POSTERS

Assignment	Title	Authors
SF-39	Extracting Simple Motifs Under the Levenshtein Measure	Adebiyi, Ezekiel F.
SA-1	MaM: Multiple Alignment Manipulator	Alkan, Can and Tüzün, Eray and Eichler, Evan and Bailey, Jeff and Sahinalp, Cenk S.
IN-125	NIGMS Funding Opportunities for Complex Biomedical Systems Research and Training	Anderson, James J.
SA-2	G-language Genome Analysis Environment	Arakawa, Kazuharu and Mori, Koya and Tomita, Masaru
RR-85	Protein Families and Regulatory Patterns amongst the Transcription Factors of E. coli	Babu, M. Madan and Teichmann, Sarah A.
SA-3	mreps: A Program for Exhaustive Search for Tandem Repeats in DNA Sequences	Bana, Ghizlane and Kolpakov, Roman and Giraud, Mathieu and Rabbat, Ralph and Kucherov, Gregory
PW-86	Combinatorial Analysis of Transcription Regulation in Yeast Cell-cycle	Banerjee, Nila and Zhang, Michael Q.
ME-47	An EST Cluster-Sorting Software HSAnalyst as an Universal Tool for Discovering of Genes with Unusual Expression	Baranova, A.V. and Lobashev, A.V. and Ivanov, D.V. and Krukovskaya, L.L. and Zinchenko, V.V. and Shestakov, S.V. and Yankovsky, N.K. and Kozlov, A.P.
SA-4	Building a Genome Database Using an Object-Oriented Approach	Barbasiewicz, Anna and Liu, Lin and Lang, B.Franz and Burger, Gertruad
ME-48	How to Arrange Gene Expression Profiles in Linear Orders	Beißbarth, Tim and Vingron, Martin
RR-74	The E. coli Promoter Region: A Statistical Analysis	Bejerano, Gill and Margalit, Hanah and Tishby, Naftali
PA-112	Enumerating Optimal Sequences of Reversals: Tools and Experiments	Bergeron, Anne and Chauve, Cedric and Hartman, Tzvika and Saint-Onge, Karine
PS-94	Ligand Binding to the Pregnane X Receptor by Geometric Matching of Hydrogen Bonds	Berretty, Robert-Paul and Hsu, David and Kettner, Lutz and Mascarenhas, Ajith and Redinbo, Matthew R. and Snoeyink, Jack and Watkins, Ryan
PA-113	MGR - A Web Tool for Multiple Genome Rearrangements	Bourque, Guillaume and Tesler, Glenn
SA-5	A Supervised Learning Approach for Detecting Significant Local Alignments	Breimer, Eric A. and Goldberg, Mark K.
SA-6	CHAOS: A Heuristic Algorithm for Local Alignment	Brudno, Michael and Morgenstern, Burkhard
PA-114	Mitochondrial Eve and Population Bottlenecks	Buss, Samuel R. and Clote, Peter G.
SA-7	A Fast String Matching Method for Database Queries	Campbell, Shannon R.
PA-115	Genomic Signature: A Global Sequence Analysis Concept Applied to Phylogeny	Chapus, Charles and Fertil, Bernard and Giron, Alain and Deschavanne, Patrick
RR-75	Characterization and Prediction of the Nanos Response Element with Sequence Analysis in Drosophila	Chen, Gengxin and Zhang, Michael Q.
SN-44	SNP Mapping Using Genome-wide Marker Sequences	Chen, Leslie Y.Y. and Lu, Szu-Hsien and Shih, Edward S.C. and Hwang, Ming-Jing
RR-76	Finding Recurrent Binding Site Clusters	Cheng, Yizong and Aronow, Bruce
RR-77	PromoterFootprint: A New Method for Alignment of Regulatory Genomic Sequences. Phylogenetic Footprinting of TF Binding Sites.	Cheremushkin, Eugene and Kel, Alexander
RR-78	Quantifying Sequence Correlates of Gene Regulation	Clarke, Neil D. and Granek, Joshua A. and Liu, Xiao
SA-8	Pooled Genomic Indexing	Csürös, Miklós and Milosavljevic, Aleksandar
PW-87	Predicting Protein Interaction Paths and Multimeric Complex Configuration: A Binding Site Recognition Based Approach	Del Carpio-Muñoz, Carlos A.
