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1.

図書

図書
Inge Jonassen, Junhyong Kim (eds.)
出版情報: Berlin : Springer, c2004  ix, 476 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 3240 . Lecture notes in bioinformatics
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2.

図書

図書
sponsored by IEEE Computer Society ; in cooperation with the Information Technology Research Institute Wright at State University and the IEEE Neural Networks Society
出版情報: Los Alamitos, California : IEEE Computer Society, c2003  xii, 442 p. ; 28 cm
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Message from the General Chair
BIBE 2003 Program Committee
Protein Structures and Pathways / Bioinfo-1:
A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale / M. Shah ; S. Passovets ; D. Kim ; K. Ellrott ; L. Wang ; I. Vokler ; P. LoCascio ; D. Xu ; Y. Xu
A Fast Algorithm for RNA Secondary Structure Prediction Including Pseudoknots / F. Tahi ; S. Engelen ; M. Regnier
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data / Y. Chen ; T. Joshi
Prediction of Contact Maps Using Support Vector Machines / Y. Zhao ; G. Karypis
Biomedical Data Engineering / Bioeng-1:
Performance Comparison of Generalized PSSM in Signal Peptide Cleavage Site and Disulfide Bond Recognition / P. Clote
Analysis of Atlantic Salmon Skin Mucus: COPS--A Computer-Based System for Protein Pattern Analysis of 1D SDS-PAGE Gels / R. Eibrand ; P. Kennedy ; D. Cotter ; U. MacEvilly ; B. Wu
An Open Multiple Instance Learning Framework and Its Application in Drug Activity Prediction Problems / X. Huang ; S.-C. Chen ; M.-L. Shyu
Analysis of Spontaneous Activity in Cultured Brain Tissue Using the Discrete Wavelet Transform / J. D. Johnson ; D. Plenz ; J. Beggs ; W. Li ; M. Mieier ; N. Miltner ; K. Owen
Phylogenetic Tress / Bioinfo-2:
An Empirical Comparison of Tools for Phylogenetic Footprinting / M. Blanchette ; S. Kwong ; M. Tompa
An Investigation of Phylogenetic Likelihood Methods / T. L. Williams ; B. M. E. Moret
Nodal Distance Algorithm: Calculating a Phylogenetic Tree Comparison Metric / J. Bluis ; D.-G. Shin
A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees / M. Hu ; P. Kearney ; J. Badger
Medical Image Processing I / Bioeng-2:
Comparison of Bicubic and Bezier Polynomials for Surface Parameterization in Volumetric Images / F. Quek ; V. Kulkarni ; C. Kirbas
Evolving Bubbles for Prostate Surface Detection from TRUS Images / F. Shao ; L. V. Ling ; W. S. Ng
Structure-Trageting Fast Magnetic Resonance Imaging Angiography with Partial Collection of the Inverse Space (k-Space) Based on the Orientation of the Vessel in Real Space / D. Gui ; N. V. Tsekos
Respiratory Gating for MRI and MRS in Rodents (Short Paper) / J. R. Garbow ; J. P. Dugas ; M. S. Conradi
Bio-Databases I / Bioinfo-3:
A Novel Laboratory Version Management System for Tracking Complex Biological Experiments / W. M. Shui ; N. Lam ; R. K. Wong
Requirements of Phylogenetic Databases / L. Nakhleh ; D. Miranker ; F. Barbancon ; W. H. Piel ; M. Donoghue
Filtration of String Proximity Search via Transformation / S. A. Aghili ; D. Agrawal ; A. El Abbabi
GenoMosaic: On-Demand Multiple Genome Comparison and Comparative Annotation / C. Gibas ; D. Sturgill ; J. Weller
Biomedical Imaging, Signaling, and Computation / Bioeng-3:
Automatic Detection of Premature Ventricular Contraction Using Quantum Neural Networks / J. Zhou
Vessel Extraction in Medical Images by 3D Wave Propagation and Traceback / F. K. H. Quek
A New Approach to Detect Similar Proteins from 2D Gel Electrophoresis Images / N. Khan ; S. Rahman
A Robotic Device for Minimally Invasive Breast Interventions with Real-Time MRI Guidance / B. T. Larson ; A. G. Erdman
Sequences and Searching / Bioinfo-4:
An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level / F.-X. Wu ; W.-J. Zhang ; A. J. Kusalik
A Model of Random Sequences for de novo Peptide Sequencing / K. D. Jarman ; W. R. Cannon ; K. H. Jarman ; A. Heredia-Langner
Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites / S. Sinha
Medical Image Processing II / Bioeng-4:
