Schedule and Program

Papers released by their authors/lecturers are now available for download.

Theme for each day:
The programme for each day is devoted to a topic, where both educational and research presentations will be delivered.
BioInfoSummer starts on Monday afternoon, a day devoted to provision of background knowledge in biology.
The themes for Tuesday to Friday are: Sequence to Structure, Comparative Genomics, Analysis of Gene Expressions and Regulatory Networks.

Mornings:
The morning session of each day starting Tuesday will start with background lectures, which will target students but also be applicable to academics moving into bioinformatics, and those who wish to learn about other areas of bioinformatics. Presentation of a keynote speaker will end the morning sessions.

Afternoons:
Each afternoon will be filled by presentation of contributed papers, followed by a keynote lecture. Workshops will be run in parallel with these presentations.

	MONDAY	TUESDAY	WEDNESDAY	THURSDAY	FRIDAY
	BIOLOGY	SEQUENCE TO STRUCTURE	COMPARATIVE GENOMICS	ANALYSIS OF GENE EXPRESSIONS	REGULATORY NETWORKS
9 - 10 AM Lectures		Sue Wilson	Robert Beiko	Conrad Burden	Terry Speed
10-10:30 AM		Morning tea
10:30- 11:30 AM Lectures		Graham Wood	Mark Ragan	Gordon Smyth	Terry Speed
11:30AM - 12:30PM Keynote	Registration	Dirk Husmeier	Jens Lagergren	Tim Beißbarth	Eric Schadt
12:30-1:30 PM	Registration	Lunch
1:30 - 2:30 PM	Matthew Wakefield	Fabien Huard Braddon Lance Saravanan Dayalan	Nikki Appleby Khaleel Petrus Brett Easton	Dorothy Wong Hong Hu Andreas Schreiber	Tim Conrad Markus Hegland Tony Reverter
2:30 - 3:30 P.M.	Hilary Booth (2004 video presentation)	Miles Davenport Tech presentation: CRAY	Tony Papenfuss Tech presentations: Ceanet	Yvonne Pittelkow John Maindonald Mark Robinson	Eric Schadt
3:30 - 4 PM	Afternoon Tea
4 - 5 PM Keynote	Matthew Wakefield	Dirk Husmeier	Jens Lagergren	Tim Beißbarth
5 - 6 PM		Welcome drinks Poster Session
6 - 7 PM		Public Lecture Chris Goodnow

Venue

All talks will take place in the Manning Clark Centre, ANU (Bldg 26a, ref g3 on the ANU map).

Titles of presentations

Monday 28/11/2005

1:30 - 2:30 PM	Introduction to Biology	Matthew Wakefield
2:30 - 3:30 PM	Modelling Gene Regulation using the Stochastic Master Equation	Hilary Booth (video presentation of 2004 lecture)
4:00 - 5:00 PM	Molecular biology Tools and Techniques	Matthew Wakefield

Tuesday 29/11/2005

9-10 AM	Sequence Comparison: Dynamic Programming, BLAST & D₂	Sue Wilson
10:30-11:30 AM	Proteins: Background, structure prediction and open problems	Graham Wood
11:30AM-12:30PM	Predicting mosaic structures in DNA sequence alignments with factorial Hidden Markov Models	Dirk Husmeier
1:30-1:50PM	Modelling sequential protein folding using HP lattice models	Fabien Huard
1:50-2:10PM	Fragment shape and comparative modelling	Braddon Lance
2:10-2:30 PM	Using disulfide bond based classification in protein structure prediction	Saravanan Dayalan
2:30-2:50 PM	Biological, chemical and physical behavioural analyses for protein classifications	Rauf Malick
2:50-3:10 PM	The genetic recombination underlying public T cell receptors: an example of convergent evolution?	Miles Davenport
3:10-3:40 PM	Technical presentation: Implications of an accelerated Smith-Waterman algorithm implementation	CRAY
4:00 - 5:00 PM	Ab initio prediction of protein interactions	Dirk Husmeier

