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Associate Professor Regina Berretta

Associate Professor

School of Elect Engineering and Computer Science (Computer Science and Software Engineering)

Computer science meets health innovation

Associate Professor Regina Berretta has long been interested in the crossover of the disciplines of computer science, mathematics and health, particularly where computer science has a key role to play in health innovation.

Associate Professor Regina Berretta 

With a degree in Computational and Applied Mathematics and a Master and PhD in the area of Metaheuristic methods for addressing Integer Programming problems, Associate Professor Berretta's research interests include combinatorial optimisation modelling with applications in the bioinformatics area with an emphasis on personalised medicine, and the development of metaheuristic methods including TABU search and memetic algorithms.

As a founding member of the Priority Research Centre for Bioinformatics, Biomarker Discovery and Information Based Medicine (CIBM), Associate Professor Berretta is a leading member of a multidisciplinary team that specialises in large-scale data analytics. The Centre excels in delivering novel, scientifically insightful, mathematically-literate, supercomputing-based processes for exploring and interpreting the massive datasets now being generated by modern society's deluge of information.

The team at the CIBM has spent a year analysing data from the international Alzheimer's Neuroimaging Initiative (ADNI) database, the most comprehensive collection of Alzheimer's data in the world. The research found that there is potential for a simple blood test to identify those in the early stages of Alzheimer's disease, before the onset of noticeable symptoms. The team believes the results are likely to be significant for the way Alzheimer's disease is diagnosed and point towards cheap, non-invasive testing techniques.

"One of the most fulfilling aspects of our work in bioinformatics is the perception that the outcomes are for the common good. Even when you are doing something that may look like a tiny incremental step on the existing knowledge, you have the satisfaction that it will contribute to improving someone's health or to have a better understanding of the cause of a disease", explains Associate Professor Berretta.

If her recent output is anything to go by, Berretta has established a strong reputation in the multidisciplinary field of bioinformatics. She has co-authored more than 60 papers and book chapters, presented at international conferences and received over $2 million in funding through 23 grants.

In 2014, Associate Professor Berretta and co-investigator Professor Pablo Moscato received a substantial Australian Research Council grant for their work on unleashing the power of a supernetwork-driven approach for bioinformatics. This research, now strengthened by the incorporation of graph theory expert Dr Luke Mathieson to the team, aims to push big-data based bioinformatics to the next level by developing practical techniques for analysing multiple large-scale network datasets in concert.

By combining multiple datasets, richer, more insightful relationships can be uncovered that would otherwise remain hidden when analysing the individual datasets alone. These techniques have wide application such as developing targeted therapies for diseases, generated by isolating and identifying the metabolic pathways employed by the disease, or to develop more robust understanding of regulatory networks by comparing networks across pathologies and species.

Currently a Chief Investigator at the ARC Training Centre for Food and Beverage Supply Chain Optimisation, Associate Professor Berretta's expertise in metaheuristics and integer programming mathematical models will be used in a different field. This Centre has received over $2 million in funding and will train the next generation of multidisciplinary researchers capable of designing, building, and managing these supply chains. Determining the best trade-off between the associated costs and the benefits so as to optimize the total profit is a critical problem facing fresh-product producers and distributors. This research project focuses on developing optimisation models to assist in the design and evaluation of cost-effective cold chains.

Associate Professor Berretta knows well that computer science and complex mathematics have an ever-increasing role to play in the future of health research and innovation, and is inspired to continue to combine her expertise to furthering the exciting and fulfilling field of bioinformatics, personalised medicine and Innovative solutions for the industry.

Associate Professor Regina Berretta

Computer science meets health innovation

Associate Professor Regina Berretta has long been interested in the crossover of the disciplines of computer science, mathematics and health, particularly where

Read more

Career Summary

Biography

Research Expertise
Computer Science Bioinformatics Heuristics and metaheuristics Evolutionary algorithms Operations Research

Teaching Expertise
computer programming languages

Administrative Expertise
Deputy Head of School of Electrical Engineering and Computer Science Head of Discipline of Computer Science and Software Engineering - Feb/2011 - Feb/2014 Computer Science Convernor - Feb/2007 - Feb/2011 Computer Science Convenor - Feb/2004 - Feb/2011

