In order to enhance the efficiency of radio frequency identification (RFID) and lower system computational complexity, this paper proposes three novel tag anticollision protocols for passive RFID systems. The three proposed protocols are based on a binary tree slotted ALOHA (BTSA) algorithm. In BTSA, tags are randomly assigned to slots of a frame and if some tags collide in a slot, the collided tags in the slot will be resolved by binary tree splitting while the other tags in the subsequent slots will wait. The three protocols utilize a dynamic, an adaptive, and a splitting method to adjust the frame length to a value close to the number of tags, respectively. For BTSA, the identification efficiency can achieve an optimal value only when the frame length is close to the number of tags. Therefore, the proposed protocols efficiency is close to the optimal value. The advantages of the protocols are that, they do not need the estimation of the number of tags, and their efficiency is not affected by the variance of the number of tags. Computer simulation results show that splitting BTSA's efficiency can achieve 0.425, and the other two protocols efficiencies are about 0.40. Also, the results show that the protocols efficiency curves are nearly horizontal when the number of tags increases from 20 to 4,000.

BACKGROUND: Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo. RESULTS: Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we developed a novel computational approach to identify dynamic nucleosome positions at promoters by combining transcriptional interaction and genomic sequence information. Our approach successfully identified experimentally determined nucleosome positioning dynamics available in three cellular conditions, and significantly improved the prediction accuracy which is based on sequence information alone. We then applied our approach to various cellular conditions and established a comprehensive landscape of dynamic nucleosome positioning in yeast. CONCLUSION: Analysis of this landscape revealed that the majority of nucleosome positions are maintained during most conditions. However, nucleosome occupancy at most promoters fluctuates with the corresponding gene expression level and is reduced specifically at the phase of peak expression. Further investigation into properties of nucleosome occupancy identified two gene groups associated with distinct modes of nucleosome modulation. Our results suggest that both the intrinsic sequence and regulatory proteins modulate nucleosomes in an altered manner.

BACKGROUND: It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages. RESULTS: The paper explores the feasibility of doing missing value imputation with the help of gene regulatory mechanism. An imputation framework called histone acetylation information aided imputation method (HAIimpute method) is presented. It incorporates the histone acetylation information into the conventional KNN(k-nearest neighbor) and LLS(local least square) imputation algorithms for final prediction of the missing values. The experimental results indicated that the use of acetylation information can provide significant improvements in microarray imputation accuracy. The HAIimpute methods consistently improve the widely used methods such as KNN and LLS in terms of normalized root mean squared error (NRMSE). Meanwhile, the genes imputed by HAIimpute methods are more correlated with the original complete genes in terms of Pearson correlation coefficients. Furthermore, the proposed methods also outperform GOimpute, which is one of the existing related methods that use the functional similarity as the external information. CONCLUSION: We demonstrated that the using of histone acetylation information could greatly improve the performance of the imputation especially at high missing percentages. This idea can be generalized to various imputation methods to facilitate the performance. Moreover, with more knowledge accumulated on gene regulatory mechanism in addition to histone acetylation, the performance of our approach can be further improved and verified.