Determining the Asymmetries of Skin Lesions with Fuzzy Borders / V. T. Y. Ng ; T. Lee ; B. Y. M. Fung
Unsupervised Iterative Segmentation and Recognition of Anatomic Structures in Medical Imagery Using Second-Order B-Spline Descriptors and Geometric Quasi-Invariants / T. A. El Doker
Vessel Extraction Techniques and Algorithms: A Survey
Prostate Gland and Extra-Capsular Tissue 3D Reconstruction and Measurement (Short Paper) / F. McKenzie ; R. Hussein ; J. Seevinck ; P. Schellhammer ; J. Diaz
Bio-Databases II / Bioinfo-5:
Empirical Evaluation of Ensemble Feature Subset Selection Methods for Learning from a High-Dimensional Database in Drug Design (Short Paper) / H. Mamitsuka
Streamlining Biological Data Analysis Using BioFlow (Short Paper) / Z. Guan ; H. M. Jamil
BioSeek: Exploiting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources (Short Paper) / L. Liu ; D. Buttler ; T. Critchlow ; W. Han ; H. Paques ; C. Pu ; D. Rocco
Biological Systems and Models / Bioeng-5:
A Computational Model of the Role of Deficit-Related Drives in Sequential Movement Learning in a T-Maze Environment (Abstract)
A Biological Mapping of a Learned Avoidance Behavior Model to the Basal Ganglia (Short Paper) / K. M. Biddell ; J. Li
Influence of the Thermal Treatment Applied to PAN Gel on Its Length Change and Generated Force (Short Paper) / H. Tamagawa ; F. Nogata ; T. Watanabe ; A. Abe ; S. Popovic
Panel
Bioinformatics and Biotechnology Research Issues
Gene Expressions / Bioinfo-6:
Analyzing the Escherichia coli Gene Expression Data by a Multilayer Adjusted Tree Organizing Map / N. Wei ; L. Gruenwald ; T. Conway
A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome / H. Huang ; H. Chang ; T. Tsou ; B. Liu ; C.-Y. Kao ; J. Horng
Time Series Analysis of Gene Expression and Location Data / C.-H. Yeang ; T. Jaakkola
Regulating Gene Expression Using Optimal Control Theory / Y. Liu ; H. B. Sun ; H. Yokota
Clustering Algorithms and Molecular Structures / Bioinfo-7:
Enhanced Biclustering on Expression Data / J. Yang ; H. Wang ; W. Wang ; P. Yu
Hierarchical Clustering of Gene Expression Data / F. Luo ; K. Tang ; L. Khan
MotifMiner: A General Toolkit for Efficiently Identifying Common Substructures in Molecules / M. Coatney ; S. Parthasarathy
Augmenting SSEs with Structural Properties for Rapid Protein Structure Comparison / C.-H. Chionh ; Z. Huang ; K.-L. Tan ; Z. Yao
Bio-Databases III / Bioinfo-8:
Load Balancing: A Case Study of a Pharmaceutical Drug Candidate Database / Z. Ben Miled ; S. Li ; J. Martin ; C. Balagoplakrishna ; O. Bukhres ; R. J. Oppelt
Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases / O. Ozturk ; H. Ferhatosmanoglu
Application of XML Schema and Active Rules System in Management and Integration of Heterogeneous Biological Data
An Assessment of a Metric Space Database Index to Support Sequence Homology / R. Mao ; W. Xu ; N. Singh ; D. P. Miranker
Clustering Algorithms / Bioinfo-9:
Detecting Experimental Noises in Protein-Protein Interactions with Iterative Sampling and Model-Based Clustering
DHC: A Density-Based Hierarchical Clustering Method for Time Series Gene Expression Data / D. Jiang ; J. Pei ; A. Zhang
Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-Means Clustering
A Repulsive Clustering Algorithm for Gene Expression Data (Short Paper) / C.-S. Cheng ; S.-S. Wang
Prediction, Simulation and Mining Models / Bioinfo-10:
Combining Few Neural Networks for Effective Secondary Structure Prediction / K. S. Guimaraes ; J. C. B. Melo ; G. D. C. Cavalcanti
Uses of Multiagents Systems for Simulation of MAPK Pathway (Short Paper) / G. Querrec ; V. Rodin ; J. F. Abgrall ; S. Kerdelo ; J. Tisseau
A Framework for Cancer-Related Genes Mining over the Internet / J. J. P. Tsai ; J. G. Chang ; S. H. Shih ; R. M. Chen ; H. W. Hsiao ; R. M. Hu ; S. N. Chen ; M. M. Lee ; F. M. Liu ; W. L. Chan
Predictive Model for Yeast Protein Functions Using Modular Neural Approach (Short Paper) / D. Hwang ; F. Fotouhi ; R. L. Filey, Jr. ; W. I. Grosky
Author Index
Message from the General Chair
BIBE 2003 Program Committee
Protein Structures and Pathways / Bioinfo-1:
3.

