RECOMB 2000 List of accepted posters

List of Accepted Posters

Comparative Study of Clustering Techniques for Gene Expression Microarray Data
--- Sonia Leach, Larry Hunter
[ PDF ] [ PS ]
A Computer Program for Generating Gene-Specific Fragments for Microarrays
--- Dong Xu, Ying Xu, Gary Li, Jizhong Zhou
[ PDF ] [ PS ]
Approaching Causality: Discovering Time-Lag Correlations in Genetic Expression Data with Static and Dynamic Relevance Networks
--- Ben Y. Reis, Atul J. Butte, Isaac S. Kohane
[ PDF ] [ PS ]
CLICK: A Clustering Algorithm for Gene Expression Analysis
--- Ron Shamir, Roded Sharan
[ PDF ] [ PS ]
Inference of Nonlinear Biological Systems by Using Linear Programming
--- Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
[ PDF ] [ PS ]
Template-Based Gene Expression Analysis
--- Torgeir R. Hvidsten, Tor-Kristian Jenssen, Jan Komorowski, Astrid Lægreid, Arne Sandvik, Dyre Tjeldvoll
[ PDF ] [ PS ]
Gene Expression Analysis by DNA Computing
--- Akira Suyama, Nao Nishida, Ken-ichi Kurata, Katsumi Omagari
[ PDF ] [ PS ]
Ordering Genes by Significance of Occurrences
--- Jun Sese, Shinichi Morishita, Kousaku Okubo
[ PDF ] [ PS ]
Diagnosis System of Drug Sensitivity of Cancer Using cDNA Microarray and Multivariate Statistical Analysis
--- Tatsuhiko Tsunoda, Yoshiaki Hojo, Chikashi Kihara, Norihiko Shiraishi, Osamu Kitahara, Kenji Ono, Toshihiro Tanaka, Toshihisa Takagi, Yusuke Nakamura
[ PDF ] [ PS ]
An Evaluation of Single Nucleotide Polymorphism Detection Programs
--- Rosalind Cutts, Ravi Mehta, Suzanne Orton, Philip East, Robert Gill, Philippe Sanseau, Paul Mathews
[ PDF ] [ PS ]
Arrayed Primer Extension on DNA Microchips (APEX). Molecular Computation of Satisfaction (SAT) Problems
--- Micheal Pirrung, Richard Connors, Amy Odenbaugh, Michael Montague-Smith, Nathan Walcott, Jeff Tollett
[ PDF ] [ PS ]
ViewDesigner: A Tool of Designing Views on Data in Discovery System Hypothesis Creator
--- Osamu Maruyama, Yoshinori Tamada, Satoshi Matsumoto, Satoru Miyano
[ PDF ] [ PS ]
A System to Find Genetic Networks Based on Weighted Majority Algorithm
--- Ayumi Shinohara, Masayuki Takeda, Tomohiro Moriyama, Osamu Maruyama, Takao Goto, Satoru Miyano, Shigeru Muta, Koushuke Tashiro, Satoru Kuhara
[ PDF ] [ PS ]
Induction Mechanism Description of l Phage by Hybrid Petri Net
--- Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
[ PDF ] [ PS ]
Bio-calculus: Its Concept, and An Application for Molecular Interaction
--- Masao Nagasaki, Shuichi Onami, Satoru Miyano, Hiroaki Kitano
[ PDF ] [ PS ]
Software Platform for Systems Biology
--- Adam Arkin, Hamid Bolouri, Mark T. Borisuk, John Doyle, Koji, M.Kyoda, Eric Mjolsness, Mineo Morohashi, Hiroaki Kitano
[ PDF ] [ PS ]
Reverse Engineering in Systems Biology: Towards Inference of a Gene Regulatory Network
--- Mineo Morohashi, Koji M. Kyoda, Shuichi Onami, Eric Mjolsness, Hiroaki Kitano
[ PDF ] [ PS ]
Development of a System for Automatic Construction of Cell Lineage of C. elegans from Nomarski DIC Microscope Images
--- Tomohiro Yasuda, Hideo Bannai, Shuichi Onami, Satoru Miyano, Hiroaki Kitano
[ PDF ] [ PS ]
Systematic Analysis of the Robustness in Complex Reaction Networks of Bacteria
--- Hiroyuki Kurata, Kazunari Taira
[ PDF ] [ PS ]
