organized by IEEE Serbia and Montenegro Section - ED/SSC Chapter ; under the co-sponsorship of IEEE Electron Devices Society ; with the cooperation of IEEE Solid-State Circuits Society
出版情報:
Piscataway, N.J. : Electron Devices Society of the IEEE, c2008 v. ; 28 cm
sponsored by Pavements Committee of the Geo-Institute, American Society of Civil Engineers ... [et al.] ; edited by Zhanping You, Ala R. Abbas, Linbing Wang
出版情報:
Reston, Va. : American Society of Civil Engineers, c2008 x, 167 p. ; 22 cm
Geotechnical Earthquake Engineering and Soil Dynamics ; American Society of Civil Engineers
出版情報:
Reston, VA : American Society of Civil Engineers , Red Hook, NY : Printed from e-media with permission by Curran Associates, c2008 p. 1543-2319 ; 28 cm
U.S. Symposium on Rock Mechanics ; US-Canada Rock Mechanics Symposium ; American Rock Mechanics Association
出版情報:
Alexandria, Va. : American Rock Mechanics Association , Red Hook, NY : Printed from e-media with permission by: Curran Associates, c2008 653 p. ; 27 cm
U.S. Symposium on Rock Mechanics ; US-Canada Rock Mechanics Symposium ; American Rock Mechanics Association
出版情報:
Alexandria, Va. : American Rock Mechanics Association , Red Hook, NY : Printed from e-media with permission by: Curran Associates, c2008 p. 654-1308 ; 27 cm
U.S. Symposium on Rock Mechanics ; US-Canada Rock Mechanics Symposium ; American Rock Mechanics Association
出版情報:
Alexandria, Va. : American Rock Mechanics Association , Red Hook, NY : Printed from e-media with permission by: Curran Associates, c2008 p. 1309-1953 ; 27 cm
Arsenite Resistance in Leishmania and Possible Drug Targets / Gaganmeet Singh ; K.G. Jayanarayan ; Chinmoy S. Dey1:
Abstract
Introduction
Arsenite Resistance in Leishmania
Potential Drug Targets
Conclusion
Unique Characteristics of the Kinetoplast DNA Replication Machinery Provide Potential Drug Targets in Trypanosomatids / Dotan Sela ; Neta Milman ; Irit Kapeller ; Aviad Zick ; Rachel Bezalel ; Nurit Yaffe ; Joseph Shlomai2:
Reevaluating the Kinetoplast as a Potential Target for Anti-Trypanosomal Drugs
The kDNA Network and Its Monomeric Components
Unique Characteristics of the kDNA Replication System
Replication of Free kDNA Minicircles and Catenated Maxicircles
Regulation of kDNA Replication
Concluding Remarks
Drugs and Transporters in Kinetoplastid Protozoa / Scott M. Landfear3:
Roles of Membrane Transport Proteins among the Kinetoplastida
Leishmania Glucose Transporters
Leishmania Purine Transporters
Selective Lead Compounds Against Kinetoplastid Tubulin / R.E. Morgan ; K.A. Werbovetz4:
Oryzalin as a Lead Compound against Kinetoplastid Tubulin
Aromatic Thiocyanates as Lead Compounds
Generating New Leads
Fishing for Anti-Leishmania Drugs: Principles and Problems / Emanuela Handman ; Lukasz Kedzierski ; Alessandro D. Uboldi ; James W. Goding5:
The Disease Burden of Leishmaniasis
Transmission and Epidemiology
Disease Manifestations
Management and Control of Leishmaniasis
The Impact of New Technologies on Drug Discovery
High Throughput Screening
Structure-Based Drug Discovery
Proteomics
Monoclonal Antibodies
Natural Products
Target Selection and Validation
Proteins and Metabolic Pathways Unique to the Parasite
Proteins Essential for Parasite Survival and Virulence Factors
Target Validation
Sterol 14-Demethylase Inhibitors for Trypanosoma Cruzi Infections / Frederick S. Buckner6:
Chagas Disease
Drug Development for Changes Disease
Sterol Biosynthesis-Overview
Sterol 14-Demethylase (CYP51) and Azole Inhibitors
Sterols of T. cruzi
Activity of Azole Compounds against T. cruzi
The Development Status of Sterol 14-Demethylase Inhibitors
Can a Better Sterol 14-Demethylase Inhibitor Be Developed against T. cruzi?
