the bioinformatics chat

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

https://bioinformatics.chat

Eine durchschnittliche Folge dieses Podcasts dauert 1h1m. Bisher sind 70 Folge(n) erschienen. Alle 4 Wochen erscheint eine Folge dieses Podcasts.

Gesamtlänge aller Episoden: 3 days 1 hour 46 minutes

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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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 September 10, 2020  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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 August 19, 2020  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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 July 29, 2020  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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 June 24, 2020  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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 May 27, 2020  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

If you enjoyed this episode, please consider supporting the podcast on Patreon.


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 May 20, 2020  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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 April 29, 2020  45m
 
 

episode 43: Generalized PCA for single-cell data with William Townes


Will Townes proposes a new, simpler way to analyze scRNA-seq data with unique molecular identifiers (UMIs). Observing that such data is not zero-inflated, Will has designed a PCA-like procedure inspired by generalized linear models (GLMs) that, unlike the standard PCA, takes into account statistical properties of the data and avoids spurious correlations (such as one or more of the top principal components being correlated with the number of non-zero gene counts)...


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 March 27, 2020  59m
 
 

episode 42: Spectrum-preserving string sets and simplitigs with Amatur Rahman and Karel Břinda


In this episode, we hear from Amatur Rahman and Karel Břinda, who independently of one another released preprints on the same concept, called simplitigs or spectrum-preserving string sets. Simplitigs offer a way to efficiently store and query large sets of k-mers—or, equivalently, large de Bruijn graphs...


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 February 28, 2020  53m
 
 

episode 41: Epidemic models with Kris Parag


Kris Parag is here to teach us about the mathematical modeling of infectious disease epidemics. We discuss the SIR model, the renewal models, and how insights from information theory can help us predict where an epidemic is going...


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 January 27, 2020  1h8m