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RECOMB
2008
Springer
16 years 3 months ago
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, ...
Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel
RECOMB
2007
Springer
16 years 3 months ago
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications
Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorith...
Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller,...
RECOMB
2009
Springer
15 years 10 months ago
Inferring the Recent Duplication History of a Gene Cluster
Abstract. Much important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to evolve new functions. Computational methods to extract evolutionary in...
Giltae Song, Louxin Zhang, Tomás Vinar, Web...
ASM
2000
ASM
15 years 7 months ago
Modeling the Dynamics of UML State Machines
We define the dynamic semantics of UML State Machines which integrate statecharts with the UML object model. The use of ASMs allows us (a) to rigorously model the event driven run...
Egon Börger, Alessandra Cavarra, Elvinia Ricc...
BICOB
2009
Springer
15 years 7 months ago
Constrained Fisher Scores Derived from Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Predictio
Protein-protein interaction plays critical roles in cellular functions. In this work, we propose a computational method to predict protein-protein interaction by using support vec...
Alvaro J. González, Li Liao