Genius: An Automated System for Assigning Genome ORFs to 3D Structures, Using a Novel Multiple Intermediate Sequence Search
--- Makiko Suwa, Henrik T. Yudate, Yasuhiko Masuho, Asaf A. Salamov, Christine A. Orengo, Mark B. Swindells
[ PDF ] [ PS ]
High-Throughput Function Assignment for Novel Gene Products using Annotation Clustering
--- Alexander Renner, Hilmar Lapp, Andras Aszodi
[ PDF ] [ PS ]
CANVAS: A Clone Annotation and Validation System
--- Zhong Li, Junping Jing, Jeffrey S. Aaronson
[ PDF ] [ PS ]
A 1.7 Mb Sequence Analysis of Rice Chromosome 1
--- Atsuko Idonuma, Hideki Nagasaki, Masatoshi Masukawa, Manami Negishi, Koji Arikawa, Yoshiyuki Mukai, Isamu Ohta, Baltazar A. Antonio, Katsumi Sakata, Takuji Sasaki
[ PDF ] [ PS ]
Web-Based System for Sample Tracking in Rice Genome Research Program
--- Kazunori Waki, Kimiko Yamamoto, Isamu Ohta, Masaki Kise, Katsumi Sakata, Takuji Sasaki
[ PDF ] [ PS ]
Pubgen: Discovering and Visualising Gene-Gene Relations
--- Tor-Kristian Jenssen, Astrid Lagreid, Jan Komorowski, Evind Hovig
[ PDF ] [ PS ]
Genome Analysis and Gene Discovery Tools
--- Christian Iseli, C.Victor Jongeneel, Marco Pagni, Thomas Junier, Philipp Bucher
[ PDF ] [ PS ]
Gene Discovery and Presentation Systems for Arabidopsis Genome Sequencing Project at Kazusa DNA Research Institute
--- Yasukazu Nakamura, Satoshi Tabata
[ PDF ] [ PS ]
GeneHacker Plus: Yet Another Gene-Finding Program with Top-Class Accuracy in Locating Start Codons
--- Tetsushi Yada, Yasushi Totoki, Toshihisa Takagi, Kenta Nakai
[ PDF ] [ PS ]
Predicting Gene Boundary
--- Sridhar S. Hannenhalli, James W. Fickett
[ PDF ] [ PS ]
A Workbench for the Research and Development of Biological Diversity
--- Hideaki Sugawara, Satoru Miyazaki
[ PDF ] [ PS ]
A New File Format and Tools for the Large-Scale Data Submission to DNA Data Bank of Japan(DDBJ)
--- Satoru Miyazaki, Hiroyuki Hashimoto, Akemi Shimada, Yoshio Tateno, Hideaki Sugawara
[ PDF ] [ PS ]
A Proposal for Integration of BLAST-Related Software Tools Using CORBA
--- Pethuru Raj, Naohiro Ishii
[ PDF ] [ PS ]
GeneNet: A Meta-Sequence Similarity Analysis System
--- Dong-Sun Park, Sung Hwan Kim, Tae-Jin Ahn, Yang-Suk Kim, Hong-gil Nam
[ PDF ] [ PS ]
Visualysis: A Tool for Biological Sequence Analysis
--- SungHwan Kim, YangSuk Kim, TaeJin Ahn, Hong Kil Nam, Byung Jun Han, Sam Myo Kim
[ PDF ] [ PS ]
GeneAtlas^TM: A High-Throughput Pipeline for Automated Model Building and Functional Annotation of the Genome
--- David Edwards, Zhan-yang Zhu, Azat Badretdinov, David Kitson, Krzysztof Olszewski, Lisa Yan
[ PDF ] [ PS ]
GeneAtlas^TM - An Automatic High-Throughput Pipeline for Structure Prediction and Function Assignment for Genomic Sequences
--- Lisa Yan, Zhan-Yang Zhu, Azat Badredinov, David Kitson, Krzysztof Olszewski, David Edwards
[ PDF ] [ PS ]
The 2D Gel Electrophoresis Simulator: SimGel
--- Chungfan Kim, Akihiko Konagaya
[ PDF ] [ PS ]
EstSearch: A Tool for More Informative EST Alignments
--- Vera Asodi, Alex Diber, Raveh Gill-More, Hershel Safer, Mor Amitai
[ PDF ] [ PS ]
Clustering and Assmbly of a Large Number of EST and cDNA Sequences Using Hyseq's Proprietary Software
--- John Tillinghast, Ankura Sinku, Y. Tom Tang
[ PDF ] [ PS ]
Can General-Purpose Compression Schemes Really Compress DNA Sequences?
