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Here we collect our writing on various topics from our day-to-day work and our reading clubs.

Four Topics in Computational Biology

I will be giving a course with these lecture in TH18 at a advanced undergraduate course at the Department of Statistics

1 Enumeration in Phylogenetics
2. Tree Generating Processes
3. Compatibility
4. Statistical Alignment

5 Physics of Molecules: QM and MM
6 Integrators and Approximations
7 Applications I: Reactions
8 Applications II: Protein Folding

9 Small Molecules
10 Polya Enumeration
11 Graph Grammars and Reaction Prediction
12 3D Prediction from Graphs

13 Modeling the Evolution of Complex Objects: Languages, Patterns, Movements
14 The Comparative Method
15 Example I: Proteins
16 Example II: Networks

They will appear on this page as I finish them:

https://heingroupoxford.com/learning-resources/lectures/

Skype Book Discussion Group in “Computational Complexity of Sampling”

The present version can be found here:

Click to access ComputationalComplexityOfCountingAndSampling.pdf

The author – Istvan Miklos – believes he will always be ahead of the readers in writing. We would then write a review that would be published about the same time as the book was published and we put an extended report on this page:

https://heingroupoxford.com/learning-resources/lectures/

We also give a summarizing lecture when we have finished the book. Earlier when we did this, we met every 2nd day doing about 20 pages each time, but it can depend on the individual book. We did a similar thing to Mike Steels 2016-book, which I believe was beneficial to both authors and readers.

The ideal number of participants in such a group is 3-5. It would have to be online since I will be Israel. I like to choose a time that is either starting or ending of working day so it interpheres minimally with work. If you know somebody interested in participating in this, please tell me. If it proves a crappy book, we will stop reading, but that is not what I expect.

Jotun gave 2 talks [31.5 1.6]

Combinatorics of Recombination:  https://www.dropbox.com/s/magvyy1jkkgin63/graduate%20lecture%201.6.17%20recombi.pptx?dl=0

Research Collaboration: https://www.dropbox.com/s/gveaj5rwp0f7eok/A%20Few%20Things.pptx?dl=0

2 Distinguished Speakers: Wim Hordijk and Dave Swofford

 

Topics – both devoted to modelling in evolution: Models of Origins of Life & Phylogenetic 

Time:  Friday June 9th  2.00 PM – 4.30 PM

Venue:  Department of Statistics, Oxford, Large Lecture Theatre 

  1. 2.00 PM Generality and Robustness of the SVDQuartets Method for Phylogenetic Species Tree Estimation (Swofford)

 

Methods for inferring evolutionary trees based on phylogenetic invariants were first proposed nearly three decades ago, but have been virtually ignored by biologists.   A new invariants-based method for estimating species trees under the multispecies coalescent model was recently developed by Julia Chifman and Laura Kubatko, building on earlier work by Elizabeth Allman, John Rhodes, and Nicholas Eriksson.  This method comes from algebraic statistics and uses singular value decomposition to estimate the rank of matrices of site pattern frequencies.  Although the approach shows great promise, its performance on empirical and simulated data sets has not been adequately evaluated.

I will give a general introduction to the SVDQuartets method and present some results from a simulation study currently in progress (collaboration with Laura Kubatko and Colby Long) that demonstrate that SVDQuartets is potentially highly robust to deviations from the standard evolutionary models assumed by other species-tree estimation methods.

BREAK

  1. 3.30PM Autocatalytic Sets and the Origin of Life (Hordijk)

The main paradigm in origin of life research is that of an RNA world, where the idea is that life started with one or a few self-replicating RNA molecules. However, so far nobody has been able to show that RNA can catalyze its own template-directed replication. What has been shown experimentally, though, is that certain sets of RNA molecules can mutually catalyze each other’s formation from shorter RNA fragments. In other words, rather than having each RNA molecule replicate itself, they all help each other’s formation from basic building blocks, in a self-sustaining network of molecular cooperation.

Such a cooperative molecular network is an instance of an autocatalytic set, a concept that was formalized and studied mathematically and computationally as RAF theory.This theory has shown that autocatalytic sets are highly likely to exist in simple polymer models of chemical reaction networks, and that such sets can, in principle, be evolvable due to their hierarchical structure of many autocatalytic subsets. Furthermore, the framework has been applied succesfully to study real chemical and biological examples of autocatalytic sets.

In this talk I will give a general (and gentle) introduction to RAF theory, present its main results and how they could be relevant to the origin of life, and argue that the framework could possibly also be useful beyond chemistry, such as in analyzing ecosystems or even economic systems.

Screenshot 2017-06-02 17.59.00WINE IN COMMON AREA AFTER TALKS

Talk by BLAST INVENTOR

Speaker: Stephen Altschul

Screenshot 2017-05-17 10.51.14Title: Dirichlet Mixtures, the Dirichlet Process, and the Topography of Amino Acid Multinomial Space

Venue: Tuesday May 23rd 3.30 PM  Department of Statistics, Lecture Theatre (Lower Ground)

Abstract:   The Dirichlet Process is used to estimate probability distributionsthat are mixtures of an unknown and unbounded number of components.Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we have used the Dirichlet Process to construct such distributions.  The resulting mixtures describe multiple alignment data substantially better than do those previously derived.  They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on protein structure.  Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino-acid multinomial space.

The slides will be made available after the talk.

Comment: Stephen Altschul has finally proven that I can’t add 2 and 2. I have attended Altschul Dinners at my College [University College, Oxford] and never thought of connecting the two words Altschul and Altschul despite their obvious similarity. It is in honour of Stephen’s grandmother, whose brother was Arthur Lehman Goodhart and Master of UNIV 1951–63.