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Guillaume Filion
Lives in Barcelona
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"Spock is also the scientist that I thought I would meet. Someone who would listen more than talk, and be detached and objective. Someone who could set aside ego and emotion in order to focus more clearly on Why. A teacher or colleague who wanted to touch me, but only to transfer information back and forth from my mind. This is not who I met. Instead, I think that Spock’s world is closer to the version of Science that I am still hoping to create."

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"This review describes our current understanding of how these functional genomic “secondary and tertiary structures” form a blueprint for global nuclear architecture and the potential they hold for understanding and manipulating genomic regulation."
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Guillaume Filion

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cette fois y avait pas de pastiche, mais le prochain...
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The legendary bioinformatician Gene Myers strikes back, and this time it is with long read alignments. “I pulled every trick I ever learned” with Daligner to get 25x – 40x speed improvement over BLASR”.
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Analysis of pop music by Music Information Retrieval.

"We show that, although pop music has evolved continuously, it did so with particular rapidity during three stylistic "revolutions" around 1964, 1983 and 1991. We conclude by discussing how our study points the way to a quantitative science of cultural change."
Abstract: In modern societies, cultural change seems ceaseless. The flux of fashion is especially obvious for popular music. While much has been written about the origin and evolution of pop, most claims about its history are anecdotal rather than scientific in nature.
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This is my latest article, published in GigaScience. The experience is very positive, and it was a pleasure to work together with the editor on this.

"The underlying hypotheses of the KS test are intrinsically incompatible with this approach and the test can produce false positives supported by extremely low p-values. This potentially makes the signed KS test a tool of p-hacking, which should be discouraged by replacing it with standard tests such as the t-test and by providing confidence intervals instead of p-values."

#statistics   #bioinformatics  
The two-sample Kolmogorov-Smirnov (KS) test is often used to decide whether two random samples have the same statistical distribution. A popular modification of the KS test is to use a signed version of the KS statistic to infer whether the values of one sample are statistically larger than the values of the other. The underlying hypotheses of the KS test are intrinsically incompatible with this approach and the test can produce false positives s...
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Have him in circles
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In this paper we present an efficient algorithm for sequence clustering. It is much faster than anything else we tested, and believe it or not, it is not a heuristic.

Starcode is now part of the standard toolbox of the team and is a key step of the TRIP pipeline. The source code is of course freely available. We have spent a lot of time trying to make it user-friendly, your feedback would be extremely very valuable!

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"We then illustrate how one can test for p-hacking when performing a meta-analysis and show that, while p-hacking is probably common, its effect seems to be weak relative to the real effect sizes being measured. This result suggests that p-hacking probably does not drastically alter scientific consensuses drawn from meta-analyses."
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The open reviews of my latest article are available from the pre-publication history (under editor's comment of February 27). There you can discover the discussion about the most appropriate test, and a power analysis of the KS test (courtesy Garrett Jenkison).
#statistics   #bioinformatics  
The two-sample Kolmogorov-Smirnov (KS) test is often used to decide whether two random samples have the same statistical distribution. A popular modification of the KS test is to use a signed version of the KS statistic to infer whether the values of one sample are statistically larger than the values of the other. The underlying hypotheses of the KS test are intrinsically incompatible with this approach and the test can produce false positives s...
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Writing email with Python can be very useful. For instance you can spam many people, or you can send yourself an email when a long script finishes running. Andrew Wheeler explains how to it on his blog.

"There are basically two parts of emailing within Python, 1) building the message and 2) opening your server and sending the mail."
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About my latest paper on the Kolmogorov-Smirnov test and p-hacking.

"After publishing the initial idea on my blog, several readers suggested to publish the argument with more visibility for the target audience. This gave me the motivation to find the right journal for this and to make the text more accurate and more accessible for biologists. This is my first community-driven publication, and for this reason, I am very proud of it."

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Computing the Levenshtein distance between two random words is quite a challenge. Most likely, the answer involves some Extreme Value Theory... Perhaps you have an idea on how to approach this question? #statistics
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Team leader at the CRG, Barcelona
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Randomness is an attitude
Introduction

"Because I give a fuck!"

That's why I am doing what I do. I give a fuck that everbody gets a chance to learn. I give a fuck that knowledge be shared. I give a fuck that children will live in a better world than ours.

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Barcelona
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Starcode: sequence clustering based on all-pairs search
bioinformatics.oxfordjournals.org

Abstract Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology.

The Extent and Consequences of P-Hacking in Science
journals.plos.org

Publication bias resulting from so-called "p-hacking" is pervasive throughout the life sciences; however, its effects on general conclusions

Emailing with Python and SPSS
andrewpwheeler.wordpress.com

Emailing automated messages using Python was on my bucket list for a few projects, so here I will illustrate how to do that within SPSS. Bas

"What then should we teach about hypothesis testing?" - Statistical Mode...
andrewgelman.com

Someone who wishes to remain anonymous writes in: Last week, I was looking forward to a blog post titled “Why continue to teach and use hypo

If cars were made by bioinformaticians...
blog.thegrandlocus.com

If cars were made by bioinformaticians... | Filed under cars, bioinformatics, software.

Our Paper: Genome-wide inference of ancestral recombination graphs
haldanessieve.org

This guest post is by Adam Siepel (@asiepel) on his paper with Matthew Rasmussen (@mattrasmus): Rasmussen and Siepel “Genome-wide inference

Longest runs and DNA alignments
blog.thegrandlocus.com

Longest runs and DNA alignments | Filed under sequence alignment, BLAST, bioinformatics.

COPE statement on inappropriate manipulation of peer review processes | ...
publicationethics.org

The Committee on Publication Ethics (COPE) has become aware of systematic, inappropriate attempts to manipulate the peer review processes of

Getting Genetics Done
gettinggeneticsdone.blogspot.com

A colleague needed some help getting Illumina BeadArray gene expression data loaded into R for data analysis with limma. Hopefully whoever r

Why Linux is awesome
blog.thegrandlocus.com

Why Linux is awesome | Filed under self-learning, open source, Linux.

How to Use libwireshark in C Program to Decode Network Packets
www.thegeekstuff.com

Wireshark is an open source network packet analyzer. It can capture, dissect, and decode various protocols. This helps Linux sysadmin to tro

A paper by Maggie Simpson and Edna Krabappel was accepted by two scienti...
www.vox.com

It's pretty funny. But it's also a sign of a bigger problem.

http://www.the-scientist.com/?articles.view/articleNo/41483/title/Illumi...
www.the-scientist.com

A massive screen yields the most comprehensive map of binary human protein interactions to date.

Creating a bioinformatics nation : Article : Nature
www.nature.com

Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all discipline

Because Reading is Fundamental
blog.codinghorror.com

26 Nov 2014. Because Reading is Fundamental. Most discussions show a bit of information next to each user: What message does this send? The

Gene blind analysis
yabib.blogspot.com

The problem I am starting to recognise a lot of known cancer genes, and while that is useful in many ways it also introduces a risk of confi

Hash functions.
www.azillionmonkeys.com

IMPORTANT NOTE: Since there has been a lot of interest for the code below, I have decided to additionally provide it under the LGPL 2.1 lice

I found the service at ShBarcelona to be good, with high level of responsiveness. The personnel is committed, foreigner-friendly and amicable. Negative point, I found the repair services (plumbers, electricians etc.) they contract overpriced. But overall they left me a good impression.
Public - 4 months ago
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