--- Toshiko Matsumoto, Kunihiko Sadakane, Hiroshi Imai, Takumi Okazaki
[ PDF ] [ PS ]
The Eukaryotic Promoter Database
--- Rouaida Cavin Perier, Viviane Praz, Thomas Junier, Claude Bonnard, Christian Iseli, Philipp Bucher
[ PDF ] [ PS ]
CAMUS DB: Development of Structural Database for Homology Search
--- Masayuki Kikuchi, Sadahiko Misu, Tadashi Imanishi, Naruya Saitou
[ PDF ] [ PS ]
Upgraded Aberrant Splicing Database Supports the Scanning Mechanism of 3' Splice-Site Selection
--- Takashi Yamanaka, Tetsushi Yada, Toshihisa Takagi, Kenta Nakai
[ PDF ] [ PS ]
Receptor Database (RDB) As an Analytical Tool
--- Kotoko Nakata, Takako Takai, Tatsuya Nakano, Tsuguchika Kaminuma
[ PDF ] [ PS ]
Transcript Sequence Registry
--- Junping Jing, Jian Jiang, Jeffrey S. Aaronson
[ PDF ] [ PS ]
Building Integrated Pathway Genome Database in Cell Type Specific Manner - Encyclopedia of Human Liver
--- Taejin Ahn, YangSuk Kim, SungHwan Kim, DongSun Park, HongGil Nam
[ PDF ] [ PS ]
A Structured Genome Document Database System for Making High-Level Queries on Diverse Genome Data
--- Aaron Stokes, Hideo Matsuda, Akihiko Hashimoto
[ PDF ] [ PS ]
SST: An Algorithm for Searching Sequence Databases in Time Proportional to the Logarithm of the Database Size
--- Eldar Giladi, Michael G. Walker, James Ze Wang, Wayne Volkmuth
[ PDF ] [ PS ]
Design of the Comprehensive Fold Recognition Benchmark. Application to SeqFold, Training and Validation.
--- Krzysztof A. Olszewski
[ PDF ] [ PS ]
Isothermic Oligonucleotide Libraries
--- Jacek Blazewicz, Piotr Formanowicz, Marta Kasprzak, Wojciech T.Markiewicz
[ PDF ] [ PS ]
Estimation of Stochastic Parameters
--- Michael A. Gibson, Jehoshua Bruck
[ PDF ] [ PS ]
Computational Prediction of Gene Regulation by DNA Conformation
--- Mick Noordewier, Peter Morrison, Craig Benham
[ PDF ] [ PS ]
Method for Recognition of Composite Regulatory Units in Promoters. Analysis of Cell-Cycle Control Genes
--- Alexander Kel, Olga Kel-Margoulis, Edgar Wingender
[ PDF ] [ PS ]
Algorithm Determining All Cut-off Values of TF-DNA Binding Score Calculated Using PWMs in TRANSFAC
--- Tatsuhiko Tsunoda, Toshihisa Takagi
[ PDF ] [ PS ]
Structure-Based Target Prediction of Transcription Factors
--- Akinori Sarai, Hidetoshi Kono
[ PDF ] [ PS ]
An Approach to Alternative Gene Transcripts Discovery through Assembly of Fragmental cDNA Sequences
--- Ryotaro Irie, Yasuhiko Masuho, Keiichi Nagai
[ PDF ] [ PS ]
Association of Binding Specificity and Disordered Regions in Zinc Finger Motifs
--- Takeshi Nagashima, Akihiko Konagaya
[ PDF ] [ PS ]
A New Method for Matching Protein Secondary Structure Elements or C-alpha Atoms in Protein Structure Comparison
--- Edward S.C. Shih, Tsan-Fu Wang, Ming-Jing Hwang
[ PDF ] [ PS ]
Sequence Codes for Extended Conformation: A Neighbor-Dependent Sequence Analysis of Loops in Proteins
--- Jin-an Feng, Chiquito J. Crasto
[ PDF ] [ PS ]
Extending HP Lattice Model with Non-Local Hydration
--- Jarmo T. Alander
[ PDF ] [ PS ]