Qualifications

  • PhD, Universidade Estadual de Campinas - Brazil
  • Teachers Certificate, Universidade Estadual de Campinas - Brazil
  • Bachelor of Mathematics, Universidade Estadual de Campinas - Brazil
  • Master of Engineering (Electrical), Universidade Estadual de Campinas - Brazil

Keywords

  • Java
  • bioinformatics
  • combinatorial optimization
  • computer programming languages
  • evolutionary computation
  • heuristics and metaheuristics
  • heuristics/metaheuristics
  • memetic algorithms
  • object oriented computer languages
  • operations research

Languages

  • Portuguese (Fluent)
  • Spanish (Fluent)

Fields of Research

Code Description Percentage
060499 Genetics not elsewhere classified 20
080108 Neural, Evolutionary and Fuzzy Computation 40
080199 Artificial Intelligence and Image Processing not elsewhere classified 40

Professional Experience

UON Appointment

Title Organisation / Department
Associate Professor University of Newcastle
School of Elect Engineering and Computer Science
Australia

Academic appointment

Dates Title Organisation / Department
1/02/2003 -  Lecturer University of Newcastle
Faculty of Engineering and Built Environment
Australia
1/07/1999 -  Lecturer San Francisco University
United States

Invitations

Participant

Year Title / Rationale
2006 Combinatorial optimization models for finding genetic signature from gene expression
Organisation: 2006 Student Symposium in Bioinformatics Description: tutorial Auckland, 1115 July
2006 Combinatorial optimization models for finding genetic signatures from gene expression
Organisation: 2006 Winter School in Mathematical and Computational Biology Description: tutorial Queensland Bioscience Precint, Brisbane, 2630 June.
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Chapter (8 outputs)

Year Citation Altmetrics Link
2014 Lachiondo JA, Ujaldón M, Berretta R, Moscato P, 'Quantifying the regeneration of bone tissue in biomedical images via Legendre moments', Computational Vision and Medical Image Processing IV, CRC Press, Boca Raton, FL 289-294 (2014) [B1]
DOI 10.1201/b15810-51
Co-authors Pablo Moscato
2012 Berretta RE, Cotta C, Moscato PA, 'Memetic algorithms in bioinformatics', Handbook of Memetic Algorithms, Springer, Berlin, Germany 261-271 (2012) [B1]
Co-authors Pablo Moscato
2011 Moscato PA, Berretta RE, Cotta C, 'Memetic algorithms', , Hoboken, NJ 1-24 (2011) [D1]
Co-authors Pablo Moscato
2009 Ravetti MG, Berretta RE, Moscato PA, 'Novel biomarkers for prostate cancer revealed by ([alpha, beta]) -k-feature sets', Foundations of Computational Intelligence Volume 5: Functional Approximation and Classification, Springer, Berlin 149-175 (2009) [C2]
DOI 10.1007/978-3-642-01536-6
Citations Scopus - 2
Co-authors Pablo Moscato
2008 Berretta R, Costa W, Moscato P, 'Combinatorial optimization models for finding genetic signatures from gene expression datasets', 363-377 (2008) [B1]

The aim of this chapter is to present combinatorial optimization models and techniques for the analysis of microarray datasets. The chapter illustrates the application of a novel ... [more]

The aim of this chapter is to present combinatorial optimization models and techniques for the analysis of microarray datasets. The chapter illustrates the application of a novel objective function that guides the search for high-quality solutions for sequential ordering of expression profiles. The approach is unsupervised and a metaheuristic method (a memetic algorithm) is used to provide high-quality solutions. For the problem of selecting discriminative groups of genes, we used a supervised method that has provided good results in a variety of datasets. This chapter illustrates the application of these models in an Alzheimer's disease microarray dataset. © 2008 Humana Press, a part of Springer Science+Business Media, LLC.

DOI 10.1007/978-1-60327-429-6_19
Citations Scopus - 13
Co-authors Pablo Moscato
2008 Hourani MA, Berretta RE, Mendes ADS, Moscato PA, 'Genetic signatures for a rodent model of Parkinson's disease using combinatorial optimization methods', Bioinformatics, Humana Press, New York 379-392 (2008) [B1]
DOI 10.1007/978-1-60327-429-6
Citations Scopus - 6
Co-authors Alexandre Mendes, Pablo Moscato
2004 Berretta RE, Cotta C, Moscato PA, 'Enhancing the performance of memetic algorithms by using a matching-based recombination algorithm', Metaheuristics: Computer Decision-Making, Kluwer Academic Publishers, The Netherlands 719 (2004) [B1]
Citations Web of Science - 6
Co-authors Pablo Moscato
1999 Berretta RE, moscato, 'The Number Partitioning Problem, An Open Challenge For Evolutionary Computation?', New Ideas In Optimisation, McGraw-Hill, Maidenhead, UK, England (1999)
Co-authors Pablo Moscato
Show 5 more chapters