SA-9	Discovering Common Mutually-Correlated Pairs of Positions for the Families of Immunoglobulin Fold	Dement'ev, Andrey and Galitsky, Boris
SW-123	A User Friendly Bioinformatical Pipeline Environment	Dunbar, Donald and Proutski, Vitali
ME-49	A Variance-Stabilizing Transformation for Microarray Data	Durbin, Blythe and Hardin, Johanna and Hawkins, Douglas and Rocke, David
LA-45	Superlink: A New Program for Exact Genetic Linkage Analysis of General Pedigrees	Fishelson, Ma'ayan and Geiger, Dan
SA-10	Substitution Matrices Derived from Structurally Constrained Protein Evolution Simulations	Fornasari, Maria and Parisi, Gustavo and Echave, Julián
PW-88	Inferring Gene Networks from Perturbed Expression Profiles	de la Fuente, Alberto and Brazhnik, Paul and Mendes, Pedro
SA-11	Contextual Alignment of Biological Sequences	Gambin, Anna and Lasota, Slawomir and Szklarczyk, Radoslaw and Tiuryn, Jerzy and Tyszkiewicz, Jerzy
SA-12	Substitution Tables for Contextual Alignment	Gambin, Anna and Tyszkiewicz, Jerzy
SA-13	Rare and Frequent n-Grams in Whole-Genome Protein Sequences	Ganapathiraju, Madhavi and Klein-Seetharaman, Judith and Rosenfeld, Roni and Carbonell, Jaime and Reddy, Raj
SA-14	`DNA Kinases' -- Computational Insights	Ganji, Gopinath and Li, Yingfu and Cuticchia, A. Jamie
RR-79	Promoter Prediction Using Hidden Markov Model	Gao, Feng and Goldstein, Richard A.
ME-50	Measurement Error and Reproducibility of Affymetrix Microarray Data with Application to Autism	Geller, Sue and Zhou, Lei and Gregg, Jeff and Hagerman, Paul and Rocke, David M.
PS-95	A Fast Pattern-Matching System on a Protein Topology Database	Gilbert, David and Torrance, Gilleain and Viksna, Juris and Dhulia, Neha and Mamtora, Darshit and Westhead, David and Michalopoulos, Ioannis
SA-15	Improving Shotgun Sequencing Through Learning	Goldberg, Mark and Lim, Darren
SA-16	Closest Strings, Primer Design, and Motif Search	Gramm, Jens and Hüffner, Falk and Niedermeier, Rolf
ME-51	Performance Analysis of Differential Expression Prediction Algorithms Using Simulated Array Data	Grant, Gregory and Manduchi, Elisabetta and Sokolovski, Sam and Stoeckert, Chris
ME-52	Discovery of Correlation of Tissue Gene Expression Using cDNA Libraries	Horng, Jorng-Tzong and Huang, Hsien Da and Tseng, Kuo-Yen and Tsou, Tsung-Shan and Liu, Baw-Jhiune and Kao, Cheng-Yan
PS-96	Mining Functional Domain Sharing in Protein Structures	Horng, Jorng-Tzong and Huang, Hsien Da and Wang, Shih-Hsien and Tsou, Tsung-Shan and Liu, Baw-Jhiune and Kao, Cheng-Yan and Hwang, Jenn-Kang
PS-97	Evolution of Protein Tyrosine Phosphatase Superfamilies: Evidences from Structures and Genome Data	Huang, Jing-Fei and Lin, Jun
PS-98	Automated Determination of Protein Structures from NMR Data by Iterative Analysis of Self-Consistent NOE Contact Patterns	Huang, Y. Janet and Tejero, Roberto and Montelione, Gaetano T.
ME-53	Instructional Movie: cDNA Microarrays for Gene Expression Analysis	Huber, Wolfgang and Sültmann, Holger and Poustka, Annemarie and Sawitzki, Günther
ON-121	A Mathematical Modeling of GO Hierarchy for Gene Expression Profiling Analysis	Hur, Jung and Lee, Sung and Oh, Ji and Chung, Tae and Kim, Yang
SA-17	Construction of Integrated Database for Protein Kinases and Proteases	Hur, Jung and Park, Dong and Kim, Yang
ME-54	Inferring Genetic Network from Microarray Gene Expression Data by Bayesian Network and Nonparametric Regression	Imoto, Seiya and Goto, Takao and Miyano, Satoru
RR-80	A Heuristic Approach to Identify Common RNA Structural Motifs in Homologous Sequences	Ji, Yongmei and Stormo, Gary D.
