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Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can(More)
Protein-protein interactions (PPIs) play a critical role in many cellular functions. A number of experimental techniques have been applied to discover PPIs; however, these techniques are expensive in terms of time, money, and expertise. There are also large discrepancies between the PPI data collected by the same or different techniques in the same(More)
It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate(More)
A goal of the post-genomics era has been to elucidate a detailed global map of protein-protein interactions (PPIs) within a cell. Here, we show that the presence of co-occurring short polypeptide sequences between interacting protein partners appears to be conserved across different organisms. We present an algorithm to automatically generate PPI prediction(More)
BACKGROUND Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing alpha-helices, beta-strands, and non-regular structures) from(More)
This paper presents a moving average method for estimating and removing electrocardiogram (ECG) artifact in surface electromyography (sEMG) recordings. This method does not require an ECG-only recording (e.g., with muscles relaxed), which is often required by other methods. The moving average method is compared to a common template subtraction method using(More)
Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of(More)
Much like the shape of a tool suggests its intended purpose, knowledge of a protein's structure can provide substantial insight into its function. Therefore, computational prediction of protein structure based solely on protein sequence data is a challenge of fundamental importance to biomedical research. An effective solution promises significant advances(More)
Thyroid hormones play an essential role in early vertebrate development as well as other key processes. One of its modes of action is to bind to the thyroid hormone receptor (TR) which, in turn, binds to thyroid response elements (TREs) in promoter regions of target genes. The sequence motif for TREs remains largely undefined as does the precise chromosomal(More)
Interactions among proteins are essential to many biological functions in living cells but experimentally detected interactions represent only a small fraction of the real interaction network. Computational protein interaction prediction methods have become important to augment the experimental methods; in particular sequence based prediction methods that(More)