図書

図書
Gary Benson, Roderic Page (eds.)
出版情報: Berlin ; Tokyo : Springer, c2003  x, 528 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 2812 . Lecture notes in bioinformatics
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Comparative Genomics
A Local Chaining Algorithm and Its Applications in Comparative Genomics / M.I. Abouelhoda ; E. Ohlebusch
Common Intervals of Two Sequences / G. Didier
Database Searching
A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring / J. Colinge ; A. Masselot ; J. Magnin
Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity / B. Brejová ; D.G. Brown ; T. Vinař
Gene Finding and Expression
A Stochastic Approach to Count RNA Molecules Using DNA Sequencing Methods / B. Hollas ; R. Schuler
A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence / P. Bonizzoni ; G. Pesole ; R. Rizzi
Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency
Genome Mapping
New Algorithm for the Simplified Partial Digest Problem / J. Błażewicz ; M. Jaroszewski
Noisy Data Make the Partial Digest Problem NP-hard / M. Cieliebak ; S. Eidenbenz ; P. Penna
Pattern and Motif Discovery
Pattern Discovery Allowing Wild-Cards, Substitution Matrices, and Multiple Score Functions / A. Mancheron ; I. Rusu
A Combinatorial Approach to Automatic Discovery of Cluster-Patterns / R. Eres ; G.M. Landau ; L. Parida
Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology / S. Rahmann
Phylogenetic Analysis
Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees / B. Holland ; V. Moulton
Efficient Generation of Uniform Samples from Phylogenetic Trees / P. Kearney ; J.I. Munro ; D. Phillips
New Efficient Algorithm for Detection of Horizontal Gene Transfer Events / A. Boc ; V. Makarenkov
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard / L. Addario-Berry ; B. Chor ; M. Hallett ; J. Lagergren ; A. Panconesi ; T. Wareham
A Linear-Time Majority Tree Algorithm / N. Amenta ; F. Clarke ; K. St. John
Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model / G. Lunter ; I. Miklós ; A. Drummond ; J.L. Jensen ; J. Hein
Better Hill-Climbing Searches for Parsimony / G. Ganapathy ; V. Ramachandran ; T. Warnow
Computing Refined Buneman Trees in Cubic Time / G.S. Brodal ; R. Fagerberg ; A. Östlin ; C.N.S. Pedersen ; S.S. Rao
Distance Corrections on Recombinant Sequences / D. Bryant ; D. Huson ; T. Kloepper ; K. Nieselt-Struwe
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks / Y.S. Song
Polymorphism
Identifying Blocks and Sub-populations in Noisy SNP Data / G. Kimmel ; R. Sharan ; R. Shamir
Designing Optimally Multiplexed SNP Genotyping Assays / Y. Aumann ; E. Manisterski ; Z. Yakhini
Minimum Recombinant Haplotype Configuration on Tree Pedigrees / K. Doi ; J. Li ; T. Jiang
Protein Structure
Efficient Energy Computation for Monte Carlo Simulation of Proteins / I. Lotan ; F. Schwarzer ; J.-C. Latombe
Speedup LP Approach to Protein Threading via Graph Reduction / J. Xu
Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment / J.C. Prasad ; M. Silberstein ; C.J. Camacho ; S. Vajda
Side-Chain Structure Prediction Based on Dead-End Elimination: Single Split DEE-criterion Implementation and Elimination Power / J.A. Spriet
Sequence Alignment
A Large Version of the Small Parsimony Problem / J. Fredslund ; T. Scharling
Optimal Multiple Parsimony Alignment with Affine Gap Cost Using a Phylogenetic Tree / B. Knudsen
Composition Alignment / G. Benson
String Algorithms
Match Chaining Algorithms for cDNA Mapping / T. Shibuya ; I. Kurochkin
Sequencing from Compomers: Using Mass Spectrometry for DNA De-Novo Sequencing of 200+ nt / S. Böcker
Bounds for Resequencing by Hybridization / D. Tsur
Selecting Degenerate Multiplex PCR Primers / R. Souvenir ; J. Buhler ; G. Stormo ; W. Zhang
Author Index
Comparative Genomics
A Local Chaining Algorithm and Its Applications in Comparative Genomics / M.I. Abouelhoda ; E. Ohlebusch
Common Intervals of Two Sequences / G. Didier
4.

