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A podcast about computational biology, bioinformatics, and next generation sequencing.
In this episode, Marie Sadler talks about her recent Cell Genomics paper, Multi-layered genetic approaches to identify approved drug targets...
Today on the podcast we have Tomasz Kociumaka and Dominik Kempa , the authors of the preprint Collapsing the Hierarchy of Compressed Data St...
In this episode, David Dylus talks about Read2Tree , a tool that builds alignment matrices and phylogenetic trees from raw sequencing reads....
This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022, with Amelie Stein , now an associate...
This is the second episode in the AlphaFold series, originally recorded on February 14, 2022, with Janani Durairaj , a postdoctoral research...
In this episode, originally recorded on February 9, 2022, Roman talks to Pedro Beltrao about AlphaFold, the software developed by DeepMind t...
In this episode, Jacob Schreiber interviews Žiga Avsec about a recently released model, Enformer . Their discussion begins with life differe...
The Bioinformatics Contest is back this year, and we are back to discuss it! This year’s contest winners Maksym Kovalchuk (1st prize) and Ma...
In this episode, Apostolos Chalkis presents sampling steady states of metabolic networks as an alternative to the widely used flux balance a...
In this episode, Jacob Schreiber interviews Da-Inn Erika Lee about data and computational methods for making sense of 3D genome structure. T...
In this episode, Michael Love joins us to talk about the differential gene expression analysis from bulk RNA-Seq data. We talk about the his...
In this episode, Lindsay Pino discusses the challenges of making quantitative measurements in the field of proteomics. Specifically, she dis...
In this episode, we learn about B cell maturation and class switching from Hamish King . Hamish recently published a paper on this subject i...
In this episode, Jacob Schreiber interviews Molly Gasperini about enhancer elements. They begin their discussion by talking about Octant Bio...
Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict the phenotype based on the genotype. However, the...
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 l...
In this episode, Markus Schmidt explains how seeding in read alignment works. We define and compare k-mers, minimizers, MEMs, SMEMs, and max...
In this episode, Jacob Schreiber interviews Devin Schweppe about the analysis of mass spectrometry data in the field of proteomics. They beg...
In this episode, Will Freyman talks about identity-by-descent (IBD): how it’s used at 23andMe , and how the templated positional Burrows-Whe...
In this episode, Jacob Schreiber interviews David Kelley about machine learning models that can yield insight into the consequences of mutat...
In this episode, Jacob Schreiber interviews Jill Moore about recent research from the ENCODE Project . They begin their discussion with an o...
In systems biology, Boolean networks are a way to model interactions such as gene regulation or cell signaling. The standard interpretations...
In this episode, Jacob Schreiber interviews Marinka Zitnik about applications of machine learning to drug development. They begin their disc...
NGLess is a programming language specifically targeted at next generation sequencing (NGS) data processing. In this episode we chat with its...
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk . If you missed the previous episode , you should pr...
In this episode, Sergey Nurk and Sergey Koren from the NIH share their thoughts on genome assembly. The two Sergeys tell the stories behind...
Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA called molecular bits , or molbits for short. These...
Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not...
In this episode, we hear from Amatur Rahman and Karel Břinda , who independently of one another released preprints on the same concept, call...
Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal models...
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...
In this episode, Benjamin Callahan talks about some of the issues faced by microbiologists when conducting amplicon sequencing and metagenom...
In this episode, Luke Anderson-Trocmé talks about his findings from the 1000 Genomes Project. Namely, the early sequenced genomes sometimes...
In this episode, I talk with Irineo Cabreros about causality. We discuss why causality matters, what does and does not imply causality, and...
In this episode, we hear from Romain Lopez and Gabriel Misrachi about scVI—Single-cell Variational Inference. scVI is a probabilistic model...
Even though the double-stranded DNA has the famous regular helical shape, there are small variations in the geometry of the helix depending...
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...
Modern genome assembly projects are often based on long reads in an attempt to bridge longer repeats. However, due to the higher error rate...
In this episode, we hear from Jacob Schreiber about his algorithm, Avocado. Avocado uses deep tensor factorization to break a three-dimensio...
The third Bioinformatics Contest took place in February 2019. Alexey Sergushichev , one of the organizers of the contest, and Gennady Korotk...
Hi-C is a sequencing-based assay that provides information about the 3-dimensional organization of the genome. In this episode, Simeon Carst...
Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at th...
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 mod...
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 Wo...
Relief is a statistical method to perform feature selection. It could be used, for instance, to find genomic loci that correlate with a trai...
Kaushik Panda and Keith Slotkin come on the podcast to educate us about repetitive DNA and transposable elements. We talk LINEs, SINEs, LTRs...
Antoine Limasset joins me to talk about NGS read correction. Antoine and his colleagues built the read correction tool Bcool based on the de...
In this episode, I talk to Fernando Portela , a software engineer and amateur scientist who works on RNA design — the problem of composing a...
In this episode I’m joined by Chang Xu . Chang is a senior biostatistician at QIAGEN and an author of smCounter2, a low-frequency somatic va...
Linear mixed models are used to analyze GWAS data and detect QTLs . Andrey Ziyatdinov recently released an R package, lme4qtl , that can be...