Preface:Introduction to APBC2009&Michael Q.Zhang,Michael S.Waterman,Xuegong Zhang 1
Oral Presentations 4
Keynote David J.Lipman:A Molecular Picture of Seasonal Influenza 4
Keynote Michael S.Waterman:Sequence Analysis Using Eulerian Graphs 5
Invited Michael B.Eisen:Understanding and Exploiting the Evolution of Drosophila Regulatory Sequences 6
Invited Bailin Hao:Independent Verification of 16S rRNA Based Prokaryotic Phylogeny By Composition Vector Approach 8
Invited John Mattick:A New Understanding of the Human Genome 9
Invited Pavel Pevzner:EULER:From Assembling Short DNA Reads to Shotgun Protein Sequencing by Assembling Mass Spectra 10
Invited Martin Vingron:A Molecular Picture of seawnd Influenza 11
A—DNA Sequence 12
sA1.Sequence alignment and evolution 12
A1-01 Genome aliquoting with double cut and join.&Robert Warren and David Sankoff. 12
A1-02 Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution.&GongXin Yu. 22
A1-03 SE:An algorithm for deriving sequence alignment from a pair of superimposed structures.&Chin-Hsien Tai,James J.Vincent,Changhoon Kim and Byungkook Lee. 32
A1-04 ComPhy:prokaryotic composite distance phylogenies inferred from whole-genome gene sets.&Guan Ning Lin,Zhipeng Cai,Guohui Lin,Sounak Chakraborty and Dong Xu. 40
A1-05 Maximum independent sets of commuting and noninterfering inversions.&Krister Swenson,Yokuki To,Jijun Tang and Bernard Moret. 53
A1-06 Inversion-based genomic signatures.&Krister Swenson and Bernard Moret. 63
A1-07 Triplet supertree heuristics for the tree of life.&Harris T.Lin,J.Gordon Burleigh and Oliver Eulenstein. 72
A1-08 Sorting by reversals,block interchanges,tandem duplications,and deletions.&Martin Bader. 83
A1-09 Improved algorithms for approximate string matching(extended abstract).&Dimitris Papamichail and Georgios Papamichail. 94
A1-10 Simultaneous phylogeny reconstruction and multiple sequence alignment.&Feng Yue,Jian Shi and Jijun Tang. 105
A1-11 Methods for comparative metagenomics.&Daniel Huson,Daniel C Richter,Suparna Mitra,Alexander F Auch and Stephan C Schuster. 115
A1-12 DNA motif alignment by evolving a population of Markov chains.&Chengpeng Bi. 126
A1-13 Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Reconstruction of Ancestral States.&Bin Ma and Louxin Zhang. 138
A2.Sequence assembly 141
A2-01 Parallel short sequence assembly of transcriptomes.&Benjamin G Jackson,Patrick S.Schnable and Srinivas Aluru. 141
A2-02 Finding optimal threshold for correction error reads in DNA assembling.&Francis Y.L.Chin,Henry C.M.Leung,Weilin Li and Siu-Ming Yiu. 153
A2-03 Crystallizing short-read assemblies around seeds.&Mohammad Sajjad Hossain,Navid Azimi and Steven Skiena. 162
A2-04 Short read DNA fragment anchoring algorithm.&Wendi Wang,Peiheng Zhang,Xinchun Liu 173
B—Expression and Regulation. 185
B1.Gene expression,microarray data analysis and disease classification. 185
B1-01 REMAS:a new regression model to identify alternative splicing events from exon array data.&Hao Zheng,Xingyi Hang,Ji Zhu,Minping Qian,Wubin Qu,Chenggang Zhang,Minghua Deng. 185
B1-02 A voting approach to identify a small number of highly predictive genes using multiple classifiers.&Md.Rafiul Hassan,M.Maruf Hossain,James Bailey,Geoff Macintyre,Joshua W.K.Ho and Kotagiri Ramamohanarao. 194
B1-03 Knowledge driven decomposition of tumor expression profiles.&M.H.van Vliet,L.F.A.Wessels and M.J.T.Reinders. 201