PA-116	Dynamics of Myb Gene Family Evolution in Arabidopsis	Jia, Li and Jiang, Tao and Clegg, Michael
GF-34	Identification and Analysis of Alternative Splicing Events in the Human Genome	Kan, Zhengyan and Gish, Warren and States, David
SF-40	Discovering Motifs in Amino Acid Sequences using a Modified PrefixSpan Method	Kanbara, Tomoki and Mori, Yasuma and Kitakami, Hajime and Kuroki, Susumu and Yamazaki, Yukiko
ME-55	Genes in Cocaine Addiction	Keskin, Ozlem and Munshi, Rajan and Bahar, Ivet
SA-18	ConPath: Views Scaffolds and Calculates the Relative Orders, Orientations and Gaps of Contigs by Using Fosmid	Kim, Pan-Gyu and Jung, Haeyoung and Park, Kiejung
SA-19	Finding All Normalized Local Alignments Above a Threshold	Kim, Sangtae and Sim, Jeong S. and Park, Heejin and Park, Kunsoo and Park, Hyunseok and Seo, Jeong-Sun
ME-56	Effects of Sparse Time-Series Data on the Prediction of Gene Networks: A Study with a Boolean Network System Simulator.	Kim, Sohyoung and Weinstein, John N. and Grefenstette, John J.
RS-36	Ribosome Builder: A Software Project to Simulate the Ribosome in Real-Time	Knight, William and Hill, Walter E. and Lodmell, J. Stephen
DS-37	Distributions of Thermodynamic Values for DNA Oligomers: A Theoretical Survey of Tm and Hybridization Extent	Koehler, Ryan T. and Peyret, Nicolas
ME-57	An Analysis of Matched mRNA Measurements from the High-Density HU6800 and cDNA Microarrays	Kuo, Winston Patrick and Jenssen, Tor-Kristian and Kim, Ju Han and Kohane, Isaac S. and Ohno-Machado, Lucila
PS-99	A Method to Assess the Performance of Knowledge-Based Potentials with Respect to Amino Acid Types.	Kuznetsov, Igor and Rackovsky, S.
SA-20	How Can We Quantitatively Describe Growth of Proteome Complexity Due to Evolution?	Kuznetsov, Vladimir A.
RR-81	Deciphering cis-Acting Regulatory Elements in Plant and Drosophila Promoter Sequences	Lescot, Magali and Rombauts, Stephane and Dèhais, Patrice and Thijs, Gert and Martin, David and Thieffry, Denis and Jacq, Bernard and Moreau, Yves and Rouzè, Pierre and van Helden, Jacques
RR-82	Identification of cis-Regulatory Elements and Their Combination in Mammalian Promoter Sequences	Leykin, Igor and Kao, Ming-Chih and Wong, Wing Hung
SA-21	Double-End Clone Sequence Assembly: Some Statistical Issues	Li, Xiaoman and Waterman, Michael S.
PW-89	MetEx Viewer: A Visualization System for Metabolomics and Transcriptomics	Li, Xing Jing and Lee, Christine and Hoops, Stefan and Mendes, Pedro
PS-100	Modeling Protein Flexibility for Structure-Based Active Site Redesign	Lilien, Ryan H. and Anderson, Amy C. and Donald, Bruce R.
SW-124	The Design of an Agent-Based Workflow Tool for Bio-informatics	Liu, Chung-Shyan and Ch'ang, Lan-Yang and Lin, Wen-Chang
SA-22	Remote Homology Detection Using Feature Vectors Formed Using Alignments of Small Motifs	Logan, Beth and Moreno, Pedro and Suzek, Baris and Weng, Zhiping and Kasif, Simon
ME-58	Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data	Magwene, Paul M. and Lizardi, Paul and Kim, Junhyong
SF-41	Fast Algorithm for Extracting Multiple Unordered Short Motifs	Maruyama, Osamu and Bannai, Hideo and Tamada, Yoshinori and Kuhara, Satoru and Miyano, Satoru
PW-90	Genomic Object Net: On-going Report on Biopathway Modeling and Simulation	Matsuno, Hiroshi and Hirata, Yuichi and Doi, Atsushi and Miyano, Satoru
ME-59	Gene Expression Analysis by a Novel Dynamically Extendable Self-Organized Map Integrating Unsupervised and Supervised Learning	Mavroudi, Seferina and Papadimitriou, Stergios and Bezerianos, Anastasios
PS-101	Extraction of Functionally Relevant Structural Templates from Protein Structures	Milik, Mariusz and Szalma, Sandor and Olszewski, Krzystof A.
