International Conference on Research in Computational Molecular Biology, Takeo Kanade, Satoru Miyano, Simon Kasif, Jill Mesirov, Pavel Pevzner, Michael Waterman
出版情報:
Springer eBooks Computer Science , Springer Berlin / Heidelberg, 2005
Informatics Infrastructure and Policy Considerations
Public Health Information Fusion for Situation Awareness / Henry Rolka ; Jean C. O'Connor ; David Walker
Biosurveillance, Case Reporting, and Decision Support: Public Health Interactions with a Health Information Exchange / Rebecca A. Hills ; William B. Lober ; Ian S. Painter
Bio-surveillance Event Models, Open Source Intelligence, and the Semantic Web / Nancy Grady ; Lowell Vizenor ; Jeanne Sappington Marin ; Laura Peitersen
Foresight China II: Identification and Detection of Infectious Diseases / Jiayuan Feng ; Jianshi (Jesse) Huang ; Angus Nicoll
Public Health Preparedness Informatics Infrastructure. A Case Study in Integrated Surveillance and Response: 2004-2005 National Influenza Vaccine Shortage / Ivan J. Gotham ; Linh H. Le ; Debra L. Sottolano ; Kathryn J. Schmit
Network-Based Data Analytics
Dynamic Network Model for Predicting Occurrences of Salmonella at Food Facilities / Purnamrita Sarkar ; Lujie Chen ; Artur Dubrawski
Network-Based Analysis of Beijing SARS Data / Xiaolong Zheng ; Daniel Zeng ; Aaron Sun ; Yuan Luo ; Quanyi Wang ; Feiyue Wang
Tutte Polynomials and Topological Quantum Algorithms in Social Network Analysis for Epidemiology, Bio-surveillance and Bio-security / Mario Velez ; Juan Ospina ; Doracelly Hincapie
Biosurveillance Models and Outbreak Detection
Integrating a Commuting Model with the Bayesian Aerosol Release Detector / Aurel Cami ; Garrick L. Wallstrom ; William R. Hogan
A Temporal Extension of the Bayesian Aerosol Release Detector / Xiaohui Kong
A Z-Score Based Multi-level Spatial Clustering Algorithm for the Detection of Disease Outbreaks / Jialan Que ; Fu-Chiang Tsui ; Jeremy Espino
Epidemic Thresholds in SIR and SIIR Models Applying an Algorithmic Method / Doracelly Hincapie P. ; Juan Ospina G. ; Anthony Uyi Afuwape ; Ruben D. Gomez A.
Test Power for Drug Abuse Surveillance / Jarad Niemi ; Meredith Smith ; David Banks
Model Assessment and Case Studies
Assessing the Accuracy of Spatiotemporal Epidemiological Models / James H. Kaufman ; Joanna L. Conant ; Daniel A. Ford ; Wakana Kirihata ; Barbara Jones ; Judith V. Douglas
Simulation of Multivariate Spatial-Temporal Outbreak Data for Detection Algorithm Evaluation / Min Zhang
Analysis and Prediction of Epidemiological Trend of Scarlet Fever from 1957 to 2004 in the Downtown Area of Beijing / Yanhui Shen ; Chu Jiang ; Zhe Dun
Environmental Biosurveillance and Case Studies
Environmental Biosurveillance for Epidemic Prediction: Experience with Rift Valley Fever / Jean-Paul Chretien ; Assaf Anyamba ; Jennifer Small ; Compton J. Tucker ; Seth C. Britch ; Kenneth J. Linthicum
Spatial Regression-Based Environmental Analysis in Infectious Disease Informatics / Daniel D. Zeng ; Ping Yan ; Su Li
Author Index
Informatics Infrastructure and Policy Considerations
Public Health Information Fusion for Situation Awareness / Henry Rolka ; Jean C. O'Connor ; David Walker
Biosurveillance, Case Reporting, and Decision Support: Public Health Interactions with a Health Information Exchange / Rebecca A. Hills ; William B. Lober ; Ian S. Painter
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations / Jean-Philippe Doyon ; Cedric Chauve ; Sylvie Hamel
Limitations of Pseudogenes in Identifying Gene Losses / James C. Costello ; Mira V. Han ; Matthew W. Hahn
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates / Paul Ryvkin ; Jin Jun ; Edward Hemphill ; Craig Nelson
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution / Ion Mandoiu
Discovering Local Patterns of Co-evolution / Yifat Felder ; Tamir Tuller
Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions / Miklos Csuros
An Alignment-Free Distance Measure for Closely Related Genomes / Bernhard Haubold ; Mirjana Domazet-Loso ; Thomas Wiehe
Gene Team Tree: A Compact Representation of All Gene Teams / Melvin Zhang ; Hon Wai Leong
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer / Cuong Than ; Guohua Jin ; Luay Nakhleh
An Evolutionary Study of the Human Papillomavirus Genomes / Dunarel Badescu ; Abdoulaye Banire Diallo ; Mathieu Blanchette ; Vladimir Makarenkov
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree / Matthias Bernt ; Daniel Merkle ; Martin Middendorf
Perfect DCJ Rearrangement / Severine Berard ; Annie Chateau ; Christophe Paul ; Eric Tannier
Sorting Genomes with Insertions, Deletions and Duplications by DCJ / Sophia Yancopoulos ; Richard Friedberg
A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach / Andrew Wei Xu
A Phylogenetic Approach to Genetic Map Refinement / Denis Bertrand ; Nadia El-Mabrouk
Sorting Cancer Karyotypes by Elementary Operations / Michal Ozery-Flato ; Ron Shamir
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios / Anne Bergeron ; Julia Mixtacki ; Jens Stoye
Hurdles Hardly Have to Be Heeded / Krister M. Swenson ; Yu Lin ; Vaibhav Rajan ; Bernard M.E. Moret
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny / David Sankoff ; Chunfang Zheng ; P. Kerr Wall ; Claude dePamphilis ; Jim Leebens-Mack ; Victor A. Albert
Author Index
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations / Jean-Philippe Doyon ; Cedric Chauve ; Sylvie Hamel
Limitations of Pseudogenes in Identifying Gene Losses / James C. Costello ; Mira V. Han ; Matthew W. Hahn
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates / Paul Ryvkin ; Jin Jun ; Edward Hemphill ; Craig Nelson
Qualitative Modeling and Simulation of Bacterial Regulatory Networks / Hidde de Jong
Integrated Analysis from Abstract Stochastic Process Algebra Models / Jane Hillston ; Federica Ciocchetta ; Adam Duguid ; Stephen Gilmore
An Exact Brownian Dynamics Method for Cell Simulation / Koichi Takahashi
Multiscale Modelling of Neuronal Signalling / Nicolas Le Novere
Systems Biology of Halophilic Archaea / Dieter Oesterhelt
A Partial Granger Causality Approach to Explore Causal Networks Derived from Multi-parameter Data / Ritesh Krishna ; Shuixia Guo
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe / Alexander Ullrich ; Christoph Flamm
Component-Based Modelling of RNA Structure Folding / Carsten Maus
A Language for Biochemical Systems / Michael Pedersen ; Gordon Plotkin
The Attributed Pi Calculus / Mathias John ; Cedric Lhoussaine ; Joachim Niehren ; Adelinde M. Uhrmacher
The Continuous [pi]-Calculus: A Process Algebra for Biochemical Modelling / Marek Kwiatkowski ; Ian Stark
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems / Dirk Lebiedz ; Dominik Skanda ; Marc Fein
Formal Analysis of Abnormal Excitation in Cardiac Tissue / Pei Ye ; Radu Grosu ; Scott A. Smolka ; Emilia Entcheva
The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock / Laurence Loewe
SED-ML - An XML Format for the Implementation of the MIASE Guidelines / Dagmar Kohn
On Parallel Stochastic Simulation of Diffusive Systems / Lorenzo Dematte ; Tommaso Mazza
Large-Scale Design Space Exploration of SSA / Matthias Jeschke ; Roland Ewald
Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway / Edmund M. Clarke ; James R. Faeder ; Christopher J. Langmead ; Leonard A. Harris ; Sumit Kumar Jha ; Axel Legay
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology / Aurelien Rizk ; Gregory Batt ; Francois Fages ; Sylvain Soliman
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways / Robin Donaldson ; David Gilbert
Compositional Definitions of Minimal Flows in Petri Nets
On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network / Abdelhalim Larhlimi ; Alexander Bockmayr
A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data / Markus Durzinsky ; Annegret Wagler ; Robert Weismantel
Analyzing a Discrete Model of Aplysia Central Pattern Generator / Ashish Tiwari ; Carolyn Talcott
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis / D. Bosnacki ; H.M.M. ten Eikelder ; M.N. Steijaert ; E.P. de Vink
A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics / Richard C. van der Wath ; Pietro Lio'
Author Index
Qualitative Modeling and Simulation of Bacterial Regulatory Networks / Hidde de Jong
Integrated Analysis from Abstract Stochastic Process Algebra Models / Jane Hillston ; Federica Ciocchetta ; Adam Duguid ; Stephen Gilmore
An Exact Brownian Dynamics Method for Cell Simulation / Koichi Takahashi
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems / David Harel ; Yaki Setty
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions / Jasmin Fisher ; Thomas A. Henzinger ; Maria Mateescu ; Nir Piterman
Computational Probability for Systems Biology / Werner Sandmann ; Verena Wolf
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets / Elzbieta Krepska ; Nicola Bonzanni ; Anton Feenstra ; Wan Fokkink ; Thilo Kielmann ; Henri Bal ; Jaap Heringa
Combining Intra- and Inter-cellular Dynamics to Investigate Intestinal Homeostasis / Oksana Tymchyshyn ; Marta Kwiatkowska
Approximating Continuous Systems by Timed Automata / Oded Maler ; Gregory Batt
From Reaction Models to Influence Graphs and Back: A Theorem / Francois Fages ; Sylvain Soliman
Rule-Based Modelling, Symmetries, Refinements / Vincent Danos ; Jerome Feret ; Walter Fontana ; Russell Harmer ; Jean Krivine
One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II / Adelinde M. Uhrmacher ; Jan Himmelspach ; Matthias Jeschke ; Mathias John ; Stefan Leye ; Carsten Maus ; Mathias Rohl ; Roland Ewald
Author Index
Contributed Papers
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems / David Harel ; Yaki Setty
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions / Jasmin Fisher ; Thomas A. Henzinger ; Maria Mateescu ; Nir Piterman
Knowledge Discovery and Emergent Complexity in Bioinformatics / Ronald Westra ; Karl Tuyls ; Yvan Saeys ; Ann Nowe
Boolean Algebraic Structures of the Genetic Code: Possibilities of Applications / Ricardo Grau ; Maria del C. Chavez ; Robersy Sanchez ; Eberto Morgado ; Gladys Casas ; Isis Bonet
Discovery of Gene Regulatory Networks in Aspergillus fumigatus / Reinhard Guthke ; Olaf Kniemeyer ; Daniela Albrecht ; Axel A. Brakhage ; Ulrich Moller
Complexity Measures for Gene Assembly / Tero Harju ; Chang Li ; Ion Petre ; Grzegorz Rozenberg
Learning Relations from Biomedical Corpora Using Dependency Trees / Sophia Katrenko ; Pieter Adriaans
Advancing the State of the Art in Computational Gene Prediction / William H. Majoros ; Uwe Ohler
Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection / Yves Van de Peer
The Net Generator Algorithm: Reconstruction of Gene Regulatory Networks / Susanne Toepfer ; Dominik Driesch ; Dirk Woetzel ; Michael Pfaff
On the Neuronal Morphology-Function Relationship: A Synthetic Approach / Ben Torben-Nielsen ; Eric O. Postma
