-
ICDM 2010, The 10th IEEE International Conference on Data Mining, Sydney, Australia, 14-17 December 2010; 01/2010
-
Service Oriented Computing and Applications. 01/2010; 4:291-305.
-
4th IEEE International Symposium on Theoretical Aspects of Software Engineering, TASE 2010, Taipei, Taiwan, 25-27 August 2010; 01/2010
-
2010 IEEE Wireless Communications and Networking Conference, WCNC 2010, Proceedings, Sydney, Australia, 18-21 April 2010; 01/2010
-
Algorithmic Learning Theory, 21st International Conference, ALT 2010, Canberra, Australia, October 6-8, 2010. Proceedings; 01/2010
-
IEEE Transactions on Systems, Man, and Cybernetics, Part A. 01/2010; 40:76-89.
-
IEEE International Symposium on Information Theory, ISIT 2010, June 13-18, 2010, Austin, Texas, USA, Proceedings; 01/2010
-
Leveraging Applications of Formal Methods, Verification, and Validation - 4th International Symposium on Leveraging Applications, ISoLA 2010, Heraklion, Crete, Greece, October 18-21, 2010, Proceedings, Part I; 01/2010
-
Pacific Asia Conference on Information Systems, PACIS 2010, Taipei, Taiwan, 9-12 July 2010; 01/2010
-
Formal Methods and Software Engineering - 12th International Conference on Formal Engineering Methods, ICFEM 2010, Shanghai, China, November 17-19, 2010. Proceedings; 01/2010
-
[show abstract]
[hide abstract]
ABSTRACT: Protein folding rate is an important property of a protein. Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Most previous methods of predicting protein folding rate require the tertiary structure of a protein as an input. And most methods do not distinguish the different kinetic nature (two-state folding or multi-state folding) of the proteins. Here we developed a method, SeqRate, to predict both protein folding kinetic type (two-state versus multi-state) and real-value folding rate using sequence length, amino acid composition, contact order, contact number, and secondary structure information predicted from only protein sequence with support vector machines.
We systematically studied the contributions of individual features to folding rate prediction. On a standard benchmark dataset, the accuracy of folding kinetic type classification is 80%. The Pearson correlation coefficient and the mean absolute difference between predicted and experimental folding rates (sec-1) in the base-10 logarithmic scale are 0.81 and 0.79 for two-state protein folders, and 0.80 and 0.68 for three-state protein folders. SeqRate is the first sequence-based method for protein folding type classification and its accuracy of fold rate prediction is improved over previous sequence-based methods. Its performance can be further enhanced with additional information, such as structure-based geometric contacts, as inputs.
Both the web server and software of predicting folding rate are publicly available at http://casp.rnet.missouri.edu/fold_rate/index.html.
BMC Bioinformatics 01/2010; 11 Suppl 3:S1. · 2.75 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.
The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB), protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models.
A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.
BMC Plant Biology 01/2010; 10:14. · 3.45 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this paper, we address retransmission strategies of the generation-based network coding in the packet network. Our discussion focuses on how to make the retransmission more efficient. We investigate four retransmission strategies, quasi Classical ReTransmission strategy (CRT), Random ReTransmission strategy (RRT), Packet-Loss-Edge-based ReTransmission strategy (PLERT) and Minimum ReTransmission strategy (MRT). The PLERT strategy and the MRT strategies are the main contributions of this paper.
Communications, 2009. APCC 2009. 15th Asia-Pacific Conference on; 11/2009
-
[show abstract]
[hide abstract]
ABSTRACT: Multiple Unmanned Helicopters (UH) formation control is a difficult problem due to the highly nonlinear model and extensively existing uncertainties. In this paper, basing on the concept of relative dynamics and Leader-Follower formation strategy, a new formation control algorithm is given to partially solve this problem. First, the formation control problem is transformed into tracking problems of multiple Leader-Follower partners, and the relative dynamics model is derived by combining a fully dynamics model of follower UH system and a simplified model of leader UH system. Second, with the approximate feedback linearization method, a nonlinear robust tracking controller is designed by the H¿ control technology. Finally, simulations of the new proposed method with two UH systems are conducted, and the results are compared with the normal Leader-Follower formation control algorithm to show the improvement.
Mechatronics and Automation, 2009. ICMA 2009. International Conference on; 09/2009
-
[show abstract]
[hide abstract]
ABSTRACT: Test data generation is one of the important tasks during software testing. This paper proposes an approach to generating test cases automatically for the unit test of C programs with derived types including pointers, structures and arrays. Our approach combines symbolic execution and concrete execution. The approach captures operations on variables precisely by concrete execution, and thus it is capable of handling derived types. Benefited from symbolic execution, accessing variables as array index can be solved by a substitution strategy. The substitution strategy also translates a path constraint involving variables of derived type to the one containing only primitive variables. An implementation of this approach is integrated into our test case generation tool called CAUT. Experimental results show that our approach is effective to generate test data for derived types.
Theoretical Aspects of Software Engineering, 2009. TASE 2009. Third IEEE International Symposium on; 08/2009
-
[show abstract]
[hide abstract]
ABSTRACT: Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008. Both NNcon server and software are available at http://casp.rnet.missouri.edu/nncon.html.
Nucleic Acids Research 06/2009; 37(Web Server issue):W515-8. · 8.03 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Evaluating the quality of protein structure models is important for selecting and using models. Here, we describe the MULTICOM series of model quality predictors which contains three predictors tested in the CASP8 experiments. We evaluated these predictors on 120 CASP8 targets. The average correlations between predicted and real GDT-TS scores of the two semi-clustering methods (MULTICOM and MULTICOM-CLUSTER) and the one single-model ab initio method (MULTICOM-CMFR) are 0.90, 0.89, and 0.74, respectively; and their average difference (or GDT-TS loss) between the global GDT-TS scores of the top-ranked models and the best models are 0.05, 0.06, and 0.07, respectively. The average correlation between predicted and real local quality scores of the semi-clustering methods is above 0.64. Our results show that the novel semi-clustering approach that compares a model with top ranked reference models can improve initial quality scores generated by the ab initio method and a simple meta approach.
Proteins Structure Function and Bioinformatics 06/2009; 77 Suppl 9:181-4. · 3.39 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Nanoscale CMOS technologies are posing new network-on-chip (NoC) concepts to gigascale system-on-chip (SoCs). However, electronic network on chip designs face several problems like energy consumption, bandwidth and latency. Optical NoC (ONoC) promises to solve these problems. The advances in nanoscale photonic technology make ONoCs possible. This paper proposes a new non-blocking optical router, OXY, and uses it to build a 2D mesh ONoC. OXY based optical mesh NoC fully utilizes the properties of XY routing in 2D networks, and significantly reduce the number of microring resonators required for ONoCs. We compared OXY based optical mesh NoC with three other schemes in number of microring resonators, loss and energy consumption. The results show that OXY based optical mesh NoC achieves the best in all the comparisons. We simulated 2D optical mesh ONoC based on OXY, and showed the end-to-end delay and throughput under different traffic loads and network sizes.
Circuits and Systems, 2008. APCCAS 2008. IEEE Asia Pacific Conference on; 01/2009
-
Proceedings of the 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP 2009, Raleigh, NC, USA, February 14-18, 2009; 01/2009
-
Proceedings of the 2009 ACM SIGPLAN Conference on Programming Language Design and Implementation, PLDI 2009, Dublin, Ireland, June 15-21, 2009; 01/2009