B1-04 Network-based support vector machine for classification of microarray samples.&Yanni Zhu,Xiaotong Shen and Wei Pan. 220
B1-05 Using random forest for reliable classification and cost-sensitive learning for medical diagnosis.&Fan Yang,Hua-zhen Wang,Hong Mi,Cheng-de Lin,Wei-wen Cai. 231
B1-06 A statistical framework for integrating two microarray data sets in differential expression analysis.&Yinglei Lai,Sarah E.Eckenrode and Jin-Xiong She. 245
B1-07 Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations.&Reija Autio,Sami Kilpinen,Matti Saarela,Olli Kallioniemi,Sampsa Hautaniemi,Jaakko Astola. 257
B1-08 Integrative disease classification based on cross-platform microarray data.&Chun-Chi Liu,Jianjun Hu,Mrinal Kalakrishnan,Haiyan Huang,Xianghong Jasmine Zhou. 269
B1-09 Principal component tests:applied to temporal gene expression data.&Wensheng Zhang,Hong-bin Fang,Jiuzhou Song. 278
B1-10 Biclustering of gene expression data using reactive greedy randomized adaptive search procedure.&Smitha Dharan,Achuthsankar S Nair. 287
B1-11 Mutual information estimation reveals global associations between stimuli and biological processes.&Taiji Suzuki,Masashi Sugiyama,Takafumi Kanamori and Jun Sese. 297
B1-12 Human gene expression sensitivity according to large scale meta-analysis.&Pei Hao,Siyuan Zheng,Jie Ping,Kang Tu,Christian Gieger,Rui Wang-Sattler,Yang Zhong,Yixue Li. 310
B1-13 Advanced analysis and visualization of gene copy number and expression data.&Reija Autio,Matti Saarela,Anna-Kaarina J？rvinen,Sampsa Hautaniemi,Jaakko Astola. 317
B2.Gene regulation 325
B2-01 Identification of histone modifications in biomedical text for supporting epigenomic research.&Corinna Kolárik,Roman Klinger and Martin Hofmann-Apitius. 325
B2-02 Searching for bidirectional promoters in Arabidopsis thaliana.&Quan Wang,Lin Wan,Dayong Li,Lihuang Zhu,Minping Qian,Minghua Deng. 336
B2-03 ModuleDigger:an itemset mining framework for the detection of cis-regulatory modules.&Hong Sun,Tijl De Bie,Valerie Storms,Qiang Fu,Thomas Dhollander,Karen Lemmens,Annemieke Verstuyf,Bart De Moor,Kathleen Marcha. 347
B2-04 Transcriptional interaction-assisted identification of dynamic nucleosome positioning.&Zhiming Dai,Xianhua Dai,Qian Xiang,Jihua Feng,Yangyang Deng,Jiang Wang,Caisheng He. 360
C—Non-coding RNAs 374
C1.miRNAs and RNAi 374
C1-01 Predicting microRNA targets in time-series microarray experiments via functional data analysis.&Brian J Parker,Jiayu Wen. 374
C1-02 A structural interpretation of the effect of GC-content on efficiency of RNA interference.&Chi Yu Chan,C.Steven Carmack,Dang D.Long,Anil Maliyekke,Yu Shao,Igor B.Roninson,and Ye Ding. 385
C1-03 Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information.&Je-Gun Joung,Zhangjun Fei. 392
C1-04 HHMMiR:Efficient de novo prediction of microRNAs using hierarchical hidden Markov models.&Sabah Kadri,Veronica Hinman,Panayiotis V.Benos. 401
C1-05 CComputational prediction of novel non-coding RNAs in Arabidopsis thaliana.&Dandan Song,Yang Yang,Bin Yu,Binglian Zheng,Zhidong Deng,Bao-Liang Lu,Xuemei Chen and Tao Jiang. 413
C2.RNA structure 426
C2-01 Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA.&Fei Xia,Yong Dou,Xingming Zhou,Xuejun Yang,Jiaqing Xu and Yang Zhang. 426
C2-02 Prediction of RNA secondary structure with pseudoknots using integer programming.&Unyanee Poolsap,Yuki Kato and Tatsuya Akutsu. 439
