We consider the following problem: given a forest of gene family trees on a set of genomes, find a first speciation which splits these genomes into two subsets and minimizes the ...
Abstract. We describe a probabilistic model, implemented as a dynamic Bayesian network, that can be used to predict nucleosome positioning along a chromosome based on one or more g...
Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, ...
We study two problems in the double cut and join (DCJ) model: sorting – transforming one multilinear genome into another and halving – transforming a duplicated genome into a p...
Abstract. In a horizontal gene transfer (HGT) event a gene is transferred between two species that do not share an ancestor-descendant relationship. Typically, no more than a few g...
Abstract. Emerging research demonstrates the potential of proteinprotein interaction (PPI) networks in uncovering the mechanistic bases of cancers, through identification of intera...
Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, ...
Immense amounts of raw instrument data (i.e., images of fluorescence) are currently being generated using ultra high-throughput sequencing platforms. An important computational cha...
Abstract. Recent genome sequencing studies have shown that the somatic mutations that drive cancer development are distributed across a large number of genes. This mutational heter...
In this work we consider an inference task that biologists are very good at: deciphering biological processes by bringing together knowledge that has been obtained by experiments u...
Christian Widmer, Jose Leiva, Yasemin Altun, Gunna...