Summary
Histone Deacetylases / David Horn7:
The Deacetylases
The Inhibitors
Current Research
Targeting Glycoproteins or Glycolipids and their Metabolic Pathways for Antiparasite Therapy / Sumi Mukhopadhyay nee Bandyopadhyay ; Chitra Mandal8:
An Introduction to the Kinetoplastid Parasites
Trypanosomiasis
Leishmaniasis
Why Target Glycoproteins and Glycolipids?
Glycoconjugates of Trypanosomes
Biological Relevance of Glycoconjugates in Trypanosomiasis
Targeting VSG Epitopes
Targeting Mucin Glycoproteins
Lactose Derivatives Are Inhibitors of Trans-Sialidase Present in the Mucins
Glycoconjugate Biosynthetic Machinery in Trypanosome
Targeting Enzymes of the Biosynthetic Pathway
Glycoconjugates of Leishmania
Biological Relevance
Development of Anti-Leishmanials by Targeting
gp63 Producing Enzymes
Galactofuranose on LPG
Sialoglycans
Other Glyoconjugates
PPG
Glycosylphosphatidylinositol (GPI) Lipids
Enzymes Producting Glycoproteins
As Drug Carrier
Perspective
DNA Topoisomerases of Leishmania: The Potential Targets for Anti-Leishmanial Therapy / Benu Brata Das ; Agneyo Ganguly ; Hemanta K. Majumder9:
DNA Topoisomerases: The Wonder Enzyme
Classification of DNA Topoisomerases
Topoisomerases of Kinetoplastid Parasites
Topoisomerases as Therapeutic Targets
Antiparasitic Chemotherapy: Tinkering with the Purine Salvage Pathway / Alok Kumar Datta ; Rupak Datta ; Banibrata Sen10:
General Strategies for Development and Characterisation of Drug Targets in Trypanosomatids
Acquisition and Assimilation of Purines in L. donovani Promastigotes
Purine Metabolism in L. donovani Amastigotes
Purine Salvage Enzymes as Targets for Structure-Based Inhibitor Design
Prospects of Adenosine Kinase (AdK) as the Drug Target
General Biochemical Properties of the L. donovani AdK
Structure of AdK from Different Sources
Sequence Characteristics of LdAdK Gene and Homology Model-Based Structural Analysis of the Protein
Identification of Potential Amino Acid Residues Involved in Catalysis
Mechanism of Ado Binding
Mechanism of Phosphate Transfer
Product-Mediated Enzyme Regulation
Conclusions and Perspectives
Searching The Tritryp Genomes for Drug Targets / Peter J. Myler11:
Tritryp Genome Content
Computational Approaches for Drug Target Selection
Databases of Tritrype Metabolism
Identification of Metabolic "Choke-Points"
Searching for Parasite Orthologues of Known Drug Targets
Matching Drug-Like Chemicals to Parasite Proteins
Purine and Pyrimidine Metabolism in Leishmania / Nicola S. Carter ; Phillip Yates ; Cassandra S. Arendt ; Jan M. Biotz ; Buddy Ullman12:
Nomenclature
Purine Metabolism
Purine Transport in Leishmania
Purine Transporters as Drug Targets in Leishmania
Structure-Function Studies on Purine Transporters
Purine Salvage Enzymes of Leishmania
Purine Salvage Enzymes as Drug Targets in Leishmania
The Compartmentalization of Purine Salvage in Leishmania
Pyrimidine Metabolism
Pyrimidine Biosynthesis in Leishmania
Pyrimidine Salvage and Nucleotide Synthesis in Leishmania
The Pyrimidine Pathway as a Drug Target in Leishmania
Index
Arsenite Resistance in Leishmania and Possible Drug Targets / Gaganmeet Singh ; K.G. Jayanarayan ; Chinmoy S. Dey1:
Centralized Indirect Control of an Anaerobic Digestion Bioprocess Using Recurrent Neural Identifier / Ieroham S. Baruch ; Rosalba Galvan-Guerra ; Boyka Nenkova
Logical Analysis of Mappings between Medical Classification Systems / Elena Cardillo ; Claudio Eccher ; Andrei Tamilin
