the bioinformatics chat

A podcast about computational biology, bioinformatics, and next generation sequencing.

https://bioinformatics.chat

Eine durchschnittliche Folge dieses Podcasts dauert 1h3m. Bisher sind 63 Folge(n) erschienen. Alle 4 Wochen erscheint eine Folge dieses Podcasts.

Gesamtlänge aller Episoden: 2 days 20 hours 19 minutes

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episode 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 begin by delving into the different types of mass spectrometry methods, including MS1, MS2, and, MS3, and the reasons for using each...


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 2020-11-18  1h3m
 
 

episode 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 Burrows-Wheeler transform can find IBD segments in the presence of genotyping and phasing errors.

Links:

  • Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform (William A. Freyman, Kimberly F. McManus, Suyash S. Shringarpure, Ethan M...


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 2020-10-27  42m
 
 

episode 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 of mutations on the genome. They begin their discussion by talking about Calico Labs, and then delve into a series of papers that David has written about using models, named Basset and Basenji, that connect genome sequence to functional activity and so can be used to quantify the effect of any mutation...


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 2020-10-07  1h13m
 
 

episode 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 overview and goals of the ENCODE Project, and then discuss a bundle of papers that were recently published in various Nature journals and the flagship paper, Expanded encyclopaedias of DNA elements in the human and mouse genomes...


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 2020-09-10  56m
 
 

episode 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 of Boolean networks are the synchronous, asynchronous, and fully asynchronous semantics.

In this episode, Loïc Paulevé explains how the same Boolean networks can be interpreted in a new, “most permissive” way...


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 2020-08-19  1h4m
 
 

episode 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 discussion with an overview of open research questions in the field, including limiting the search space of high-throughput testing methods, designing drugs entirely from scratch, predicting ways that existing drugs can be repurposed, and identifying likely side-effects of combining existing drugs in novel ways...


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 2020-07-29  1h25m
 
 

episode 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 main developer, Luis Pedro Coelho, about the benefits of domain-specific languages, pros and cons of Haskell in bioinformatics, reproducibility, and of course NGLess itself...


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 2020-06-24  57m
 
 

episode 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 probably start there. Otherwise, join us to learn about HiFi reads, the tradeoff between read length and quality, and what tricks HiCanu employs to resolve highly similar repeats...


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 2020-05-27  1h9m
 
 

episode 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 their amazing careers as well as behind some of the best known genome assemblers: Celera assembler, Canu, and SPAdes.

Links:

  • Canu on GitHub
  • SPAdes on GitHub


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 2020-05-20  1h16m
 
 

episode 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 short. These DNA tags then can be rapidly sequenced on an Oxford Nanopore MinION device without any need for library preparation.

In this episode, Katie Doroschak explains how Porcupine works—how molbits are designed and prepared, and how they are directly recognized by the software without an intermediate basecalling step...


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 2020-04-29  45m