THURSDAY, FRIDAY, 2 – 3 SEPTEMBER (MASSEY UNIVERSITY, ALBANY CAMPUS)

Pre-Conference Workshop on Parallel Computing in Bioinformatics

SUNDAY, 5 SEPTEMBER 2004, EVENING

1600 – 2100 Registration, Aotea Centre Conference Rooms

MONDAY , 6 SEPTEMBER 2004, MORNING

0730	Registration
0830	Delegates to be seated Conference Room NZ3
0845	Powhiri and Welcoming addresses
0945	Opening Address: Professor Bruce Weir, North Carolina State University An evolutionary perspective for bioinformatics
1030	Morning Tea
	Genome Bioinformatics -- NZ1 Chair: Christian Schoenbach	Applied Bioinformatics -- NZ3 Chair: Prasit Palittapongarnpim	Evolutionary Bioinformatics --NZ4 Chair: Bruce Rannala
1100	Satoru Miyano, University of Tokyo Computational Challenges in Systems Biology	Shoba Ranganathan, Macquarie University Alternative Splicing: bridging the gap between the genome and the transcriptome	Mike Hendy, Massey University Interpreting nested micro-satellite evolution
1145	Peter Wills, Auckland University Bioinformatic significance of cellular dynamics	Yoshiaki Minezaki, DDBJ, National Institute of Genetics Comparative Genomics of Transcription Factors	Howard Ross, Auckland University Sources of variation in ancestral sequence reconstruction (ASR)
1205	Stephen Rice, Auckland University DNA Strand Bias in Mammalian Gene Clusters	Tekaporn Siriwan, Rajamangala Institute of Technology Single Nucleotide Polymorphism Prediction using Frame Shift and Artificial Neural Network	Brett Easton, Australian National University Evolutionary modelling and phylogenetic reconstruction through non-reversible Markov models
1230	Lunch

MONDAY, 6 SEPTEMBER 2004, AFTERNOON

	Biomedical Bioinformatics --NZ1 Chair: Shoba Ranganathan	Biodiversity Bioinformatics -- NZ3 Chair: Howard Ross	Evolutionary Bioinformatics -- NZ4 Chair: Mike Hendy
1400	Garth Cooper, Protemix & University of Auckland Pharmaceutical Discovery by Proteomics-based Analysis of Adipocyte Conversion	Mark Costello, Auckland University Informatics Enables a New Era of Discovery in Marine Biology and Ecology	Keith Crandall, Brigham Young University Comparing network approaches for estimating gene genealogies
1445	Te Ming Huang, Auckland University Gene Extraction for Cancer Diagnosis by Support Vector Machines	Robbie Price, Landcare Research, New Zealand Computing in Environmental Space	Barbara Holland, Massey University Super networks : Combining gene trees on overlapping sets of species
1505		Shane Lavery, Auckland University Web-based DNA taxonomy: www.DNA-surveillance as a model for the future	Matthew Goode, Auckland University DNA Surveillance 2.0
1530	Afternoon Tea
1600 – 1800	Poster Session
1730 -- 2400	Conference Dinner Wintergarden (under the Civic Theatre) Dinner Speaker: Prof Denis Dutton, University of Canterbury Through a Glass Darkly. Very Darkly Indeed

TUESDAY, 7 SEPTEMBER 2004, MORNING

	Applied Bioinformatics -- NZ1 Chair: Paul Bickerstaff	Microarrays and Proteomics -- NZ3 Chair: Geoff McLachlan	Phylogenetics and Rapidly Evolving Pathogens --NZ4 Chair: Jeff Thorne
0900	Christian Schoenbach, RIKEN Genomic Sciences Center Interspersed Repeats as Mediators of Gene Product and Species-specific Variation	Terry Speed, University of California, Berkeley Statistical Analysis of Replicated Microarray Time Series Data	Mike Steel, University of Canterbury Phylogenetic Networks and Biodiversity
0945	Lesley Collins, Massey University Data management for small scale genomics	Mik Black, University of Auckland Empirical false discovery rate control, with application to microarray experimentation.	Roderic Page, University of Glasgow Viruses, clocks, and cospeciation
1005	Chiao-Yun Yang, National Chiao Tung University A Hierarchical Protein Fold Classification Scheme Using Data Fusion	Mohd Saberi Mohamad, Universiti Teknologi Malaysia Genetic Algorithms Wrapper Approach to Select Informative Genes for Gene Expression Microarray Classification using Support Vector Machines
1030	Morning Tea
1100	Limsoon Wong, Institute for Infocomm Research Assessing Reliability of Protein-Protein Interaction Experiments	Robert Gentleman, Dana Farber Cancer Institute Exploring Genomic Data using GO	Thomas Leitner, Los Alamos National Laboratories Recombination, 3D network structure, multiple transmission, and subpopulation frequency shifts in a mother-to-child transmission case.
1145	John Cleary, Reel Two & Waikato University SureGene, a Scalable System for Automated Term Disambiguation of Gene and Protein Names	Katya Ruggiero, CSIRO Mathematical and Information Sciences The challenges of designing a large two-phase microarray experiment	Marc Suchard, University of California, Los Angeles Resolving the intra-host evolution of rapidly evolving pathogens: common patterns and shared indel information under a Bayesian framework
1205		Beatrix Jones, Massey University Modeling Microarray Data with Gaussian Graphical Models