C2-03 Sequence-structure relations of pseudoknot RNA.&Fenix WD Huang,Linda YM Li and Christian M Reidys. 449
D—Proteins and Proteomics 464
D1.Protein structure,location and function 464
D1-01 Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures.&Weitao Sun,Jing He. 464
D1-02 Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses.&Jhang-Wei Huang,Chwan-Chuen King,Jinn-Moon Yang. 474
D1-03 Predicting disordered regions in proteins using the profiles of amino acid indices.&Pengfei Han,Xiuzhen Zhang and Zhi-Ping Feng. 484
D1-04 A method to improve protein subcellular localization prediction by integrating various biological data sources.&Thai Quang Tung,Doheon Lee. 494
D1-05 Studying the unfolding process of protein G and protein L under physical property space.&Liling Zhao,Jihua Wang,Xianghua Dou Zanxia Cao. 505
D1-06 Prediction of amyloid fibril-forming segments based on a support vector machine.&Jian Tian,Ningfeng Wu,Jun Guo,Yunliu Fan. 513
D1-07 Towards comprehensive structural motif mining for better fold annotation.&Yi Jia.Jun Huan,Vincent Buhr,Jintao Zhang and Leonidas N.Carayannopoulos. 523
D1-08 Semi-supervised protein subcellular localization.&Qian Xu,Derek Hao Hu,Hong Xue,Weichuan Yu and Qiang Yang. 537
D1-09 A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction:implication for structure and active site binding mechanism.&Krongsakda Phakthanakanok,Khanok Ratanakhanokchai,Khin Lay Kyu,Pornthep Sompornpisut,Aaron Watts,and Surapong Pinitglang. 548
D2.Mass spectrometry data processing. 556
D2-01 Quality assessment of tandem mass spectra using support vector machine(SVM).&An-Min Zou,Fang-Xiang Wu and Jia-Rui Ding and Guy G.Pcirier. 556
D2-02 Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences.&Yan Fu,Wei Jia,Zhuang Lu,Haipeng Wang,Zuofei Yuan,Hao Chi,You Li,Liyun Xiu,Wenping Wang,Chao Liu,Leheng Wang,Ruixiang Sun,Wen Gao,Xiaohong Qian,Si-Min He. 568
D2-03 Analysis of mass spectrometry data using sub-spectra.&Wouter Meuleman,Judith Y.M.N.Engwegen,Marie-Christine W.Gast,Lodewyk F.A.Wessels and Marcel J.T.Reinders. 579
E—Pathways and Networks 588
E1.Pathways 588
E1-01 Predicting allosteric communication pathways using motion correlation network.&Tu-Liang Lin and Guang Song. 588
E1-02 Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach.&Hong-Hee Won,Inho Park,Eunjung Lee,Jong-Won Kim and Doheon Lee. 599
E1-03 Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data.&Dongxiao Zhu. 607
E1-04 Analysis on relationship between extreme pathways and correlated reaction sets.&Yanping Xi,Yi-Ping Phoebe Chen,Ming Cao,Weirong Wang and Fei Wang. 619
E2.Networks and systems biology 631
E2-01 Extract interaction detection methods from the biological literature.&Hongning Wang,Minlie Huang and Xiaoyan Zhu. 631
E2-02 Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting.&Jisu Kim,Kyungsook Han. 644
E2-03 A new graph-based method for pairwise global network alignment.&Gunnar W.Klau. 652
E2-04 GAIA:a gram-based interaction analysis tool-an approach for identifying interacting domains in yeast.&Kelvin X.Zhang and B.F.Francis Ouellette. 662
F-Genetic Variations and Complex Diseases 673
F1.Disease classification and metabolism modeling 673
F1-01 On optimal comparability editing with applications to molecular diagnostics.&Sebastian B？ecker,Sebastian Briesemeister and Gunnar W.Klau. 673