Wednesday 30/11/2005

9-10 AM	Comparative evolutionary genomics: how genomes (and organisms) evolve - part I	Robert Beiko
10:30-11:30 AM	Comparative evolutionary genomics: how genomes (and organisms) evolve - part II	Mark Ragan
11:30AM-12:30PM	Probabilistic and combinatorial analysis of gene families with respect to gene duplications and lateral gene transfers	Jens Lagergren
1:30-1:50PM	The extraction and characterisation of data subsets for comparative genomic analysis	Nikki Appleby
1:50-2:10 PM	Combining gene expression data and gene ontology with the use of a data mining tool	Khaleel Petrus
2:10-2:30 PM	A probabilistic method for the identification of compensatory substitutions for pathogenic mutations	Brett Easton
2:30-2:50 PM	Analysis of conserved non-coding sequences in the mammalian MHC class III region	Tony Papenfuss
2:50-3:20 PM	Technical presentation: Developing and Deploying Bioinformatics Applications with MATLAB	Ceanet
4:00 - 5:00 PM	A tree-based Gibbs motif sampler for unaligned orthologous upstream sequences	Jens Lagergren

Thursday 1/12/2005

9-10 AM	Adsorption Models of Oligonucleotide Microarrays	Conrad Burden
10:30-11:30 AM	A calibration data set of mixtures for evaluating microarray platform accuracy	Gordon Smyth
11:30AM-12:30PM	Using Gene Ontology and Gene Expression Data	Tim Beißbarth
1:30-1:50 PM	Imputation in microarray experiments	Dorothy Wong
1:50-2:10 PM	Studying microarray data pre-processing for classification	Hong Hu
2:10-2:30 PM	The generalised singular value decomposition and its use in combining gene expression data from diverse platforms	Andreas Schreiber
2:30-2:50 PM	Challenges for molecular classification: a case study of breast cancer survival	Yvonne Pittelkow
2:50-3:10 PM	Plots that are designed to show groups in expression array data	John Maindonald
3:10-3:30 PM	Differential expression in liquid chromatography-mass spectrometry (LC-MS) data	Mark Robinson
4:00-5:00 PM	Estimating Networks from Microarray Data and RNAi Experiments	Tim Beißbarth

Friday 2/12/2005

9-10 AM	Transcriptional regulation in eukaryotes: a brief introduction	Terry Speed
10:30-11:30 AM	Methods for the discovery of cis-regulatory modules in eukaryotes: a brief overview	Terry Speed
11:30AM-12:30PM	Novel Integrative Genomics Strategies to Identify Genes and Reconstruct Networks Associated with Disease	Eric Schadt
1:30-1:50 PM	Fingerprinting in MALDI-TOF-MS: from ion counts to patters to impact on diseases	Tim Conrad
1:50-2:10 PM	Computational techniques for gene regulatory networks	Markus Hegland
2:10-2:30 PM	Gene networks at work using digital organisms	Tony Reverter
2:30-3:30 PM	Causal Inferences from Genetic and Gene Expression Data: Moving towards an unbiased approach to the identification of key drivers of disease	Eric Schadt

Posters

Sequence and structures
1.	Molecular dynamics simulation analysis of human CYP1B1 mutations associated with primary congenital glaucoma	Malkaram S. Achary and Hampapathalu A. Nagarajaram
2.	Parallel solutions for bioinformatics algorithms	Manal Helal, Lenore Mullin, Bruno Gaeta and Hossam El-Gindy
3.	Expression and sequence analysis of recombinant Diaminopropionate ammonia lyase from non-virulent Salmonella typhimurium PU001	K.R. Rupesh, K.R. Padma, P. Saravanan and S. Jayachandran
4.	A comparative study on identification techniques of tandem repeats in DNA sequences	M. Shah, J. Miah and Saleh A. Wasimi
Comparative Genomics
5.	Comparative evolutionary sequence analysis of nucleotide and amino acid sequences of haemolysin gene in various haemolysin producing bacteria	Mahdieh Khosroheydari and K.R. Rupesh
6.	Random amplified polymorphic DNA (RAPD) PCR analysis of genetically modified organism (GMO)	Cheah Yoke Kqueen and Son Radu
Analysis of Gene Expression
7.	Microarray data analysis	Irina Rusinova
8.	Enhancing predicted gene interaction networks from microarray data using additional genomics data	William J Wilson and Harri T. Kiiveri
9.	QC of Affymetrix GeneChips with R/Bioconductor and affyPLM	SJ Ohms, K Peng, YE Pittelkow
10.	Screening and analysis of transcription factors in Arabidopsis thaliana	Elke G. Rosche, Yvonne E. Pittelkow, Murray R. Badger and Susan R. Wilson
Regulatory Networks
11.	Modelling Gene regulation in the Bacteriophage Lambda	Hilary S. Booth, Conrad J. Burden, Lucia Santoso and Markus Hegland