Biomedical subjects

Ye Ding

Publications and source records attributed to Ye Ding.

3 recordsLinked to original sources

PubMed2004

Sfold web server for statistical folding and rational design of nucleic acids.

The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives of this software is to offer computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies. The methodology for siRNA design is based on a combination of RNA target accessibility prediction, siRNA duplex thermodynamic properties and empirical design rules. Our approach to target accessibility evaluation is an original extension of the underlying RNA folding algorithm to account for the likely existence of a population of structures for the target mRNA. In addition to the application modules Sirna, Soligo and Sribo for siRNAs, antisense oligos and ribozymes, respectively, the module Srna offers comprehensive features for statistical representation of sampled structures. Detailed output in both graphical and text formats is available for all modules. The Sfold server is available at http://sfold.wadsworth.org and http://www.bioinfo.rpi.edu/applications/sfold.

Algorithms↗

PubMed2003

A statistical sampling algorithm for RNA secondary structure prediction.

An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative sample of structures. With cubic run time for the forward step, quadratic run time in the worst case for the sampling step, and quadratic storage, the algorithm is efficient for broad applicability. We demonstrate that, by classifying sampled structures, the algorithm enables a statistical delineation and representation of the Boltzmann ensemble. Applications of the algorithm show that alternative biological structures are revealed through sampling. Statistical sampling provides a means to estimate the probability of any structural motif, with or without constraints. For example, the algorithm enables probability profiling of single-stranded regions in RNA secondary structure. Probability profiling for specific loop types is also illustrated. By overlaying probability profiles, a mutual accessibility plot can be displayed for predicting RNA:RNA interactions. Boltzmann probability-weighted density of states and free energy distributions of sampled structures can be readily computed. We show that a sample of moderate size from the ensemble of an enormous number of possible structures is sufficient to guarantee statistical reproducibility in the estimates of typical sampling statistics. Our applications suggest that the sampling algorithm may be well suited to prediction of mRNA structure and target accessibility. The algorithm is applicable to the rational design of small interfering RNAs (siRNAs), antisense oligonucleotides, and trans-cleaving ribozymes in gene knock-down studies.

Algorithms↗

PubMed2002

Cyclin E and survival in patients with breast cancer.

BACKGROUND: Cyclin E, a regulator of the cell cycle, affects the behavior of breast-cancer cells. We investigated whether levels of cyclin E in the tumor correlated with survival among patients with breast cancer. METHODS: Tumor tissue from 395 patients with breast cancer was assayed for cyclin E, cyclin D1, cyclin D3, and the HER-2/neu oncogene with the use of Western blot analysis. Full-length, low-molecular-weight, and total cyclin E were measured. Immunohistochemical assessments of cyclin E were also made of 256 tumors. We sought correlations between levels of these molecular markers and disease-specific and overall survival. RESULTS: The median follow-up was 6.4 years. A high level of the low-molecular-weight isoforms of cyclin E, as detected by Western blotting, correlated strongly with disease-specific survival whether axillary lymph nodes were negative or positive for metastases (P<0.001). Among 114 patients with stage I breast cancer, none of the 102 patients with low levels of cyclin E in the tumor had died of breast cancer by five years after diagnosis, whereas all 12 patients with a high level of low-molecular-weight cyclin E had died of breast cancer within that period. In multivariate analysis, a high total cyclin E level or high levels of the low-molecular-weight forms of cyclin E were significantly correlated with poor outcome. The hazard ratio for death from breast cancer for patients with high total cyclin E levels as compared with those with low total cyclin E levels was 13.3--about eight times as high as the hazard ratios associated with other independent clinical and pathological risk factors. CONCLUSIONS: Levels of total cyclin E and low-molecular-weight cyclin E in tumor tissue, as measured by Western blot assay, correlate strongly with survival in patients with breast cancer.

Adult↗