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Matsen Group: home

Say we care about a function on pairs of trees (such as subtree-prune-regraft distance) that doesn’t make reference to the labels as such, but simply uses them as markers to ensure that the leaves end up in the right place. We’d like to calculate this function for all trees of a certain type. However, doing so for. Pair of labeled trees is a waste, because if we just relabel the two trees in the same way, we will get the same result. So, how many computations do we actually need to do? The answer is rath...

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Say we care about a function on pairs of trees (such as subtree-prune-regraft distance) that doesn’t make reference to the labels as such, but simply uses them as markers to ensure that the leaves end up in the right place. We’d like to calculate this function for all trees of a certain type. However, doing so for. Pair of labeled trees is a waste, because if we just relabel the two trees in the same way, we will get the same result. So, how many computations do we actually need to do? The answer is rath...
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Matsen Group: home | matsen.fredhutch.org Reviews

https://matsen.fredhutch.org

Say we care about a function on pairs of trees (such as subtree-prune-regraft distance) that doesn’t make reference to the labels as such, but simply uses them as markers to ensure that the leaves end up in the right place. We’d like to calculate this function for all trees of a certain type. However, doing so for. Pair of labeled trees is a waste, because if we just relabel the two trees in the same way, we will get the same result. So, how many computations do we actually need to do? The answer is rath...

INTERNAL PAGES

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Matsen Group: photos

http://matsen.fredhutch.org/photos.html

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Matsen Group: home

http://matsen.fredhutch.org/general/2014/05/13/sprmix.html}

Raquo; Incorporating new sequences into posterior distributions using SMC. The Bayesian approach is a beautiful means of statistical inference in general, and phylogenetic inference in particular. In addition to getting posterior distributions on trees and mutation model parameters, the Bayesian approach has been used to get posteriors on complex model parameters such as geographic location and ancestral population sizes of viruses, among other applications. The bummer about Bayesian computation? Softwar...

3

Matsen Group: members

http://matsen.fredhutch.org/members.html

Frederick A. "Erick" Matsen. Statistics PhD student (joint with Vladimir Minin). Programmer/analyst and PhD applicant. Statistics PhD student (joint with Vladimir Minin).

4

New paper on molecular evolution of B cells

http://matsen.fredhutch.org/general/2014/03/23/mebcell.html

New paper on molecular evolution of B cells. 23 Mar 2014, by Erick. Over the past year we’ve started in on a completely new research direction, which concerns B cells, the cells that make antibodies. Antibodies have to be able to bind a very large number of different molecules in order to neutralize pathogens or to mark them for destruction. As part of improving their binding for a given antigen they go through an evolutionary process of mutation (yes, the human genome mutating itself on purpose! We do e...

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Matsen Group: service

http://matsen.fredhutch.org/service.html

We started and run these initiatives:. A free online seminar about phylogenetics, since 2009. A discussion forum for phylogenetics, since 2014. To educate about and promote access to computational resources at the Fred Hutch, since 2014. A discussion forum for adaptive immune repertoire analysis, since 2016.

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What is this? · fredhutch.io

http://www.fredhutch.io/about

Education and access to computational methods at the Fred Hutchinson Cancer Research Center. Fredhutch.io is an initiative to facilitate education about and promote access to computational resources at the Fred Hutchinson Cancer Research Center. Maintain the Fred Hutch Galaxy instance, adding tools as needed. Offer training and consulting for researchers using Galaxy in their work. Offer a seven-week bioinformatics training course for beginners. The initiative was started by Erick Matsen.

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Raquo; Postdoc opening to learn about antibody development during HIV superinfection. Please see https:/ b-t.cr/t/506. Raquo; Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. This central message is not new, but it’s worth emphasizing because doing germline set inference is not part of most current studies of B cell receptor (BCR) sequences. Unsurprisingly, aligning sequences one by one to the. (full post). In this particular case, the starting point was the stunnin...

matsen.fredhutch.org matsen.fredhutch.org

Matsen Group: home

Say we care about a function on pairs of trees (such as subtree-prune-regraft distance) that doesn’t make reference to the labels as such, but simply uses them as markers to ensure that the leaves end up in the right place. We’d like to calculate this function for all trees of a certain type. However, doing so for. Pair of labeled trees is a waste, because if we just relabel the two trees in the same way, we will get the same result. So, how many computations do we actually need to do? The answer is rath...

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