Roman Cheplyaka
the bioinformatics chat
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Roman Cheplyaka
the bioinformatics chatClaimedEpisodes
Roman Cheplyaka
the bioinformatics chat
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Episodes of the bioinformatics chat
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In this episode, Marie Sadler talksabout her recent Cell Genomics paper, Multi-layered genetic approaches toidentify approved drug targets.Previous studies have found that the drugs that target a gene linked to thedisease are
Today on the podcast we have Tomasz Kociumaka and Dominik Kempa,the authors of the preprintCollapsing the Hierarchy of Compressed Data Structures: Suffix Arrays in Optimal Compressed Space.The suffix array is one of the founda
In this episode,David Dylus talks aboutRead2Tree,a tool that builds alignment matrices and phylogenetic trees from rawsequencing reads.By leveraging the database of orthologous genes called OMA, Read2Tree bypasses traditional
This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022,with Amelie Stein, now an associate professor at the University of Copenhagen.In the episode, Amelie explains what 𝛥𝛥G is,
This is the second episode in the AlphaFold series, originally recorded on February 14, 2022,with Janani Durairaj, a postdoctoralresearcher at the University of Basel.Janani talks about how she used shape-mers and topic modell
In this episode, originally recorded on February 9, 2022,Roman talks to Pedro Beltraoabout AlphaFold, the software developed by DeepMind that predicts a protein’s3D structure from its amino acid sequence.Pedro is an associate
In this episode, Jacob Schreiber interviews Žiga Avsec abouta recently released model, Enformer. Their discussion begins with lifedifferences between academia and industry, specifically about how researchis conducted in the two
The Bioinformatics Contest is back this year, and we are back to discussit!This year’s contest winnersMaksym Kovalchuk (1st prize) andMatt Holt (2nd prize)talk about how they approachparticipating in the contest and what st
In this episode, Apostolos Chalkis presents sampling steadystates of metabolic networks as an alternative to the widely used flux balanceanalysis (FBA). We also discuss dingo, aPython package written by Apostolos that employs g
In this episode, Jacob Schreiber interviews Da-Inn Erika Lee aboutdata and computational methods for making sense of 3D genome structure. They begin their discussion by talking about 3D genome structure at a high level and the
In this episode, Michael Love joins us to talk about the differential geneexpression analysis from bulk RNA-Seq data.We talk about the history of Mike’s own differential expression package,DESeq2, as well as other packages in
In this episode, Lindsay Pino discusses thechallenges of making quantitative measurements in the field of proteomics.Specifically, she discusses the difficulties of comparing measurements acrossdifferent samples, potentially ac
In this episode, we learn about B cell maturation and class switching fromHamish King. Hamish recently published apaper on this subject in Science Immunology, where he and his coauthorsanalyzed gene expression and antibody repe
In this episode, Jacob Schreiber interviews Molly Gasperini aboutenhancer elements. They begin their discussion by talking about Octant Bio,and then dive into the surprisingly difficult task of defining enhancers anddetermining
Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS)to predict the phenotype based on the genotype. However, the predictionaccuracy suffers when GWAS from one population are used to calculate PRS within
In this episode, we chat about phylogenetics with Xiang Ji. We start with ageneral introduction to the field and then go deeper into the likelihood-basedmethods (maximum likelihood and Bayesian inference). In particular, we talk
In this episode, Markus Schmidt explains how seeding in read alignment works.We define and compare k-mers, minimizers, MEMs, SMEMs, and maximal spanning seeds.Markus also presents his recent work on computing variable-sized seed
In this episode, Jacob Schreiber interviews Devin Schweppe aboutthe analysis of mass spectrometry data in the field of proteomics. They beginby delving into the different types of mass spectrometry methods, including MS1, MS2,
In this episode, Will Freyman talks about identity-by-descent (IBD): howit’s used at 23andMe, and how the templatedpositional Burrows-Wheeler transform can find IBD segments in the presence ofgenotyping and phasing errors.
In this episode, Jacob Schreiber interviews David Kelley aboutmachine learning models that can yield insight into the consequences ofmutations on the genome. They begin their discussion by talking about Calico Labs, and then de
In this episode, Jacob Schreiber interviews Jill Moore aboutrecent research from the ENCODE Project. They begin theirdiscussion with an overview and goals of the ENCODE Project, and thendiscuss a bundle of papers that were rece
In systems biology, Boolean networks are a way to model interactions such asgene regulation or cell signaling. The standardinterpretations of Boolean networks are the synchronous, asynchronous, andfully asynchronous semantics.
In this episode, Jacob Schreiber interviews Marinka Zitnik aboutapplications of machine learning to drug development.They begin their discussion with an overview of open research questions in thefield, including limiting the se
NGLess is a programming language specificallytargeted at next generation sequencing (NGS) data processing.In this episode we chat with its main developer, Luis PedroCoelho, about the benefits of domain-specificlanguages, pros
In this episode, I continue to talk (but mostly listen) to Sergey Koren and Sergey Nurk.If you missed the previous episode, you should probably start there.Otherwise, join us to learn about HiFi reads, the tradeoff between read
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