PhD Publications & Presentations

Ryan van Laar

ryan.vanlaar@petermac.org

Title:

Optimisation of cDNA microarray based tumour profiling and molecular profiling of ovarian cancer.

Research proposal:

Microarray technology allows for the rapid quantification of the entire human genome within a given tissue. Several important factors surrounding this technology such as the appropriate reference RNA for large-scale tumour profiling studies, normalisation, replication and hardware considerations will be tested and evaluated.

Following on from optimizing of several aspects of cDNA microarray profiling, analysis of ovarian cancer gene expression data will be carried out to investigate genes and pathways that correlate with patient outcome and also invasive and non-invasive forms of the disease.

Below is an archive of presentations, posters and articles I have either created or collaborated on during the period of my PhD candidature.

Date	Title	Description	Link
Aug 2002	The use of synthetic control genes for statistical validation of cDNA microarray data, within and between experiments	Essay for 'Statistics for Research Workers' postgraduate course @ Melbourne University.	PDF (0.9MB)
Aug 2002	Moods median test & array spatial bias	Presentation about the use of a statistical test to quantify spatial bias across the surface of a microarray.	JPEGS
Sep 2002	Integrating clinical & Molecular datasets to develop microarray-based cancer diagnostic tools	2002 Peter Mac PhD Student Committee talks.	PDF (0.7MB)
Sep 2002	Getting the most out of your microarray experiments - A comparison of reference RNA options on downstream data analysis	Peter Mac Research Hub Presentation.	JPEGS
Dec 2002	Options available - from start to finish - for obtaining data from DNA microarrays II	Nature Genetics Review article (co-author).	Pubmed\| PDF (0.5MB)
Dec 2002	Peter Mac Microarray data manipulation macro workbook	Visual Basic code for manipulation of raw microarray gene expression data files - implemented in Microsoft Excel.	Excel (0.2MB)
Jan 2003	Summary of publications involving microarray & clinical data integration	Table of relevant or novel journal articles where clinical or other non-molecular information is used in conjunction with expression data.	PDF (0.2MB)
Feb 2003	Bioinformatics tools for expression-based tumor classification	Talk given at Bioinformatics Workshop/Seminar held at St.Vincents hospital.	JPGs (<1MB)
Mar 2003	Comparison of data generated from Packard ScanArray 4000, ScanArray 5000 & Agilent Microarray slide scanners	Report & Centre for Cancer Genomics Hub presentation on statistical analysis and comparison of data generated on three different microarray scanners.	Report: PDF (0.3MB) Presentation: JPG
Mar 2003	PhD Confirmation	Written report & presentation for PhD confirmation process.	Report: PDF\| Presentation: JPEGS
Oct 2003	Student Committee Progress report	Tumor biology PhD Student Committee report	JPEGS
Jan 2004	School of graduate studies - Progress report	Two page summary of PhD progress to date.	PDF (1.5MB)
Feb 2004	Microarray Expression Analysis of Ovarian Cancer and Prediction of Patient Outcome	Poster presentation - Lorne Cancer Conference 2004	JPG (0.6MB)
Jun 2004	Genotypic and phenotypic analyses of a mouse model of spontaneous breast cancer metastasis	Molecular Cancer Research paper (co-author)	Pubmed
Aug 2004	Microarray profiling of invasive and low malignant potential ovarian cancer	Presentation at 2004 AOCS & Familial Cancer Clinics of Australia Conference	JPEGS
Sep 2004	Molecular Prognosis of Epithelial Ovarian Cancer	Review written for Cancer Council Gynecological Cancer Update newsletter	PDF (0.2MB)
Oct 2004	Identification and functional significance of genes regulated by structurally diverse histone deacetylase inhibitors	PNAS paper from collaborative project (co-author)	Pubmed \| PDF
Jan 2005	An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin	Cancer Research from collaborative project (co-author)	Pubmed \| PDF
Feb 2005	Understanding invasive ovarian cancer by microarray analysis and comparison with the low malignant potential phenotype.	Oral presentation and poster for AACR Oncogenomics Conference, San Diego, USA. [Astra-zenica Scholar-in-training award]	Poster: JPEG (1MB); Presentation JPEGS