Wednesday, June 18, 2014

Blog posts and formal publications

One possible use of blog posts is as first drafts of ideas that might make their appearance in a refereed publication at a later date. Thus, many of my blog posts have appeared in one form or another in my recent publications. Here I have listed the ones that I can remember using, just in case anyone wants a citable reference for the information in these posts.

A. Morrison DA (2013) Phylogenetic networks are fundamentally different from other kinds of biological networks. In W.J. Zhang (ed.) Network Biology: Theories, Methods and Applications (Nova Science Publishers, New York) pp. 23-68.

    9 Biological versus phylogenetic networks
  13 Network measures and phylogenetic networks
  23 An explanation of graph types
  25 Networks and bootstraps as tree-support criteria
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  53 Are mathematical constraints biologically realistic?
  54 Some odd network definitions and terms
  63 Human races, networks and fuzzy clusters
  69 Is this the first network from conflicting datasets?
  70 Why do we still use trees for the Neandertal genealogy?
  72 Networks and most recent common ancestors
  74 Open questions about evolutionary networks, part 1
  75 Open questions about evolutionary networks, part 2
  76 Open questions about evolutionary networks, part 3
  88 When is there support for a large phylogeny?
  90 Explanation of the names for phylogenetic networks
  94 Phylogenetic position of turtles: a network view
  99 How networks differ from bootstrapped trees
107 We should present bayesian phylogenetic analyses using networks
115 Is there a philosophy of phylogenetic networks?

B. Morrison DA (2014) Phylogenetic networks — a new form of multivariate data summary for data mining and exploratory data analysis. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 4: in press.

  29 Network analysis of scotch whiskies
  50 Phylogenetic network of the FIFA World Cup
  61 How to interpret splits graphs
101 Distortions and artifacts in Principal Components Analysis analysis of genome data
103 Networks can outperform PCA ordinations in phylogenetic analysis
114 Network analysis of Genesis 1:3
119 Network of ancient Thai bronze Buddha images
134 A network analysis of Simon and Garfunkel
159 Networks and human inter-population variation
172 The acoustics of the Sydney Opera House

C. Morrison DA (2014) Next generation sequencing and phylogenetic networks. EMBnet.journal: Bioinformatics in Action 20: e760.

191 Next Generation Sequencing and phylogenetic networks

D. Morrison DA (2014) Phylogenetic networks: a review of methods to display evolutionary history. Annual Research and Review in Biology 4: 1518-1543.

    2 The first phylogenetic network (1755)
  21 The second phylogenetic network (1766)
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  67 Metaphors for evolutionary relationships
  89 Relationship trees drawn like real trees
168 Who first used the term "phylogenetic network"?
182 Affinity networks updated
183 Reticulation patterns and processes in phylogenetic networks
187 What are evolutionary networks currently used for?

E. Morrison DA (2014) Rooted phylogenetic networks for exploratory data analysis. Advances in Research 2: 145-152.

  43 Rooted networks for exploratory data analysis

F. Morrison DA (2014) Is the Tree of Life the best metaphor, model or heuristic for phylogenetics? Systematic Biology 63: 628-638.

  23 An explanation of graph types
  34 Networks of affinity rather than genealogy
  36 Networks of genealogy
  58 Who published the first phylogenetic tree?
  89 Relationship trees drawn like real trees
143 Resistance to network thinking
144 Destroying the Tree of Life?
147 Should phylogenetic modelling proceed from simple to complex or vice versa?
171 Conflicting placental roots: network or tree?
182 Affinity networks updated

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