CIBM News in Brief
September 2011
Ahmed Arefin won the Computer Science and Software Engineering Research Days Award for 2011 as a result of his doctoral work under the supervision of Prof Moscato and Dr Berretta.
May 2011
Journal of Clinical Bioinformatics: Thematic Series on Biomarkers in Human Disease
Due to rapid progress in highthroughput technologies and in the development of related bioinformatic methods in recent years, biomarker discovery efforts increasingly incorporate next generation sequencing or MS-based profiling of complex biological mixtures. Interest in the discovery of novel biomarkers unambiguously originates from their broad range of potential clinical applications and fundamental impact on pharmaceutical industry and the current public health burden.
We invite investigators to contribute original research articles, review articles or short reports that will stimulate the continuing efforts to understand the molecular mechanisms of disease, the development of technologies and computational tools to identify, verify and interpret novel biomarkers, and the evaluation and validation of outcomes.
March 2011
New paper in PLoS One!
In the paper, researchers from CIBM, Moscato, Berretta and Rocha de Paula, show that a specific pattern of cell signalling imbalance in blood plasma has valuable information to distinguish between Non Demented Controls (NDC) and Alzheimer's Disease (AD) samples. They obtained signatures that were able to predict AD in patients that already had a Mild Cognitive Impairment (MCI) with up to 84% of sensitivity, while maintaining also a strong prediction accuracy of 90% on an independent dataset with NDC and AD samples.
Stacked values of the Z-Scores of the 5-protein signature
March 2011
Scholarships available
We are seeking candidates for two PhD scholarships with a background in at least one of the following areas: computer science, mathematics, and statistics. Molecular or cell biology would also be desirable.
Interested applicants should first send an Expression of Interest to Prof. Pablo Moscato (CIBM Co-Director), a short email and a copy of CV and academic transcripts would be enough. Shortlisted candidates will be required to provide a 2-3 page research plan/interests. We need to ascertain whether your research interests match those of CIBM and its current research infrastructure for computing.
Please check our CIBM Cluster Summary information for more details on CIBM's infrastructure, or contact the Centre Manager if you require any further assistance.
February 2011
Prof Pablo Moscato, Mr Daniel Johnston and 4 other researchers from CIBM were awarded $50,000 by the Maitland Cancer Appeal in a ceremony on February 11.
The project, entitled "University of Newcastle Brain Tumour Drug Combination Project" will help determine new treatments for people diagnosed with malignant brain tumours.
An article with coverage of the ceremony can be found in the Maitland Mercury.
January 2011
New paper in PLoS One!
In this paper, CIBM researchers Moscato and Berretta and former CIBM member Inostroza-Ponta present a new data visualization approach (QAPgrid) that reveals patterns of similarities and differences in large datasets of objects for which a similarity measure can be computed. They use the Quadratic Assignment Problem (QAP) as a mathematical model to provide an objective function for assignment of objects to positions on the grid and employ a Memetic Algorithm (a powerful metaheuristic) to tackle the large instances of this NP-hard combinatorial optimization problem showing its performance on the visualization of real data sets.
A layout of the 24 clusters found by QAPgrid using as extra input the result of the MSTkNN algorithm on the Shanghai Jiao Tong University Academic Ranking of World Universities dataset.
December 2010
Our Biomarker Discovery Conference (BDC 2010) was a great success! Thanks to all who participated.
The inaugural Biomarker Discovery Conference (BDC 2010). BDC 2010 was held from 6 December to 10 December 2010 at Shoal Bay, NSW hosted by the Priority Research Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine. On the photo above, from left to right, Prof Jason Moore (Dartmouth Medical School, USA), Prof Pablo Moscato (CIBM, Australia), Dr Regina Berretta (CIBM, Australia) and Prof Greg Gibson (Georgia Tech, USA).
Conference Statistics:
12 invited Speakers - 6 from the USA
89 Registrations - 70 Scientists and 19 Students from 26 Institutions such as: Australian Research Council, University of California, Centre for Eye Research Australia, Charles Darwin University, Charles University Prague, Stanford University, China Academy of Medical Sciences, CSIRO, Garvan Institute,, Geneworks, Griffith University, Macquarie University, Osmania University India, Uni of Sydney, etc
9 Countries: Australia, Austria, USA, Singapore, China, Czech Republic, India, S. Korea, Taiwan
Sponsors:
ILLUMINA, MILLENNIUM SCIENCE/AFFYMETRIX, AusDIAGNOSTICS, BIOLINE, CBMI / HMRI, THE UNIVERSITY OF NEWCASTLE, NEWCASTLE INNOVATION, THERMO-FISHER, DSB, GRA - GENETIC REPOSITORIES AUSTRALIA.
The Hunter Medical Research Institute(HMRI) awarded $7,500 to the best presentations and posters by Students and Early Career Researchers. Professor John Rostas handed out the cetificates (and cheques!) to the happy winners (from left to right Mr Brian Gloss (Garvan Institute), Prof John Rostas (HMRI), Prof Pablo Moscato (CIBM), Dr Emilie Cameron (CIBM), Mr Dan Johnstone (CIBM), Ms Bushra Nasir (Griffith University), Mr William Tao (Melbourne University), Dr Kristina Warton (Garvan Institute), and Dr Christina Selinger (Royal Prince Albert Hospital).
Overview:
The Inaugural Biomarker Discovery Conference showcased the latest innovations in biomarker discovery using genomic, proteomic and metabolomic tools and methods. International experts in all these fields and bioinformatics presented at the meeting. Cancer and Neurobiology were important topics and specialist workshops on aspects of biomarker discovery, bioinformatics and applications were held. The main conclusion of the 5-day-long gathering was that the era of univariate biomarkers is passing, and that emerging bioinformatics applications applied to genome-scale datasets will provide fresh ways to think about the risks of disease.
In the media:
Articles about the conference can be found in Future Medicine (Pharmacogenomics) and in the Australian Epigenetics Alliance news page.