Schedule and Program

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		Warren Kaplan	Lars Jermiin	Yvonne Pittelkow	Terry Speed
10-10:30 AM		Morning tea
10:30- 11:30 AM Lectures		Warren Kaplan	Lars Jermiin	Geoff McLachlan	Terry Speed
11:30AM - 12:30PM Keynote		Anna Tramontano	Susan Holmes	Robert Gentleman	Hidde de Jong
12:30-1:30 PM	Registration	Lunch
1:30 - 2:30 PM		Hong Gu Vanessa Venturi	Brett Easton Kinshore Sakharkar	Susan Kim Serban Nacu	Mark Fellmann Florian Hahne
2:30 - 3:30 P.M.	Bruno Gaëta	Ignatius Pang Conrad Burden	Sylvain Forêt Gowri Shankar	Mark Robinson Cameron Craddock	Joshua Ho (2:30-3:00pm)
3:30 - 4 PM	Afternoon Tea				Hidde de Jong (3:00-4:00pm)
4 - 5 PM Keynote	Bruno Gaëta	Anna Tramontano	Susan Holmes	Robert Gentleman
5 - 6 PM		Welcome drinks Poster Session
6 - 7 PM		Public Lecture

Venue

The talks will take place in:

• Monday 4 - Thursday 7 December 2006, Robertson Lecture theatre, Research School of Biological Sciences, ANU (Building 46 ref E4 on the ANU map).
• Friday 8 December 2006, Haydon Allen Lecture Theatre (The Tank), ANU (Building 23, ref F3 on the ANU map).
• Public lecture at the Robertson Lecture theatre, Research School of Biological Sciences, ANU (Building 46 ref E4 on the ANU map).

Please note that no food or drinks are allowed in the lecture theatres and seminar rooms.

Titles of presentations

Monday 04/12/2006
2:30 - 3:30 PM	The biology you need to know to do bioinformatics part I	Bruno Gaëta
4:00 - 5:00 PM	The biology you need to know to do bioinformatics part II	Bruno Gaëta
Tuesday 05/12/2006
9:00-10:00 AM	Protein Structures - An Introduction	Warren Kaplan
10:30-11:30 AM	Protein Structures - Prediction Methods	Warren Kaplan
11:30AM-12:30PM	Protein Structure Prediction: Prognosis and diagnosis	Anna Tramontano
1:30-2:00PM	Examining Protein Structure And Similarities and predicting	Hong Gu
2:00-2:30PM	Sharing of T Cell Receptors In Antigen-Specific Responses Is Driven By Convergent Recombination	Vanessa Venturi
2:30-3:00 PM	Surface accessibility of post-translational modifications and protein-protein interactivity	Ignatius Pang
3:00-3:30 PM	Anisotropic atomic motion in proteins: comparison of experiment with theory	Conrad Burden
4:00 - 5:00 PM	Protein Structure Prediction: Applications and pitfalls	Anna Tramontano
Wednesday 06/12/2006
9:00-10:00 AM	Comparative Genomics: How Genomes Change, and Why We Should Care	Lars Jermiin
10:30-11:30 AM	Phylogenomics: Inferring the Phylogeny of Genomes using Maximum Likelihood	Lars Jermiin
11:30AM-12:30PM	Using Distances between Phylogenetic Trees	Susan Holmes
1:30-2:00PM	A few things about coevolution	Brett Easton
2:00-2:30PM	Gene Fusion in H.Pylori - Making the Ends Meet	Kinshore Sakharkar
2:30-3:00 PM	Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences	Sylvain Forêt
3:00-3:30 PM	Cytochrome P450 structures - A phylogenetic approach	Gowri Shankar
4:00 - 5:00 PM	Tree shape: can we detect non standard events from tree shape?	Susan Holmes
Thursday 07/12/2006
9:00-10:00 AM	Challenges in analysing Microarray Data	Yvonne Pittelkow
10:30-11:30 AM	Testing for Differential Gene Expression	Geoff McLachlan
11:30AM-12:30PM	Quality Assessment and Processing Affymetrix data	Robert Gentleman
1:30-2:00PM	Identification of Important Docking Parameters, Examplified for Calpain Inhibitors, with Cluster Analysis	Susan Kim
2:00-2:30PM	Gene Expression Network Analysis, and Applications to Immunology	Serban Nacu
2:30-3:00 PM	Statistical Analysis of SAGE Data	Mark Robinson
3:00-3:30 PM	Evaluation of Single Channel Oligonucleotide Microarray Preprocessing Pipelines Using Predictability and Reproducibility	Cameron Craddock
4:00-5:00 PM	Gene Set Enrichment Analysis	Robert Gentleman
Friday 08/12/2006
9:00-10:00 AM	Signal transduction for mathematicians: examples from the JAK-STAT and the EGFR pathways	Terry Speed
10:30-11:30 AM	Computational aspects of intracellular signalling	Terry Speed
11:30AM-12:30PM	Modelling and Simulation of Genetic Regulatory Networks	Hidde de Jong
1:30-2:00PM	Delineating breast cancer gene expression networks by RNA interference and global microarray analysis in human tumor cells	Mark Fellmann
2:00-2:30PM	Pipeline for the automated analysis of high-throughput reverse genetic assays using flow cytometry readouts	Florian Hahne
2:30-3:00 PM	Structure and Evolution of Gene Regulatory Networks	Joshua Ho
3:00-4:00 PM	Qualitative Simulation of the Carbon Starvation Response in Escherichia coli	Hidde de Jong