Multiple Genome Alignment by Clustering Pairwise Matches
We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwisegenome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each cluster. To use a sequence clustering algorithm for genome alignment, it is necessary to handle numerous local alignments between a pair of genomes. We propose a multiple genome alignment method that converts the multiple genome alignment problem to the sequence clustering problem. This method does not need to make a guide tree to determine the order of multiple alignment, and it accurately detects multiple homologous regions. As a result, our multiple genome alignment algorithm performs competitively over existing algorithms. This is shown using an experiment which compares the performance of TBA, MultiPipMaker (MPM) and our algorithm in aligning 12 groups of 56 microbial genomes and by evaluating the number of common COGs detected.

title: PLATCOM: a Platform for Computational Comparative Genomics
abstract: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely.



PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes.



http://platcom.informatics.indiana.edu/platcom

title: PLATCOM: Current Status and Plan for the Next Stages
abstract: We have been developing a web-based system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational tools. PLATCOM is built on internal databases such as GenBank, COG, KEGG, and Pairwise Comparison Database (PCDB) that contains all pairwise comparisons (97,034 entries) of protein sequence files (.faa) and whole genome sequence files (.fna) of 312 replicons. Since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool, we also developed and incorporated high performance sequence data mining tools such as sequence clustering and neighborhood prediction. The next plan includes defining several data types for genome analysis and integrating system modules using data mining tools that operate on the genome data types. PLATCOM is available at http://platcom.informatics.indiana.edu.

title: A Korean-Japanese-Chinese Aligned Wordnet with Shared Semantic Hierarchy
abstract: A Korean-Japanese-Chinese aligned wordnet, “CoreNet” is introduced. For the purpose of this paper, the term “wordnet” refers to a network of words. It is constructed based on a shared semantic hierarchy that is originated from NTT Goidaikei (Lexical Hierarchical System). Korean wordnet was constructed through the semantic category assignment to every meaning of Korean words in a dictionary. Verbs and adjectives’ word senses are assigned to the same semantic hierarchy as that of nouns. Each sense of verbs is investigated from corpora for their usage, and compared with Japanese translation. Chinese wordnet with the same semantic hierarchy was built up based on the comparison with Korean wordnet. Each sense of Chinese verb corresponds to Korean with its argument structure. The use of the same semantic hierarchy for nouns and predicates has several advantages. First, the surface forms of nouns and predicates share the similar one, especially in Chinese words. In case of Korean and Japanese, the typical formation is like “do+Noun” in English like “Noun+suru” in Japanese and “Noun+hada” in Korean. Second, the language generation from conceptual structures takes freedom to choose the surface form whether it chooses noun phrases or verb phrases. CoreNet has been constructed by the following principles: word sense mapping to concept, corpus-based, multi-lingualism, and single concept system for multi-languages. The overall flow of construction is based on dictionary-based bootstrapping, incremental similarity-based classification and manual post-editing. Among consideration points, the followings are introduced: multiple concept mapping, verbal noun, and concept splitting. For multiple concept mapping, a word is mapped into numerous concepts that comprise respective meanings of the word. For example, school is an “institution for the instruction of students.” The word school is mapped into three concepts such as location, organization, and facility. For verbal noun, a word that is a verb is assigned to concepts after it is transformed to a noun. For example, “write” is transformed to its noun form “writing” that is mapped into a concept writing falling under event. For concept splitting, every time inconsistency among nodes of concepts is discovered, a node may be added. What differs between CoreNet and NTT Goidaikei is that CoreNet features mapping between word senses (not just words) and concepts. These works have lasted since 1994.

title: Implicit ambiguity resolution using incremental clustering in cross-language information retrieval
abstract: This paper presents a method to implicitly resolve ambiguities using dynamic incremental clustering in cross-language information retrieval (CLIR) such as Korean-to-English and Japanese-to-English CLIR. The main objective of this paper shows that document clusters can effectively resolve the ambiguities tremendously increased in translated queries as well as take into account the context of all the terms in a document. In the framework we propose, a query in Korean/Japanese is first translated into English by looking up bilingual dictionaries, then documents are retrieved for the translated query terms based on the vector space retrieval model or the probabilistic retrieval model. For the top-ranked retrieved documents, query-oriented document clusters are incrementally created and the weight of each retrieved document is recalculated by using the clusters. In the experiment based on TREC CLIR test collection, our method achieved 39.41% and 36.79% improvement for translated queries without ambiguity resolution in Korean-to-English CLIR, and 17.89% and 30.46% improvements in Japanese-to-English CLIR, on the vector space retrieval and on the probabilistic retrieval, respectively. Our method achieved 12.30% improvement for all translation queries, compared with blind feedback for the probabilistic retrieval in Korean-to-English CLIR. These results indicate that cluster analysis help to resolve ambiguity.

title: Good spaced seeds for homology search
abstract: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. 
 
 Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.

title: PA-ZSA (Power-Aware Zero-Slack Algorithm): A Graph-Based Timing Analysis for Ultra-Low Power CMOS VLSI
abstract: This paper describes a slack budget distribution algorithm for ultra-low power CMOS logic circuits in a VLSI design environment. We introduce Power-Aware Zero-Slack Algorithm (PA-ZSA), which distributes the surplus time slacks into the most power-hungry modules. The PA-ZSA ensures that the total slack budget is near-maximal and the total power is minimal as a power-aware version of the well-known zero-slack algorithm (ZSA). Based on these time slacks, we have conducted the low-power optimization at gate level by using technology scaling technique. The experimental results show that our strategy reduces average 36% of the total (static and dynamic) power over the conventional slack budget distribution algorithms.

title: Research problems in clothing simulation
abstract: Clothing simulation and animation are of great importance in computer animation. If cloth simulations could be improved to the point that they could generate realistic cloth motion in real-time, they would find uses in many aspects of daily life such as in fashion design and manufacturing. The area of cloth simulation and animation is full of technical challenges: creating more realistic results, achieving faster run-times, and developing methods capable of constructing and simulating more complex garments. This paper provides an overview of the key procedures involved in the creation of clothed characters, describes the current state-of-the-art techniques, and proposes the research problems that most require further study. Three technical aspects of cloth simulation are considered in this paper: garment construction, physically based simulation, and collision resolution.