Yaping Feng

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In adult mammals, restoration of function after peripheral nerve injury is often poor and effective therapies are not available. Previously we have shown in mice that a peptide which functionally mimics the human natural killer cell (HNK)-1 trisaccharide epitope significantly improves the outcome of femoral nerve injury. Here we evaluated the translational(More)
Spinal cord injury (SCI) in mammals not only damages the focal area, but also leads to wallerian degeneration (WD) of axons and myelin distal to the injury. In the present study, we investigated cellular responses within areas of WD of a sensory pathway, the fasciculus gracilis, after a T8-9 lateral spinal hemisection in the adult monkey Macaca(More)
Two-body inter-residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are(More)
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode(More)
BACKGROUND Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online. RESULTS Our new knowledge-based potential server makes available many of these(More)
Two-component signaling systems (TCSs) are major mechanisms by which bacteria adapt to environmental conditions. It follows then that TCSs would play important roles in the adaptation of pathogenic bacteria to host environments. However, no pathogen-associated TCS has been identified in uropathogenic Escherichia coli (UPEC). Here, we identified a novel TCS,(More)
The orientational geometry of residue packing in proteins was studied in the past by superimposing clusters of neighboring residues with several simple lattices (Bagci et al., Proteins 2003;53:56-67; Raghunathan et al., Protein Sci 1997;6:2072-2083). In this work, instead of a lattice we use the regular polyhedron, the icosahedron, as the model to describe(More)
—UCMs (Use Case Maps) model describes functional requirements and high-level designs with causal paths superimposed on a structure of components. It could provide useful resources for software acceptance testing. However until now statistical testing technologies for large scale software is not considered yet in UCMs model. Thus if one applies UCMs model to(More)
In human immune system, V(D)J recombination produces an enormously large repertoire of immunoglobulins (Ig) so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of(More)
The synthesis of information across microarray studies has been performed by combining statistical results of individual studies (as in a mosaic), or by combining data from multiple studies into a large pool to be analyzed as a single data set (as in a melting pot of data). Specific issues relating to data heterogeneity across microarray studies, such as(More)