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Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. Herein, a new web server, KinasePhos 2.0,(More)
—Recent study shows that the nonuniform thermal distribution not only has an impact on the substrate but also interconnects. Hence, three–dimensional (3-D) thermal analysis is crucial to analyze these effects. In this paper, the authors present and develop an efficient 3-D transient thermal simulator based on the alternating direction implicit (ADI) method(More)
This paper presents a fast algorithm to optimize both the widths and lengths of power/ground networks under reliability and power dip/ground bounce constraints. The space-sizing which allows the length to change gives more flexibility in solving practical problems. There are two major contributions of this paper. First, we prove that for general topology, a(More)
Understanding the overall patterns of information flow within the brain has become a major goal of neuroscience. In the current study, we produced a first draft of the Drosophila connectome at the mesoscopic scale, reconstructed from 12,995 images of neuron projections collected in FlyCircuit (version 1.1). Neuron polarities were predicted according to(More)
With the growing power dissipation in modern high performance VLSI designs, nonuniform temperature distribution and limited heat-conduction capability have caused thermal induced performance and reliability degradation. However, the problem modeled by finite difference method for interconnect reliability analysis has huge size if we require the resolution(More)
Due to the dramatic increase of clock frequency and integration density, power density and on-chip temperature in high-end VLSI circuits rise significantly. To ensure the timing correctness and the reliability of high-end VLSI design, efficient and accurate chip-level transient thermal simulations are of crucial importance. In this paper, we develop and(More)
Recent studies show that the nonuniform thermal distribution on the substrate and interconnects has impact on the circuit reliability and performance. Hence three-dimensional (3-D) thermal analysis is crucial to analyze these effects. In this paper, we present and develop an efficient 3-D transient thermal simulator based on the alternating direction(More)
Tyrosine sulfation is a post-translational modification of many secreted and membrane-bound proteins. It governs protein-protein interactions that are involved in leukocyte adhesion, hemostasis, and chemokine signaling. However, the intrinsic feature of sulfated protein remains elusive and remains to be delineated. This investigation presents SulfoSite,(More)
Studies over the last few years have identified protein methylation on histones and other proteins that are involved in the regulation of gene transcription. Several works have developed approaches to identify computationally the potential methylation sites on lysine and arginine. Studies of protein tertiary structure have demonstrated that the sites of(More)
With the increasing power density and heat-dissipation cost of modern VLSI designs, thermal and power integrity has become serious concern. Although the impacts of thermal effects on transistor and interconnect performance are well-studied, the interactions between power-delivery and thermal effects are not clear. As a result, power-delivery design without(More)