Alle afleveringen
70 afleveringen, van nieuw naar oud
-
#20 B cell receptor substitution profile prediction and SPURF with Kristian Davidsen and Amrit Dhar
30 april 2018 · 2 uur 1 min
In this episode
Kristian Davidsen
and
Amrit Dhar
present their project called SPURF.
SPURF can predict the B cell receptor (BCR) substitution profile of a given clonal
family based on a single representative sequence from that family.
SPURF works by fitting a tensor regression model to publicly available
Rep-seq data. Lees meerLinks:
Preprint: Predicting B Cell Receptor Substitution Profiles Using Public Repertoire Data
Blog post about SPURF by Erick Matsen
SPURF on GitHub
-
#19 Genome fingerprints with Gustavo Glusman
7 april 2018 · 1 uur 29 min
In this episode, Gustavo Glusman explains his method of reducing a VCF file
to a small “fingerprint”, which could be then used to detect duplicate genomes,
infer relatedness, map the population structure, and more. Lees meerLinks:
The genome fingerprints paper
The genotype fingerprints preprint
The data fingerprints preprint
The blog post about time series visualization
-
#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi
3 maart 2018 · 1 uur 53 min
The final round of Bioinformatics Contest 2018 was held on February 24-25th,
and the qualification round took place two weeks earlier. Lees meerI invited the organizers of the contest, Alexey Sergushichev and Ekaterina Vyahhi,
to discuss the problems and find out what it was like to organize the contest.Timestamps for the problems:
Qualification round
0:41:38 Problem 1. Synthesis of ATP
0:48:46 Problem 2. Restriction Sites
1:06:42 Problem 3. Tandem Repeats
Final round
1:14:00 Problem 1. Recombination of Plasmids
1:25:30 Problem 2. Species Recovering
1:28:39 Problem 3. Haplotype Phasing
1:36:34 Problem 4. Cluster the Reads
1:40:25 Problem 5. Cattle Breeding
Links:
The contest problems on Stepik
The final scoreboard
Bioinformatics Institute
-
#17 Rarefaction, alpha diversity, and statistics with Amy Willis
22 januari 2018 · 1 uur 14 min
In this episode, Amy Willis joins me to talk about good and bad ways to
estimate taxonomic richness in microbial ecology studies. Lees meerLinks:
Rarefaction, alpha diversity, and statistics
Estimating Diversity via Frequency Ratios
Estimating the Number of Species in Microbial Diversity Studies
Summer Institutes 2018 at the University of Washington
STAMPS: Strategies and Techniques for Analyzing Microbial Population Structures
bio2040, a new podcast by Flavio Rump
-
#16 Javier Quilez on what makes large sequencing projects successful
24 december 2017 · 1 uur 4 min
Javier Quilez and I discuss what it’s like to be
a bioinformatician, how to improve communication between the wet and dry labs
and make the research more reproducible. Lees meerMake sure to read Javier’s paper we are discussing; it’s a light and entertaining read.
The last author on this paper is Guillaume Filion, whom you may
remember from the episode on generating functions.Links:
Parallel sequencing lives, or what makes large sequencing projects successful
-
#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger
26 november 2017 · 1 uur 9 min
Geoffrey Schiebinger explains
how reconstructing developmental trajectories from single-cell RNA-seq data can be reduced to the
mathematical problem called optimal transport. Lees meerLinks:
Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.