Modeling Reuse on Case-Based Reasoning with Application to Breast Cancer Diagnosis / Carles Pous ; Pablo Gay ; Albert Pla ; Joan Brunet ; Judit Sanz ; Teresa Ramon y Cajal ; Beatriz Lopez
Toward Expert Knowledge Representation for Automatic Breast Cancer Detection / Marina Velikova ; Maurice Samulski ; Nico Karssemeijer ; Peter Lucas
Hybrid Wavelet-RBFNN Model for Monthly Anchovy Catches Forecasting / Nibaldo Rodriguez ; Broderick Crawford ; Carlos Castro ; Eleuterio Yanez
Trilateration Analysis for Movement Planning in a Group of Mobile Robots / Svetoslav Genchev ; Pencho Venkov ; Boris Vidolov
Posters / 7:
Dynamic and Neuro-Dynamic Optimization of a Fed-Batch Fermentation Process / Tatiana Ilkova ; Mitko Petrov
Classification Model for Estimation of Risk Factors in Cardiological Diagnostics / Plamena Andreeva
A Hybrid Approach to Distributed Constraint Satisfaction / David Lee ; Kit-Ying Hui
Interleaved Alldifferent Constraints: CSP vs. SAT Approaches / Frederic Lardeux ; Eric Monfroy
Adaptation of Personality-Based Decision Making to Crowd Behavior Simulations / Fatemeh Alavizadeh ; Caro Lucas ; Behzad Moshiri
Conceptualizing Interactions with Matchmakers and Front-Agents Using Formal Verification Methods / Amelia Badica ; Costin Badica
A Social and Emotional Model for Obtaining Believable Emergent Behaviors / Javier Asensio ; Marta Jimenez ; Susana Fernandez
A Learning Approach to Eary Bug Prediction in Deployed Softward / Saeed Parsa ; Somaye Arabi ; Mojtaba Vahidi-Asl
Evolutionary Decision Support System for Stock Market Trading / Piotr Lipinski
Suboptimal Nonlinear Predictive Control Based on Neural Wiener Models
Author Index
Agents / 1:
Context Model for Multi-Agent System Reconfiguration / Krzysztof Stebel ; Dariusz Choinski
NN-Based Multiagent Platform for Testing Investing Strategies / Darius Plikynas
A Study of SAT-Based Branching Heuristics for the CSP / Yannis Argyropoulos ; Kostas Stergiou
Autonomy in Virtual Agents: Integrating Perception and Action on Functionally Grounded Representations / Argyris Arnellos ; Spyros Vosinakis ; George Anastasakis ; John Darzentas
A Sparse Regression Mixture Model for Clustering Time-Series / K. Blekas ; N. Galatsanos ; A. Likas
Human Distress Sound Analysis and Characterization Using Advanced Classification Techniques / Charalampos Doukas ; Ilias Maglogiannis
A Genetic Programming Environment for System Modeling / Efstratios F. Georgopoulos ; George P. Zarogiannis ; Adam V. Adamopoulos ; Anastasios P. Vassilopoulos ; Spiridon D. Likothanassis
Mining Gene Expression Profiles and Gene Regulatory Networks: Identification of Phenotype-Specific Molecular Mechanisms / Alexandros Kanterakis ; Dimitris Kafetzopoulos ; Vassilis Moustakis ; George Potamias
MOpiS: A Multiple Opinion Summarizer / Fotis Kokkoras ; Efstratia Lampridou ; Konstantinos Ntonas ; Ioannis Vlahavas
Human Behavior Classification Using Multiple Views / Dimitrios I. Kosmopoulos ; Panagiota Antonakaki ; Konstandinos Valasoulis ; Anastasios Kesidis ; Stavros Perantonis
A Hamming Maxnet That Determines all the Maxima / Konstantinos Koutroumbas
Item-Based Filtering and Semantic Networks for Personalized Web Content Adaptation in E-Commerce / Panayiotis Koutsabasis
Fuzzy Representation and Synthesis of Concepts in Engineering Design / Vassilis C. Moulianitis ; Nikos A. Aspragathos ; Argiris J. Dentsoras
Phonotactic Recognition of Greek and Cypriot Dialects from Telephone Speech / Iosif Mporas ; Todor Ganchev ; Nikos Fakotakis
