User: Douglas S. Stones

Reputation:
260
Status:
New User
Location:
Melbourne, Australia
Website:
https://sites.google.c...
Last seen:
6 years, 10 months ago
Joined:
8 years, 7 months ago
Email:
t****************@yahoo.com

My primary research interest is Latin squares (combinatorics) and problems relating to Latin squares. Recently I have been expanding my interests into computer science and computational biology. Please visit my website for more info (e.g. a list of publications).

Posts by Douglas S. Stones

<prev • 15 results • page 1 of 2 • next >
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Software For Hydrogen Bond Detection In Pdb Data?
... In order to study the network structure of proteins, I'm looking for software that can predict the existence of hydrogen bonds in proteins from PDB data. I'm intending on running this software for ~1000 PDB files. After searching around with Google, there appears to be a range of software availabl ...
pdb protein written 7.3 years ago by Douglas S. Stones260 • updated 7.3 years ago by Keith Callenberg890
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How Can I Find The Distances Between Alpha Helices And Beta Strands In Proteins?
... I'm attempting to repeat a computational experiment performed in: Ron Milo, et al., Superfamilies of Evolved and Designed Network, Science 303, 1538 (2004). Among other experiments, they look for network motifs in protein structures. According to their paper, their protein networks were generated ...
network protein written 7.6 years ago by Douglas S. Stones260 • updated 7.2 years ago by Chris1.6k
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Comment: C: Is There Interest In K-Node Network Motifs For Large K?
... Thanks for that -- I think I can safely make the above claim. Also, your second paragraph raises quite an important point. Hmm... ...
written 7.9 years ago by Douglas S. Stones260
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Is There Interest In K-Node Network Motifs For Large K?
... A motif in a network is a connected subgraph that occurs significantly more frequently as an induced subgraph than would be expected in a similar random network. From what I've read in various papers, it seems that the vast majority of interest in network motifs is focussed on k-node motifs for k=3 ...
network motif graphs written 8.0 years ago by Douglas S. Stones260 • updated 8.0 years ago by Casin Winner0
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Comment: C: A Food Web Whose Species Have Been Dna Sequenced?
... Hmm... It looks like finding a decent food web is going to be the difficult part. I don't really expect 100% closed, but it would be nice to have external influences minimal. ...
written 8.3 years ago by Douglas S. Stones260
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Comment: C: A Food Web Whose Species Have Been Dna Sequenced?
... Thanks for that. In fact, I plan to use the data to identify what diet changes are likely to have occurred in the food web as it evolved. ...
written 8.3 years ago by Douglas S. Stones260
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A Food Web Whose Species Have Been Dna Sequenced?
... I'm currently looking into the evolution of food webs and wonder: Is there DNA sequence data around for all species belonging to some food web? Ideally, I would like the species in this food web to have been fairly isolated on an evolutionary time scale. I would like to find the phylogenetic tree ...
phylogenetics dna written 8.3 years ago by Douglas S. Stones260 • updated 9 weeks ago by kasdfd0
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Comment: C: In Mrbayes, What Does It Mean For A Node To Have More Than Two Descendants?
... Thanks, that's really helpful. ...
written 8.4 years ago by Douglas S. Stones260
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In Mrbayes, What Does It Mean For A Node To Have More Than Two Descendants?
... In MrBayes it's possible to generate phylograms that contain nodes with more than two descendants. Such an example arises in the MrBayes manual (see this) for the basic primates.nex. Question: How should nodes with more than two descendants be interpreted? Strictly speaking these should be bi ...
phylogenetics written 8.4 years ago by Douglas S. Stones260 • updated 8.4 years ago by Rvosa570
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Seeking Random Graph Models Of Evolving Food Webs
... Recently I've started to become interested in network motifs and the surrounding issues. In particular, it seems difficult to be able to theoretically classify whether or not a certain frequency of a subgraph in a network constitutes a motif or not. With this in mind, I'm thinking about using rand ...
motif random written 8.4 years ago by Douglas S. Stones260 • updated 8.4 years ago by Larry_Parnell16k

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