Prediction of translation initiation site for microbial genomes with TriTISA (2009)
Hu, Gang-Qing, Zheng, Xiaobin, Zhu, Huai-Qiu, She, Zhen-Su
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...
Dating the time of viral subtype divergence (2008)
O'Brien, John D, She, Zhen-Su, Suchard, Marc A
Abstract 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...
Huai-qiu Zhu, Gang-qing Hu, Zheng-qing Ouyang, Jin Wang, Zhen-su She
improvement for identifying translation
Computational evaluation of TIS annotation for prokaryotic genomes (2008)
Hu, Gang-Qing, Zheng, Xiaobin, Ju, Li-Ning, Zhu, Huaiqiu, She, Zhen-Su
Abstract Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in...
A dynamic Bayesian network approach to protein secondary structure prediction (2008)
Yao, Xin-Qiu, Zhu, Huaiqiu, She, Zhen-Su
Abstract Background Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant...
Hu, Gang-Qing, Zheng, Xiaobin, Yang, Yi-Fan, Ortet, Philippe, She, Zhen-Su, Zhu, Huaiqiu
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...
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes (2007)
Zhu, Huaiqiu, Hu, Gang-Qing, Yang, Yi-Fan, Wang, Jin, She, Zhen-Su
Abstract 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...
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes (2007)
Zhu, Huaiqiu, Hu, Gang-Qing, Yang, Yi-Fan, Wang, Jin, She, Zhen-Su
Abstract 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...
Tree and rate estimation by local evaluation of heterochronous nucleotide data (2007)
Yang, Zhu, O'Brien, John D., Zheng, Xiaobin, Zhu, Huai-Qiu, She, Zhen-Su
Motivation: Heterochronous gene sequence data is important for characterizing the evolutionary processes of fast-evolving organisms such as RNA viruses. A limited set of algorithms exists for...
Characterizing large scale base composition structures of genomes (2004)
Ouyang, Zhengqing, Liu, Jian, She, Zhen-Su
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally...
Hierarchical structure description of spatiotemporal chaos (2004)
Liu, Jian, She, Zhen-Su, Guo, Hongyu, Li, Liang, Ouyang, Qi
We develop a hierarchical structure (HS) analysis for quantitative description of statistical states of spatially extended systems. Examples discussed here include an experimental reaction-diffusion...
Accuracy improvement for identifying translation initiation sites in microbial genomes (2004)
Zhu, Huai-Qiu, Hu, Gang-Qing, Ouyang, Zheng-Qing, Wang, Jin, She, Zhen-Su
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 improvement for identifying translation initiation sites in microbial genomes (2004)
Zhu, Huai-Qiu, Hu, Gang-Qing, Ouyang, Zheng-Qing, Wang, Jin, She, Zhen-Su
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...
Accuracy improvement for identifying translation initiation sites in microbial genomes (2004)
Zhu, Huai-Qiu, Hu, Gang-Qing, Ouyang, Zheng-Qing, Wang, Jin, She, Zhen-Su
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...
Extended Self-Similarity and Hierarchical Structure in Turbulence (2001)
Ching, Emily S. C., She, Zhen-Su, Su, Weidong, Zou, Zhengping
It is shown that the two remarkable properties of turbulence, the Extended Self-Similarity (ESS) [R. Benzi {\it et al.}, Phy. Rev. E {\bf 48}, R29, (1993)] and the She-Leveque Hierarchical Structure...
Anomalous self-similarity in two-dimensional turbulence (2001)
Baroud, Charles N., Plapp, Brendan B., She, Zhen-Su, Swinney, Harry L.
Our velocity measurements on a quasi-two-dimensional turbulent flow in a rapidly rotating annulus yield an inverse cascade with E(k)~k^{-2} rather than the expected E(k)~k^{-5/3}. The probability...
Scalings in Homogeneous and Inhomogeneous Turbulence (1998)
Program Objective: Understand the fundamental processes which leads to the generation of small-scale fluctuations. Describe the scaling properties of turbulence based on features of fluid structures....
Universal Laws of Cascade of Turbulent Fluctuations (1998)
this paper, we present a few new ideas aiming at establishing a basis for a dual mechanical-statistical approach. The ideas presented throughout this paper form what will be referred to as the...
Hierarchical Structures and Scalings in Turbulence (1997)
. Turbulence is a mixture of hierarchical structures (eddies) of different sizes, different amplitudes and different degree of coherence. The size distributes continuously from the integral scale `0...
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Zhu, Huaiqiu, Hu, Gang-Qing, Yang, Yi-Fan, Wang, Jin, She, Zhen-Su
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes
Hu, Gang-Qing, Zheng, Xiaobin, Yang, Yi-Fan, Ortet, Philippe, She, Zhen-Su, Zhu, Huaiqiu
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...
Computational evaluation of TIS annotation for prokaryotic genomes
Hu, Gang-Qing, Zheng, Xiaobin, Ju, Li-Ning, Zhu, Huaiqiu, She, Zhen-Su
Dating the time of viral subtype divergence
O'Brien, John D, She, Zhen-Su, Suchard, Marc A
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...
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...