図書

図書
Olivier Gascuel, Marie-France Sagot (eds.)
出版情報: Berlin : Springer, c2001  x, 163 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 2066
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Speeding Up the DIALIGN Multiple Alignment Program by Using the `Greedy Alignment of BIOlogical Sequences LIBraryÆ (GABIOS-LIB) / Said Abdeddaim ; Burkhard Morgenstern
GeMCore, a Knowledge Base Dedicated to Mapping Mammalian Genomes / Gisèle Bronner ; Bruno Spataro ; Christian Gautier ; François Rechenmann
Optimal Agreement Supertrees / David Bryant
Segmentation by Maximal Predictive Partitioning According to Composition Biases / Laurent Guéguen
Can We Have Confidence in a Tree Representation? / Alain Guenoche ; Henri Garréta
Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition / Vsevolod Makeev ; Vasily Ramensky ; Mikhail Gelfand ; Mikhail Roytberg ; Vladimir Tumanyan
Exact and Asymptotic Distribution of the Local Score of One i.i.d. Random Sequence / Sabine Mercier ; Dominique Cellier ; François Charlot ; Jean-Jacques Daudin
Phylogenetic Reconstruction Algorithms Based on Weighted 4-Trees / Vincent Ranwez ; Olivier Gascuel
Computational Complexity of Word Counting / Mireille Régnier
EuGene: An Eukaryotic Gene Finder That Combines Several Sources of Evidence / Thomas Schiex ; Annick Moisan ; Pierre Rouzé
Tree Reconstruction via a Closure Operation on Partial Splits / Charles Semple ; Mike Steel
InterDB, a Prediction-Oriented Protein Interaction Database for C. elegans / Nicolas Thierry-Mieg ; Laurent Trilling
Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data / Jacques van Helden ; David Gilbert ; Lorenz Wernisch ; Michael Schroeder ; Shoshana Wodak
Author Index
Speeding Up the DIALIGN Multiple Alignment Program by Using the `Greedy Alignment of BIOlogical Sequences LIBraryÆ (GABIOS-LIB) / Said Abdeddaim ; Burkhard Morgenstern
GeMCore, a Knowledge Base Dedicated to Mapping Mammalian Genomes / Gisèle Bronner ; Bruno Spataro ; Christian Gautier ; François Rechenmann
Optimal Agreement Supertrees / David Bryant
5.

図書

図書
Olivier Gascuel, Bernard M.E. Moret (eds.)
出版情報: Berlin ; Tokyo : Springer, c2001  x, 306 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 2149
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An Improved Model for Statistical Alignment / Istvan Miklós ; Zoltán Toroczkai
Improving Profile-Profile Alignments via Log Average Scoring / Niklas von Öhsen ; Ralf Zimmer
False Positives in Genomic Map Assembly and Sequence Validation / Thomas Anantharaman ; Bud Mishra
Boosting EM for Radiation Hybrid and Genetic Mapping / Thomas Schiex ; Patrick Chabrier ; Martin Bouchez ; Denis Milan
Placing Probes along the Genome Using Pairwise Distance Data / Will Casey ; Mike Wigler
Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar / Arun Jagota ; Rune B. Lyngsø ; Christian N.S. Pedersen
Assessing the Statistical Significance of Overrepresented Oligonucleotides / Alain Denise ; Mireille Régnier ; Mathias Vandenbogaert
Pattern Matching and Pattern Discovery Algorithms for Protein Topologies / Juris Viksna ; David Gilbert
Computing Linking Numbers of a Filtration / Herbert Edelsbrunner ; Afra Zomorodian
Side Chain-Positioning as an Integer Programming Problem / Olivia Eriksson ; Yishao Zhou ; Arne Elofsson
A Chemical-Distance-Based Test for Positive Darwinian Selection / Tal Pupko ; Roded Sharan ; Masami Hasegawa ; Ron Shamir ; Dan Graur
Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time / Ganeshkumar Ganapathysaravanabavan ; Tandy Warnow
Experiments in Computing Sequences of Reversals / Anne Bergeron ; François Strasbourg
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes / Li-San Wang
Finding an Optimal Inversion Median: Experimental Results / Adam C. Siepel ; Bernard M.E. Moret
Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sites / Benny Chor ; Michael Hendy ; David Penny
The Performance of Phylogenetic Methods on Trees of Bounded Diameter / Luay Nakhleh ; Usman Roshan ; Katherine St. John ; Jerry Sun
(1=?)-Approximation of Sorting by Reversals and Transpositions / Niklas Eriksen
On the Practical Solution of the Reversal Median Problem / Alberto Caprara
Algorithms for Finding Gene Clusters / Steffen Heber ; Jens Stoye
Determination of Binding Amino Acids Based on Random Peptide Array Screening Data / Peter J. van der Veen ; L.F.A. Wessels ; J.W. Slootstra ; R.H. Meloen ; M.J.T. Reinders ; J. Hellendoorn
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites / Yoseph Barash ; Gill Bejerano ; Nir Friedman
Comparing Assemblies Using Fragments and Mate-Pairs / Daniel H. Huson ; Aaron L. Halpern ; Zhongwu Lai ; Eugene W. Myers ; Knut Reinert ; Granger G. Sutton
Author Index
An Improved Model for Statistical Alignment / Istvan Miklós ; Zoltán Toroczkai
Improving Profile-Profile Alignments via Log Average Scoring / Niklas von Öhsen ; Ralf Zimmer
False Positives in Genomic Map Assembly and Sequence Validation / Thomas Anantharaman ; Bud Mishra
6.