Analyzing Stigmergetic Algorithms Through Automata Games / Peter Vrancx ; Katja Verbeeck
The Identification of Dynamic Gene-Protein Networks / Ronald L. Westra ; Goele Hollanders ; Geert Jan Bex ; Marc Gyssens
Knowledge Discovery and Emergent Complexity in Bioinformatics / Ronald Westra ; Karl Tuyls ; Yvan Saeys ; Ann Nowe
Boolean Algebraic Structures of the Genetic Code: Possibilities of Applications / Ricardo Grau ; Maria del C. Chavez ; Robersy Sanchez ; Eberto Morgado ; Gladys Casas ; Isis Bonet
Discovery of Gene Regulatory Networks in Aspergillus fumigatus / Reinhard Guthke ; Olaf Kniemeyer ; Daniela Albrecht ; Axel A. Brakhage ; Ulrich Moller
Protein: Structure, Function, and Interaction / Part I：
Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai
Predicting SUMOylation Sites / Denis C. Bauer ; Fabian A. Buske ; Mikael Boden
DFS Based Partial Pathways in GA for Protein Structure Prediction / Md Tamjidul Hoque ; Madhu Chetty ; Andrew Lewis ; Abdul Sattar
Evaluation of the Stability of Folding Nucleus upon Mutation / Mathieu Lonquety ; Zoe Lacroix ; Jacques Chomilier
Prediction of Protein Beta-Sheets: Dynamic Programming Versus Grammatical Approach / Yuki Kato ; Tatsuya Akutsu ; Hiroyuki Seki
Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types / QiPeng Li ; Shao Wu Zhang ; Quan Pan
Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces / Satoshi Koizumi ; Keisuke Imada ; Tomonobu Ozaki ; Takenao Ohkawa
Learning, Classification, and Clustering / Part II：
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis / Pengyi Yang ; Zili Zhang
A Modified Markov Clustering Approach for Protein Sequence Clustering / Lehel Medves ; Laszlo Szilagyi ; Sandor M. Szilagyi
Feature Selection and Classification for Small Gene Sets / Gregor Stiglic ; Juan J. Rodriguez ; Peter Kokol
Pseudoknot Identification through Learning TAG[subscript RNA] / Sahar Al Seesi ; Sanguthevar Rajasekaran ; Reda Ammar
Support Vector Based T-Score for Gene Ranking / Piyushkumar A. Mundra ; Jagath C. Rajapakse
Prediction of Transcription Factor Families Using DNA Sequence Features / Ashish Anand ; Gary B. Fogel ; Ganesan Pugalenthi ; P.N. Suganthan
g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines / Xiaonan Ji ; James Bailey ; Kotagiri Ramamohanarao
Bio-Molecular Networks and Pathways Analysis / Part III：
Domain-Domain Interaction Identification with a Feature Selection Approach / Xing-Ming Zhao ; Luonan Chen
Dividing Protein Interaction Networks by Growing Orthologous Articulations / Pavol Jancura ; Jaap Heringa ; Elena Marchiori
Constraint Minimization for Efficient Modeling of Gene Regulatory Network / Ramesh Ram ; Dieter Bulach
Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models / Iti Chaturvedi
TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees / Tingting Zhou ; Keith C.C. Chan ; Zhenghua Wang
Generating Synthetic Gene Regulatory Networks
Microarray and Gene Expression Analysis / Part IV：
Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm / Edmundo Bonilla Huerta ; Beatrice Duval ; Jin-Kao Hao
Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem / Lili Wang ; Alioune Ngom ; Luis Rueda
On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments / Yvonne E. Pittelkow ; Susan R. Wilson
Microarray Design Using the Hilbert-Schmidt Independence Criterion / Justin Bedo
Exploratory Data Analysis for Investigating GC-MS Biomarkers / Ken McGarry ; Kim Bartlett ; Morteza Pourfarzam
Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins / Karen T. Girao ; Fatima C.E. Oliveira ; Kaio M. Farias ; Italo M.C. Maia ; Samara C. Silva ; Carla R.F. Gadelha ; Laura D.G. Carneiro ; Ana C.L. Pacheco ; Michel T. Kamimura ; Michely C. Diniz ; Maria C. Silva ; Diana M. Oliveira
Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-Genomic Knowledge Discovery / Muhammad Shoaib B. Sehgal ; Iqbal Gondal ; Laurence S. Dooley ; Ross Coppel
Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis / Xiaoxu Han ; Joseph Scazzero
Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer / Geoff Macintyre ; Daniel Gustafsson ; Alex Boussioutas ; Izhak Haviv ; Adam Kowalczyk
Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data / Cem Meydan ; Alper Kucukural ; Deniz Yorukoglu ; O. Ugur Sezerman
Applications of High Performance Computing / Part VI：
Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study / Alexandros Stamatakis ; Michael Ott
Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA / Jan Schroder ; Lars Wienbrandt ; Gerd Pfeiffer ; Manfred Schimmler
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences / Chen Chen ; Bertil Schmidt ; Liu Weiguo ; Wolfgang Muller-Wittig
Accelerating BLASTP on the Cell Broadband Engine / Huiliang Zhang
Author Index
Protein: Structure, Function, and Interaction / Part I：
Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai
Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen
Reconstructing the Evolutionary History of Complex Human Gene Clusters / Yu Zhang ; Giltae Song ; Tomas Vinar ; Eric D. Green ; Adam Siepel ; Webb Miller
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads / Paul Medevedev ; Michael Brudno
Orchestration of DNA Methylation (Keynote) / Howard Cedar
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes / Tien-ho Lin ; Pradipta Ray ; Geir K. Sandve ; Selen Uguroglu ; Eric P. Xing
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors / Yanxin Shi ; Itamar Simon ; Tom Mitchell ; Ziv Bar-Joseph
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery / Raluca Gordan ; Leelavati Narlikar ; Alexander J. Hartemink
The Statistical Power of Phylogenetic Motif Models / John Hawkins ; Timothy L. Bailey
Transcriptional Regulation and Cancer Genomics (Keynote) / Edison Liu
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans / Fuhui Long ; Hanchuan Peng ; Xiao Liu ; Stuart Kim ; Gene Myers
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing / Ritendra Datta ; Marshall Bern
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry / Yu Lin ; Yantao Qiao ; Shiwei Sun ; Chungong Yu ; Gongjin Dong ; Dongbo Bu
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics / Yong Fuga Li ; Randy J. Arnold ; Yixue Li ; Predrag Radivojac ; Quanhu Sheng ; Haixu Tang
De Novo Sequencing of Nonribosomal Peptides / Nuno Bandeira ; Julio Ng ; Dario Meluzzi ; Roger G. Linington ; Pieter Dorrestein ; Pavel A. Pevzner
Systems Metabolic Engineering (Keynote) / Sang Yup Lee
Protein Function Prediction Based on Patterns in Biological Networks / Mustafa Kirac ; Gultekin Ozsoyoglu
Automatic Parameter Learning for Multiple Network Alignment / Jason Flannick ; Antal Novak ; Chuong B. Do ; Balaji S. Srinivason ; Serafim Batzoglou
An Integrative Network Approach to Map the Transcriptome to the Phenome / Michael R. Mehan ; Juan Nunez-Iglesias ; Mrinal Kalakrishnan ; Michael S. Waterman ; Xianghong Jasmine Zhou
Fast and Accurate Alignment of Multiple Protein Networks / Maxim Kalaev ; Vineet Bafna ; Roded Sharan
High-Resolution Modeling of Cellular Signaling Networks / Michael Baym ; Chris Bakal ; Norbert Perrimon ; Bonnie Berger
At the Origin of Life: How Did Folded Proteins Evolve? (Keynote) / Andrei Lupas
Locating Multiple Gene Duplications through Reconciled Trees / J. Gordon Burleigh ; Mukul S. Bansal ; Andre Wehe ; Oliver Eulenstein
Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information / Jing Zhang ; Xin Gao ; Jinbo Xu ; Ming Li
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins / Wei Zheng ; Alan M. Friedman ; Chris Bailey-Kellogg
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework / Christophe Dessimoz ; Daniel Margadant ; Gaston H. Gonnet
Computation of Median Gene Clusters / Sebastian Bocker ; Katharina Jahn ; Julia Mixtacki ; Jens Stoye
BCL-2: From Translocation to Therapy (Keynote) / Suzanne Cory
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles / Igor Ulitsky ; Richard M. Karp ; Ron Shamir
Constructing Treatment Portfolios Using Affinity Propagation / Delbert Dueck ; Brendan J. Frey ; Nebojsa Jojic ; Vladimir Jojic ; Guri Giaever ; Andrew Emili ; Gabe Musso ; Robert Hegele
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs / Michael Sammeth ; Gabriel Valiente ; Roderic Guigo
More Efficient Algorithms for Closest String and Substring Problems / Bin Ma ; Xiaoming Sun
Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia (Keynote) / Denis Smirnov ; Vivian G. Cheung
Accounting for Non-genetic Factors Improves the Power of eQTL Studies / Oliver Stegle ; Anitha Kannan ; Richard Durbin ; John Winn
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA / Andreas Sundquist ; Eugene Fratkin
On the Inference of Ancestries in Admixed Populations / Sriram Sankararaman ; Gad Kimmel ; Eran Halperin ; Michael I. Jordan
Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information / Eleazar Eskin
Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information / Sivan Bercovici ; Dan Geiger ; Liran Shlush ; Karl Skorecki ; Alan Templeton
Constructing Level-2 Phylogenetic Networks from Triplets / Leo van Iersel ; Judith Keijsper ; Steven Kelk ; Leen Stougie ; Ferry Hagen ; Teun Boekhout
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony / Rune B. Lyngso ; Yun S. Song ; Jotun Hein
Author Index
Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen
A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport / Paras Chopra ; Andreas Bender
Punctuated Equilibrium in Statistical Models of Generalized Coevolutionary Resilience: How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection / Rodrick Wallace ; Deborah Wallace
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways / Roberto Barbuti ; Andrea Maggiolo-Schettini ; Paolo Milazzo ; Paolo Tiberi ; Angelo Troina
The BlenX Language with Biological Transactions / Federica Ciocchetta
Author Index
A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport / Paras Chopra ; Andreas Bender
Punctuated Equilibrium in Statistical Models of Generalized Coevolutionary Resilience: How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection / Rodrick Wallace ; Deborah Wallace
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways / Roberto Barbuti ; Andrea Maggiolo-Schettini ; Paolo Milazzo ; Paolo Tiberi ; Angelo Troina
Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps / Marco Vassura ; Luciano Margara ; Pietro Di Lena ; Filippo Medri ; Piero Fariselli ; Rita Casadio
Bringing Folding Pathways into Strand Pairing Prediction / Jieun K. Jeong ; Piotr Berman ; Teresa M. Przytycka
A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage / Loredana M. Genovese ; Filippo Geraci ; Marco Pellegrini
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies / Phil Hyoun Lee ; Hagit Shatkay
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity / Justin Kennedy ; Ion Mandoiu ; Bogdan Pasaniuc
