
aaron wrote a new post, stochastic tunnelling, on the site de Koning Lab Intranet 3 years, 5 months ago
Sorry for the delay.
Here’s the paper: Genetics 2004 Iwasa. Have a glance, its pretty straight forward.
Aaron.
I’ll let you know the room as soon as I can. July 11 at 1:30.

aaron posted an update 3 years, 6 months ago
Duh, 3rd rule of fight club: No shirt or shoes

aaron changed their profile picture 3 years, 7 months ago

aaron wrote a new post, Random Walks in Gene Space, on the site de Koning Lab Intranet 3 years, 7 months ago
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: HitNDdriveSahinalp2014
aaron

aaron posted an update 3 years, 7 months ago
Working through dank’s paper, way easier than I thought it would be. I hang my head in shame now.

chenzhe and aaron are now friends 3 years, 7 months ago

arnab and aaron are now friends 3 years, 7 months ago

aaron posted an update 3 years, 7 months ago
Network Theory, here I come.

aaron posted an update 3 years, 8 months ago
Finally got the approximation method validated. Feels good to be me.

aaron commented on the post, A few curious papers., on the site de Koning Lab Intranet 3 years, 8 months ago
Got it. Thanks.

aaron changed their profile picture 4 years, 4 months ago

aaron commented on the post, HolbothJensen EM method, on the site de Koning Lab Intranet 4 years, 5 months ago
The equation I implemented was the general solution, and in the case of irreversibility spits out complex numbers. In the case of reversibility, it is sometimes more beneficial to work with the matrix S, because […]

aaron commented on the post, Mutation Selection Model, on the site de Koning Lab Intranet 4 years, 5 months ago
Post is empty…

aaron wrote a new post, HolbothJensen EM method, on the site de Koning Lab Intranet 4 years, 5 months ago
Based on the work by Holboth & Jensen, the mathematical formalism for modelling DNA sequences via the EM algorithm is as follows;
$$P_{ab}(t)=sqrt{(frac{pi_{b}}{pi_{a}})} sum […]

aaron commented on the post, Success….kinda., on the site de Koning Lab Intranet 4 years, 5 months ago
Wasn’t really “mathy”, my apologies. But the deviance is due to the fact that the scaling of the Qmatrix in a population model requires more work. To be continued….

aaron wrote a new post, Success….kinda., on the site de Koning Lab Intranet 4 years, 5 months ago
As promised a more mathematicallyformulated description of the latest assignment…
Once we were confident about the program we previously constructed, it was time to expand the horizon, so to speak. A brief […] 
aaron wrote a new post, On to “bigger” things…, on the site de Koning Lab Intranet 4 years, 6 months ago
After finally being able to implement an equation(and know that it works) in matlab, the journey has only begun.
It’s now time to expand this idea to instead of a state space of just 4 nucleotides, how about […]

aaron wrote a new post, Circles, on the site de Koning Lab Intranet 4 years, 6 months ago
First week on the job, and it has been somewhat of a roller coaster.
Day 1: My assignment is simple: Implement equation 54 from Minin and Suchard’s paper, “Counting labeled transitions in continoustime Markov […]

aaron posted an update 4 years, 6 months ago
I spoke to Vladmir Minin, he tells me that the results are calculated using eqn 50 and 51. Something I had a suspicion of, but wanted to verify.@jason

aaron posted an update 4 years, 6 months ago
Dr. de Koning, you once told me that the first Minin and Suchard paper you had me read was the most math intensive. That was clearly a lie. Haha@jason
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