A "Bag" or a "Window" of Words for Information Filtering? / Nikolaos Nanas ; Manolis Vavalis
A Fuzzy Clustering Algorithm to Estimate the Parameters of Radial Basis Functions Neural Networks and Its Application to System Modeling / Antonios D. Niros ; George E. Tsekouras
Speech/Music Discrimination Based on Discrete Wavelet Transform / Stavros Ntalampiras
Comparing Datasets Using Frequent Itemsets: Dependency on the Mining Parameters / Irene Ntoutsi ; Yannis Theodoridis
A Theory of Action, Knowledge and Time in the Event Calculus / Theodore Patkos ; Dimitris Plexousakis
Tensor Space Models for Authorship Identification / Spyridon Plakias ; Efstathios Stamatatos
Efficient Incremental Model for Learning Context-Free Grammars from Positive Structural Examples / Gend Lal Prajapati ; Narendra S. Chaudhari ; Manohar Chandwani
Histogram-Based Visual Object Recognition for the 2007 Four-Legged RoboCup League / Souzana Volioti ; Michail G. Lagoudakis
Learning Ontologies of Appropriate Size / Elias Zavitsanos ; Sergios Petridis ; Georgios Paliouras ; George A. Vouros
Short Papers
Bayesian Model of Recognition on a Finite Set of Events / Vladimir Berikov ; Gennady Lbov
The DR-Prolog Tool Suite for Defeasible Reasoning and Proof Explanation in the Semantic Web / Constantinos Papatheodorou
Modeling Stroke Diagnosis with the Use of Intelligent Techniques / S. Lalas ; N. Ampazis ; A. Tsakonas ; G. Dounias ; K. Vemmos
Introducing Parallel Computations to a PTTP-Based First-Order Reasoning Process in the Oz Language / Adam Meissner
A Dense Stereo Correspondence Algorithm for Hardware Implementation with Enhanced Disparity Selection / Lazaros Nalpantidis ; Georgios Ch. Sirakoulis ; Antonios Gasteratos
MyCites: An Intelligent Information System for Maintaining Citations / George Papadakis
Improving the Integration of Neuro-Symbolic Rules with Case-Based Reasoning / Jim Prentzas ; Ioannis Hatzilygeroudis ; Othon Michail
Rule-Based Fuzzy Logic System for Diagnosing Migraine / Svetlana Simic ; Dragan Simic ; Petar Slankamenac ; Milana Simic-Ivkov
An Individualized Web-Based Algebra Tutor Based on Dynamic Deep Model Tracing / Dimitrios Sklavakis ; Ioannis Refanidis
Design and Optimization of IIR Digital Filters with Non-standard Characteristics Using Continuous Ant Colony Optimization Algorithm / Adam Slowik ; Michal Bialko
An Empirical Study of Lazy Multilabel Classification Algorithms / E. Spyromitros ; G. Tsoumakas ; I. Vlahavas
An Algorithm of Decentralized Artificial Immune Network and Its Implementation / Mariusz Swiecicki
Predicting Defects in Software Using Grammar-Guided Genetic Programming / Athanasios Tsakonas ; Georgios Dounias
A Clustering Framework to Build Focused Web Crawlers for Automatic Extraction of Cultural Information / Damianos Gavalas ; Stefanos Filios ; George Bafaloukas
Non-negative Matrix Factorization for Endoscopic Video Summarization / Spyros Tsevas ; Dimitris Iakovidis ; Dimitris Maroulis ; Emmanuel Pavlakis ; Andreas Polydorou
Nature Inspired Intelligence for the Constrained Portfolio Optimization Problem / Vassilios Vassiliadis
CLIVE - An Artificially Intelligent Chat Robot for Conversational Language Practice / John Zakos ; Liesl Capper
Author Index
Invited Talks
Grounding Concrete Motion Concepts with a Linguistic Framework / Gutemberg Guerra-Filho ; Yiannis Aloimonos
Emotion in Cognitive Systems Architectures / Tom Ziemke