Talk by Geoffrey and Lénaïc Chizat
-
#14 Generating functions for read mapping with Guillaume Filion
13 november 2017 · 1 uur 10 min
Guillaume Filion recently published a preprint in which he applies
generating functions, a concept from analytic combinatorics,
to estimating the optimal seed length for read mapping. Lees meerIn this episode, Guillaume and I attempt to explain the core concepts from
analytic combinatorics and why they are useful in modeling sequences.Links:
Guillaume’s preprint: Analytic combinatorics for bioinformatics I: seeding methods
Once upon a BLAST
Guillaume’s blog, «The Grand Locus»
Dan Gusfield’s home page
featuring the fast fourier transform lectures I mention in the podcastAfter we recorded the podcast, Guillaume wrote to me to clarify the
relationship between read mapping and BLAST:I looked into my notes about BLAST. The problem that it solves is the following: “Given that a local alignment has score S, what is the probability that it does not contain a word of score T or greater”? The background work of Karlin and Altschul is used to give a statistical significance for S (what is the probability that a “Smith-Waterman random walk” starting at height 0 would reach height S, i.e. what is the probability that aligning two random proteins would yield a score S). The authors write in the original paper “Theory does not yet exist to calculate the probability q that such segment pair will contain a word pair with a score of at least T. However, one argument suggests that q should depend exponentially upon the score of the MSP”.
This is the part that I did not remember well. MSP stands for Maximal Segment Pair, this is the “longest fragment” with “highest score” in the alignment. I thought that Karlin and Altschul solved this part as well, but the authors just go empirical and they calibrate the relationship between T and S with simulations.
I realize a little bit better now that my work is precisely about this problem that the authors of BLAST could not solve, but as you pointed out, I am attacking only a very specific sub-case that is much easier because the models of …
-
#13 Bracken with Jennifer Lu
21 oktober 2017 · 47 min
Jennifer Lu joins me to discuss species abundance estimation from metagenomic sequencing data. Lees meer
Links:
The Bracken paper
The Kraken paper
The preprint that applies Kallisto to metagenomics
-
#12 Modelling the immune system and C-ImmSim with Filippo Castiglione
8 oktober 2017 · 1 uur 7 min
In this episode, Filippo Castiglione and I discuss different ways to model the immune system. Lees meer
Links:
Celada’s and Seiden’s 1992 paper, “A computer model of cellular interactions in the immune system”
Filippo’s 2001 paper, “Design and implementation of an immune system simulator”
PLOS One paper, “Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System”
A paper about modelling sea bass vaccination using C-ImmSim
C-ImmSim homepage
The online simulator based on C-ImmSim and the paper describing it
Special thanks to Martina Stoycheva for bringing this work to my attention.
-
#11 Collective cell migration with Linus Schumacher
18 september 2017 · 1 uur
In this episode, Linus Schumacher joins me to discuss mathematical models of collective cell migration and multidisciplinary research. Lees meer
Links:
Semblance of Heterogeneity in Collective Cell Migration and associated code
Multidisciplinary approaches to understanding collective cell migration in developmental biology
Linus’s homepage
-
#10 Spatially variable genes and SpatialDE with Valentine Svensson
3 september 2017 · 58 min
Valentine Svensson
explains how he analyzes spatially-annotated single cell gene expression data
using Gaussian processes. Lees meerLinks:
Valentine’s preprint, “SpatialDE - Identification Of Spatially Variable Genes”
SpatialDE code on GitHub
Valentine’s personal page
The Integrative Biology & Medicine conference
-
#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing
18 augustus 2017 · 46 min
Michael Tessler
and
Christopher Mason
join me to talk about their comparison of
16S amplicon sequencing and
shotgun sequencing for quantifying microbial diversity. Lees meerLinks:
The 2017 Nature paper that we discuss: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
Michael’s et al. 2016 paper that describes their original 16S study: A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil
The sequencing data for these studies is available from NCBI:
PRJNA310230
(16S),
PRJNA389803
(shotgun)Michael’s website
Christopher’s lab website
The Integrative Biology & Medicine
conference, featuring the talk on Postmodern Synthesis by Eugene Koonin -
#8 Perfect k-mer hashing in Sailfish
5 augustus 2017 · 22 min
The original version of Sailfish,
an RNA-Seq quantification tool, used minimal perfect hash functions to
replace k-mers with unique integers.
