Mathematical Modeling for Functional Divergence after Gene Duplication
In this paper, I present a statistical framework for modeling the functional divergence after gene duplication. A rate-component model to describe the rate covariation among homologous genes of a gene family is implemented when a phylogenetic tree is known. The Markov chain model is rigorous but may require a huge amount of computational time when the number of sequences is large. On the other hand, the Poisson-based model is mathematically analytical so that computation is very fast even for a large dataset. Moreover, under the posterior framework, we have developed a site-specific profile for predicting important amino acid residues responsible for these functional differences between member genes of a gene family. Our study may have great potential for functional genomics because it is cost-effective, and these predictions can be further tested by biological experimentation.

title: A Greedy Algorithm for Optimal Recombination
abstract: Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = ajaj+1 . . . an+s2 = b1b2 . . . bj bj+1 . . . bn ∈ Σn, a recombination of s1 and s2 at position j is defined as an operation that crosses s1 and s2 at position j and generates t1 = a1a2 . . .  . bn and t2 = b1b2 . . .  Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for finding the optimal recombination evolutionary history from S to any tree A of sequences when |S| = 2.

title: Multiple Genome Rearrangement by Reversals
abstract: In this paper, we discuss a multiple genome rearrangement problem: Given a collection of genomes represented by permutations, we generate the collection from some fixed genome, e.g., the identity permutation, in a minimum number of signed reversals. It is NP-hard, so efficient heuristics is important for finding its optimal solution. We at first discuss how to generate two and three genomes from a fixed genome by polynomial algorithms for some special cases. Then based on the polynomial algorithms, we obtain some approximation algorithms for generating two and three genomes in general, respectively. Finally, we apply these approximation algorithms to design a new approximation algorithm for generating more genomes. We also show by some experimental examples that the algorithms are efficient.

title: Functional Divergence in TGF-b Signaling Pathway

title: DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
abstract: DetectIng Variability in Evolutionary Rates among GEnes (DIVERGE) is a software system to study functional divergence of a protein family by detecting site-specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given phylogenetic tree. The program first conducts a statistical test for site-specific rate shifts along the tree, and predicting candidate amino acid residues responsible for functional divergence based on posterior analysis. These results can then be mapped on the 3D protein structure if available.


AVAILABILITY
DIVERGE is available free of charge from http://xgu1.zool.iastate.edu/. Distribution packages for both Linux and Microsoft Windows operating systems are available, including manual and example files.

title: Performance evaluation of DCCP: A focus on smoothness and TCP-friendliness
abstract: Recent years have seen dramatic increases of the use of multimedia applications on the Internet, which typically either lack congestion control or use proprietary congestion control mechanisms. This can easily cause congestion collapse or compatibility problems. Datagram Congestion Control Protocol (Dccp) fills the gap betweenUdp andTcp, featuring congestion control rather than reliability for packet-switched rich content delivery with high degree of flexibility. We present aDccp model designed and implemented withOpnet Modeler, and the experiments and evaluation focused on largely the smoothness of the data rates, and the fairness between concurrentDccp flows andTcp flows. We foundDccp-ccid3 demonstrates stable data rates under different scenarios, and the fairness betweenDccp andTcp is only achieved under certain conditions. We also validated that the throughput ofDccp-Ccid3 is proportional to the average packet size, and relatively fixed packet size is critical for the optimal operation ofDccp. Problems in the slow start phase and insufficient receiver buffer size were identified and we hereby proposed solutions on this.RésuméLe nombre d’applications multimédias sur l’internet a considérablement augmenté ces dernières années. Ces applications généralement ne gèrent pas les congestions ou bien utilisent des mécanismes de contrôle propriétaires. Il peut en résulter facilement des congestions graves ou des problèmes d’incompatibilité. Le protocoleDccp (Datagram Congestion Control Protocol) se positionne entreUdp etTcp puisqu ’il fournit, pour des paquets multimédias, un contrôle de congestion hautement flexible mais sans la fiabilité de délivrance. Cet article présente un modèleDccp conçu et implémenté avec le simulateurOpnet. Les expérimentations et les analyses portent principalement sur le lissage des débits et l’équité entre des fluxDccp etTcp concurrents. On montre queDccp-Ccid3 affiche des débits stables sous divers scénarios et que l’équité entreDccp etTcp n’est atteinte que sous certaines conditions. On valide également que le débit deDccp-Ccid3 est proportionnel à la taille moyenne des paquets et que le fait d’avoir des paquets de taille relativement constante est un facteur essentiel pour un fonctionnement optimal deDccp. Les problèmes pendant la phase de démarrage lent et ceux dus à une mémoire tampon insuffisante côté récepteur sont également analysés et résolus.

title: Evolutionary analysis of functional divergence in TGF- signaling pathway
abstract: TGF-β cytokines and their interacting receptors form an intricate signaling network and play important roles in cell differentiation and development. Members in gene families involved in this complicated pathway are usually conserved in sequence but distinct in temporal and tissue-specific expression. Starting from an evolutionary perspective, we have statistically tested the functional divergence in major pathway components, targeted the critical amino acid residues responsible for functional divergence. Our results show that altered functional constraints is a common pattern in the evolution of TGF-β pathway. Moreover, we have found the correlation between structural divergence and functional divergence in the extracellular ligand-binding domain of Type II receptors. This study helps understand the complex intrinsic mechanisms of signaling.

title: Computational methodologies for modelling, analysis and simulation of signalling networks
abstract: This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.

title: Adaptive offloading inference for delivering applications in pervasive computing environments
abstract: Pervasive computing allows a user to access an application on heterogeneous devices continuously and consistently. However it is challenging to deliver complex applications on resource-constrained mobile devices, such as cellular telephones and PDA. Different approaches, such as application-based or system-based adaptations, have been proposed to address the problem. However existing solutions often require degrading application fidelity. We believe that this problem can be overcome by dynamically partitioning the application and offloading part of the application execution to a powerful nearby surrogate. This will enable pervasive application delivery to be realized without significant fidelity degradation or expensive application rewriting. Because pervasive computing environments are highly dynamic, the runtime offloading system needs to adapt to both application execution patterns and resource fluctuations. Using the fuzzy control model, we have developed an offloading inference engine to adaptively solve two key decision-making problems during runtime offloading: (1) timely triggering of adaptive offloading, and (2) intelligent selection of an application partitioning policy. Extensive trace-driven evaluations show the effectiveness of the offloading inference engine.

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.