MicroRNAs (miRNAs) have recently been discovered as an important class of non-coding RNA genes that play a major role in regulating gene expression, providing a means to control th...
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseu...
In this paper, we present CONTRAlign, an extensible and fully automatic framework for parameter learning and protein pairwise sequence alignment using pair conditional random field...
We present a model for predicting HLA class I restricted CTL epitopes. In contrast to almost all other work in this area, we train a single model on epitopes from all HLA alleles a...
David Heckerman, Carl Myers Kadie, Jennifer Listga...
Abstract. We present a fast converging method for distance-based phylogenetic inference, which is novel in two respects. First, it is the only method (to our knowledge) to guarante...
Constantinos Daskalakis, Cameron Hill, Alexander J...
Abstract. A probabilistic graphical model is developed in order to detect the dependent evolution between different sites in biological sequences. Given a multiple sequence alignme...
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gen...
Computational and comparative analysis of protein-protein interaction (PPI) networks enable understanding of the modular organization of the cell through identification of functio...
Abstract. This paper presents a new method for studying protein folding kinetics. It uses the recently introduced Stochastic Roadmap Simulation (SRS) method to estimate the transit...
Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L...