F1-02 Genome-scale analysis to the impact of gene deletion on the metabolism of E.coli:constraint-based simulation approach.&Zixiang Xu,Xiao Sun,Shihai Yu. 683
F1-03 An unsupervised partition method based on association delineated revised mutual information.&Jing Chen,Guangcheng Xi. 694
F1-04 A new classification method using array Comparative Genome Hybridization data,based on the concept of Limited Jumping Emerging Patterns.&Tomasz Gambin and Krzysztof Walczak. 706
F2. Association study and genomic variation 717
F2-01 Copy-number-variation and copy-number-alteration region detection by cumulative plots.&Wentian Li,Annette Lee and Peter K Gregersen. 717
F2-02 Identifying disease associations via genome-wide association studies.&Wenhui Huang,Pengyuan Wang,Zhen Liu and Liqing Zhang. 729
F2-03 Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies.&Erdahl T Teber,Jason Y Liu,Sara Ballouz,Diane Fatkin and Merridee A Wouters. 738
F2-04 CGTS:a site-clustering graph based tagSNP selection algorithm in genotype data.&Jun Wang,Mao-zu Guo,Chun-yu Wang. 751
F2-05 PCA.based population structure inference with generic clustering algorithms.&Chih Lee,Ali Abdool and Chun-Hsi Huang. 761
F2-06 A fast algorithm for genome-wide haplotype pattern mining.&S？ren Besenbacher,Christian N.S.Pedersen and Thomas Mailund. 772
F2-07 Detecting Disease-Associated Genotype Patterns.&Quan Long,Qingrun Zhang and Jurg Ott. 781
F2-08 A random forest approach to the detection of epistatic interactions in case-control studies.&Rui Jiang,Wanwan Tang,Xuebing Wu and Wenhui Fu. 788
F2-09 Partial correlation analysis indicates causal relationships between GC-content,exon density and recombination rate variation in the human genome.&Jan Freudenberg,Mingyi Wang,Yaning Yang and Wentian Li. 801
F2-10 Minimizing recombinations in consensus networks for phylogeographic studies.&Laxmi Parida,Asif Javed,Marta Melé,Francesc Calafell and Jaume Bertranpetit and Genographic Consortium. 811
Posters 823
PA1-01 Evolutionary and genomic analyses of cee,a novel but ancient gene involved in development.&Jorge Fernandes,Daniel Macqueen,Hung-Tai Lee and Ian Johnston. 823
PA1-03 Heterogeneous Computing for Bioinformatics Applications.&Xiandong Meng and Vipin Chaudhary. 824
PA1-04 De Novo Exon Acquisition during Human Evolution.&Yoonsoo Hahn and Byungkook Lee. 825
PA1-05 Feasibility Study of Using Massively Parallel Pyrosequencing in Detecting Variation in Dengue Virus Genome.&Kwanrutai Chin-inmanu,Aroonroong Jairungsri,Duangjai Sangsrakru,Sithichoke Tangphatsornruang,Somvong Tragoonrung and Prapat Suriyaphol. 826
PA1-07 SE:An algorithm for deriving sequence alignment from a pair of superimposed structures.&Chin-Hsien Tai,Changhoon kim,James J.Vincent and Byungkook(BK)Lee. 827
PA1-08 Discovery of Unknown Bacteria:A Metagenomic Analysis.&Divya Suryakumar,Raveesh Chilakapati,Qingzhong Liu and Andrew Sung. 828
PA1-09 An annotation system focused on metabolic reconstruction and comparative genomics:characterization of an acidophilic microbial community.&Aida Arcas,Noemi Alvarez,Marina Postigo,Mercedes Moreno,Victor Parro and Manuel J Gómez. 829
PA1-10 Multiple Weighted Sequence Alignment for Functional Residue Prediction on Carbohydrate Binding Modules.&Wei-Yao Chou,Wei-I Chou,Tun-Wen Pai,Shu-Chuan Lin，Ting-Ying Chiang,Chuan Yi Tang and Margaret Dah-Tsyr Chang. 830
