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by ivan

A talk by Dr. Skinner May 16th

May 14, 2014 in Labwide Announcements

Just a little reminder about the talk we will have on Friday.

It is by Dr. Michael Skinner, who's big claim to fame (?) is that non-genetic mechanisms can produce inheritable traits (i.e. chemical modifications that do not change the DNA sequence). I shall not pass any judgement (even though this disclaimer makes my bias obvious). The article attached tells a good story about his research, its implications and reception.

Please read this: Skinner Science

As one of the not-so-many evolutionary biology labs on campus, I believe that we should be able to ask a few provocative questions this Friday.

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by arnab

Combined Annotation–Dependent Depletion

May 11, 2014 in Labwide Announcements

Following up,

I will be discussing the paper CADD published not so long ago in Nature Genetics http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html, which implements a hyper-plane support vector machine trained to rank pathogenic variants in the human genome. The discussion will take place on friday, May16 from 3:00 pm to 4:30 pm

-Arnab

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by aaron

Random Walks in Gene Space

May 11, 2014 in Labwide Announcements

Gentleman,

I will be leading out in a discussion on Sahinalp's paper on random walks and driver genes, May 13 if anyone is around.

Here is the paper: HitNDdrive-Sahinalp-2014

 

-aaron

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by shams

Polar Bear Genome

May 10, 2014 in Shams' Blog

Hey guys!

So it looks like they recently published a reference genome for a polar bear. There's a bit of an interesting discussion over the genes found to be under positive selection on the polar bear lineage

Here's the article:
http://www.cell.com/cell/abstract/S0092-8674%2814%2900488-7

Toodles
-Shams

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by Jason

Something awesome

May 4, 2014 in Jason's Blog

This is hilarious. Thanks Ivan.

PE-genomics

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by ivan

A few curious papers.

April 3, 2014 in Ivan's Blog, Labwide Announcements

Here are a few intereseting recent development that have happened in the past week:

1) The paper I would like to talk about next Thursday: http://www.pnas.org/content/early/2014/03/19/1220873111

2) A paper about "machine teaching": http://www.tandfonline.com/doi/abs/10.1080/09540091.2014.885279#.Uz3HInXqfbg

3) A paper on differential gene expression detection: http://www.biomedcentral.com/1471-2105/15/79

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by Jason

Detailed analysis of Neanderthal genomes

December 18, 2013 in Jason's Blog, Labwide Announcements

Svante Pääbo's lab has just published a detailed analysis of the newer high-resolution Neanderthal genome sequences! This is very exciting and worth a look; someone, maybe me, should present this paper in lab meeting in January.

See the paper here.

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by ivan

A simple bridge between perl and C++

November 5, 2013 in Labwide Announcements

I have created a simple example script that wraps around the perlapi. This allows perl code to use C++ functions. There are a few accessory functions, that allow to convert a perl array into a c array and back. This may require a little cleanup so that it's not mandatory to de-reference the array in perl.

Hopefully the code is not too hard to understand. I would like to give a quick rundown of this on the Friday meeting if possible - it seems like a few people can benefit from this.

I will also write a short blogpost on my blog, and let you know when that's done.

The code is hosted here.

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by Jason

Machine Learning Toolkit, Mahout

November 3, 2013 in Labwide Announcements

For anyone who's project or interests touch on machine learning, I came across the Apache project Mahout. It focuses on scalable implementations of machine learning algorithms, and appears to have a pretty active user community. It's written in Java.

The main project site is: Apache Mahout.

There is also an article about it in the current issue of Dr. Dobbs (the programming magazine).

mantle-mahout

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by ivan

Short update on the Palantir visualization

September 26, 2013 in Ivan's Blog

I have put together a simplistic R script that draws a few circles next to the branches on a tree.

Screenshot - 09252013 - 06:27:27 PM
Thus far, it is a rather simple hack that uses a the obscure numbering of branches provided by APE. I foresee that it might be necessary to come up with a better way to encode branch identity. This really depends on what the output from Palantir is.

Another problem is that I am using the plotrix library for drawing things. Sadly, it does not scale well when a window is resized, so you might end up with elliptical circles. Additionally, I will have to play with the coordinates of the circle offsets to make sure they consistently fit on the picture.

Hopefully, when I get the data, it will not be too hard to make work properly.

The current usage information is provided in the repository description.

 

 

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