Haplotype Inference Via Hierarchical Genotype Parsing / Pasi Rastas ; Esko Ukkonen
Seeded Tree Alignment and Planar Tanglegram Layout / Antoni Lozano ; Ron Y. Pinter ; Oleg Rokhlenko ; Gabriel Valiente ; Michal Ziv-Ukelson
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion (Extended Abstract) / Hadas Birin ; Zohar Gal-Or ; Isaac Elias ; Tamir Tuller
An [Omega](n[superscript 2]/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem / Mukul S. Bansal ; Oliver Eulenstein
Incremental Discovery of Irredundant Motif Bases in Time O([vertical bar Sigma vertical bar]n[superscript 2] log n) (Extended Abstract) / Alberto Apostolico ; Claudia Tagliacollo
A Graph Clustering Approach to Weak Motif Recognition / Christina Boucher ; Daniel G. Brown ; Paul Church
Informative Motifs in Protein Family Alignments / Hatice Gulcin Ozer ; William C. Ray
Topology Independent Protein Structural Alignment / Joe Dundas ; T.A. Binkowski ; Bhaskar DasGupta ; Jie Liang
Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction / Giuseppe Nicosia ; Giovanni Stracquadanio
Alignment-Free Local Structural Search by Writhe Decomposition / Degui Zhi ; Maxim Shatsky ; Steven E. Brenner
Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment / Xueyi Wang ; Jack Snoeyink
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding / Mihaela Pertea ; Steven L. Salzberg
Genomic Signatures in De Bruijn Chains / Lenwood S. Heath ; Amrita Pati
Fast Kernel Methods for SVM Sequence Classifiers / Pavel Kuksa ; Vladimir Pavlovic
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences / Rastislav Sramek ; Brona Brejova ; Tomas Vinar
Predicting Protein Folding Kinetics Via Temporal Logic Model Checking (Extended Abstract) / Christopher James Langmead ; Sumit Kumar Jha
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops / Ankur Dhanik ; Peggy Yao ; Nathan Marz ; Ryan Propper ; Charles Kou ; Guanfeng Liu ; Henry van den Bedem ; Jean-Claude Latombe
Algorithms for the Extraction of Synteny Blocks from Comparative Maps / Vicky Choi ; Chunfang Zheng ; Qian Zhu ; David Sankoff
Computability of Models for Sequence Assembly / Paul Medvedev ; Konstantinos Georgiou ; Gene Myers ; Michael Brudno
Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data / Jaime Davila ; Sudha Balla ; Sanguthevar Rajasekaran
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound / Chunmei Liu ; Yinglei Song ; Louis Shapiro
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding / Hosna Jabbari ; Anne Condon ; Ana Pop ; Cristina Pop ; Yinglei Zhao
Homology Search with Fragmented Nucleic Acid Sequence Patterns / Axel Mosig ; Julian J.-L. Chen ; Peter F. Stadler
Fast Computation of Good Multiple Spaced Seeds / Lucian Ilie ; Silvana Ilie
Inverse Sequence Alignment from Partial Examples / Eagu Kim ; John Kececioglu
Novel Approaches in Psychiatric Genomics (Keynote) / Maja Bucan
The Point Placement Problem on a Line - Improved Bounds for Pairwise Distance Queries / Francis Y.L. Chin ; Henry C.M. Leung ; W.K. Sung ; S.M. Yiu
Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach / Alexander Schliep ; Roland Krause
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data / Yonghui Wu ; Prasanna Bhat ; Timothy J. Close ; Stefano Lonardi
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence / Reka Albert ; Riccardo Dondi ; Sema Kachalo ; Eduardo Sontag ; Alexander Zelikovsky ; Kelly Westbrooks
Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation / Geoffrey Koh ; Lisa Tucker-Kellogg ; David Hsu ; P.S. Thiagarajan
Author Index
Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial
The First Section: Modeling and Simulation of Societies and Collective Behavior
Phase Synchronization of Circadian Oscillators Induced by a Light-Dark Cycle and Extracellular Noise / Ying Li ; Jianbao Zhang ; Zengrong Liu
Detecting RNA Sequences Using Two-Stage SVM Classifier / Xiaoou Li ; Kang Li
Frequency Synchronization of a Set of Cells Coupled by Quorum Sensing / Luonan Chen
A Stochastic Model for Prevention and Control of HIV/AIDS Transmission Dynamics / Min Xu ; Yongsheng Ding ; Liangjian Hu
Simulation of Artificial Life of Bee's Behaviors / Bin Wu ; Hongying Zhang ; Xia Ni
Hybrid Processing and Time-Frequency Analysis of ECG Signal / Ping Zhang ; Chengyuan Tu ; Xiaoyang Li ; Yanjun Zeng
Robust Stability of Human Balance Keeping / Minrui Fei ; Lisheng Wei ; Taicheng Yang
Modelling Pervasive Environments Using Bespoke and Commercial Game-Based Simulators / Marc Davies ; Vic Callaghan ; Liping Shen
The Research of Artificial Animal's Behavior Memory Based on Cognition / Xiaojuan Ban ; Shurong Ning ; Jing Shi ; Dongmei Ai
The Second Section: Computational Methods and Intelligence in Biomechanical Systems, Tissue Engineering and Clinical Bioengineering
How to Ensure Safety Factors in the Development of Artificial Heart: Verified by the Usage of "Modeling and Simulation" Technology / Mitsuo Umezu
Parametric-Expression-Based Construction of Interior Features for Tissue Engineering Scaffold with Defect Bone / Chunxiang Dai ; Qingxi Hu ; Minglun Fang
Computation of Uniaxial Modulus of the Normal and Degenerated Articular Cartilage Using Inhomogeneous Triphasic Model / Haijun Niu ; Qing Wang ; Yongping Zheng ; Fang Pu ; Yubo Fan ; Deyu Li
Effect of the Plantar Ligaments Injury on the Longitudinal Arch Height of the Human Foot / Yunfeng Yang ; Guangrong Yu ; Wenxin Niu ; Jiaqian Zhou ; Yanxi Chen ; Feng Yuan ; Zuquan Ding
Internet Living Broadcast of Medical Video Stream / Shejiao Li ; Bo Li ; Fan Zhang
Predicting Syndrome by NEI Specifications: A Comparison of Five Data Mining Algorithms in Coronary Heart Disease / Jianxin Chen ; Guangcheng Xi ; Yanwei Xing ; Jing Chen ; Jie Wang
Application of Image Processing and Finite Element Analysis in Bionic Scaffolds' Design Optimizing and Fabrication / Liulan Lin ; Huicun Zhang ; Yuan Yao ; Aili Tong
The Mechanical Properties of Bone Tissue Engineering Scaffold Fabricating Via Selective Laser Sintering
The Third Section: Computational Intelligence in Bioinformatics and Biometrics
Informational Structure of Agrobacterium Tumefaciens C58 Genome / Zhihua Liu ; Xiao Sun
Feature Extraction for Cancer Classification Using Kernel-Based Methods / Shutao Li ; Chen Liao
A New Hybrid Approach to Predict Subcellular Localization by Incorporating Protein Evolutionary Conservation Information / ShaoWu Zhang ; YunLong Zhang ; JunHui Li ; HuiFeng Yang ; YongMei Cheng ; GuoPing Zhou
Support Vector Machine for Prediction of DNA-Binding Domains in Protein-DNA Complexes / Jiansheng Wu ; Hongtao Wu ; Hongde Liu ; Haoyan Zhou
Feature Extraction for Mass Spectrometry Data / Yihui Liu
An Improved Algorithm on Detecting Transcription and Translation Motif in Archaeal Genomic Sequences / Minghui Wu ; Xian Chen ; Fanwei Zhu ; Jing Ying
Constructing Structural Alignment of RNA Sequences by Detecting and Assessing Conserved Stems / Xiaoyong Fang ; Zhigang Luo ; Bo Yuan ; Zhenghua Wang ; Fan Ding
Iris Verification Using Wavelet Moments and Neural Network / Zhiqiang Ma ; Miao Qi ; Haifeng Kang ; Shuhua Wang ; Jun Kong
Comprehensive Fuzzy Evaluation Model for Body Physical Exercise Risk / Yizhi Wu ; Hongan Xu
The Fourth Section: Brain Stimulation, Neural Dynamics and Neural Interfacing
The Effect of Map Information on Brain Activation During a Driving Task / Tao Shang ; Shuoyu Wang ; Shengnan Zhang
Worm 5: Pseudo-organics Computer and Natural Live System / Yick Kuen Lee ; Ying Ying Lee
Comparisons of Chemical Synapses and Gap Junctions in the Stochastic Dynamics of Coupled Neurons / Jiang Wang ; Xiumin Li ; Dong Feng
Distinguish Different Acupuncture Manipulations by Using Idea of ISI / Wenjie Si ; Limei Zhong ; Feng Dong
The Study on Internet-Based Face Recognition System Using PCA and MMD / Jong-Min Kim
Simulation of Virtual Human's Mental State in Behavior Animation / Zhen Liu
Hemodynamic Analysis of Cerebral Aneurysm and Stenosed Carotid Bifurcation Using Computational Fluid Dynamics Technique / Yi Qian ; Tstsuji Harada ; Koichi Fukui ; Hiroyuki Takao ; Yuichi Murayama
Active/Inactive Emotional Switching for Thinking Chain Extraction by Type Matching from RAS / JeongYon Shim
Pattern Recognition for Brain-Computer Interfaces by Combining Support Vector Machine with Adaptive Genetic Algorithm / Banghua Yang ; Shiwei Ma ; Zhihua Li
The Fifth Section: Biological and Biomedical Data Integration, Mining and Visualization
Improved Locally Linear Embedding by Cognitive Geometry / Guihua Wen ; Lijun Jiang ; Jun Wen
Predicting the Free Calcium Oxide Content on the Basis of Rough Sets, Neural Networks and Data Fusion / Yunxing Shu ; Shiwei Yun ; Bo Ge
Classification of Single Trial EEG Based on Cloud Model for Brain-Computer Interfaces / Shaobin Li ; Chenxi Shao
The Modified Self-organizing Fuzzy Neural Network Model for Adaptability Evaluation / Zuohua Miao ; Hong Xu ; Xianhua Wang
Predicting Functional Protein-Protein Interactions Based on Computational Methods / Luwen Zhang ; Wu Zhang
The Chaos Model Analysis Based on Time-Varying Fractal Dimension / Jianrong Hou ; Dan Huang ; Hui Zhao
Bi-hierarchy Medical Image Registration Based on Steerable Pyramid Transform / Xiuying Wang ; David Feng
The Sixth Section: Computational Methods and Intelligence in Organism Modeling and Biochemical Networks and Regulation
A Multiagent Quantum Evolutionary Algorithm for Global Numerical Optimization / Chaoyong Qin ; Jianguo Zheng ; Jiyu Lai
Developing and Optimizing a Finite Element Model of Phalange Using CT Images / Quan Zhang
Reverse Engineering Methodology in Broken Skull Surface Model Reconstruction / Luyue Ju ; Gaojian Zhong ; Xia Liu
Identification and Application of Nonlinear Rheological Characteristics of Oilseed Based on Artificial Neural Networks / Xiao Zheng ; Guoxiang Lin ; Dongping He ; Jingzhou Wang ; Yan You
Prediction of Death Rate of Breast Cancer Induced from Average Microelement Absorption with Neural Network / Shouju Li ; Jizhe Wang ; Yingxi Liu ; Xiuzhen Sun
An Adaptive Classifier Based on Artificial Immune Network / Zhiguo Li ; Jiang Zhong ; Yong Feng ; ZhongFu Wu
Investigation of a Hydrodynamic Performance of a Ventricular Assist Device After Its Long-Term Use in Clinical Application / Yuma Kokuzawa ; Tomohiro Shima ; Masateru Furusato ; Kazuhiko Ito ; Takashi Tanaka ; Toshihiro Igarashi ; Tomohiro Nishinaka ; Kiyotaka Iwasaki
The Seventh Section: Computational Methods and Intelligence in Modeling of Molecular, Cellular, Multi-cellular Behavior and Design of Synthetic Biological Systems
QSAR and Molecular Docking Study of a Series of Combretastatin Analogues Tubulin Inhibitors / Yubin Ji ; Ran Tian ; Wenhan Lin
A Software Method to Model and Fabricate the Defective Bone Repair Bioscaffold Using in Tissue Engineering / Hongfei Yang
Using Qualitative Technology for Modeling the Process of Virus Infection / Hailin Feng