TUESDAY, 7 SEPTEMBER 2004, AFTERNOON

1230	Lunch
	Applied Bioinformatics -- NZ1 Chair: Mik Black	Genome Bioinformatics -- NZ3 Chair: Limsoon Wong	Phylogenetics and Rapidly Evolving Pathogens --NZ4 Chair: Marc Suchard
1400	Peter Johnstone, AgResearch Ltd. Bioinformatics in Agriculture	Bailin Hao, Fudan University Finding Genes in the Rice Genome	Alexei Drummond, University of Oxford Modeling virus evolution and population dynamics
1445	Antonio Reverter, CSIRO Livestock Industries Identification of Differential Gene Expression from Massively Parallel Signature Sequencing (MPSS) Data based on Bootstrap Percentile Confidence Intervals	Gautam Aggarwal, Seattle Biomedical Research Institute A novel method for identifying syntenic regions between Trypanosomatid Genomes	Jeff Thorne, North Carolina State University Making evolutionary inferences when there is dependent change among sequence positions, with emphasis on protein tertiary structure and viral antigenicity.
1505	Fei Zhang, CSIRO’s Bioinformatics Facility, Plant Industry Division, High-Throughput Bioinformatics Applications on Linux Clusters	Noppadon Khiripet, National Electronics and Computer Technology Center, Thailand Discovering Common Genes Using Approximate Maximal Clique Detection
Free

WEDNESDAY, 8 SEPTEMBER 2004, MORNING

	Evolutionary Bioinformatics -- NZ1 Chair: Barbara Holland	Platforms and Applications -- NZ3 Chair: John Cleary	Phylogenetics and Rapidly Evolving Pathogens --NZ4 Chair: Mike Steel
0900	David Penny, Massey University RNA processing in the Eukaryotic Ancestor	Haruki Nakamura, Osaka University Protein Informatics: Database studies and Molecular Simulations with GRID Architectures	Bruce Rannala, University of Alberta Imperfect Molecular Clocks
0945	Mihaela Baroni, University of Canterbury A digraph-based approach to study hybrid evolution	Paul Bickerstaff GeneThresher Bioinformatics	Geoff Nicholls, University of Auckland Measurably evolving memes: new models and inference tools for meme-trait data
1005		Allison Soo & Aaron Chuah, Temasek Life Sciencces GloBLAST: Distributed Customizable BLAST on the Web
1030	Morning Tea
1100	Lindell Bromham, University of Sussex Can we trust the molecular clock?	Prasit Palittapongarnpim In Silico Characterization of Leucine-rich Repeat (LRR) Motif from Leptospira interrogans Genomes: a homology modeling approach	Ben Redelings, University of California, Los Angeles Incorporating Indel Information into Phylogeny Estimation for Rapidly Emerging Diseases
1120			Gregory Ewing, University of Auckland Measurably Evolving Populations and the structured coalescent
1145	Haryadi Sugiarto, Massey University Evolutionary Relationship and the Multifunctional Roles of b‑Defensins	Kitiporn Plaimas, Chulalongkorn University Resolving Ambiguous Nucleotide Symbol from DNA Sequences	Allen Rodrigo, University of Auckland Measurably Evolving Populations: where to next?
1205	David Welch, Auckland University Combining genealogy and epidemiology using a stochastic model	T. Madhan Mohan, Ministry of Science and Technology, India Integration of Bioinfo-Resources on Biogrid India Developed Through Biotechnology Information System Network (BTISnet)

WEDNESDAY, 8 SEPTEMBER 2004, AFTERNOON

1230	Lunch
	Evolutionary Bioinformatics -- NZ1 Chair: Keith Crandall	Platforms and Applications -- NZ3 Chair: Lindell Bromham	Microarrays and Proteomics -- NZ4 Chair: Kathy Ruggiero
1400	James I . Mullins, University of Washington HIV evolutionary dynamics: Implications for pathogenesis and vaccine development	Russell Gray, Auckland University Language Trees Meet Bioinformatics: Can Computational Methods Help Resolve Debates About Our Past?	Geoff MacLachlan, Queensland University Classification of Microarray Gene-Expression Data
1445	Stephane Guindon, Auckland University Modeling the Site-specific Variation of Selection Patterns Along Lineages	Sarinder Kaur, University of Malaya Bio-Data Mining through Communication Engineering: The Role of DiGIR	Yeo Lee Chin, Universiti Teknologi Malaysia Improved Gene Selection Technique by Combining Model-Based Clustering and Statistical Methods for Classification of Microarrays Gene Expression Data
1505	Jack da Silva, University of Adelaide Monte Carlo Simulation of HIV Adaptation to Immune Surveillance	Maheswary Vellupilai, MARDI, Malaysia Application of Arrayinformatics in the Analysis of Gene Expression Data from Pummelo Fruit Peel Development	Chiou-Nan Chen,, National Tsing Hua University Boolean Logic Modeling of Microarray Regulatory Pathway
1530	CLOSING (NZ3)