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the bioinformatics chat

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Roman Cheplyaka

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

#69

#69 Suffix arrays in optimal compressed space and δ-SA with Tomasz Kociumaka and Dominik Kempa

Today on the podcast we have [Tomasz Kociumaka] (https://mimuw.edu.pl/~kociumaka/) and [Do... more

29 Sep 2023

56 MINS

56:46

29 Sep 2023

#68

#68 Phylogenetic inference from raw reads and Read2Tree with David Dylus

In this episode, [David Dylus] (https://www.unil.ch/dee/en/home/menuguid/people/previous-c... more

28 Aug 2023

49 MINS

49:11

28 Aug 2023

#67

#67 AlphaFold and variant effect prediction with Amelie Stein

This is the third and final episode in the AlphaFold series, originally recorded on Februa... more

29 Jul 2023

35 MINS

35:25

29 Jul 2023

#66

#66 AlphaFold and shape-mers with Janani Durairaj

This is the second episode in the AlphaFold series, originally recorded on February 14, 20... more

10 Jul 2023

20 MINS

20:51

10 Jul 2023

#65

#65 AlphaFold and protein interactions with Pedro Beltrao

In this episode, originally recorded on February 9, 2022, Roman talks to [Pedro Beltrao] (... more

21 Jun 2023

52 MINS

52:23

21 Jun 2023

#64

#64 Enformer: predicting gene expression from sequence with Žiga Avsec

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Žiga Avsec] (... more

09 Nov 2021

59 MINS

59:41

09 Nov 2021

#63

#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt

The [Bioinformatics Contest] (https://bioinf.me/en/contest) is back this year, and we are ... more

27 Sep 2021

1 HR 00 MINS

1:00:47

27 Sep 2021

#62

#62 Steady states of metabolic networks and Dingo with Apostolos Chalkis

In this episode, [Apostolos Chalkis] (https://tolischal.github.io/) presents sampling stea... more

28 Jul 2021

38 MINS

38:25

28 Jul 2021

#61

#61 3D genome organization and GRiNCH with Da-Inn Erika Lee

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Da-Inn Erika ... more

23 Jun 2021

1 HR 09 MINS

1:09:41

23 Jun 2021

#60

#60 Differential gene expression and DESeq2 with Michael Love

In this episode, [Michael Love] (https://mikelove.github.io/) joins us to talk about the d... more

12 May 2021

1 HR 31 MINS

1:31:15

12 May 2021

#59

#59 Proteomics calibration with Lindsay Pino

In this episode, [Lindsay Pino] (https://lindsaykpino.com/) discusses the challenges of ma... more

21 Apr 2021

48 MINS

48:26

21 Apr 2021

#58

#58 B cell maturation and class switching with Hamish King

In this episode, we learn about B cell maturation and class switching from [Hamish King] (... more

31 Mar 2021

1 HR 29 MINS

1:29:11

31 Mar 2021

#57

#57 Enhancers with Molly Gasperini

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Molly Gasperi... more

10 Mar 2021

46 MINS

46:57

10 Mar 2021

#56

#56 Polygenic risk scores in admixed populations with Bárbara Bitarello

Polygenic risk scores (PRS) rely on the genome-wide association studies (GWAS) to predict ... more

17 Feb 2021

1 HR 30 MINS

1:30:12

17 Feb 2021

#55

#55 Phylogenetics and the likelihood gradient with Xiang Ji

In this episode, we chat about phylogenetics with [Xiang Ji] (http://xiang-ji-ncsu.github.... more

13 Jan 2021

57 MINS

57:02

13 Jan 2021

#54

#54 Seeding methods for read alignment with Markus Schmidt

In this episode, [Markus Schmidt] (http://itbe.hanyang.ac.kr/staff-members/markus-schmidt/... more

16 Dec 2020

1 HR 00 MINS

1:00:46

16 Dec 2020

#53

#53 Real-time quantitative proteomics with Devin Schweppe

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Devin Schwepp... more

18 Nov 2020

1 HR 03 MINS

1:03:13

18 Nov 2020

#52

#52 How 23andMe finds identical-by-descent segments with William Freyman

In this episode, [Will Freyman] (http://willfreyman.org) talks about identity-by-descent (... more

27 Oct 2020

42 MINS

42:40

27 Oct 2020

#51

#51 Basset and Basenji with David Kelley

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [David Kelley]... more

07 Oct 2020

1 HR 13 MINS

1:13:58

07 Oct 2020

#50

#50 ENCODE3 with Jill Moore

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Jill Moore] (... more

10 Sep 2020

56 MINS

56:02

10 Sep 2020

#49

#49 Most Permissive Boolean Networks with Loïc Paulevé

In systems biology, Boolean networks are a way to model interactions such as gene regulati... more

19 Aug 2020

1 HR 04 MINS

1:04:01

19 Aug 2020

#48

#48 Machine learning for drug development with Marinka Zitnik

In this episode, [Jacob Schreiber] (https://jmschrei.github.io/) interviews [Marinka Zitni... more

29 Jul 2020

1 HR 25 MINS

1:25:08

29 Jul 2020

#47

#47 Reproducible pipelines and NGLess with Luis Pedro Coelho

[NGLess] (http://ngless.embl.de/) is a programming language specifically targeted at next ... more

24 Jun 2020

57 MINS

57:34

24 Jun 2020

#46

#46 HiFi reads and HiCanu with Sergey Nurk and Sergey Koren

In this episode, I continue to talk (but mostly listen) to [Sergey Koren] (https://genomei... more

27 May 2020

1 HR 09 MINS

1:09:08

27 May 2020

#45

#45 Genome assembly and Canu with Sergey Koren and Sergey Nurk

In this episode, [Sergey Nurk] (https://genomeinformatics.github.io/people/nurk/) and [Ser... more

20 May 2020

1 HR 16 MINS

1:16:34

20 May 2020

#44

#44 DNA tagging and Porcupine with Kathryn Doroschak

Porcupine is a molecular tagging system—a way to tag physical objects with pieces of DNA c... more

29 Apr 2020

45 MINS

45:00

29 Apr 2020

#43

#43 Generalized PCA for single-cell data with William Townes

[Will Townes] (https://willtownes.github.io/) proposes a new, simpler way to analyze scRNA... more

27 Mar 2020

59 MINS

59:44

27 Mar 2020

#42

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

In this episode, we hear from [Amatur Rahman] (https://orcid.org/0000-0002-9166-1220) and ... more

28 Feb 2020

53 MINS

53:20

28 Feb 2020

#41

#41 Epidemic models with Kris Parag

[Kris Parag] (https://www.imperial.ac.uk/people/k.parag) is here to teach us about the mat... more

27 Jan 2020

1 HR 08 MINS

1:08:08