AOC-by-Self-discovery Modeling and Simulation for HIV / Chunxiao Zhao ; Ning Zhong ; Ying Hao
A Simulation Study on the Encoding Mechanism of Retinal Ganglion Cell / Chao-Feng Cai ; Pei-Ji Liang ; Pu-Ming Zhang
Modelling the MAPK Signalling Pathway Using a Two-Stage Identification Algorithm / Padhraig Gormley ; George W. Irwin
The Eighth Section: Others
Design and Path Planning for a Remote-Brained Service Robot / Shigang Cui ; Xuelian Xu ; Zhengguang Lian ; Li Zhao ; Zhigang Bing
Adaptive Fuzzy Sliding Mode Control of the Model of Aneurysms of the Circle of Willis / Peijun Ju ; Guocai Liu ; Li Tian ; Wei Zhang
Particle Swarm Optimization Applied to Image Vector Quantization / Xubing Zhang ; Zequn Guan ; Tianhong Gan
Face Detection Based on BPNN and Wavelet Invariant Moment in Video Surveillance / Hongji Lin ; Zhengchun Ye
Efficient Topological Reconstruction for Medical Model Based on Mesh Simplification / Ying Jiang
Repetitive Motion Planning of Redundant Robots Based on LVI-Based Primal-Dual Neural Network and PUMA560 Example / Yunong Zhang ; Xuanjiao Lv ; Zhonghua Li ; Zhi Yang
Tensile Test to Ensure a Safety of Cannula Connection in Clinical Ventricular Assist Device (VAD)
A Reproduction of Inflow Restriction in the Mock Circulatory System to Evaluate a Hydrodynamic Performance of a Ventricular Assist Device in Practical Conditions / ZhiKun Yan ; Ling Zhu
Author Index
The First Section: Modeling and Simulation of Societies and Collective Behavior
Phase Synchronization of Circadian Oscillators Induced by a Light-Dark Cycle and Extracellular Noise / Ying Li ; Jianbao Zhang ; Zengrong Liu
Detecting RNA Sequences Using Two-Stage SVM Classifier / Xiaoou Li ; Kang Li
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation / Fereydoun Hormozdiari ; Petra Berenbrink ; Natasa Przulj ; Cenk Sahinalp
Probabilistic Paths for Protein Complex Inference / Hailiang Huang ; Lan V. Zhang ; Frederick P. Roth ; Joel S. Bader
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting / Hans-Michael Kaltenbach ; Sebastian Bocker ; Sven Rohmann
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells / Celine Lefebvre ; Wei Keat Lim ; Katia Basso ; Riccardo Dalla Favera ; Andrea Califano
Identification and Evaluation of Functional Modules in Gene Co-expression Networks / Jianhua Ruan ; Weixiong Zhang
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast / Mingzhou (Joe) Song ; Z. Lewis Liu
A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry / Yin Wu ; Yehia Mechref ; Iveta Klouckova ; Milos V. Novotny ; Haixu Tang
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Arialysis / Derek Ruths ; Jen-Te Tseng ; Luay Nakhleh ; Prahlad T. Ram
Alignment of Mass Spectrometry Data by Clique Finding and Optimization / Daniel Fasulo ; Anne-Katrin Emde ; Lu-Yong Wang ; Karin Noy ; Nathan Edwards
Author Index
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation / Fereydoun Hormozdiari ; Petra Berenbrink ; Natasa Przulj ; Cenk Sahinalp
Probabilistic Paths for Protein Complex Inference / Hailiang Huang ; Lan V. Zhang ; Frederick P. Roth ; Joel S. Bader
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting / Hans-Michael Kaltenbach ; Sebastian Bocker ; Sven Rohmann
Multi-label Hierarchical Classification of Protein Functions with Artificial Immune Systems / Roberto T. Alves ; Myriam R. Delgado ; Alex A. Freitas
Operon Prediction in Bacterial Genomes / Matheus B.S. Barros ; Simone de L. Martins ; Alexandre Plastino
An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures / Miguel M.F. Bugalho ; Arlindo L. Oliveira
Top-Down Hierarchical Ensembles of Classifiers for Predicting G-Protein-Coupled-Receptor Functions / Eduardo P. Costa ; Ana C. Lorena ; Andre C.P.L.F. Carvalho
A Hybrid Method for the Protein Structure Prediction Problem / Marcio Dorn ; Ardala Breda ; Osmar Norberto de Souza
Detecting Statistical Covariations of Sequence Physicochemical Properties / Moshe A. Gadish ; David K.Y. Chiu
Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase / Diego E.B. Gomes ; Roberto D. Lins ; Pedro G. Pascutti ; Tjerk P. Straatsma ; Thereza A. Soares
On the Toric Graph as a Tool to Handle the Problem of Sorting by Transpositions / Rodrigo de A. Hausen ; Luerbio Faria ; Celina M.H. de Figueiredo ; Luis Antonio B. Kowada
A Customized Class of Functions for Modeling and Clustering Gene Expression Profiles in Embryonic Stem Cells / Shenggang Li ; Miguel Andrade-Navarro ; David Sankoff
Extracting Information from Flexible Receptor-Flexible Ligand Docking Experiments / Karina S. Machado ; Evelyn K. Schroeder ; Duncan D. Ruiz ; Ana Wink
Transposition Distance Based on the Algebraic Formalism / Cleber V.G. Mira ; Zanoni Dias ; Hederson P. Santos ; Guilherme A. Pinto ; Maria Emilia M.T. Walter
Using BioAgents for Supporting Manual Annotation on Genome Sequencing Projects / Celia Ghedini Ralha ; Hugo W. Schneider ; Lucas O. da Fonseca ; Marcelo M. Brigido
Application of Genetic Algorithms to the Genetic Regulation Problem / Maria Fernanda B. Wanderley ; Joao C.P. da Silva ; Carlos Cristiano H. Borges ; Ana Tereza R. Vasconcelos
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion / Ximing Xu
Extended Abstracts
Identity Transposon Networks in D. melanogaster / Alcides Castro-e-Silva ; Gerald Weber ; Romuel F. Machado ; Elizabeth F. Wanner ; Renata Guerra-Sa
Prediction of Protein-Protein Binding Hot Spots: A Combination of Classifiers Approach / Roberto Hiroshi Higa ; Clesio Luis Tozzi
AGN Simulation and Validation Model / Fabricio M. Lopes ; Roberto M. Cesar-Jr. ; Luciano da F. Costa
A Practical Evaluation of BioProvider / Maira Ferreira de Noronha ; Sergio Lifschitz ; Antonio Basilio de Miranda
Evaluation of Models for the Recognition of Hadwritten Digits in Medical Forms / Willian Zalewski ; Huei Diana Lee ; Adewole M.J.F. Caetano ; Andre G. Maletzke ; Joao Jose Fagundes ; Claudio Saddy ; Rodrigues Coy ; Feng Chung Wu
Author Index
Selected Articles
Multi-label Hierarchical Classification of Protein Functions with Artificial Immune Systems / Roberto T. Alves ; Myriam R. Delgado ; Alex A. Freitas
Operon Prediction in Bacterial Genomes / Matheus B.S. Barros ; Simone de L. Martins ; Alexandre Plastino
Multichromosomal Genome Median and Halving Problems / Eric Tannier ; Chunfang Zheng ; David Sankoff
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem / Meng Zhang ; William Arndt ; Jijun Tang
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions / Andrew Wei Xu
Read Mapping Algorithms for Single Molecule Sequencing Data / Vladimir Yanovsky ; Stephen M. Rumble ; Michael Brudno
Exact Transcriptome Reconstruction from Short Sequence Reads / Vincent Lacroix ; Michael Sammeth ; Roderic Guigo ; Anne Bergeron
Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments / Florian Battke ; Carsten Muller-Tidow ; Hubert Serve ; Kay Nieselt
NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem / Glenn Hickey ; Paz Carmi ; Anil Maheshwari ; Norbert Zeh
Minimum Common String Partition Parameterized / Peter Demaschke
Hardness and Approximability of the Inverse Scope Problem / Zoran Nikoloski ; Sergio Grimbs ; Joachim Selbig ; Oliver Ebenhoh
Rapid Neighbour-Joining / Martin Simonsen ; Thomas Mailund ; Christian N. S. Pedersen
Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices / Seung-Jin Sul ; Grant Brammer ; Tiffani L. Williams
Efficient Genome Wide Tagging by Reduction to SAT / Arthur Choi ; Noah Zaitlen ; Buhm Han ; Knot Pipatsrisawat ; Adnan Darwiche ; Eleazar Eskin
Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming / Serdar Bozdag ; Timothy J. Close ; Stefano Lonardi
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem / Rumen Andonov ; Nicola Yanev ; Noel Malod-Dognin
A Faster Algorithm for RNA Co-folding / Michal Ziv-Ukelson ; Irit Gat-Viks ; Ydo Wexler ; Ron Shamir
An Automated Combination of Kernels for Predicting Protein Subcellular Localization / Cheng Soon Ong ; Alexander Zien
Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach / Thomas Lingner ; Peter Meinicke
Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles / Nico Pfeifer ; Oliver Kohlbacher
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks / Alexander Medvedovsky ; Vineet Bafna ; Uri Zwick ; Roded Sharan
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network / Ludovic Cottret ; Paulo Vieira Milreu ; Vicente Acuna ; Alberto Marchetti-Spaccamela ; Fabio Viduani Martinez ; Marie-France Sagot ; Leen Stougie
Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach / Xiuwei Zhang ; Bernard M.E. Moret
Fast Bayesian Haplotype Inference Via Context Tree Weighting / Pasi Rastas ; Jussi Kollin ; Mikko Koivisto
Genotype Sequence Segmentation: Handling Constraints and Noise / Qi Zhang ; Wei Wang ; Leonard McMillan ; Jan Prins ; Fernando Pardo-Manuel de Villena ; David Threadgill
Constructing Phylogenetic Supernetworks from Quartets / Stefan Grunewald ; Andreas Spillner ; Kristoffer Forslund ; Vincent Moulton
Summarizing Multiple Gene Tree Using Cluster Networks / Daniel H. Huson ; Regula Rupp
Fast and Adaptive Variable Order Markov Chain Construction / Marcel H. Schulz ; David Weese ; Tobias Rausch ; Andreas Doring ; Knut Reinert ; Martin Vingron
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata / Inke Herms ; Sven Rahmann
The Relation between Indel Length and Functional Divergence: A Formal Study / Raheleh Salari ; Alexander Schonhuth ; Fereydoun Hormozdiari ; Artem Cherkasov ; S. Cenk Sahinalp
Detecting Repeat Families in Incompletely Sequenced Genomes / Jose Augusto Amgarten Quitzau ; Jens Stoye
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models (Extended Abstract) / Sagi Snir ; Tamir Tuller
A Local Move Set for Protein Folding in Triangular Lattice Models / Hans-Joachim Bockenhauer ; Abu Zfer M. Dayem Ullah ; Leonidas Kapsokalivas ; Kathleen Steinhofel
Protein Decoy Generation Using Branch and Bound with Efficient Bounding / Martin Paluszewski ; Pawel Winter
Author Index
Multichromosomal Genome Median and Halving Problems / Eric Tannier ; Chunfang Zheng ; David Sankoff
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem / Meng Zhang ; William Arndt ; Jijun Tang
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions / Andrew Wei Xu
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems / David Harel ; Yaki Setty
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions / Jasmin Fisher ; Thomas A. Henzinger ; Maria Mateescu ; Nir Piterman
Computational Probability for Systems Biology / Werner Sandmann ; Verena Wolf
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets / Elzbieta Krepska ; Nicola Bonzanni ; Anton Feenstra ; Wan Fokkink ; Thilo Kielmann ; Henri Bal ; Jaap Heringa
Combining Intra- and Inter-cellular Dynamics to Investigate Intestinal Homeostasis / Oksana Tymchyshyn ; Marta Kwiatkowska