SA-23	Development of the Bacteria Analysis System on G-language Genome Analysis Environment	Mori, Koya and Arakawa, Kazuharu and Tomita, Masaru
ON-122	Building Front End to the Common-Sense Genome Ontology	Moucka, Gina and Galitsky, Boris
PA-117	Comparative Structural Phylogeny of Potassium Channels	Palaniappan, Ashok and Jakobsson, Eric G.
PS-102	Structural Constrained Protein Evolution Simulations of Members of the Left-Handed Beta Helix Superfamily	Parisi, Gustavo and Echave, Julián
ME-60	Principal Variables Analysis of Microarray Data	Park, Peter J. and Kohane, Isaac S.
PW-91	A Fast and Robust Method to Infer and Characterize an Active Regulator Set for Molecular Pathways	Pe'er, Dana and Regev, Aviv and Tanay, Amos
RR-83	Regulation of the Heat Shock Response of $\beta$-, $\gamma$- and $\epsilon$- Proteobacteria	Permina, Elizabeth and Gelfand, Mikhail
GF-35	Stable RNA Secondary Structure of Human Donor Splice Sites	Pervouchine, Dmitri and Graber, Joel and Kasif, Simon
SA-24	STROMA: Structurally Optimized Score Matrix for Sequence Alignment	Qian, Bin and Goldstein, Richard A.
PA-118	A New Formulation of Evolutionary Models	Rahmann, Sven and Müller, Tobias
SF-42	Using Gibbs Sampling Strategies to Identify Motif Families in Networks of Interacting Proteins	Reiss, David J. and Schwikowski, Benno
ME-61	Gene Expression Based Class Discovery of Familial Non-BRCA1/BRCA2 Breast Cancer	Ringnér, Markus and Hedenfalk, Ingrid and Ben-Dor, Amir and Yakhini, Zohar and Chen, Yidong and Meltzer, Paul and Borg, Åke and Trent, Jeffrey
PS-103	Computing Mutational Constraints Within Protein Domains Using Naturally-Occurring Sequence Variation	Ruby, J. Graham and Zadeh, Joseph N. and Kao, Ming-Yang
RR-84	Analysis of Topological Representations of Transcriptional Regulatory Regions	Sand, Olivier and Vu, Tien Deng and Gilbert, David and Viksna, Juris
SA-25	Development of Gene Ontology Analysis and Classification Tools for Microbial Genome Annotation	Seo, Hwajung and Kim, Ki-Bong and Tae, Hongseok and Park, Wan and Park, Kiejung
PS-104	Compression of Protein Conformational Space	Shao, Yu and Magdon-Ismail, Malik and Freedman, Daniel and Akella, Srinivas and Zaki, Mohammed and Bystroff, Chris
PS-105	Optimal Knowledge-Based Potentials and Threading Score Functions Derived from the Most Informative Sequence-Dependent Structural Probability Distributions	Solis, Armando D. and Rackovsky, S.
PS-106	Using Solvation Model with Implicit Membrane for Transmembrane Protein Structure Modeling	Spassov, Velin and Yan, Lisa and Szalma, Sandor
SA-26	PIR Non-Redundant Reference Protein Database (PIR-NREF)	Suzek, Baris E. and Huang, Hongzhan and Orcutt, Bruce C. and Chen, Yongxing and Hu, Zhang-Zhi and Zhang, Jian and Wu, Cathy H.
