Browsing by Author "Huang, KT"

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Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites
(2005-07-30)
Huang, HD
;
Lee, TY
;
Tzeng, SW
;
Wu, LC
;
Horng, JT
Protein phosphorylation, which is an important mechanism in posttranslational modification, affects essential cellular processes such as metabolism, cell signaling, differentiation, and membrane transportation. Proteins are phosphorylated by a variety of protein kinases. In this investigation, we develop a novel tool to computationally predict catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the concepts of profile Hidden Markov Models (HMM), computational models are trained from the kinase-specific groups of phosphorylation sites. After evaluating the trained models, we select the model with highest accuracy in each kinase-specific group and provide a Web-based prediction tool for identifying protein phosphorylation sites. The main contribution here is that we have developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. (c) 2005 Wiley Periodicals, Inc.
Low leakage reliability characterization methodology for advanced CMOS with gate oxide in the 1nm range
(2004)
Chung, SS
;
Feng, HJ
;
Hsieh, YS
;
Liu, A
;
Lin, WM
A low leakage characterization technique for the lateral profiling of interface and oxide traps in a 12Angstrom-16Angstrom range gate oxide CMOS devices has been demonstrated. The approach being taken includes an incremental frequency Charge-Pumping(IFCP) measurement and a neutralization procedure such that interface and oxide traps can be separated. The most critical steps are the elimination of leakage current during measurement and a neutralization procedure, which enables accurate detennination of interface and oxide traps. This method has been demonstrated successfully for an advanced sub-100nm CMOS devices. As an important merit for its application, evaluations of HC reliability and NBTI effect have also been demonstrated. Evaluations of gate oxide qualities with plasma nitridation in both n- and p-MOSFET reliabilities have been properly described based on the current analysis technique.