Approximating Continuous Systems by Timed Automata / Oded Maler ; Gregory Batt
From Reaction Models to Influence Graphs and Back: A Theorem / Francois Fages ; Sylvain Soliman
Rule-Based Modelling, Symmetries, Refinements / Vincent Danos ; Jerome Feret ; Walter Fontana ; Russell Harmer ; Jean Krivine
One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II / Adelinde M. Uhrmacher ; Jan Himmelspach ; Matthias Jeschke ; Mathias John ; Stefan Leye ; Carsten Maus ; Mathias Rohl ; Roland Ewald
Author Index
Contributed Papers
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems / David Harel ; Yaki Setty
Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions / Jasmin Fisher ; Thomas A. Henzinger ; Maria Mateescu ; Nir Piterman
Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps / Marco Vassura ; Luciano Margara ; Pietro Di Lena ; Filippo Medri ; Piero Fariselli ; Rita Casadio
Bringing Folding Pathways into Strand Pairing Prediction / Jieun K. Jeong ; Piotr Berman ; Teresa M. Przytycka
A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage / Loredana M. Genovese ; Filippo Geraci ; Marco Pellegrini
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies / Phil Hyoun Lee ; Hagit Shatkay
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity / Justin Kennedy ; Ion Mandoiu ; Bogdan Pasaniuc
Haplotype Inference Via Hierarchical Genotype Parsing / Pasi Rastas ; Esko Ukkonen
Seeded Tree Alignment and Planar Tanglegram Layout / Antoni Lozano ; Ron Y. Pinter ; Oleg Rokhlenko ; Gabriel Valiente ; Michal Ziv-Ukelson
Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion (Extended Abstract) / Hadas Birin ; Zohar Gal-Or ; Isaac Elias ; Tamir Tuller
An [Omega](n[superscript 2]/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem / Mukul S. Bansal ; Oliver Eulenstein
Incremental Discovery of Irredundant Motif Bases in Time O([vertical bar Sigma vertical bar]n[superscript 2] log n) (Extended Abstract) / Alberto Apostolico ; Claudia Tagliacollo
A Graph Clustering Approach to Weak Motif Recognition / Christina Boucher ; Daniel G. Brown ; Paul Church
Informative Motifs in Protein Family Alignments / Hatice Gulcin Ozer ; William C. Ray
Topology Independent Protein Structural Alignment / Joe Dundas ; T.A. Binkowski ; Bhaskar DasGupta ; Jie Liang
Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction / Giuseppe Nicosia ; Giovanni Stracquadanio
Alignment-Free Local Structural Search by Writhe Decomposition / Degui Zhi ; Maxim Shatsky ; Steven E. Brenner
Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment / Xueyi Wang ; Jack Snoeyink
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding / Mihaela Pertea ; Steven L. Salzberg
Genomic Signatures in De Bruijn Chains / Lenwood S. Heath ; Amrita Pati
Fast Kernel Methods for SVM Sequence Classifiers / Pavel Kuksa ; Vladimir Pavlovic
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences / Rastislav Sramek ; Brona Brejova ; Tomas Vinar
Predicting Protein Folding Kinetics Via Temporal Logic Model Checking (Extended Abstract) / Christopher James Langmead ; Sumit Kumar Jha
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops / Ankur Dhanik ; Peggy Yao ; Nathan Marz ; Ryan Propper ; Charles Kou ; Guanfeng Liu ; Henry van den Bedem ; Jean-Claude Latombe
Algorithms for the Extraction of Synteny Blocks from Comparative Maps / Vicky Choi ; Chunfang Zheng ; Qian Zhu ; David Sankoff
Computability of Models for Sequence Assembly / Paul Medvedev ; Konstantinos Georgiou ; Gene Myers ; Michael Brudno
Fast Algorithms for Selecting Specific siRNA in Complete mRNA Data / Jaime Davila ; Sudha Balla ; Sanguthevar Rajasekaran
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound / Chunmei Liu ; Yinglei Song ; Louis Shapiro
HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding / Hosna Jabbari ; Anne Condon ; Ana Pop ; Cristina Pop ; Yinglei Zhao
Homology Search with Fragmented Nucleic Acid Sequence Patterns / Axel Mosig ; Julian J.-L. Chen ; Peter F. Stadler
Fast Computation of Good Multiple Spaced Seeds / Lucian Ilie ; Silvana Ilie
Inverse Sequence Alignment from Partial Examples / Eagu Kim ; John Kececioglu
Novel Approaches in Psychiatric Genomics (Keynote) / Maja Bucan
The Point Placement Problem on a Line - Improved Bounds for Pairwise Distance Queries / Francis Y.L. Chin ; Henry C.M. Leung ; W.K. Sung ; S.M. Yiu
Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach / Alexander Schliep ; Roland Krause
Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data / Yonghui Wu ; Prasanna Bhat ; Timothy J. Close ; Stefano Lonardi
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence / Reka Albert ; Riccardo Dondi ; Sema Kachalo ; Eduardo Sontag ; Alexander Zelikovsky ; Kelly Westbrooks
Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation / Geoffrey Koh ; Lisa Tucker-Kellogg ; David Hsu ; P.S. Thiagarajan
Author Index
Shotgun Protein Sequencing (Keynote) / Pavel A. Pevzner
Locality Kernels for Protein Classification / Evgeni Tsivtsivadze ; Jorma Boberg ; Tapio Salakoski
When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features / Roy Varshavsky ; Menachem Fromer ; Amit Man ; Michal Linial
Multichromosomal Genome Median and Halving Problems / Eric Tannier ; Chunfang Zheng ; David Sankoff
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem / Meng Zhang ; William Arndt ; Jijun Tang
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions / Andrew Wei Xu
Read Mapping Algorithms for Single Molecule Sequencing Data / Vladimir Yanovsky ; Stephen M. Rumble ; Michael Brudno
Exact Transcriptome Reconstruction from Short Sequence Reads / Vincent Lacroix ; Michael Sammeth ; Roderic Guigo ; Anne Bergeron
Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments / Florian Battke ; Carsten Muller-Tidow ; Hubert Serve ; Kay Nieselt
NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem / Glenn Hickey ; Paz Carmi ; Anil Maheshwari ; Norbert Zeh
Minimum Common String Partition Parameterized / Peter Demaschke
Hardness and Approximability of the Inverse Scope Problem / Zoran Nikoloski ; Sergio Grimbs ; Joachim Selbig ; Oliver Ebenhoh
Rapid Neighbour-Joining / Martin Simonsen ; Thomas Mailund ; Christian N. S. Pedersen
Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices / Seung-Jin Sul ; Grant Brammer ; Tiffani L. Williams
Efficient Genome Wide Tagging by Reduction to SAT / Arthur Choi ; Noah Zaitlen ; Buhm Han ; Knot Pipatsrisawat ; Adnan Darwiche ; Eleazar Eskin
Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming / Serdar Bozdag ; Timothy J. Close ; Stefano Lonardi
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem / Rumen Andonov ; Nicola Yanev ; Noel Malod-Dognin
A Faster Algorithm for RNA Co-folding / Michal Ziv-Ukelson ; Irit Gat-Viks ; Ydo Wexler ; Ron Shamir
An Automated Combination of Kernels for Predicting Protein Subcellular Localization / Cheng Soon Ong ; Alexander Zien
Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach / Thomas Lingner ; Peter Meinicke
Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles / Nico Pfeifer ; Oliver Kohlbacher
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks / Alexander Medvedovsky ; Vineet Bafna ; Uri Zwick ; Roded Sharan
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network / Ludovic Cottret ; Paulo Vieira Milreu ; Vicente Acuna ; Alberto Marchetti-Spaccamela ; Fabio Viduani Martinez ; Marie-France Sagot ; Leen Stougie
Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach / Xiuwei Zhang ; Bernard M.E. Moret
Fast Bayesian Haplotype Inference Via Context Tree Weighting / Pasi Rastas ; Jussi Kollin ; Mikko Koivisto
Genotype Sequence Segmentation: Handling Constraints and Noise / Qi Zhang ; Wei Wang ; Leonard McMillan ; Jan Prins ; Fernando Pardo-Manuel de Villena ; David Threadgill
Constructing Phylogenetic Supernetworks from Quartets / Stefan Grunewald ; Andreas Spillner ; Kristoffer Forslund ; Vincent Moulton
Summarizing Multiple Gene Tree Using Cluster Networks / Daniel H. Huson ; Regula Rupp
Fast and Adaptive Variable Order Markov Chain Construction / Marcel H. Schulz ; David Weese ; Tobias Rausch ; Andreas Doring ; Knut Reinert ; Martin Vingron
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata / Inke Herms ; Sven Rahmann
The Relation between Indel Length and Functional Divergence: A Formal Study / Raheleh Salari ; Alexander Schonhuth ; Fereydoun Hormozdiari ; Artem Cherkasov ; S. Cenk Sahinalp
Detecting Repeat Families in Incompletely Sequenced Genomes / Jose Augusto Amgarten Quitzau ; Jens Stoye
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models (Extended Abstract) / Sagi Snir ; Tamir Tuller
A Local Move Set for Protein Folding in Triangular Lattice Models / Hans-Joachim Bockenhauer ; Abu Zfer M. Dayem Ullah ; Leonidas Kapsokalivas ; Kathleen Steinhofel
Protein Decoy Generation Using Branch and Bound with Efficient Bounding / Martin Paluszewski ; Pawel Winter
Author Index
Multichromosomal Genome Median and Halving Problems / Eric Tannier ; Chunfang Zheng ; David Sankoff
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem / Meng Zhang ; William Arndt ; Jijun Tang
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions / Andrew Wei Xu
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations / Jean-Philippe Doyon ; Cedric Chauve ; Sylvie Hamel
Limitations of Pseudogenes in Identifying Gene Losses / James C. Costello ; Mira V. Han ; Matthew W. Hahn
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates / Paul Ryvkin ; Jin Jun ; Edward Hemphill ; Craig Nelson
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution / Ion Mandoiu
Discovering Local Patterns of Co-evolution / Yifat Felder ; Tamir Tuller
Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions / Miklos Csuros
An Alignment-Free Distance Measure for Closely Related Genomes / Bernhard Haubold ; Mirjana Domazet-Loso ; Thomas Wiehe
Gene Team Tree: A Compact Representation of All Gene Teams / Melvin Zhang ; Hon Wai Leong
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer / Cuong Than ; Guohua Jin ; Luay Nakhleh
An Evolutionary Study of the Human Papillomavirus Genomes / Dunarel Badescu ; Abdoulaye Banire Diallo ; Mathieu Blanchette ; Vladimir Makarenkov
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree / Matthias Bernt ; Daniel Merkle ; Martin Middendorf
Perfect DCJ Rearrangement / Severine Berard ; Annie Chateau ; Christophe Paul ; Eric Tannier
Sorting Genomes with Insertions, Deletions and Duplications by DCJ / Sophia Yancopoulos ; Richard Friedberg
A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach / Andrew Wei Xu
A Phylogenetic Approach to Genetic Map Refinement / Denis Bertrand ; Nadia El-Mabrouk
Sorting Cancer Karyotypes by Elementary Operations / Michal Ozery-Flato ; Ron Shamir
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios / Anne Bergeron ; Julia Mixtacki ; Jens Stoye
