Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that are attached to the nuclear matrix, and participate in many cellular processes. The nuclear matrix is a complex structure consisting of various elements. In this paper we compared frequencies of simple nucleotide motifs in S/MAR sequences and in sequences extracted directly from various nuclear matrix elements, such as nuc...

MOTIVATION One of the limiting factors in deciphering transcriptional regulatory networks is the effectiveness of motif-finding software. An emerging avenue for improving motif-finding accuracy aims to incorporate generalized binding constraints of related transcription factors (TFs), named familial binding profiles (FBPs), as priors in motif identification methods. A motif-finder can thus be '...

Gene or protein expression data are usually represented by metric or at least ordinal variables. In order to translate a continuous variable into a clinical decision, it is necessary to determine a cutoff point and to stratify patients into two groups each requiring a different kind of treatment. Currently, there is no standard method or standard software for biomarker cutoff determination. The...

We present a new spectral-method based algorithm for finding apparent horizons in three-dimensional spacelike hypersurfaces without symmetries. While there are already a wide variety of algorithms for finding apparent horizons, our new algorithm does not suffer from the same weakness as previous spectral apparent horizon finders: namely the monopolar coefficient (l = 0 in terms of the spherical...

One of the important prospects for the national information infrastructure is the wide-spread availability of on-line data and information services on a large scale. However, existing means of information access will not scale up to a network of this size. We believe that access to appropriate information, the ability to contact the right source at the right time, is the most significant obstac...