Advanced search    

Search: authors:"Zhen-Su She"

12 papers found.
Use AND, OR, NOT, +word, -word, "long phrase", (parentheses) to fine-tune your search.

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

Background Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea. However, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the SD-led initiation way...

New perspective in statistical modeling of wall-bounded turbulence

Despite dedicated effort for many decades, statistical description of highly technologically important wall turbulence remains a great challenge. Current models are unfortunately incomplete, or empirical, or qualitative. After a review of the existing theories of wall turbulence, we present a new framework, called the structure ensemble dynamics (SED), which aims at integrating...

A Spike-Timing Pattern Based Neural Network Model for the Study of Memory Dynamics

It is well accepted that the brain's computation relies on spatiotemporal activity of neural networks. In particular, there is growing evidence of the importance of continuously and precisely timed spiking activity. Therefore, it is important to characterize memory states in terms of spike-timing patterns that give both reliable memory of firing activities and precise memory of...

Universal hierarchical symmetry for turbulence and general multi-scale fluctuation systems

Zhen-Su She Zhi-Xiong Zhang Scaling is an important measure of multi-scale fluctuation systems. Turbulence as the most remarkable multi-scale system possesses scaling over a wide range of scales

A dynamic Bayesian network approach to protein secondary structure prediction

Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relationship. However, at present, the prediction accuracy of pure HMM-type methods is much lower than that of machine learning-based methods such as neural networks (NN) or support...

Dating the time of viral subtype divergence

Precise dating of viral subtype divergence enables researchers to correlate divergence with geographic and demographic occurrences. When historical data are absent (that is, the overwhelming majority), viral sequence sampling on a time scale commensurate with the rate of substitution permits the inference of the times of subtype divergence. Currently, researchers use two...

Prediction of translation initiation site for microbial genomes with TriTISA

Summary: We report a new and simple method, TriTISA, for accurate prediction of translation initiation site (TIS) of microbial genomes. TriTISA classifies all candidate TISs into three categories based on evolutionary properties, and characterizes them in terms of Markov models. Then, it employs a Bayesian methodology for the selection of true TIS with a non-supervised, iterative...

Computational evaluation of TIS annotation for prokaryotic genomes

Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. Results Based on a homogeneity assumption that gene translation-related signals are uniformly...

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

Background Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative...

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes...

Accuracy improvement for identifying translation initiation sites in microbial genomes

Motivation: At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3′ end), but a much lower accuracy of the translation initiation site (TIS, 5′ end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the...