Hurdles Hardly Have to Be Heeded / Krister M. Swenson ; Yu Lin ; Vaibhav Rajan ; Bernard M.E. Moret
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny / David Sankoff ; Chunfang Zheng ; P. Kerr Wall ; Claude dePamphilis ; Jim Leebens-Mack ; Victor A. Albert
Author Index
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations / Jean-Philippe Doyon ; Cedric Chauve ; Sylvie Hamel
Limitations of Pseudogenes in Identifying Gene Losses / James C. Costello ; Mira V. Han ; Matthew W. Hahn
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates / Paul Ryvkin ; Jin Jun ; Edward Hemphill ; Craig Nelson
Qualitative Modeling and Simulation of Bacterial Regulatory Networks / Hidde de Jong
Integrated Analysis from Abstract Stochastic Process Algebra Models / Jane Hillston ; Federica Ciocchetta ; Adam Duguid ; Stephen Gilmore
An Exact Brownian Dynamics Method for Cell Simulation / Koichi Takahashi
Multiscale Modelling of Neuronal Signalling / Nicolas Le Novere
Systems Biology of Halophilic Archaea / Dieter Oesterhelt
A Partial Granger Causality Approach to Explore Causal Networks Derived from Multi-parameter Data / Ritesh Krishna ; Shuixia Guo
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe / Alexander Ullrich ; Christoph Flamm
Component-Based Modelling of RNA Structure Folding / Carsten Maus
A Language for Biochemical Systems / Michael Pedersen ; Gordon Plotkin
The Attributed Pi Calculus / Mathias John ; Cedric Lhoussaine ; Joachim Niehren ; Adelinde M. Uhrmacher
The Continuous [pi]-Calculus: A Process Algebra for Biochemical Modelling / Marek Kwiatkowski ; Ian Stark
Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems / Dirk Lebiedz ; Dominik Skanda ; Marc Fein
Formal Analysis of Abnormal Excitation in Cardiac Tissue / Pei Ye ; Radu Grosu ; Scott A. Smolka ; Emilia Entcheva
The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock / Laurence Loewe
SED-ML - An XML Format for the Implementation of the MIASE Guidelines / Dagmar Kohn
On Parallel Stochastic Simulation of Diffusive Systems / Lorenzo Dematte ; Tommaso Mazza
Large-Scale Design Space Exploration of SSA / Matthias Jeschke ; Roland Ewald
Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway / Edmund M. Clarke ; James R. Faeder ; Christopher J. Langmead ; Leonard A. Harris ; Sumit Kumar Jha ; Axel Legay
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology / Aurelien Rizk ; Gregory Batt ; Francois Fages ; Sylvain Soliman
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways / Robin Donaldson ; David Gilbert
Compositional Definitions of Minimal Flows in Petri Nets
On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network / Abdelhalim Larhlimi ; Alexander Bockmayr
A Combinatorial Approach to Reconstruct Petri Nets from Experimental Data / Markus Durzinsky ; Annegret Wagler ; Robert Weismantel
Analyzing a Discrete Model of Aplysia Central Pattern Generator / Ashish Tiwari ; Carolyn Talcott
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis / D. Bosnacki ; H.M.M. ten Eikelder ; M.N. Steijaert ; E.P. de Vink
A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics / Richard C. van der Wath ; Pietro Lio'
Author Index
Qualitative Modeling and Simulation of Bacterial Regulatory Networks / Hidde de Jong
Integrated Analysis from Abstract Stochastic Process Algebra Models / Jane Hillston ; Federica Ciocchetta ; Adam Duguid ; Stephen Gilmore
An Exact Brownian Dynamics Method for Cell Simulation / Koichi Takahashi
Informatics Infrastructure and Policy Considerations
Public Health Information Fusion for Situation Awareness / Henry Rolka ; Jean C. O'Connor ; David Walker
Biosurveillance, Case Reporting, and Decision Support: Public Health Interactions with a Health Information Exchange / Rebecca A. Hills ; William B. Lober ; Ian S. Painter
Bio-surveillance Event Models, Open Source Intelligence, and the Semantic Web / Nancy Grady ; Lowell Vizenor ; Jeanne Sappington Marin ; Laura Peitersen
Foresight China II: Identification and Detection of Infectious Diseases / Jiayuan Feng ; Jianshi (Jesse) Huang ; Angus Nicoll
Public Health Preparedness Informatics Infrastructure. A Case Study in Integrated Surveillance and Response: 2004-2005 National Influenza Vaccine Shortage / Ivan J. Gotham ; Linh H. Le ; Debra L. Sottolano ; Kathryn J. Schmit
Network-Based Data Analytics
Dynamic Network Model for Predicting Occurrences of Salmonella at Food Facilities / Purnamrita Sarkar ; Lujie Chen ; Artur Dubrawski
Network-Based Analysis of Beijing SARS Data / Xiaolong Zheng ; Daniel Zeng ; Aaron Sun ; Yuan Luo ; Quanyi Wang ; Feiyue Wang
Tutte Polynomials and Topological Quantum Algorithms in Social Network Analysis for Epidemiology, Bio-surveillance and Bio-security / Mario Velez ; Juan Ospina ; Doracelly Hincapie
Biosurveillance Models and Outbreak Detection
Integrating a Commuting Model with the Bayesian Aerosol Release Detector / Aurel Cami ; Garrick L. Wallstrom ; William R. Hogan
A Temporal Extension of the Bayesian Aerosol Release Detector / Xiaohui Kong
A Z-Score Based Multi-level Spatial Clustering Algorithm for the Detection of Disease Outbreaks / Jialan Que ; Fu-Chiang Tsui ; Jeremy Espino
Epidemic Thresholds in SIR and SIIR Models Applying an Algorithmic Method / Doracelly Hincapie P. ; Juan Ospina G. ; Anthony Uyi Afuwape ; Ruben D. Gomez A.
Test Power for Drug Abuse Surveillance / Jarad Niemi ; Meredith Smith ; David Banks
Model Assessment and Case Studies
Assessing the Accuracy of Spatiotemporal Epidemiological Models / James H. Kaufman ; Joanna L. Conant ; Daniel A. Ford ; Wakana Kirihata ; Barbara Jones ; Judith V. Douglas
Simulation of Multivariate Spatial-Temporal Outbreak Data for Detection Algorithm Evaluation / Min Zhang
Analysis and Prediction of Epidemiological Trend of Scarlet Fever from 1957 to 2004 in the Downtown Area of Beijing / Yanhui Shen ; Chu Jiang ; Zhe Dun
Environmental Biosurveillance and Case Studies
Environmental Biosurveillance for Epidemic Prediction: Experience with Rift Valley Fever / Jean-Paul Chretien ; Assaf Anyamba ; Jennifer Small ; Compton J. Tucker ; Seth C. Britch ; Kenneth J. Linthicum
Spatial Regression-Based Environmental Analysis in Infectious Disease Informatics / Daniel D. Zeng ; Ping Yan ; Su Li
Author Index
Informatics Infrastructure and Policy Considerations
Public Health Information Fusion for Situation Awareness / Henry Rolka ; Jean C. O'Connor ; David Walker
Biosurveillance, Case Reporting, and Decision Support: Public Health Interactions with a Health Information Exchange / Rebecca A. Hills ; William B. Lober ; Ian S. Painter
Multi-label Hierarchical Classification of Protein Functions with Artificial Immune Systems / Roberto T. Alves ; Myriam R. Delgado ; Alex A. Freitas
Operon Prediction in Bacterial Genomes / Matheus B.S. Barros ; Simone de L. Martins ; Alexandre Plastino
An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures / Miguel M.F. Bugalho ; Arlindo L. Oliveira
Top-Down Hierarchical Ensembles of Classifiers for Predicting G-Protein-Coupled-Receptor Functions / Eduardo P. Costa ; Ana C. Lorena ; Andre C.P.L.F. Carvalho
A Hybrid Method for the Protein Structure Prediction Problem / Marcio Dorn ; Ardala Breda ; Osmar Norberto de Souza
Detecting Statistical Covariations of Sequence Physicochemical Properties / Moshe A. Gadish ; David K.Y. Chiu
Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase / Diego E.B. Gomes ; Roberto D. Lins ; Pedro G. Pascutti ; Tjerk P. Straatsma ; Thereza A. Soares
On the Toric Graph as a Tool to Handle the Problem of Sorting by Transpositions / Rodrigo de A. Hausen ; Luerbio Faria ; Celina M.H. de Figueiredo ; Luis Antonio B. Kowada
A Customized Class of Functions for Modeling and Clustering Gene Expression Profiles in Embryonic Stem Cells / Shenggang Li ; Miguel Andrade-Navarro ; David Sankoff
Extracting Information from Flexible Receptor-Flexible Ligand Docking Experiments / Karina S. Machado ; Evelyn K. Schroeder ; Duncan D. Ruiz ; Ana Wink
Transposition Distance Based on the Algebraic Formalism / Cleber V.G. Mira ; Zanoni Dias ; Hederson P. Santos ; Guilherme A. Pinto ; Maria Emilia M.T. Walter
Using BioAgents for Supporting Manual Annotation on Genome Sequencing Projects / Celia Ghedini Ralha ; Hugo W. Schneider ; Lucas O. da Fonseca ; Marcelo M. Brigido
Application of Genetic Algorithms to the Genetic Regulation Problem / Maria Fernanda B. Wanderley ; Joao C.P. da Silva ; Carlos Cristiano H. Borges ; Ana Tereza R. Vasconcelos
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion / Ximing Xu
Extended Abstracts
Identity Transposon Networks in D. melanogaster / Alcides Castro-e-Silva ; Gerald Weber ; Romuel F. Machado ; Elizabeth F. Wanner ; Renata Guerra-Sa
Prediction of Protein-Protein Binding Hot Spots: A Combination of Classifiers Approach / Roberto Hiroshi Higa ; Clesio Luis Tozzi
AGN Simulation and Validation Model / Fabricio M. Lopes ; Roberto M. Cesar-Jr. ; Luciano da F. Costa
A Practical Evaluation of BioProvider / Maira Ferreira de Noronha ; Sergio Lifschitz ; Antonio Basilio de Miranda
Evaluation of Models for the Recognition of Hadwritten Digits in Medical Forms / Willian Zalewski ; Huei Diana Lee ; Adewole M.J.F. Caetano ; Andre G. Maletzke ; Joao Jose Fagundes ; Claudio Saddy ; Rodrigues Coy ; Feng Chung Wu
Author Index
Selected Articles
Multi-label Hierarchical Classification of Protein Functions with Artificial Immune Systems / Roberto T. Alves ; Myriam R. Delgado ; Alex A. Freitas
Operon Prediction in Bacterial Genomes / Matheus B.S. Barros ; Simone de L. Martins ; Alexandre Plastino
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation / Fereydoun Hormozdiari ; Petra Berenbrink ; Natasa Przulj ; Cenk Sahinalp
Probabilistic Paths for Protein Complex Inference / Hailiang Huang ; Lan V. Zhang ; Frederick P. Roth ; Joel S. Bader
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting / Hans-Michael Kaltenbach ; Sebastian Bocker ; Sven Rohmann
A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells / Celine Lefebvre ; Wei Keat Lim ; Katia Basso ; Riccardo Dalla Favera ; Andrea Califano
Identification and Evaluation of Functional Modules in Gene Co-expression Networks / Jianhua Ruan ; Weixiong Zhang
A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast / Mingzhou (Joe) Song ; Z. Lewis Liu
A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry / Yin Wu ; Yehia Mechref ; Iveta Klouckova ; Milos V. Novotny ; Haixu Tang
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Arialysis / Derek Ruths ; Jen-Te Tseng ; Luay Nakhleh ; Prahlad T. Ram
Alignment of Mass Spectrometry Data by Clique Finding and Optimization / Daniel Fasulo ; Anne-Katrin Emde ; Lu-Yong Wang ; Karin Noy ; Nathan Edwards
Author Index
Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation / Fereydoun Hormozdiari ; Petra Berenbrink ; Natasa Przulj ; Cenk Sahinalp