A New Method for Evaluating the Structural Similarity of Proteins Using Geometric Morphometrics
--- Dean C. Adams, Gavin J.P. Naylor
[ PDF ] [ PS ]
A Methodology to Optimally Extract Local Structural Information in Proteins
--- Armando D. Solis, S. Rackovsky
[ PDF ] [ PS ]
Optimal Hidden Markov Models for All Sequences of Known Structure
--- Julian Gough, Cyrus Chothia, Kevin Karplus, Christian Barrett, Richard Hughey
[ PDF ] [ PS ]
IMGT Sequence Profile: A Standardized Visualization for the Immunoglobulin and T Cell Receptor V-REGIONs Applicable to Other Protein Alignments
--- Manule Ruiz, Marie-Paule Lefranc
[ PDF ] [ PS ]
Motif Recognition in Genomes
--- Peter Clote, Sebastian Will
[ PDF ] [ PS ]
Analysis of Antisense Oligodeoxynucleotides Based on Sequence Motif Content to Predict Effectiveness
--- Michael Giddings, Olga Matveeva, Alex Tsodikov, Raymond F. Gesteland, John F. Atkins
[ PDF ] [ PS ]
Comparison of Profile and Hidden Markov Model Methods for Detecting Degenerate Motifs in Protein Sequences
--- Krzysztof M. Rajkowski, Etienne-Emile Baulieu, Michael Schumacher
[ PDF ] [ PS ]
Improving the Accuracy of Functional Inferences from Links between Proteins Detected by Computational or Experimental Methods
--- Michael Thompson, Edward Marcotte, Matteo Pellegrini, Todd Yeates, David Eisenberg
[ PDF ] [ PS ]
Evaluating Homology Search Algorithms
--- Timothy L. Bailey, Michael Gribskov
[ PDF ] [ PS ]
Protein Superfamily Building Methods Comparison
--- Kunbin Qu, Jun Zhu, Scott Pegg, Patricia Babbitt
[ PDF ] [ PS ]
Clustering Protein Sequences: Structure Prediction by Transitive Homology
--- Eva Bolten, Alexander Schliep, Sebastian Schneckener, D. Schomburg, Rainer Schrader
[ PDF ] [ PS ]
Side-Chain Clusters in Protein Structures
--- N. Kannan, S. Vishveshwara
[ PDF ] [ PS ]
Hierarchical Clustering Procedure for Grouping Orthologous Domains in Multiple Genomes
--- Ikuo Uchiyama
[ PDF ] [ PS ]
The Grammatical Structure of Protein Sequences in a Single Non-linear Hidden Markov Model; Prediction of Coding Regions, Secondary and Tertiary structure
--- Christopher Bystroff
[ PDF ] [ PS ]
The Statistics of Semi-Probabilistic Alignment
--- Yi-Kuo Yu, Terence Hwa
[ PDF ] [ PS ]
Topological Requirement for the Nucleus Formation of a Two-state Folding Reaction. First Successful Blind F-Values Predictions - Activation Domain of Human Procarboxypeptidase
--- Roumen A. Dimitrov
[ PDF ] [ PS ]
Conformer Models of TEM-1 b-lactamase
--- Christo Christov, Boris Atanasov
[ PDF ] [ PS ]
The Identification of Transmembrane Helices in the Sequences of Membrane Proteins Using a Computationally-Derived Hydrophobicity Scale
--- Lisa Bourla, Tidhar Seifer, Barry Honig, Nir Ben-Tal
[ PDF ] [ PS ]
Prediction of Hydrophobic Cores of Globular Proteins Using Multiresolution Analysis of Wavelet Analysis
--- Hideki Hirakawa, Satoru Kuhara
[ PDF ] [ PS ]
Structure Prediction of Proteins with Transmembrane Helices
--- Takatsugu Hirokawa, Makiko Suwa, Seah Boon-Chieng, Shigeki Mitaku
