In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods ...
Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2break rearrangements represent standard reversals, fusions, ...
Abstract. Side-chain prediction is an important subproblem of the general protein folding problem. Despite much progress in side-chain prediction, performance is far from satisfact...
Currently, large-scale projects are underway to perform whole genome disease association studies. Such studies involve the genotyping of hundreds of thousands of SNP markers. One o...
We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to maximize the overall match between the two networks; in c...
Genetic instability represents an important type of biological markers for cancer and many other diseases. Array Comparative Genome Hybridization (aCGH) is a high-throughput cytoge...
Transcription factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position spe...
Our group has recently developed a compact, universal protein binding microarray (PBM) that can be used to determine the binding preferences of transcription factors (TFs) [1]. Thi...
Anthony A. Philippakis, Aaron M. Qureshi, Michael ...
A centromere is a special region in the chromosome that plays a vital role during cell division. Every new chromosome created by a genome rearrangement event must have a centromere...
Abstract. Protein conformational changes play a critical role in biological functions such as ligand-protein and protein-protein interactions. Due to the noise in structural data, ...