Kernel k-Means Clustering Applied to Vector Space Embeddings of Graphs / Kaspar Riesen ; Horst Bunke
Probabilistic Models Based on the [Pi]-Sigmoid Distribution / Anastasios Alivanolgou ; Aristidis Likas
How Robust Is a Probabilistic Neural VLSI System Against Environmental Noise / C.C. Lu ; C.C. Li ; H. Chen
Supervised Learning
Sparse Least Squares Support Vector Machines by Forward Selection Based on Linear Discriminant Analysis / Shiego Abe
Supervised Incremental Learning with the Fuzzy ARTMAP Neural Network / Jean-Francois Connolly ; Eric Granger ; Robert Sabourin
Discriminatory Data Mapping by Matrix-Based Supervised Learning Metrics / M. Strickert ; P. Schneider ; J. Keilwagen ; T. Villmann ; M. Biehl ; B. Hammer
Neural Approximation of Monte Carlo Policy Evaluation Deployed in Connect Four / Stefan Fausser ; Friedhelm Schwenker
Cyclostationary Neural Networks for Air Pollutant Concentration Prediction / Monica Bianchini ; Ernesto Di Iorio ; Marco Maggini ; Augusto Pucci
Experiments with Supervised Fuzzy LVQ / Christian Thiel ; Britta Sonntag
A Neural Network Approach to Similarity Learning / Stefano Melacci ; Lorenzo Sarti
Partial Discriminative Training of Neural Networks for Classification of Overlapping Classes / Cheng-Lin Liu
Multiple Classifiers
Boosting Threshold Classifiers for High-Dimensional Data in Functional Genomics / Ludwig Lausser ; Malte Buchholz ; Hans A. Kestler
Decision Fusion on Boosting Ensembles / Joaquin Torres-Sospedra ; Carlos Hernandez-Espinosa ; Mercedes Fernandez-Redondo
The Mixture of Neural Networks as Ensemble Combiner
Combining Methods for Dynamic Multiple Classifier Systems / Amber Tomas
Researching on Multi-net Systems Based on Stacked Generalization
Applications
Real-Time Emotion Recognition from Speech Using Echo State Networks / Stefan Scherer ; Mohamed Oubbati ; Gunther Palm
Sentence Understanding and Learning of New Words with Large-Scale Neural Networks / Heiner Markert ; Zohre Kara Kayikci
Multi-class Vehicle Type Recognition System / Xavier Clady ; Pablo Negri ; Maurice Milgram ; Raphael Poulenard
A Bio-inspired Neural Model for Colour Image Segmentation / Francisco Javier Diaz-Pernas ; Miriam Anton-Rodriguez ; Jose Fernando Diez-Higuera ; Mario Martinez-Zarzuela
Bayesian Classifiers for Predicting the Outcome of Breast Cancer Preoperative Chemotherapy / Antonio P. Braga ; Euler G. Horta ; Rene Natowicz ; Roman Rouzier ; Roberto Incitti ; Thiago S. Rodrigues ; Marcelo A. Costa ; Carmen D.M. Pataro ; Arben Cela
Feature Selection
Feature Ranking Ensembles for Facial Action Unit Classification / Terry Windeatt ; Kaushala Dias
Texture Classification with Generalized Fourier Descriptors in Dimensionality Reduction Context: An Overview Exploration / Ludovic Journaux ; Marie-France Destain ; Johel Miteran ; Alexis Piron ; Frederic Cointault
Improving Features Subset Selection Using Genetic Algorithms for Iris Recognition / Kaushik Roy ; Prabir Bhattacharya
Artificial Neural Network Based Automatic Face Model Generation System from Only One Fingerprint / Seref Sagiroglu ; Necla Ozkaya
Author Index
Unsupervised Learning
Patch Relational Neural Gas - Clustering of Huge Dissimilarity Datasets / Alexander Hasenfuss ; Barbara Hammer ; Fabrice Rossi
Proving Group Protocols Secure Against Eavesdroppers / Steve Kremer ; Antoine Mercier ; Ralf Treinen
System Descriptions 1 / Session 5:
Automated Implicit Computational Complexity Analysis / Martin Avanzini ; Georg Moser ; Andreas Schnabl