[ PDF ] [ PS ]
Creating Physical Maps With Automatic Caputure of Hybridization Data
--- David Hall, Suchendra Bhandarkar, Jonathan Arnold
[ PDF ] [ PS ]
Probe Interval Graph and Its Applications to Physical Mapping of DNA
--- Peisen Zhang
[ PDF ] [ PS ]
Using Genetic Algorithms to Construct Physical Maps of Chromosomes with Unique Probes
--- Huai-Kuang Tsai, Cheng-Yan Kao
[ PDF ] [ PS ]
Graph Modeling of Metabolism
--- Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
[ PDF ] [ PS ]
A Local Alignment Algorithm for Metabolic Pathway Analysis
--- Yukako Tohsato, Hideo Matsuda, Akihiro Hashimoto
[ PDF ] [ PS ]
Optimizing RNA Secondary Structure Over All Possible Encodings of a Given Protein
--- Barry Cohen, Steven Skiena
[ PDF ] [ PS ]
PiKA²: A WWW Based System for Automated Analysis of Protein 2D-PAGE Images
--- Katsutoshi Takahashi, Masayuki Nakazawa, Yasuo Watanabe, Akihiko Konagaya
[ PDF ] [ PS ]
Improved Elastic Rod Model of 3D RNA Structure Formation
--- Eugeny Kugushev, Ekaterina Kozyreva, Aleksey Maykov
[ PDF ] [ PS ]
Phylogenetic Reconstruction of Influenza B from 1940 to 1998. Are Means Important For The End?
--- L.M. Boykin, H. Lu, C.A. Macken, P.H. Mukundan, A.K. Naik
[ PDF ] [ PS ]
Comparative Analysis of Genomic Rearrangements in Microorganisms
--- Siv G E Andersson, Daniel Dalevi, Niklas Eriksen, Kimmo Eriksson
[ PDF ] [ PS ]
Maximum Likelihood Reconstruction of Ancestral Amino-acid Sequences
--- Tal Pupko, Itsik Pe'er
[ PDF ] [ PS ]
Molecular Phylogenetics of the Genus Oryza L. (Poaceae): Evidence from the Sequences of the Internal Transcribed Spacer (ITS) of Nuclear Ribosomal DNA
--- Xie Zhongwen, Zhou Yi, Lu Baorong, Hong Deyuan
[ PDF ] [ PS ]
Incomplete Directed Perfect Phylogeny
--- Itsik Pe'er, Ron Shamir, Roded Sharan
[ PDF ] [ PS ]
Comparison of Information Criteria and Simulation Statistics Method for Topology Selection in Molecular Phylogenetic Tree
--- Soichi Ogishima, Fengrong Ren, Hiroshi Tanaka
[ PDF ] [ PS ]
Inferring a Species Tree from Gene Trees under the Deep Coalescence Cost
--- Louxin Zhang
[ PDF ] [ PS ]
Optimizing Pedigree Drawing Using Interval Graph Theory
--- Frederic Tores, Emmanuel Barillot
[ PDF ] [ PS ]
Similarity Trees for Zinc Finger Protein Design
--- Dagmar Steffen, Dusan Ihracky, Lothar Gierl
[ PDF ] [ PS ]
Singular Value Decomposition of Protein Conformational Motions: Application to HIV-1 Protease
--- Miguel L. Teodoro, George N. Phillips Jr., Lydia E. Kavraki
[ PDF ] [ PS ]
Modelling of Enantioselectivity in Candida antarctica Lipase B
--- Sami Raza, Linda Fransson, Karl Hult
[ PDF ] [ PS ]
Molecular Dynamics Study of the N-terminal Domain of Apolipoprotein E on a Mimetic-lipid Surface
--- M. Prevost
[ PDF ] [ PS ]
Modeling of Chimeric b-galactosidase Antigenic Fusion Proteins
--- N. Boutonnet, M.Prevost
[ PDF ] [ PS ]
Semianalytical Integration Method for Macromolecular Simulations
--- Dusanka Janezic, Matej Praprotnik
[ PDF ] [ PS ]