SA-27	Two Visualization Tools for Sequence Contig Assembly	Tae, Hongseok and Kim, Pan-Gyu and Park, Wan and Park, Kiejung
ME-62	XDotsReader, a Software for Automatic Analysis of cDNA Array Images	Tahi, Fariza and Achddou, Brice and Decraene, Charles and Auffray, Charles and Piétu, Geneviève
PS-107	Hierarchical Machine Learning for Characterising FAD-binding Proteins	Tan, Aik Choon and Gilbert, David
DS-38	Primer Tailing in Multiplex PCR	Tang, Mengxiang
PA-119	GRIMM: Genome Rearrangements Software	Tesler, Glenn
PW-92	Homology Searches for Pathways	Tillinghast, John and Yang, Grace and Piercy, Chris
ME-63	Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data	Troyanskaya, Olga G. and Garber, Mitchell E. and Altman, Russ B. and Botstein, David
ME-64	An Intuitive Way for Selecting Informative Genes From Microarray Data	Tsai, Huai-Kuang and Chao, Yu-Chih and Chuang, Han-Yu and Kao, Cheng-Yan
SN-43	Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases	Tsalenko, Anya and Ben-Dor, Amir and Cox, Nancy and Yakhini, Zohar
SA-28	Aligning Two Fragmented Sequences	Veeramachaneni, Vamsi and Berman, Piotr and Miller, Webb
PS-108	Sequence and Structural Analysis of APE1 Protein Family Using Physical-chemial Properties Based Motifs	Venkatarajan, Mathura S. and Schein, Catherine H. and Özgün, Numan and Braun, Werner
GF-33	A Comparative Genomic Method for Computational Identification of Prokaryotic Translation Initiation Sites	Walker, Megon and Pavlovic, Valdimir and Kasif, Simon
SA-29	A Framework Towards Efficient and Effective Protein Clustering	Wang, Wei and Yang, Jiong
SA-30	Accelerating Search of Approximate Match on Large Protein Sequence Databases	Wang, Wei and Yang, Jiong and Xia, Yi and Yu, Philip
SA-31	Pfam-A HMMs and SVMs for Protein Kinase Classification	Weber, Ryan J. and New, Michael H.
SA-32	Finding Approximate Tandem Repeats in Genomic Sequences	Wexler, Ydo and Kashi, Yechezkel and Geiger, Dan
ME-65	How Useful are the Bayesian Networks and Dynamic Bayesian Networks for Modeling Gene Expression Data	Wu, Baolin and Zhao, Hongyu
PS-109	Combinatorial Optimization Algorithms for Assignment of Protein Backbone NMR Peaks	Xu, Ying and Xu, Dong and Kim, Dongsup and Chen, Zhi-Zhong and Lin, Guohui and Jiang, Tao
ME-66	A New Framework for Biological Data Clustering Using Minimum Spanning Trees	Xu, Ying and Xu, Dong and Olman, Victor
ME-67	Improving Performance of Bicluster Discovery in a Large Data Set	Yang, Jiong and Wang, Wei and Wang, Haixun and Yu, Philip
ME-68	Feature Selection and Clustering for Tumor Classification	Yeang, Chen-Hsiang
MA-46	Relevance Network between Transcriptome and Chemosensitivity in Hepatoma Cells	Yujin, Hoshida and Masaru, Moriyama and Motoyuki, Otsuka and Nishimura, Shin-ichiro and Naoya, Kato and Yasushi, Shiratori and Naohiko, Seki and Masao, Omata
PS-110	Solving Molecular Inverse Kinematics Problems for Protein Folding and Drug Design	Zhang, Ming and Kavraki, Lydia E.
ME-69	A Unified Maximum Separability Analysis Approach for Biological Expression Data Processing	Zhang, Zhen and Zhang, Hong and Chan, Daniel W.
PS-111	Protein Structure Prediction Aided by Solution Xray Scattering Data, and Its Application in Structural Homology Study	Zheng, Wenjun and Doniach, Sebastian
PW-93	Computational Identification of Operons in Microbial Genomes	Zheng, Yu and Roberts, Richard J. and Kasif, Simon
ME-70	Construct Regulatory Networks from Gene Expression Data Using Association Rule Mining	Zhou, Jiaye and Veroff, Robert L. and Helman, Paul
ME-71	Prediction of Gene Function by Expression Transitivity using Microarray Data	Zhou, Xianghong and Kao, Ming-Chih Jeffrey and Wong, Wing Hung
ME-72	Finding Regulatory Elements from Microarray data	Zilberstein, Chaya Ben-Zaken and Geiger, Dan
ON-120	FunCatTM Controlled Vocabulary for the Human Genome: Enhancing the MIPS Yeast Functional Catalogue to Encompass the Biology of Prokaryotes, Plants and Animals	Zollner, Alfred and Albermann, Kaj and Hani, Jean and Ehrenreich, Armin and Reinfried, Goetz and Maier, Dieter and Mayer, Klaus and Schoof, Heiko and Mewes, Hans-Werner
ME_73	Exploration of Yeast Gene Expression Regulation via Classification.	van Zwet, Erik and Kechris, Katherina and Chiang, Derek and Bickel, Peter and Eisen, Michael