Journal article (26 outputs)

Year Citation Altmetrics Link
2016 Rocha de Paula M, Berretta R, Moscato P, 'A fast meta-heuristic approach for the (a, ß) - k-feature set problem', Journal of Heuristics, 22 199-220 (2016) [C1]

© 2015, Springer Science+Business Media New York.The feature selection problem aims to choose a subset of a given set of features that best represents the whole in a particular a... [more]

© 2015, Springer Science+Business Media New York.The feature selection problem aims to choose a subset of a given set of features that best represents the whole in a particular aspect, preserving the original semantics of the variables on the given samples and classes. In 2004, a new approach to perform feature selection was proposed. It was based on a NP-complete combinatorial optimisation problem called ((Formula presented.))-k-feature set problem. Although effective for many practical cases, which made the approach an important feature selection tool, the only existing solution method, proposed on the original paper, was found not to work well for several instances. Our work aims to cover this gap found on the literature, quickly obtaining high quality solutions for the instances that existing approach can not solve. This work proposes a heuristic based on the greedy randomised adaptive search procedure and tabu search to address this problem; and benchmark instances to evaluate its performance. The computational results show that our method can obtain high quality solutions for both real and the proposed artificial instances and requires only a fraction of the computational resources required by the state of the art exact and heuristic approaches which use mixed integer programming models.

DOI 10.1007/s10732-015-9307-0
Co-authors Pablo Moscato
2016 Puthiyedth N, Riveros C, Berretta R, Moscato P, 'Identification of Differentially Expressed Genes through Integrated Study of Alzheimer's Disease Affected Brain Regions.', PLoS One, 11 e0152342 (2016)
DOI 10.1371/journal.pone.0152342
Co-authors Pablo Moscato, Carlos Riveros
2016 Lachiondo JA, Ujaldón M, Berretta R, Moscato P, 'Legendre moments as high performance bone biomarkers: computational methods and GPU acceleration', Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization, 4 146-163 (2016)

© 2014 Informa UK Limited, trading as Taylor & Francis Group.We investigate the use of Legendre moments as biomarkers for an efficient and accurate classification of bone tissue ... [more]

© 2014 Informa UK Limited, trading as Taylor & Francis Group.We investigate the use of Legendre moments as biomarkers for an efficient and accurate classification of bone tissue on images coming from stem cell regeneration studies. Legendre moments are analysed from three different perspectives: (1) their discriminant properties in a wide set of preselected vectors of features based on our clinical and computational experience, providing solutions whose accuracy exceeds 90%; (2) the amount of information to be retained when using principal component analysis to reduce the dimensionality of the problem to either 2, 3, 4, 5 or 6 dimensions and (3) the use of the (Formula presented.) -k-feature set problem to identify a k¿=¿4 number of features which are more relevant to our analysis from a combinatorial optimisation approach. These techniques are compared in terms of computational complexity and classification accuracy to assess the strengths and limitations of the use of Legendre moments. The second contribution of this work goes to reduce the computational complexity by using graphics processing units (GPUs) and compute unified device architecture programming [Nvidia Developer Zone. 2014. CUDA. Available from: http:developer.nvidia.comobjectcuda.html]. We exploit single instruction multiple data parallelism and memory bandwidth on GPUs to accelerate the process to more than a 5 ׿ factor on each 64¿×¿64 image tile. The result is a powerful combination of software and hardware methods which deliver a much faster response in contrast with existing solutions coming from conventional programming on multicore CPU platforms, thus offering a high performance alternative in clinical practice for real-time imaging.