Probabilistic Paths for Protein Complex Inference / Hailiang Huang ; Lan V. Zhang ; Frederick P. Roth ; Joel S. Bader
Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting / Hans-Michael Kaltenbach ; Sebastian Bocker ; Sven Rohmann
A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport / Paras Chopra ; Andreas Bender
Punctuated Equilibrium in Statistical Models of Generalized Coevolutionary Resilience: How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection / Rodrick Wallace ; Deborah Wallace
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways / Roberto Barbuti ; Andrea Maggiolo-Schettini ; Paolo Milazzo ; Paolo Tiberi ; Angelo Troina
The BlenX Language with Biological Transactions / Federica Ciocchetta
Author Index
A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport / Paras Chopra ; Andreas Bender
Punctuated Equilibrium in Statistical Models of Generalized Coevolutionary Resilience: How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection / Rodrick Wallace ; Deborah Wallace
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways / Roberto Barbuti ; Andrea Maggiolo-Schettini ; Paolo Milazzo ; Paolo Tiberi ; Angelo Troina
Protein: Structure, Function, and Interaction / Part I：
Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai
Predicting SUMOylation Sites / Denis C. Bauer ; Fabian A. Buske ; Mikael Boden
DFS Based Partial Pathways in GA for Protein Structure Prediction / Md Tamjidul Hoque ; Madhu Chetty ; Andrew Lewis ; Abdul Sattar
Evaluation of the Stability of Folding Nucleus upon Mutation / Mathieu Lonquety ; Zoe Lacroix ; Jacques Chomilier
Prediction of Protein Beta-Sheets: Dynamic Programming Versus Grammatical Approach / Yuki Kato ; Tatsuya Akutsu ; Hiroyuki Seki
Using Multi-scale Glide Zoom Window Feature Extraction Approach to Predict Protein Homo-oligomer Types / QiPeng Li ; Shao Wu Zhang ; Quan Pan
Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces / Satoshi Koizumi ; Keisuke Imada ; Tomonobu Ozaki ; Takenao Ohkawa
Learning, Classification, and Clustering / Part II：
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis / Pengyi Yang ; Zili Zhang
A Modified Markov Clustering Approach for Protein Sequence Clustering / Lehel Medves ; Laszlo Szilagyi ; Sandor M. Szilagyi
Feature Selection and Classification for Small Gene Sets / Gregor Stiglic ; Juan J. Rodriguez ; Peter Kokol
Pseudoknot Identification through Learning TAG[subscript RNA] / Sahar Al Seesi ; Sanguthevar Rajasekaran ; Reda Ammar
Support Vector Based T-Score for Gene Ranking / Piyushkumar A. Mundra ; Jagath C. Rajapakse
Prediction of Transcription Factor Families Using DNA Sequence Features / Ashish Anand ; Gary B. Fogel ; Ganesan Pugalenthi ; P.N. Suganthan
g-MARS: Protein Classification Using Gapped Markov Chains and Support Vector Machines / Xiaonan Ji ; James Bailey ; Kotagiri Ramamohanarao
Bio-Molecular Networks and Pathways Analysis / Part III：
Domain-Domain Interaction Identification with a Feature Selection Approach / Xing-Ming Zhao ; Luonan Chen
Dividing Protein Interaction Networks by Growing Orthologous Articulations / Pavol Jancura ; Jaap Heringa ; Elena Marchiori
Constraint Minimization for Efficient Modeling of Gene Regulatory Network / Ramesh Ram ; Dieter Bulach
Fusion of Gene Regulatory and Protein Interaction Networks Using Skip-Chain Models / Iti Chaturvedi
TopEVM: Using Co-occurrence and Topology Patterns of Enzymes in Metabolic Networks to Construct Phylogenetic Trees / Tingting Zhou ; Keith C.C. Chan ; Zhenghua Wang
Generating Synthetic Gene Regulatory Networks
Microarray and Gene Expression Analysis / Part IV：
Gene Selection for Microarray Data by a LDA-Based Genetic Algorithm / Edmundo Bonilla Huerta ; Beatrice Duval ; Jin-Kao Hao
Sequential Forward Selection Approach to the Non-unique Oligonucleotide Probe Selection Problem / Lili Wang ; Alioune Ngom ; Luis Rueda
On Finding and Interpreting Patterns in Gene Expression Data from Time Course Experiments / Yvonne E. Pittelkow ; Susan R. Wilson
Microarray Design Using the Hilbert-Schmidt Independence Criterion / Justin Bedo
Exploratory Data Analysis for Investigating GC-MS Biomarkers / Ken McGarry ; Kim Bartlett ; Morteza Pourfarzam
Multi-relational Data Mining for Tetratricopeptide Repeats (TPR)-Like Superfamily Members in Leishmania spp.: Acting-by-Connecting Proteins / Karen T. Girao ; Fatima C.E. Oliveira ; Kaio M. Farias ; Italo M.C. Maia ; Samara C. Silva ; Carla R.F. Gadelha ; Laura D.G. Carneiro ; Ana C.L. Pacheco ; Michel T. Kamimura ; Michely C. Diniz ; Maria C. Silva ; Diana M. Oliveira
Heuristic Non Parametric Collateral Missing Value Imputation: A Step Towards Robust Post-Genomic Knowledge Discovery / Muhammad Shoaib B. Sehgal ; Iqbal Gondal ; Laurence S. Dooley ; Ross Coppel
Protein Expression Molecular Pattern Discovery by Nonnegative Principal Component Analysis / Xiaoxu Han ; Joseph Scazzero
Gene Ontology Assisted Exploratory Microarray Clustering and Its Application to Cancer / Geoff Macintyre ; Daniel Gustafsson ; Alex Boussioutas ; Izhak Haviv ; Adam Kowalczyk
Discovery of Biomarkers for Hexachlorobenzene Toxicity Using Population Based Methods on Gene Expression Data / Cem Meydan ; Alper Kucukural ; Deniz Yorukoglu ; O. Ugur Sezerman
Applications of High Performance Computing / Part VI：
Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study / Alexandros Stamatakis ; Michael Ott
Massively Parallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA / Jan Schroder ; Lars Wienbrandt ; Gerd Pfeiffer ; Manfred Schimmler
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences / Chen Chen ; Bertil Schmidt ; Liu Weiguo ; Wolfgang Muller-Wittig
Accelerating BLASTP on the Cell Broadband Engine / Huiliang Zhang
Author Index
Protein: Structure, Function, and Interaction / Part I：
Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins / M. Michael Gromiha ; Liang-Tsung Huang ; Lien-Fu Lai
Knowledge Discovery and Emergent Complexity in Bioinformatics / Ronald Westra ; Karl Tuyls ; Yvan Saeys ; Ann Nowe
Boolean Algebraic Structures of the Genetic Code: Possibilities of Applications / Ricardo Grau ; Maria del C. Chavez ; Robersy Sanchez ; Eberto Morgado ; Gladys Casas ; Isis Bonet
Discovery of Gene Regulatory Networks in Aspergillus fumigatus / Reinhard Guthke ; Olaf Kniemeyer ; Daniela Albrecht ; Axel A. Brakhage ; Ulrich Moller
Complexity Measures for Gene Assembly / Tero Harju ; Chang Li ; Ion Petre ; Grzegorz Rozenberg
Learning Relations from Biomedical Corpora Using Dependency Trees / Sophia Katrenko ; Pieter Adriaans
Advancing the State of the Art in Computational Gene Prediction / William H. Majoros ; Uwe Ohler
Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection / Yves Van de Peer
The Net Generator Algorithm: Reconstruction of Gene Regulatory Networks / Susanne Toepfer ; Dominik Driesch ; Dirk Woetzel ; Michael Pfaff
On the Neuronal Morphology-Function Relationship: A Synthetic Approach / Ben Torben-Nielsen ; Eric O. Postma
Analyzing Stigmergetic Algorithms Through Automata Games / Peter Vrancx ; Katja Verbeeck
The Identification of Dynamic Gene-Protein Networks / Ronald L. Westra ; Goele Hollanders ; Geert Jan Bex ; Marc Gyssens
Knowledge Discovery and Emergent Complexity in Bioinformatics / Ronald Westra ; Karl Tuyls ; Yvan Saeys ; Ann Nowe
Boolean Algebraic Structures of the Genetic Code: Possibilities of Applications / Ricardo Grau ; Maria del C. Chavez ; Robersy Sanchez ; Eberto Morgado ; Gladys Casas ; Isis Bonet
Discovery of Gene Regulatory Networks in Aspergillus fumigatus / Reinhard Guthke ; Olaf Kniemeyer ; Daniela Albrecht ; Axel A. Brakhage ; Ulrich Moller
The First Section: Modeling and Simulation of Societies and Collective Behavior
Phase Synchronization of Circadian Oscillators Induced by a Light-Dark Cycle and Extracellular Noise / Ying Li ; Jianbao Zhang ; Zengrong Liu
Detecting RNA Sequences Using Two-Stage SVM Classifier / Xiaoou Li ; Kang Li
Frequency Synchronization of a Set of Cells Coupled by Quorum Sensing / Luonan Chen
A Stochastic Model for Prevention and Control of HIV/AIDS Transmission Dynamics / Min Xu ; Yongsheng Ding ; Liangjian Hu
Simulation of Artificial Life of Bee's Behaviors / Bin Wu ; Hongying Zhang ; Xia Ni
Hybrid Processing and Time-Frequency Analysis of ECG Signal / Ping Zhang ; Chengyuan Tu ; Xiaoyang Li ; Yanjun Zeng
Robust Stability of Human Balance Keeping / Minrui Fei ; Lisheng Wei ; Taicheng Yang
Modelling Pervasive Environments Using Bespoke and Commercial Game-Based Simulators / Marc Davies ; Vic Callaghan ; Liping Shen
The Research of Artificial Animal's Behavior Memory Based on Cognition / Xiaojuan Ban ; Shurong Ning ; Jing Shi ; Dongmei Ai
The Second Section: Computational Methods and Intelligence in Biomechanical Systems, Tissue Engineering and Clinical Bioengineering
How to Ensure Safety Factors in the Development of Artificial Heart: Verified by the Usage of "Modeling and Simulation" Technology / Mitsuo Umezu
Parametric-Expression-Based Construction of Interior Features for Tissue Engineering Scaffold with Defect Bone / Chunxiang Dai ; Qingxi Hu ; Minglun Fang
Computation of Uniaxial Modulus of the Normal and Degenerated Articular Cartilage Using Inhomogeneous Triphasic Model / Haijun Niu ; Qing Wang ; Yongping Zheng ; Fang Pu ; Yubo Fan ; Deyu Li
Effect of the Plantar Ligaments Injury on the Longitudinal Arch Height of the Human Foot / Yunfeng Yang ; Guangrong Yu ; Wenxin Niu ; Jiaqian Zhou ; Yanxi Chen ; Feng Yuan ; Zuquan Ding
Internet Living Broadcast of Medical Video Stream / Shejiao Li ; Bo Li ; Fan Zhang
Predicting Syndrome by NEI Specifications: A Comparison of Five Data Mining Algorithms in Coronary Heart Disease / Jianxin Chen ; Guangcheng Xi ; Yanwei Xing ; Jing Chen ; Jie Wang
Application of Image Processing and Finite Element Analysis in Bionic Scaffolds' Design Optimizing and Fabrication / Liulan Lin ; Huicun Zhang ; Yuan Yao ; Aili Tong
The Mechanical Properties of Bone Tissue Engineering Scaffold Fabricating Via Selective Laser Sintering
The Third Section: Computational Intelligence in Bioinformatics and Biometrics
Informational Structure of Agrobacterium Tumefaciens C58 Genome / Zhihua Liu ; Xiao Sun
Feature Extraction for Cancer Classification Using Kernel-Based Methods / Shutao Li ; Chen Liao
A New Hybrid Approach to Predict Subcellular Localization by Incorporating Protein Evolutionary Conservation Information / ShaoWu Zhang ; YunLong Zhang ; JunHui Li ; HuiFeng Yang ; YongMei Cheng ; GuoPing Zhou
Support Vector Machine for Prediction of DNA-Binding Domains in Protein-DNA Complexes / Jiansheng Wu ; Hongtao Wu ; Hongde Liu ; Haoyan Zhou
Feature Extraction for Mass Spectrometry Data / Yihui Liu
An Improved Algorithm on Detecting Transcription and Translation Motif in Archaeal Genomic Sequences / Minghui Wu ; Xian Chen ; Fanwei Zhu ; Jing Ying