PA1-11 The evolution rate speed-up event of UCP1 indicates the essential residues for its characteristic high uncoupling activity.&Yaping Liu,Kun Chen,Zhiyuan Lv,Hongxiang Zheng,Jin Wang and Chenyu Zhang. 831
PA1-12 Comparative Metagenomics with MEGAN 2.0.&Suparna Mitra,Daniel Richter,Alexander Auch,Stephan Schuster and Daniel Huson. 832
PA1-13 ComPhy:Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets.&Guan Ning Lin,Zhipeng Cai,Guohui Lin,Sounak Chakraborty and Dong Xu. 833
PA1-14 Genome-wide analysis of natural selection in human repetitive DNA elements.&Jian-Huan Chen,Qian Xu,Siu-Kin Ng and Hong Xue. 834
PA1-15 Genome-wide Identification of ChIP-Seq Enriched Regions Based on a Statistical Model.&Chongzhi Zang,Chen Zeng,Weiqun Peng,Dustin E Schones,Kairong Cui and Keji Zhao. 835
PA1-16 Sorting by inversions,fast.&Krister Swenson,Vaibhav Rajan,Yu Lin and Bernard Moret. 836
PB1-01 Singular value decomposition for genome-wide spermatogenesis microarray data analysis.&Weixiang Liu,Aifa Tang,Kehong Yuan,Datian Ye,Tianfu Wang,Siping Chen. 837
PB1-02 Gene Selection with Fold Change Detection via Nonnegative Matrix Factorization.&Weixiang Liu,Tianfu Wang,Siping Chen,Aifa Tang,Kehong Yuan,Datian Ye. 838
PB1-03 A joint mixture model for clustering genes from Gaussian and beta distributed data.&Xiaofeng Dai,Timo Erkkil？,Olli Yli-Harja and Harri L？hdesm？ki. 839
PB1-04 Research on Random Forests-based gene selection of microarray data of colon cancer.&Jiangeng Li,Zhikun Gao,Zhi Yan and Youyong Lu. 840
PB1-05 Gene Set Enrichment Analysis for Replicated Microarray Time Course Data.&Jae-Young Kim,Hyungmin Lee and Miyoung Shin. 841
PB1-08 Data Analysis Tools at the UCM-CNB Bioinfo Unit.&Pedro Carmona-Saez,Ruben Nogales-Cadenas,Miguel Vazquez,Edgardo Mejía,Federico Abascal,Mariana Neves,Francisco Tirado,Jose-Maria Carazo and Alberto Pascual-Montano. 842
PB2-01 Prevalent use of bidirectional promoters generates pervasive transcription in yeast.&Zhenyu Xu,Wu Wei,Julien Gagneur and Lars Steinmetz. 843
PB2-02 Genome-wide identification of transcriptional start sites,promoters and transcriptional factor binding sites in Escherichia coli K-12 bacterial genome:Development of a bioinformatics tool for the graphical display of the high throughput sequencing data.&Enrique Morett,Alfredo Mendoza,Leticia Olvera,Maricela Olvera,Katy Juárez,contreras-moreira,Verónica Jiménez,Julio Collado-Vides,Blanca Taboada,Leticia Vega-Alvarado,Ryosuke Watanabe and Edgar Vallejo. 844
PB2-03 Prediction of translation initiation site for microbial genomes with TriTISA.&Gang-Qing Hu,Xiaobin Zheng,HuaiQiu Zhu and Zhen-Su She. 845
PB2-05 A TaqMan？ real-time PCR based method for studying copy number variations.&Xiaoqing You,Matt Xia,Kelly Li and Gene Spier. 846
PB2-06 Evaluation and expression of"drug-likeness"of small molecules using Semantic Web technologies.&Jooyoung Choi,Melissa Davis and Mark A.Ragan. 847
PB2-07 Chromatin modification similarity and coexpression of neighboring gene pairs in yeast.&Yangyang Deng,Xianhua Dai,Qian Xiang,Caisheng He,Jiang Wang,Jihua Feng and Zhiming Dai. 848
PB2-08 A comparison study of cross-platform experimental nucleosome positioning data:a nucleosome statistical distribution domain model in the S.cerevisiae genome.&Jihua Feng,Xianhua Dai,Qian Xiang,Zhiming Dai,Jiang Wang,Yangyang Deng and Caisheng He. 849