On Negative Selection Against ATG Triplets Near Start Codons in Archaebactreial Genomes
--- Rintaro Saito, Masaru Tomita
[ PDF ] [ PS ]
Computer Simulation of Human Erythorocyte and its Application to Analyses of Enzyme Deficiencies
--- Yoichi Nakayama, Ryo Matsushima, Ayako Kinoshita, Hironori Tanaka, Natsumi Noguchi, Masaru Tomita
[ PDF ] [ PS ]
Modeling a Complex Gene Regulation Network Using the E-CELL System
--- Kenta Hashimoto, Sae Seno, Fumihiko Miyoshi, Masaru Tomita
[ PDF ] [ PS ]
E-Cell: Software Environment for Whole Cell Simulation and Analysis
--- Kouichi Takahashi, Yusuke Saito, Tomohiko Aikawa, Tomoharu Iwata, Motohiro Yoneda, Masayuki Okayama, Masaru Tomita
[ PDF ] [ PS ]
Comparative Study of Overlapping Genes in Bacterial Genomes
--- Yoko Fukuda, Takanori Washio, Yoichi Nakayama, Masaru Tomita
[ PDF ] [ PS ]
On Base-Pairing Potential Between 16S rRNA and 5$B!G(BUTR in Archaebacterial Genomes
--- Yuko Osada, Rintaro Saito, Masaru Tomita
[ PDF ] [ PS ]
Stem Loop Structures in the B.subtilis Genome and Their Roles in the Transcription Machinery
--- Takanori Washio, Keio Asai, Kazuo Kobayashi, Naotake Ogasawara, Hiroki Yamamoto, Jun-ichi Sekiguchi, Ken-ichi Yoshida, Yasutaro Fujita, Masaru Tomita
[ PDF ] [ PS ]
Comparative Analysis of Location of First Intron
--- Atsushi Sakurai, Shigeo Fujimori, Hiromi Kochiwa, Takanori Washio, Masaru Tomita
[ PDF ] [ PS ]
Integrative Modeling of Mitochondrial Metabolism
--- Katsuyuki Yugi, Yuko Kanai, Masaru Tomita
[ PDF ] [ PS ]
Analysis of CpG Dinucleotide Frequency in Bacterial Genomes with respect to Genomic Regions and Codon Position
--- Mami Goto, Takanori Washio, Masaru Tomita
[ PDF ] [ PS ]
Analysis of Similarity Pattern and Selective Constraint in C. elegans and C. briggsae Genomes
--- Svetlana A. Shabalina, Alexey N. Spiridonov, Alexey S. Kondrashov
[ PDF ] [ PS ]
A Reaction-Diffusion Model for Genetic Interference
--- Youhei Fujitani, Shintaro Mori, Ichizo Kobayashi
[ PDF ] [ PS ]
Genomic Signature is Preserved in Short DNA Fragments
--- Patrik Deschavanne, Alain Giron, Joseph Vilain, Alexandra Vaury, Bernard Fertil
[ PDF ] [ PS ]
Analysis of the Context of 5' Splice Site Sequences and 5' Splice Site-like Sequences in Mammalian mRNA Precursors by a Position Tree
--- Sumie K. Abe, Nobuyuki Takahashi, Mineichi Kudo, Masaru Shimbo, Akihiro Tsutsumi
[ PDF ] [ PS ]
Insight on the Lateral Organization and the Size Distribution of the Gel and Fluid Clusters in DMPC/DSPC Lipid Bilayers
--- Ekaterina I. Michonova-Alexova, Istvan P. Sugar
[ PDF ] [ PS ]
Investigation of Nucleosides Molecular Structure
--- S.A. Krasnokutski, A.Yu. Ivanov, G.G. Sheina, Yu.P. Blagoi
[ PDF ] [ PS ]
Calculation of Thermodynamic Parameters for Helix-to-Coil Transition in Duplex and Triplex Complexes of Oligoadenilate
--- A. Shcherbakova, Yu. Blagoi, V. Zozulya
[ PDF ] [ PS ]
Calculation of the Binding Isotherms of Cu²⁺ and Ca²⁺ Ions Interacting with DNA in Aqueous Solution
--- Elene V. Hackl, Natalya Bezlepkina, Yurij P. Blagoi
[ PDF ] [ PS ]