Constructing Structural Alignment of RNA Sequences by Detecting and Assessing Conserved Stems / Xiaoyong Fang ; Zhigang Luo ; Bo Yuan ; Zhenghua Wang ; Fan Ding
Iris Verification Using Wavelet Moments and Neural Network / Zhiqiang Ma ; Miao Qi ; Haifeng Kang ; Shuhua Wang ; Jun Kong
Comprehensive Fuzzy Evaluation Model for Body Physical Exercise Risk / Yizhi Wu ; Hongan Xu
The Fourth Section: Brain Stimulation, Neural Dynamics and Neural Interfacing
The Effect of Map Information on Brain Activation During a Driving Task / Tao Shang ; Shuoyu Wang ; Shengnan Zhang
Worm 5: Pseudo-organics Computer and Natural Live System / Yick Kuen Lee ; Ying Ying Lee
Comparisons of Chemical Synapses and Gap Junctions in the Stochastic Dynamics of Coupled Neurons / Jiang Wang ; Xiumin Li ; Dong Feng
Distinguish Different Acupuncture Manipulations by Using Idea of ISI / Wenjie Si ; Limei Zhong ; Feng Dong
The Study on Internet-Based Face Recognition System Using PCA and MMD / Jong-Min Kim
Simulation of Virtual Human's Mental State in Behavior Animation / Zhen Liu
Hemodynamic Analysis of Cerebral Aneurysm and Stenosed Carotid Bifurcation Using Computational Fluid Dynamics Technique / Yi Qian ; Tstsuji Harada ; Koichi Fukui ; Hiroyuki Takao ; Yuichi Murayama
Active/Inactive Emotional Switching for Thinking Chain Extraction by Type Matching from RAS / JeongYon Shim
Pattern Recognition for Brain-Computer Interfaces by Combining Support Vector Machine with Adaptive Genetic Algorithm / Banghua Yang ; Shiwei Ma ; Zhihua Li
The Fifth Section: Biological and Biomedical Data Integration, Mining and Visualization
Improved Locally Linear Embedding by Cognitive Geometry / Guihua Wen ; Lijun Jiang ; Jun Wen
Predicting the Free Calcium Oxide Content on the Basis of Rough Sets, Neural Networks and Data Fusion / Yunxing Shu ; Shiwei Yun ; Bo Ge
Classification of Single Trial EEG Based on Cloud Model for Brain-Computer Interfaces / Shaobin Li ; Chenxi Shao
The Modified Self-organizing Fuzzy Neural Network Model for Adaptability Evaluation / Zuohua Miao ; Hong Xu ; Xianhua Wang
Predicting Functional Protein-Protein Interactions Based on Computational Methods / Luwen Zhang ; Wu Zhang
The Chaos Model Analysis Based on Time-Varying Fractal Dimension / Jianrong Hou ; Dan Huang ; Hui Zhao
Bi-hierarchy Medical Image Registration Based on Steerable Pyramid Transform / Xiuying Wang ; David Feng
The Sixth Section: Computational Methods and Intelligence in Organism Modeling and Biochemical Networks and Regulation
A Multiagent Quantum Evolutionary Algorithm for Global Numerical Optimization / Chaoyong Qin ; Jianguo Zheng ; Jiyu Lai
Developing and Optimizing a Finite Element Model of Phalange Using CT Images / Quan Zhang
Reverse Engineering Methodology in Broken Skull Surface Model Reconstruction / Luyue Ju ; Gaojian Zhong ; Xia Liu
Identification and Application of Nonlinear Rheological Characteristics of Oilseed Based on Artificial Neural Networks / Xiao Zheng ; Guoxiang Lin ; Dongping He ; Jingzhou Wang ; Yan You
Prediction of Death Rate of Breast Cancer Induced from Average Microelement Absorption with Neural Network / Shouju Li ; Jizhe Wang ; Yingxi Liu ; Xiuzhen Sun
An Adaptive Classifier Based on Artificial Immune Network / Zhiguo Li ; Jiang Zhong ; Yong Feng ; ZhongFu Wu
Investigation of a Hydrodynamic Performance of a Ventricular Assist Device After Its Long-Term Use in Clinical Application / Yuma Kokuzawa ; Tomohiro Shima ; Masateru Furusato ; Kazuhiko Ito ; Takashi Tanaka ; Toshihiro Igarashi ; Tomohiro Nishinaka ; Kiyotaka Iwasaki
The Seventh Section: Computational Methods and Intelligence in Modeling of Molecular, Cellular, Multi-cellular Behavior and Design of Synthetic Biological Systems
QSAR and Molecular Docking Study of a Series of Combretastatin Analogues Tubulin Inhibitors / Yubin Ji ; Ran Tian ; Wenhan Lin
A Software Method to Model and Fabricate the Defective Bone Repair Bioscaffold Using in Tissue Engineering / Hongfei Yang
Using Qualitative Technology for Modeling the Process of Virus Infection / Hailin Feng
AOC-by-Self-discovery Modeling and Simulation for HIV / Chunxiao Zhao ; Ning Zhong ; Ying Hao
A Simulation Study on the Encoding Mechanism of Retinal Ganglion Cell / Chao-Feng Cai ; Pei-Ji Liang ; Pu-Ming Zhang
Modelling the MAPK Signalling Pathway Using a Two-Stage Identification Algorithm / Padhraig Gormley ; George W. Irwin
The Eighth Section: Others
Design and Path Planning for a Remote-Brained Service Robot / Shigang Cui ; Xuelian Xu ; Zhengguang Lian ; Li Zhao ; Zhigang Bing
Adaptive Fuzzy Sliding Mode Control of the Model of Aneurysms of the Circle of Willis / Peijun Ju ; Guocai Liu ; Li Tian ; Wei Zhang
Particle Swarm Optimization Applied to Image Vector Quantization / Xubing Zhang ; Zequn Guan ; Tianhong Gan
Face Detection Based on BPNN and Wavelet Invariant Moment in Video Surveillance / Hongji Lin ; Zhengchun Ye
Efficient Topological Reconstruction for Medical Model Based on Mesh Simplification / Ying Jiang
Repetitive Motion Planning of Redundant Robots Based on LVI-Based Primal-Dual Neural Network and PUMA560 Example / Yunong Zhang ; Xuanjiao Lv ; Zhonghua Li ; Zhi Yang
Tensile Test to Ensure a Safety of Cannula Connection in Clinical Ventricular Assist Device (VAD)
A Reproduction of Inflow Restriction in the Mock Circulatory System to Evaluate a Hydrodynamic Performance of a Ventricular Assist Device in Practical Conditions / ZhiKun Yan ; Ling Zhu
Author Index
The First Section: Modeling and Simulation of Societies and Collective Behavior
Phase Synchronization of Circadian Oscillators Induced by a Light-Dark Cycle and Extracellular Noise / Ying Li ; Jianbao Zhang ; Zengrong Liu
Detecting RNA Sequences Using Two-Stage SVM Classifier / Xiaoou Li ; Kang Li
International Conference on Research in Computational Molecular Biology, Takeo Kanade, Satoru Miyano, Simon Kasif, Jill Mesirov, Pavel Pevzner, Michael Waterman, Sorin Istrail
出版情報:
SpringerLink Books - AutoHoldings , Springer Berlin / Heidelberg, 2005
Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen
Reconstructing the Evolutionary History of Complex Human Gene Clusters / Yu Zhang ; Giltae Song ; Tomas Vinar ; Eric D. Green ; Adam Siepel ; Webb Miller
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads / Paul Medevedev ; Michael Brudno
Orchestration of DNA Methylation (Keynote) / Howard Cedar
BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes / Tien-ho Lin ; Pradipta Ray ; Geir K. Sandve ; Selen Uguroglu ; Eric P. Xing
A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors / Yanxin Shi ; Itamar Simon ; Tom Mitchell ; Ziv Bar-Joseph
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery / Raluca Gordan ; Leelavati Narlikar ; Alexander J. Hartemink
The Statistical Power of Phylogenetic Motif Models / John Hawkins ; Timothy L. Bailey
Transcriptional Regulation and Cancer Genomics (Keynote) / Edison Liu
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans / Fuhui Long ; Hanchuan Peng ; Xiao Liu ; Stuart Kim ; Gene Myers
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing / Ritendra Datta ; Marshall Bern
A Fragmentation Event Model for Peptide Identification by Mass Spectrometry / Yu Lin ; Yantao Qiao ; Shiwei Sun ; Chungong Yu ; Gongjin Dong ; Dongbo Bu
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics / Yong Fuga Li ; Randy J. Arnold ; Yixue Li ; Predrag Radivojac ; Quanhu Sheng ; Haixu Tang
De Novo Sequencing of Nonribosomal Peptides / Nuno Bandeira ; Julio Ng ; Dario Meluzzi ; Roger G. Linington ; Pieter Dorrestein ; Pavel A. Pevzner
Systems Metabolic Engineering (Keynote) / Sang Yup Lee
Protein Function Prediction Based on Patterns in Biological Networks / Mustafa Kirac ; Gultekin Ozsoyoglu
Automatic Parameter Learning for Multiple Network Alignment / Jason Flannick ; Antal Novak ; Chuong B. Do ; Balaji S. Srinivason ; Serafim Batzoglou
An Integrative Network Approach to Map the Transcriptome to the Phenome / Michael R. Mehan ; Juan Nunez-Iglesias ; Mrinal Kalakrishnan ; Michael S. Waterman ; Xianghong Jasmine Zhou
Fast and Accurate Alignment of Multiple Protein Networks / Maxim Kalaev ; Vineet Bafna ; Roded Sharan
High-Resolution Modeling of Cellular Signaling Networks / Michael Baym ; Chris Bakal ; Norbert Perrimon ; Bonnie Berger
At the Origin of Life: How Did Folded Proteins Evolve? (Keynote) / Andrei Lupas
Locating Multiple Gene Duplications through Reconciled Trees / J. Gordon Burleigh ; Mukul S. Bansal ; Andre Wehe ; Oliver Eulenstein
Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information / Jing Zhang ; Xin Gao ; Jinbo Xu ; Ming Li
Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins / Wei Zheng ; Alan M. Friedman ; Chris Bailey-Kellogg
DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework / Christophe Dessimoz ; Daniel Margadant ; Gaston H. Gonnet
Computation of Median Gene Clusters / Sebastian Bocker ; Katharina Jahn ; Julia Mixtacki ; Jens Stoye
BCL-2: From Translocation to Therapy (Keynote) / Suzanne Cory
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles / Igor Ulitsky ; Richard M. Karp ; Ron Shamir
Constructing Treatment Portfolios Using Affinity Propagation / Delbert Dueck ; Brendan J. Frey ; Nebojsa Jojic ; Vladimir Jojic ; Guri Giaever ; Andrew Emili ; Gabe Musso ; Robert Hegele
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs / Michael Sammeth ; Gabriel Valiente ; Roderic Guigo
More Efficient Algorithms for Closest String and Substring Problems / Bin Ma ; Xiaoming Sun
Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia (Keynote) / Denis Smirnov ; Vivian G. Cheung
Accounting for Non-genetic Factors Improves the Power of eQTL Studies / Oliver Stegle ; Anitha Kannan ; Richard Durbin ; John Winn
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA / Andreas Sundquist ; Eugene Fratkin
On the Inference of Ancestries in Admixed Populations / Sriram Sankararaman ; Gad Kimmel ; Eran Halperin ; Michael I. Jordan
Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information / Eleazar Eskin
Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information / Sivan Bercovici ; Dan Geiger ; Liran Shlush ; Karl Skorecki ; Alan Templeton
Constructing Level-2 Phylogenetic Networks from Triplets / Leo van Iersel ; Judith Keijsper ; Steven Kelk ; Leen Stougie ; Ferry Hagen ; Teun Boekhout
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony / Rune B. Lyngso ; Yun S. Song ; Jotun Hein
Author Index
Computational Biology: Its Challenges Past, Present, and Future (Keynote) / Temple F. Smith
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast / Caroline C. Friedel ; Jan Krumsiek ; Ralf Zimmer
CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads / Sourav Chatterji ; Ichitaro Yamazaki ; Zhaojun Bai ; Jonathan A. Eisen
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