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Technical report TR05-18. Reconstruction of an evolutionary history for a set of organisms is an important research subject in computational biology. One approach motivated by graph theory constructs a relationship graph based on pairwise evolutionary closeness. The approach builds a tree...
Technical report TR08-07. In gene expression microarray data analysis, biclustering has been demonstrated to be one of the most effective methods for discovering gene expression patterns under various conditions. We present in this study a framework to take advantage of the homogeneously...
Technical report TR05-05. A lookahead branch-and-bound algorithm is proposed for solving the Maximum Quartet Consistency Problem where the input is a complete set of quartets on the taxa and the goal is to construct a phylogeny which satisfies the maximum number of given quartets. Such a...
Santana, Andre M., Tonhati, Humberto, Greco, Anthony J., Mishra, Bina, Cai, Zhipeng, Kumar, S. T. Bharani, Tantia, Madhu S., Jones, Brittany C., Saradhi, G. Pardha, Miziara, Melissa N., Kumar, M. Aravind, Kochan, Kelli J., Goldammer, Tom, Brunner, Ronald M., Caetano, Alexandre R., Weikard, Rosemarie, Womack, James E., Mathew, Boby, Kumar, Satish, Pelai, Vanderlei A., Filho, Edson A. R., Jeong, Jooha, Prasad, Aparna, Vijh, Ramesh K., Lin, Guohui, Moore, Stephen, Galvao, Stephan R., Mariani, Paola, Grant, Jason R., Stafuzza, Nedenia B., Fornitano, Larissa C., Riggs, Penny K., Stothard, Paul, Amaral, M. Elisabete
Background The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the...
Technical report TR10-04. This paper describes a novel and fast placement algorithm for field programmable gate array (FPGA) design space exploration. The proposed algorithm generates the placement based on the topological similarity between two configurations (netlists) in the design space....
Technical report TR08-06. The Capacitated Multicast Tree Routing Problem is considered, in which only a limited number of destination nodes are allowed to receive data in one routing tree and multiple routing trees are needed to send data from the source node to all destination nodes. The goal...
Technical report TR11-02. Given two genomic maps G1 and G2 each represented as a sequence of n gene markers, the maximal strip recovery (MSR) problem is to retain the maximum number of markers in both G1 and G2 such that the resultant subsequences, denoted as G1* and G2*, can be partitioned into...
Technical report TR03-06. Given a set of species and their similarity data, an important problem in evolutionary biology is how to reconstruct a phylogeny (also called evolutionary tree) so that species are close in the phylogeny if and only if they have high similarity. Assume that the...
Background Single nucleotide polymorphism (SNP) genotyping assays normally give rise to certain percents of no-calls; the problem becomes severe when the target organisms, such as cattle, do not have a high resolution genomic sequence. Missing SNP genotypes, when related to target traits, would...
Technical report TR04-12. For the Capacitated Multicast Routing Problem, we considered two models which are the Multicast k-Path Routing and the Multicast k-Tree Routing. We presented two improved approximation algorithms for them, which have worst case performance ratios of 3 and (2 + ρ) (ρ is...