PB2-09 A mutation degree model for identifying transcriptional regulatory elements.&Chang Q Zhang,Jin Wang,Huaiqiu Zhu and Xiang Gao. 850
PB2-10 Assessing the apparent stability of conserved sites in plant virus genomes over time.&Linda Zheng,Mark Gibbs and Brendan Rodoni. 851
PB2-11 A fast algorithm on detecting spatially locally co-expressed regions between genes from in situ hybridization data.&XiaotuMa and Wenyuan Li. 852
PB2-13 Evolutionary Dynamics of Genomic Regulatory Blocks:HCNEs and HARs,the content and the boundaries.&Xianjun Dong,Altuna Akalin,David Fredman and Boris Lenhard. 853
PB2-14 Recovering gene regulations by optimization model.&Yong Wang,Xiang-Sun Zhang and Luonan Chen. 854
PC1-01 A Target-Structure-Based Hybridization Model for Prediction of MicroRNA:Target Interactions.&Dang Long,Chi Yu Chan,Molly Hammell,Rosalind Lee,Peter Williams,Victor Ambros,and Ye Ding. 855
PC1-02 Characteristic analysis of miRNA precursors in metazoan species.&Xiaobai Zhang,Xiaofeng Song,Huinan Wang and Huanping Zhang. 856
PC1-04 The microRNAs'effects on the expression of target genes at mRNA and protein levels.&Yunfei Pei,Xi Wang and Xuegong Zhang. 857
PC1-05 Rapid Evolution of Mammalian X-linked Testis microRNAs.&Xuejiang Guo,Bin Su,Zuomin Zhou and Jiahao Sha. 858
PC1-06 sRNATarBase:a comprehensive database of bacterial sRNA targets verified by experiments.&Yalin Zhao,Yuan Cao,Xiaomin Ying,Lei Cha,Ligui Wang,NingSheng Shao and Wuju Li. 859
PC1-07 Cleavage in MicroRNA Maturation by Drosha.&Jiyuan An,Yongjun Fan,Anthony Beckhouse,Alistair Chalk and Christine Wells. 860
PC1-08 miRNA analysis,the design of highly discriminative oligonucleotides with a memetic algorithm.&Niels Tolstrup,Marc Juul Christoffersen,Nana Jacobsen,Ditte Andreasen,Peter K Busk,Lena Hansson,Jesper Salomon,Hanni Willenbrock,Jens Friis-Nielsen and Peter Mouritzen. 861
PC2-02 Incorporating Statistical Characters of Amino Acid for the Prediction of RNA-Protein Interface Residue.&Xiujun Gong,Xinmi Liu and Hua Yu. 862
PC2-03 Computational evidence of A-to-I RNA editing in the nucleus transcriptome of Arabidopsis thaliana.&Pufeng Du and Yanda Li. 863
PC2-05 Group-specific 16S rRNA probe design using MCMC methods.&Yibo Wu,Lirong Yan,Hui Liu,Hanchang Sun and Hongwei Xie. 864
PD1-04 DomML,a novel ab initio protein domain prediction method based on domain size distribution.&Yann Christinat. 865
PD1-05 A plasmid-borne O-antigen in Brachyspira hyodysenteriae.&Phatthanaphong Wanchanthuek,Karon Ryan,Paula Moolhuijzen,Zayed Albertyn,Babak Shaban,David J.Hampson,Matthew Bellgard. 866
PD1-06 Identifying Conserved Regions for Protein Structure Prediction.&Yi Wei,Dongbo Bu and Jishuang Yang. 867
PD1-07 Classification RpoS regulon in Burkholderia pseudomallei based on proteomic profile information.&Yupaporn Osiriphun,Patompon Wongtrakoongate,Sucharat Sanongkiet,Prapat Suriyaphol and Sumalee Tungpradabkul. 868
PD1-09 Evolutionary conservation in multiple faces of protein interaction.&Sanguk Kim,Yoon Sup Choi,Jae-Seong Yang and Sung Ho Ryu. 869
PD1-11 Uncovering signaling networks based on high-throughput data.&Xingming Zhao and Luonan Chen. 870
PD1-12 Order and Content of Thymine in Protein Coding Frames of mRNA Sequences.&Ekambaram Rajasekaran and Perumal Anandagopu. 871
PD1-13 Protein Function-Function Correlation Approach for Protein Functions Prediction.&Ka-Lok Ng,Chien-Hung Huang and Jin-Shuei Ciou. 872