(The current version appears to be using a Cuckoo hashmap instead.) Lees meerThis is my attempt to explain how a minimal perfect hash function could be
built. The algorithm described here is not exactly the same as the one
Sailfish used, but it follows the same idea.Sections:
Sailfish and perfect hashing (1:15)
Perfect hashing based on binary search or hash tables (4:34)
Random hash functions (7:34)
Perfect hash function based on an acyclic graph (12:16)
Links:
The Sailfish paper
The paper describing the perfect hashing algorithm
The birthday paradox
Integrative Biology & Medicine
-
#7 Metagenomics and Kraken
9 juli 2017 · 28 min
What is metagenomics and how is it different from phylotyping? Lees meer
What is Kraken and how can it be faster than BLAST?
Let’s try to sort this out.
Sections:
Culturing and its limitation (00:18)
Metagenomics vs phylotyping (1:43)
BLAST (5:53)
The idea behind Kraken (8:14)
How Kraken organizes its database (18:08)
Links:
The paper about Kraken
A freely accessible (though a bit dated) book on metagenomics
Correction: in this episode, I incorrectly state that Kraken operates on
phylogenetic trees, whereas in fact it operates on taxonomic trees.In practice this means that when Kraken cannot decide among several species,
it assigns the read to their lowest common taxon (genus, family etc.),
not their latest common evolutionary ancestor. -
#6 Allele-specific expression
25 juni 2017 · 33 min
I talk about allele-specific expression: why it arises and how it can be
reliably detected. Lees meerSections:
The biology of allele-specific expression (2:17)
Detecting allele-specific expression with RNA-seq (7:46)
Mapping and sequencing biases (16:39)
The experiment in yeast (19:47)
Statistical models (21:44)
Links:
A powerful and flexible statistical framework for testing hypotheses of
allele-specific gene expression from RNA-seq dataSupplemenal information
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
The talk by John Marioni
The blog post explaining the RSEM model
-
#5 Relative data analysis and propr with Thom Quinn
10 juni 2017 · 56 min
In this episode, Thom Quinn and I explore different ways
to transform and analyze relative data arising in genomics. Lees meerWe also discuss
propr, Thom’s R
package to compute various proportionality measures.Links:
Thom’s preprint about propr —
take a look if you feel lost in all the quantities that we discuss :)David Lovell original paper introducing proportionality for relative data
and a very detailed appendixIonas Erb’s paper introducing the ρ metric
Vignettes for propr
-
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
29 mei 2017 · 55 min
In this episode, I meet with Georg Stricker and Julien Gagneur from the Technical University of Munich
to discuss ChIP-seq data analysis and their tool, GenoGAM. Lees meerLinks:
Preprint about GenoGAM
Georg on GitHub
Julien’s lab on Twitter
[BC]2 — The Basel Computational Biology Conference (Basel, September 2017), where you can meet Georg
The European Human Genetics Conference (Copenhagen, May 2017), where you can meet Daniel Bader from Julien’s lab
Register for the Summer School in Bioinformatics & NGS Data Analysis (#NGSchool2017) (Poland, September 2017)
-
#3 miRNA target site prediction and seedVicious with Antonio Marco
12 mei 2017 · 57 min
In this episode
Antonio Marco
talks about miRNA target site prediction and his tool, seedVicious. Lees meerLinks:
seedVicious preprint
seedVicious manual
-
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk
29 april 2017 · 1 uur 9 min
In this episode
Aleksandra Kolodziejczyk
talks about single-cell RNA sequencing. Lees meerLinks:
A review paper by Aleksandra
Comparative analysis of single-cell RNA sequencing methods, including the cost table
Power Analysis of Single Cell RNA‐Sequencing Experiments
Monocle: a toolkit for analyzing single-cell gene expression experiments
Questions from listeners on
bioinformatics.chat
and
reddit -
#1 Transcriptome assembly and Scallop with Mingfu Shao
16 april 2017 · 44 min
In this episode, Mingfu Shao talks about
Scallop, an accurate reference-based transcript assembler. Lees meerLinks:
The preprint about Scallop
The preprint about flow decomposition
The video of a talk by Ben Langmead about Rail-RNA
The preprint about Rail-RNA