Multiple Genome Rearrangement by Reversals
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: 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: Functional Divergence in TGF-b Signaling Pathway

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: Enabling network-centric music performance in wide-area networks
abstract: NMP on the Internet is not only possible, its delay bounds can satisfy the tight requirements involved in human perception while generating high-end audio quality for musicians and listeners alike.

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: Polyhedral Geometry and the Two-Plane Parameterization
abstract: Recently the light-field and lumigraph systems have been proposed as general methods of representing the visual information present in a scene. These methods represent this information as a 4D function of light over the domain of directed lines. These systems use the intersection points of the lines on two planes to parameterize the lines in space. This paper explores the structure of the two-plane parameterization in detail. In particular we analyze the association between the geometry of the scene and subsets of the 4D data. The answers to these questions are essential to understanding the relationship between a lumigraph, and the geometry that it attempts to represent. This knowledge is potentially important for a variety of applications such as extracting shape from lumigraph data, and lumigraph compression.

title: An overlay based QoS-aware voice-over-IP conferencing system
abstract: Ubiquitous IP telephony has become a feasible Internet service, and it is expected to meet the quality standards of traditional telephone services. The work presents a distributed voice-over-IP (VoIP) conferencing system called Venus that is implemented as a composable application-level service overlay network. Compared to the traditional centralized approach, Venus achieves better scalability and resource utilization by efficiently aggregating resources across distributed voice mixers. Moreover, Venus provides multi-constrained quality-of-service (QoS) provisioning by establishing each conferencing session based on multiple QoS constraints (e.g., delay, loss rate) and resource requirements (e.g., bandwidth, audio channels). Venus provides a failure resilient VoIP conferencing service by leveraging the fast failure recovery capability of the application-level service overlay network. Large-scale simulation results illustrate the efficiency of the Venus system.

title: Optimal Component Composition for Scalable Stream Processing
abstract: Stream processing has become increasingly important with emergence of stream applications such as audio/video surveillance, stock price tracing, and sensor data analysis. A challenging problem is to provide optimal component composition in a distributed stream processing environment. The goal of optimal component composition is to achieve load balancing subject to multiple function, resource, and quality-of-service (QoS) constraints while composing stream applications. In this paper, we present an adaptive composition probing (ACP) approach to the problem. Different from previous work, ACP provides a new hybrid approach that combines distributed composition probing with coarse-grain global state management. Guided by the coarse-grain global state information, ACP selectively probes a subset of candidate components to discover an approximately optimal component composition. Further, ACP is self-tuning, which can adoptively adjust the number of probes to maintain a specified composition performance target (i.e., composition success rate) in a dynamic stream environment. While the optimal component composition problem is NP-hard, our ACP approach provides an adaptive polynomial approximation solution. We have conducted extensive simulation experiments to show the efficiency, scalability, and adaptability of the ACP approach by comparing with other alternative solutions