Functional Divergence in TGF-b Signaling Pathway

title: Gene Network: Model, Dynamics and Simulation
abstract: A gene network is modeled as a dynamical random graph whose vertices and edges represent genes and gene-gene interactions, respectively. The network grows through three biological mechanisms: (1) gene duplication and loss; (2) gene-gene interaction adding and removing; and (3) genome duplication. The evolutionary dynamics of gene networks is discussed. It is shown that: (1) the vertex degree distribution (i.e., the distribution of the number of the gene-gene interactions per gene) always follows power laws and the power law exponents may be changed by genome duplications; and (2) the network degree distribution (i.e., the distribution of the total number of the gene-gene interactions in the network) has a complex behavior: If no genome duplication occurs, it follows a power law. If a genome duplication occurs, it may be away from the power law state. However, after a sufficient long evolutionary time, it approaches to a power law tail. The dynamics is confirmed by computer simulations. By allowing genome duplications, our model and dynamics (describing the dynamic behavior of gene networks) are more realistic than other previous ones (containing only static behavior).

title: Global Conformal Parameterization

title: DRTF: a database of rice transcription factors
abstract: DRTF contains 2025 putative transcription factors (TFs) in Oryza sativa L. ssp. indica and 2384 in ssp. japonica, distributed in 63 families, identified by computational prediction and manual curation. It includes detailed annotations of each TF including sequence features, functional domains, Gene Ontology assignment, chromosomal localization, EST and microarray expression information, as well as multiple sequence alignment of the DNA-binding domains for each TF family. The database can be browsed and searched with a user-friendly web interface.


AVAILABILITY
DRTF is available at http://drtf.cbi.pku.edu.cn

title: Silhouette clipping
abstract: Approximating detailed with coarse, texture-mapped meshes results in polygonal silhouettes. To eliminate this artifact, we introduce silhouette clipping, a framework for efficiently clipping the rendering of coarse geometry to the exact silhouette of the original model. The coarse mesh is obtained using progressive hulls, a novel representation with the nesting property required for proper clipping. We describe an improved technique for constructing texture and normal maps over this coarse mesh. Given a perspective view, silhouettes are efficiently extracted from the original mesh using a precomputed search tree. Within the tree, hierarchical culling is achieved using pairs of anchored cones. The extracted silhouette edges are used to set the hardware stencil buffer and alpha buffer, which in turn clip and antialias the rendered coarse geometry. Results demonstrate that silhouette clipping can produce renderings of similar quality to high-resolution meshes in less rendering time.

title: On Composing Stream Applications in Peer-to-Peer Environments
abstract: Stream processing has become increasingly important as many emerging applications call for continuous real-time processing over data streams, such as voice-over-IP telephony, security surveillance, and sensor data analysis. In this paper, we propose a composable stream processing system for cooperative peer-to-peer environments. The system can dynamically select and compose stream processing elements located on different peers into user desired applications. We investigate multiple alternative approaches to composing stream applications: 1) global-state-based centralized versus local-state-based distributed algorithms for initially composing stream applications at setup phase. The centralized algorithm performs periodical global state maintenance while the distributed algorithm performs on-demand state collection. 2) Reactive versus proactive failure recovery schemes for maintaining composed stream applications during runtime. The reactive failure recovery algorithm dynamically recomposes a new stream application upon failures while the proactive approach maintains a number of backup compositions for failure recovery. We conduct both theoretical analysis and experimental evaluations to study the properties of different approaches. Our study illustrates the performance and overhead trade-offs among different design alternatives, which can provide important guidance for selecting proper algorithms to compose stream applications in cooperative peer-to-peer environments

title: An XML-based Quality of Service Enabling Language for the Web
abstract: In this paper, we introduce an XML-based hierarchical QoS markup language, called HQML, to enhance distributed multimedia applications on the World Wide Web (WWW) with quality of service (QoS) capability. The design ofHQML is based on two observations: (1) the absence of a systematic QoS specification language, that can be used by distributed multimedia applications on the WWW to utilize the state-of-the-art QoS management technology and (2) the power and popularity of XML to deliver richly structured contents over the Web. HQML allows distributed multimedia applications to specify all kinds of application-specific QoS policies and requirements. During runtime, the HQML Executor translates the HQML file into desired data structures and cooperates with the QoS proxies that assist applications in end-to-end QoS negotiation, setup and enforcement. In order to make QoS services tailored toward user preferences and meet the challenges of uncertainty in the distributed heterogeneous environments, the design of HQML is featured as interactive andflexible . In order to allow application developers to create HQML specifications correctly and easily, we have designed and developed a unified visual QoS programming environment, called QoSTalk. In QoSTalk, we adopt a grammatical approach to perform consistency check on the visual QoS specifications and generate HQML files automatically. Finally, we introduce the distributed QoS compiler, which performs the automatic mappings between application- and resource-level QoS parameters to relieve the application developer of the burden of dealing with low-level QoS specifications.