PD1-14 Improved computational prediction of prokaryotic protein subcellular localization.&Nancy Yu,James Wagner,Matthew Laird,Raymond Lo,Martin Ester and Fiona Brinkman. 873
PD1-15 Towards Comprehensive Structural Motif Mining for Better Fold Annotation in the"Twilight Zone"of Sequence Dissimilarity.&Yi Jia,Vincent Buhr,Jintao Zhang,Jun Huan and Leonidas N.Carayannopoulos. 874
PD1-17 Protease Substrate Site Predictors Based on Multilevel Substrate Phage Display Data.&Ching-Tai Chen,Ei-Wen Yang,Wen-Lian Hsu and An-Suei Yang. 875
PD1-19 Detecting protein structure flexibility via rigid structure identification.&Yu-Feng Huang,Chia-Jui Yang,Chun-Chin Huang,Chien-Kang Huang,Chun-Yi Huang,Li-Yuan Chiu,Pei-Chun Ko,Chiun-Yao Chiang. 876
PD1-20 Prediction of Protein Nuclear Localization Based on Smoothed Evolutionary Information and Probabilistic Latent Semantic Indexing.&Emily Chia-Yu Su,Jia-Ming Chang,Ting-Yi Sung and WenLian Hsu. 877
PD1-21 Computational characterisation of humanlamina-associated domains(LADs).&Wouter Meuleman,Ludo Pagie,Marcel Reinders,Bas van Steensel and Lodewyk Wessels. 878
PD1-22 Evolution of protein-protein interaction networks for plant bZIP transcription factors.&Ying He,Grigoris Amoutzias and Yves Van de Peer. 879
PD1-23 Glutamate Receptor Ion Channels and their relativesin Bacteria.&Mao-Feng Ger,Gloria Rendon and Eric Jakobsson. 880
PD1-24 CPSARST&CPDB-an efficient search tool and a comprehensive database of circular permutation in proteins.&Wei-Cheng Lo,Chi-Ching Lee,Che-Yu Lee,and Ping-Chiang Lyu. 881
PD2-02 Protein maps:Integration of Physico-Chemical Properties for Functional Annotation of Proteins.&Sumeet Dua and Pradeep Chowriappa. 882
PD2-03 Physical Encoding Based Bioinformatics Analysis for Exploring Protein Sorting Signals.&Fan Zhang and Jianjun Hu. 883
PD2-04 Protein-protein docking by simulating the process of association based on predicted interface.&Bingding Huang,Michael Schroeder and Rebecca Wade. 884
PD2-24 Assessment of contribution of genomic data sets to predicting protein functions.&Seok-Ha Ko and Hyunju Lee. 885
PE1-01 Bifurcation Analysis of Oscillation Patterns in an NF-κВ Signal Pathway Model.&Hong Yue and Baoyun Lu. 886
PE1-03 Constrained Mining of Minimal Separators with Applications to Gene Perturbation Studies.&Ying Jin,Naren Ramakrishnan,Lenwood S.Heath and Richard F.Helm. 887
PE2-02 BIOIR:An approach to public domain resource integration for human protein-protein interaction.&Hsueh-Chuan Liu,Carlos Roberto Arias and Von-Wun Soo. 888
PE2-04 Identification of disease genes via network alignment of human interactome and phenome.&Xuebing Wu,Qifang Liu and Rui Jiang. 890
PE2-05 The Influenza Virus Resource at the National Center for Biotechnology Information.&Yiming Bao,Dmitry Dernovoy,Boris Kiryutin,Leonid Zaslavsky,Tatiana Tatusova,Jim Ostell and David Lipman. 891
PE2-06 Dose mitochondrial protein network in yeast have a structure of the dissemination tree?&Yoon Kyeong Lee,Myung Ho Yeo,Tae Ho Kang,Jae Soo Yoo and Hakyong Kim. 892
PE2-07 Dao:a novel programming language for bioinformatics.&Limin Fu. 893
PE2-08 A functional canonical correlation analysis approach to reverse engineering of in silico gene regulatory networks.&Feng Zeng,Xuebing Wu,Xuegong Zhang and Rui Jiang. 894