LogAnswer - A Deduction-Based Question Answering System / Ulrich Furbach ; Ingo Glockner ; Hermann Helbig ; Bjorn Pelzer
A High-Level Implementation of a System for Automated Reasoning with Default Rules / Christoph Beierle ; Gabriele Kern-Isberner ; Nicole Koch
The Abella Interactive Theorem Prover / Andrew Gacek
LEO-II - A Cooperative Automatic Theorem Prover for Classical Higher-Order Logic / Christoph Benzmuller ; Lawrence C. Paulson ; Frank Theiss ; Arnaud Fietzke
KeYmaera: A Hybrid Theorem Prover for Hybrid Systems / Andre Platzer ; Jan-David Quesel
The Complexity of Conjunctive Query Answering in Expressive Description Logics / Carsten LutzSession 6:
Modal Logics / Session 7:
A General Tableau Method for Deciding Description Logics, Modal Logics and Related First-Order Fragments / Renate A. Schmidt ; Dmitry Tishkovsky
Terminating Tableaux for Hybrid Logic with the Difference Modality and Converse / Mark Kaminski ; Gert Smolka
Herbrand Award Ceremony / Session 8:
Description Logics / Session 9:
Automata-Based Axiom Pinpointing / Franz Baader ; Rafael Penaloza
Individual Reuse in Description Logic Reasoning / Boris Motik ; Ian Horrocks
The Logical Difference Problem for Description Logic Terminologies / Boris Konev ; Dirk Walther ; Frank Wolter
System Descriptions 2 / Session 10:
Aligator: A Mathematica Package for Invariant Generation / Laura Kovacs
IeanCoP 2.0 and ileanCoP 1.2: High Performance Lean Theorem Proving in Classical and Intuitionistic Logic / Jens Otten
iProver - An Instantiation-Based Theorem Prover for First-Order Logic / Konstantin Korovin
An Experimental Evaluation of Global Caching for ALC / Rajeev Gore ; Linda Postniece
Multi-completion with Termination Tools / Haruhiko Sato ; Sarah Winkler ; Masahito Kurihara ; Aart Middeldorp
MTT: The Maude Termination Tool / Francisco Duran ; Salvador Lucas ; Jose Meseguer
Celf - A Logical Framework for Deductive and Concurrent Systems / Anders Schack-Nielsen ; Carsten Schurmann
Canonicity! / Nachum DershowitzSession 11:
Equational Theories / Session 12:
Unification and Matching Modulo Leaf-Permutative Equational Presentations / Thierry Boy de la Tour ; Mnacho Echenim ; Paliath Narendran
Modularity of Confluence: Constructed / Vincent van Oostrom
Automated Complexity Analysis Based on the Dependency Pair Method / Nao Hirokawa ; Geory Moser
Canonical Inference for Implicational Systems / Maria Paola Bonacina
Challenges in the Automated Verification of Security Protocols / Hubert Comon-LundhSession 13:
Theorem Proving 1 / Session 14:
Deciding Effectively Propositional Logic Using DPLL and Substitution Sets / Leonardo de Moura ; Nikolaj Bjorner
Proof Systems for Effectively Propositional Logic / Juan Antonio Navarro ; Andrei Voronkov
MaLARea SG1 - Machine Learner for Automated Reasoning with Semantic Guidance / Josef Urban ; Geoff Sutcliffe ; Petr Pudlak ; Jiri Vyskocil
CASC / Session 15:
CASC-J4 - The 4th IJCAR ATP System Competition
Theorem Proving 2 / Session 16:
Labelled Splitting / Christoph Weidenbach
Engineering DPLL(T) + Saturation
THF0 - The Core of the TPTP Language for Higher-Order Logic / Florian Rabe
Logical Frameworks / Session 17:
Focusing in Linear Meta-logic / Vivek Nigam ; Dale Miller
Tree Automata / Session 18:
Certifying a Tree Automata Completion Checker / Benoit Boyer ; Thomas Genet ; Thomas Jensen
Automated Induction with Constrained Tree Automata / Adel Bouhoula ; Florent Jacquemard
