of Sailfish, an RNA-Seq quantification tool, used minimal perfect hash functions to replace k-mers with uni...
#7 Metagenomics and Kraken
09 Jul 2017
Contributed by Lukas
What is metagenomics and how is it different from phylotyping? What is Kraken and how can it be faster than BLAST? Let’s try ...
#6 Allele-specific expression
25 Jun 2017
Contributed by Lukas
I talk about allele-specific expression: why it arises and how it can be reliably detected. Sections: T...
#5 Relative data analysis and propr with Thom Quinn
10 Jun 2017
Contributed by Lukas
In this episode, Thom Quinn and I explore different ways to transform and analyze relative data arising in genomics. We also dis...
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
29 May 2017
Contributed by Lukas
In this episode, I meet with Georg Stricker and Julien Gagneur from the Technical University of Munich to discuss ChIP-seq data a...
#3 miRNA target site prediction and seedVicious with Antonio Marco
12 May 2017
Contributed by Lukas
In this episode Antonio Marco talks about miRNA target site prediction and his tool, seedVicious. Links: ...
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk
29 Apr 2017
Contributed by Lukas
In this episode Aleksandra Kolodziejczyk talks about single-cell RNA sequencing. Links: A review paper ...
#1 Transcriptome assembly and Scallop with Mingfu Shao
16 Apr 2017
Contributed by Lukas
In this episode, Mingfu Shao talks about Scallop, an accurate reference-based transcript assembler. Links: ...