Daniel Chu's research while affiliated with The University of Sydney and other places
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Publications (7)
Extending the idea of our previous algorithm (17, 18) we developed a new sequential quartet-based phylogenetic tree construction method. This new algorithm reconstructs the phylogenetic tree iteratively by examining at each merge step every possible super-quartet which is formed by four subtrees instead of simple quartet in our previous algorithm....
Protein structure prediction (also known as the protein folding problem) studies the way in which a protein will ‘fold’ into
its natural state. Due to the enormous complexities involed in accuratly predicting protein structures, many simplifications
have been proposed. The Hydrophobic-Hydrophilic (HP) method is one such method of simplifying the pr...
This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster. This algorithm constructs evolutionary trees for a given set of DNA or protein sequences based on the topological information of every possible quartet trees. Our experimental results showed that it has several...
An interesting and important, but largely ignored question associated with the ML method is whether there exists only a single maximum likelihood point for a given phylogenetic tree. Mike Steel presented a simple analytical result to argue that the ML point is not unique (11). However, his view so far attracts only little attention. Though many res...
Recently we developed a new quartet-based algorithm for phylogenetic analysis (22). This algorithm constructs a limited number of trees for a given set of DNA or protein sequences and the initial experimental results show that the probability for the correct tree to be included in this small set of trees is very high. In this paper we further exten...
The Protein Folding Problem studies the way in which a protein - a chain of amino acids - will 'fold' into its natu- ral state. Predicting the way in which various proteins fold can be fundamental in developing treatments of diseases such as Alzeihmers and Systic Fibrosis. Classical solutions to calculating the final conformation of a protein struc...
Citations
... However, the experimental results presented in this paper suggest that, because of its excellent theoretical properties, the quartet-based method should never be overlooked. The problem of high computational cost can be alleviated using highperformance , or parallel computing systems [23]. The paper is organized as follows: our quartet-based algorithm is briefly described in Section 2. Its extension is discussed in Section 3. In Section 4 we present some experimental results. ...
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... The aim of this study is to show the potential impact in the search mechanics when shifting between LANs as well as to show the actual power and utility of the proposed distributed GA to solve the DNA fragment assembly problem. Another work dealing with high dimensional data is the work proposed in (Chu & Zomaya 2006), where authors proposed a parallel ant colony optimization for 3D Protein Structure Prediction using the HP Lattice Model, and results show the performance of the distributed ACO approach in terms of accuracy and network scalability. Another optimization problem dealing with big data is the work proposed in (Luque & Alba 2011b). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/273761068908547-1442281133370_Q64/Albert-Zomaya.jpg)
... This quartet error problem greatly hinders the quartet-based approach from a wide application. Previously we developed a quartet-based algorithm for the reconstruction of evolutionary trees [17, 18, 19]. Instead of constructing only one tree as output, this algorithm constructs a limited number of trees for a given set of DNA or protein sequences. ...
... The super-quartet method [12], which places a sub-tree (which may contain a number of taxa) on each vertex of a quartet tree to form a so-called super quartet, has been designed and implemented. The experimental results show that the evaluation of super-quartets at critical points can be very effective. ...
... This quartet error problem greatly hinders the quartet-based approach from a wide application. Previously we developed a quartet-based algorithm for the reconstruction of evolutionary trees [17, 18, 19]. Instead of constructing only one tree as output, this algorithm constructs a limited number of trees for a given set of DNA or protein sequences. ...
... Swarm Intelligence or SI remains little explored for protein structure prediction as yet [34][35][36][37][38][39][40], albeit having demonstrated rapid growth in the last few years [41][42][43][44]. ...
... TREE-PUZZLE is a computer program to reconstruct phylogeny trees from molecular sequence data by ML. The name, TREE-PUZZLE, is from a fast tree search algorithm, quartet puzzling [13,29,33,37], which allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise ML distances [28] as well as branch lengths for user specified trees. ...