Author Index
Invited Talk / Session 1:
Software Verification: Roles and Challenges for Automatic Decision Procedures / Aarti Gupta
Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data (Abstract) / Dan L. Nicolae ; Omar De la Cruz ; William Wen ; Baoguan Ke ; Minsun Song
Hierarchical Clustering Using Constraints / Mariana Kant ; Maurice LeBon ; David Sankoff
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches / Mukul S. Bansal ; Oliver Eulenstein
A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes / Xintao Wei ; Lenore Cowen ; Carla Brodley ; Arthur Brady ; D. Sculley ; Donna K. Slonim
An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis / Tingting Zhou ; Keith C.C. Chan ; Yi Pan ; Zhenghua Wang
Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences / Ankit Agrawal ; Volker Brendel ; Xiaoqiu Huang
Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition / Arka Ghosh
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats / Todd J. Treangen ; Aaron E. Darling ; Mark A. Ragan ; Xavier Messeguer
Improved Alignment of Protein Sequences Based on Common Parts / David Hoksza
Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry / Nikita Arnold ; Tema Fridman ; Robert M. Day ; Andrey A. Gorin
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes / Dongsheng Che ; Guojun Li ; Shane T. Jensen ; Jun S. Liu ; Ying Xu
Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure / Leonid Zaslavsky ; Tatiana A. Tatusova
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution / Qian Zhu ; Zaky Adam ; Vicky Choi
Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure / David Campo ; Zoya Dimitrova ; Yuri Khudyakov
HCV Quasispecies Assembly Using Network Flows / Kelly Westbrooks ; Irina Astrovskaya ; Piotr Berman ; Alex Zelikovsky
A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring / Matthew A. Goto ; Eric J. Schwabe
Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies (Abstract) / Andrew S. Allen
Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data / Eyad Almasri ; Peter Larsen ; Guanrao Chen ; Yang Dai
Integrative Network Component Analysis for Regulatory Network Reconstruction / Chen Wang ; Jianhua Xuan ; Li Chen ; Po Zhao ; Yue Wang ; Robert Clarke ; Eric P. Hoffman
A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks / Min Li ; Jianxin Wang ; Jianer Chen
Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph / Alexandre P. Francisco ; Arlindo L. Oliveira ; Ana T. Freitas
Mean Squared Residue Based Biclustering Algorithms / Stefan Gremalschi ; Gulsah Altun
Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information / Ting Gong ; Rebecca B. Riggins
A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution / Xue-Qiang Zeng ; Guo-Zheng Li ; Jack Y. Yang ; Mary Qu Yang
Network-Based Inference of Cancer Progression from Microarray Data / Yongjin Park ; Stanley Shackney ; Russell Schwartz
Invited Keynote Talk: Quiet Revolution: Connectivity in the Cancer Research Community (Abstract) / Kenneth Buetow
Wavelet-Based 3-D Multifractal Spectrum with Applications in Breast MRI Images / Gordana Derado ; Kichun Lee ; Orietta Nicolis ; F. DuBois Bowman ; Mary Newell ; Fabrizio F. Ruggeri ; Brani Vidakovic
Accurate Inverse Consistent Non-rigid Image Registration and Its Application on Automatic Re-contouring / Qingguo Zeng ; Yunmei Chen
GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies / Matthew Eavenson ; Maciej Janik ; Shravya Nimmagadda ; John A. Miller ; Krys J. Kochut ; William S. York