図書

図書
Roderic Guigó, Dan Gusfield (eds.)
出版情報: Berlin ; Tokyo : Springer, c2002  x, 554 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 2452
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7.

図書

図書
editors, Arno Siebes ... [et al.]
出版情報: Melville, New York : American Institute of Physics, 2007  vii, 180 p. ; 25 cm
シリーズ名: AIP conference proceedings ; 940
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Preface
Genomics
Improving Microarray Expressions with Recalibration / K. Fraser ; Z. Wang ; Y. Li ; P. Kellam ; X. Liu
On the Measurement of Genetic Interactions / E. de Jong ; L. Franke ; A. Siebes
Cluster Assisted Mixed Effect Models (CAMM) for the Identification of Differentially Expressed Genes / P. S. McCormick ; P. Murray ; R. C. Glen
Consensus Gene Regulatory Networks: Combining Multiple Microarray Gene Expression Datasets / E. Peeling ; A. Tucker
Using Sorting by Reversal: Breakpoint Graph for Gene Assembly in Ciliates / R. Brijder ; H. J. Hoogeboom
Bayesian Median Regression for Temporal Gene Expression Data / K. Yu ; V. Vinciotti ; P. A. C. 't Hoen
Systems Biology
Minimal Direction Cuts in Metabolic Networks / A. Larhlimi ; A. Bockmayr
Modeling Evolution of Regulatory Networks in Artificial Organisms / Y. Sanchez-Dehesa ; G. Beslon ; J.-M. Pena
Medical Informatics
Polarimetric Images Segmentation for Lesion Detection / S. M. Djaouti ; A. Koudache ; A. Boudaieb
Studying Channelopathies at the Functional Level Using a System Identification Approach / A. A. Faisal
Using Simple Molecular Orbital Calculations to Predict Disease: Fast DFT Methods Applied to Enzymes Implicated in PKU, Parkinson's Disease and Obsessive Compulsive Disorder / L. Hofto ; M. Hofto ; J. Cross ; M. Cafiero
Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet / R. Hussong ; A. Tholey ; A. Hildebrandt
Calculating Mean First Passage Times from Markov Models of Proteins / C. H. Jensen ; D. Nerukh
Predicting Error Bars for QSAR Models / T. Schroeter ; A. Schwaighofer ; S. Mika ; A. Ter Laak ; D. Suelzle ; U. Ganzer ; N. Heinrich ; K.-R. Muller
Ab Initio Potential Grid Based Docking: From High Performance Computing to In Silico Screening / M. R. de Jonge ; H. M. Vinkers ; J. H. van Lenthe ; F. Daeyaert ; I. J. Bush ; H. J. J. van Dam ; P. Sherwood ; M. F. Guest
Author Index
Preface
Genomics
Improving Microarray Expressions with Recalibration / K. Fraser ; Z. Wang ; Y. Li ; P. Kellam ; X. Liu
8.

図書

図書
edited by David S. Moss, Sibila Jelaska, and Sándor Pongor
出版情報: Amsterdam : IOS Press, c2005  x, 251 p. ; 25 cm
シリーズ名: NATO science series ; ser. 1 . Life and behavioural sciences ; v. 368
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図書

図書
Mehmet M. Dalkilic, Sun Kim, Jiong Yang (eds.)
出版情報: Berlin : Springer, c2006  viii, 195 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 4316 . Lecture notes in bioinformatics
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図書

図書
Rita Casadio, Gene Myers (eds.)
出版情報: Berlin : Springer, c2005  x, 436 p. ; 24 cm
シリーズ名: Lecture notes in computer science ; 3692 . Lecture notes in bioinformatics
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