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Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp (http://cast.engr.uic.edu) is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of(More)
Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by(More)
In this paper, we present the design, implementation, and application of several families of fast multiplierless approximations of the discrete cosine transform (DCT) with the lifting scheme called the binDCT. These binDCT families are derived from Chen’s and Loeffler’s plane rotation-based factorizations of the DCT matrix, respectively, and the design(More)
Small, noncoding RNA molecules, called microRNAs (miRNAs), are thought to function as either tumor suppressors or oncogenes. Common single-nucleotide polymorphisms (SNPs) in miRNAs may change their property through altering miRNA expression and/or maturation, and thus they may have an effect on thousands of target mRNAs, resulting in diverse functional(More)
Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single(More)
This paper presents a general framework of constructing a large family of lapped transforms with symmetric basis functions by adding simple time-domain reand postprocessing modules onto existing block DCT based infrastructures. A subset of the resulting solutions is closed-form, fast computable, modular, near optimal in the energy compaction sense, and(More)
microRNAs (miRNA) are a new class of non-protein-coding, small RNAs that function as tumor suppressors or oncogenes. They participate in diverse biological pathways and function as gene regulators. Recently, we conducted a survey of common single nucleotide polymorphisms (SNP) in miRNA sequences and reported that, among four SNPs (rs2910164, rs2292832,(More)
Microsoft Windows Media 9 Series is a set of technologies that enables rich digital media experiences across many types of networks and devices. These technologies are widely used in the industry for media delivery over the internet and other media, and are also applied to broadcast, high definition DVDs, and digital projection in theaters. At the core of(More)
The shape of a protein is important for its functions. This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and(More)
We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end(More)