Pattern Matching in RNA Structures / Kejie Li ; Reazur Rahman ; Aditi Gupta ; Prasad Siddavatam ; Michael Gribskov
The Use of a Conformational Alphabet for Fast Alignment of Protein Structures / Wei-Mou Zheng
On-the-Fly Rotamer Pair Energy Evaluation in Protein Design / Andrew Leaver-Fay ; Jack Snoeyink ; Brian Kuhlman
Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling / James Lara
Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction / Shibin Qiu ; Terran Lane
Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients / Wei Zhong ; Rick Chow ; Richard Stolz ; Jieyue He ; Marsha Dowell
Computational Mutagenesis of E. Coli Lac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity / Majid Masso ; Kahkeshan Hijazi ; Nida Parvez ; Iosif I. Vaisman
Evaluating Genetic Algorithms in Protein-Ligand Docking / Rafael Ordog ; Vince Grolmusz
A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling / Huimin Geng ; Hesham H. Ali ; Wing C. Chan
Evolutionary Algorithm for Feature Subset Selection in Predicting Tumor Outcomes Using Microarray Data / Qihua Tan ; Mads Thomassen ; Kirsten M. Jochumsen ; Jing Hua Zhao ; Kaare Christensen ; Torben A. Kruse
Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data
Invited Keynote Talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments (Abstract) / Shin-Lian Lo ; Kwok-Leung Tsui ; Benjamin Barwick
Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI / Anna-Lena Lamprecht ; Tiziana Margaria ; Bernhard Steffen
Supporting Computational Systems Science: Genomic Analysis Tool Federations Using Aspects and AOP / David Stotts ; Keith Lee ; Ivan Rusyn
BioDQ: Data Quality Estimation and Management for Genomics Databases / Alexandra Martinez ; Joachim Hammer ; Sanjay Ranka
Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis / Juntao Li ; Jianhua Liu ; R. Krishna Murthy Karuturi
Bagging Multiple Comparisons from Microarray Data / Dimitris N. Politis
Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products / Shandar Ahmad
Author Index
Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data (Abstract) / Dan L. Nicolae ; Omar De la Cruz ; William Wen ; Baoguan Ke ; Minsun Song
Hierarchical Clustering Using Constraints / Mariana Kant ; Maurice LeBon ; David Sankoff
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches / Mukul S. Bansal ; Oliver Eulenstein
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
An Introduction to iTasks: Defining Interactive Work Flows for the Web / Rinus Plasmeijer ; Peter Achten ; Pieter Koopman
Proving Properties of Lazy Functional Programs with Sparkle / Maarten de Mol ; Marko van Eekelen
An Introduction to the Lambda Calculus / Zoltan Csornyei ; Gergely Devai
Abstract [lambda]-Calculus Machines / Werner E. Kluge
Programming in [Omega]mega / Tim Sheard ; Nathan Linger
A Tutorial on Object-Oriented Functional Programming / Horia F. Pop
Use Cases for Refactoring in Erlang / Tamas Kozsik ; Zoltan Horvath ; Roland Kiraly ; Robert Kitlei ; Laszlo Lovei ; Tamas Nagy ; Melinda Toth ; Aniko Vig
From Interpretation to Compilation / Jan Martin Jansen
Author Index
An Introduction to iTasks: Defining Interactive Work Flows for the Web / Rinus Plasmeijer ; Peter Achten ; Pieter Koopman
Proving Properties of Lazy Functional Programs with Sparkle / Maarten de Mol ; Marko van Eekelen
An Introduction to the Lambda Calculus / Zoltan Csornyei ; Gergely Devai