PE2-09 Semantic map generation for biological databases.&Hoan Nguyen,Nicolas Wicker,DavidKieffer and Olivier Poch. 895
PE2-10 Using the Non-negative Matrix Factorization model in Bioinformatics.&Alberto Pascual-Montano,Ruben Nogales-Cadenas,Pedro Carmona-Saez and Jose-Maria Carazo. 896
PE2-11 The Prediction of Protein-Protein Interaction Networks in Rice Blast Fungus.&He Fei,Yan Zhang,Hao Chen,Ziding Zhang and You-Liang Peng. 897
PE2-12 Modelling uncertainty in transcriptome measurements enhances network component analysis of yeast metabolic cycle.&Chunqi Chang,Yeung Sam Hung and Mahesan Niranjan. 898
PE2-14 Integrative Online Tool for Simulation of Steady-state and Dynamic Cellular Networks.&Hongseok Yun,Choamun Yun,Sang Yup Lee and Sunwon Park. 899
PE2-15 Reconstruction of a Genome-scale Metabolic Network of Clostridium acetobutylicum ATCC 824 and Flux Balance Analysis Combined with Nonlinear Programming.&Hongseok Yun,Joungmin Lee and Sang Yup Lee. 900
PE2-16 From Genome to Life-Style.&Zhaocheng Fan,Jiayuan Zhao,Xiaoyan zhu,Yang Zhong,Renyi Liu and Tao Jiang. 901
PE2-17 A systematic approach of modulization in hES cell differentiation.&Jin Hyuk Kim,Jin-il Han,Hye Young Kim,Min Jung Kim,Bo Kyung Kim and Yong Sung Lee. 902
PE2-18 Construction of comprehensive gene network for mitochondria.&Song Gao,Jie Li and Jin Wang. 903
PE2-19 Network approach for prioritizing drug candidate on gliomas.&Lisha Li,Ningbo Zhang and Shao Li. 904
PF1-01 A Case Study:The Development of a Cancer Clinical Trial Database System Using caCORE SDK.&Haibin Wang,Teresa Stilley,Fadlo Khuri and André Rogatko. 905
PF1-02 Gene Prospector:ranking genes for investigation of gene-disease associations and gene-environment interactions.&Wei Yu,Anja Wulf,Tiebin Liu,Muin Khoury and Marta Gwinn. 906
PF1-03 Computational analysis of disease-related mutation effects on transcription factor binding.&Kirsti Laurila and Harri L？hdesm？ki. 907
PF1-04 An Approach to the Recovery of Associations between Protein Domains and Complex Diseases.&Wenhui Wang,Wangshu Zhang,Rui Jiang and Yihui Luan. 908
PF1-05 Nonlinear cooperation between p53 and ING1 induces bax expression in mouse thymocyte apoptosis.&Shaojin Duan,Lin Wan,Wenjiang Fu,Hong Pan,Qi Ding,Chang Chen,Peiwei Han,Xiaoyan Zhu,Liying Du,Hongxiao Liu,Yuxia Chen,Ximing Liu,Xiting Yan,Minghua Deng and Minping Qian. 909
PF1-07 Knowledge driven decomposition of tumor expression profiles.&Martin van Vliet,Lodewyk F.A.Wessels and Marcel J.T.Reinders. 910
PF1-09 Gentrepid:a candidate gene prediction webserver.&Jason Liu,Erdahl Teer,Richard George,Sara Ballouz,Chi N Pang,Boer Xu,Naresh P.Bains,Duncan B.Sparrow,Robyn Otway,Guanglan Guo,Diane Fatkin and Merridee Wouters. 911
PF2-01 Extended multiple breakpoint graphs and a fast and exact DCJ median solver for linear genomes.&Andrew Wei Xu. 912
PF2-02 Epidemic history of HCV genotype 6 in South East Asia.&Yi Tan and Shui Shan Lee. 913
PF2-03 PBEAM:A parallel implementation of BEAM for genome-wide inference of epistatic interactions.&Tao Peng,Pufeng Du and Yanda Li. 914
PF2-04 SNPShuttle:bi-directional scan of SNP arrays to gain accuracy in missing genotype inference.&Christine Sinoquet. 915
PF2-06 A CCA-based multi-locus method for association studies on multi-phenotype data.&Wanwan Tang and Yanda Li. 926
PF2-08 Natural parameter values for generalized gene adjacency.&Zhenyu Yang and David Sankoff. 927