DOI 10.1080/21681163.2014.922437
Co-authors Pablo Moscato
2016 Naeni LM, Craig H, Berretta R, Moscato P, 'A Novel Clustering Methodology Based on Modularity Optimisation for Detecting Authorship Affinities in Shakespearean Era Plays.', PLoS One, 11 e0157988 (2016)
DOI 10.1371/journal.pone.0157988
Co-authors Hugh Craig, Pablo Moscato
2016 Haque MN, Noman N, Berretta R, Moscato P, 'Heterogeneous ensemble combination search using genetic algorithm for class imbalanced data classification', PLoS ONE, 11 (2016) [C1]

© 2016 Haque et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and repr... [more]

© 2016 Haque et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Classification of datasets with imbalanced sample distributions has always been a challenge. In general, a popular approach for enhancing classification performance is the construction of an ensemble of classifiers. However, the performance of an ensemble is dependent on the choice of constituent base classifiers. Therefore, we propose a genetic algorithm-based search method for finding the optimum combination from a pool of base classifiers to form a heterogeneous ensemble. The algorithm, called GA-EoC, utilises 10 fold-cross validation on training data for evaluating the quality of each candidate ensembles. In order to combine the base classifiers decision into ensemble's output, we used the simple and widely used majority voting approach. The proposed algorithm, along with the random sub-sampling approach to balance the class distribution, has been used for classifying class-imbalanced datasets. Additionally, if a feature set was not available, we used the (a, ß) - k Feature Set method to select a better subset of features for classification. We have tested GA-EoC with three benchmarking datasets from the UCI-Machine Learning repository, one Alzheimer's disease dataset and a subset of the PubFig database of Columbia University. In general, the performance of the proposed method on the chosen datasets is robust and better than that of the constituent base classifiers and many other well-known ensembles. Based on our empirical study we claim that a genetic algorithm is a superior and reliable approach to heterogeneous ensemble construction and we expect that the proposed GA-EoC would perform consistently in other cases.

DOI 10.1371/journal.pone.0146116
Co-authors Nasimul Noman, Mohammad Haque, Pablo Moscato
2016 Milioli HH, Vimieiro R, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset.', BioData Min, 9 2 (2016) [C1]
DOI 10.1186/s13040-015-0078-9
Citations Scopus - 1Web of Science - 1
Co-authors Pablo Moscato, Inna Tishchenko, Carlos Riveros
2015 Puthiyedth N, Riveros C, Berretta R, Moscato P, 'A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study.', PLoS One, 10 e0127702 (2015) [C1]
DOI 10.1371/journal.pone.0127702
Citations Scopus - 1Web of Science - 1
Co-authors Pablo Moscato, Carlos Riveros
2015 Milioli HH, Vimieiro R, Riveros C, Tishchenko I, Berretta R, Moscato P, 'The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set.', PLoS One, 10 e0129711 (2015) [C1]
DOI 10.1371/journal.pone.0129711
Citations Scopus - 2Web of Science - 2
Co-authors Pablo Moscato, Inna Tishchenko, Carlos Riveros
2013 Nunes LF, Galvão LC, Lopes HS, Moscato P, Berretta R, 'An integer programming model for protein structure prediction using the 3D-HP side chain model', Discrete Applied Mathematics, (2013)

© 2015 Elsevier B.V.In spite of the fact that many simplified model variants of protein structure prediction have been widely studied in the past years, few attention has been gi... [more]

© 2015 Elsevier B.V.In spite of the fact that many simplified model variants of protein structure prediction have been widely studied in the past years, few attention has been given to discrete models with side chains, for which there is no specific benchmark. In this paper, we propose an integer programming model for the 3D-HP side chain protein structure prediction problem. The model accounts for the energy resulting from all types of interactions, between pairs of backbone elements, hydrophilic side chains and hydrophobic side chains. Three sets of instances, modified from the literature, were used in the experiments, and the maximum number of non-local hydrophobic contact was found using the ILOG CPLEX optimization package. We offer the optimal solution found for several instances of the benchmark. It is expected that the mathematical model allow further studies of the protein structure prediction with side chains and may, for some cases, provide new optimal values or new bounds that would rekindle the interest to this fascinating problem domain.

DOI 10.1016/j.dam.2015.06.021
Co-authors Pablo Moscato
2013 Johnstone DM, Riveros C, Heidari M, Graham RM, Trinder D, Berretta R, et al., 'Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes', Microarrays, 2 131-152 (2013) [C1]
Co-authors Rodney Scott, Pablo Moscato, Liz Milward, Carlos Riveros
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'GPU-FS-kNN: A software tool for fast and scalable kNN computation using GPUs', PLOS One, 7 e44000 (2012) [C1]
Citations Scopus - 22Web of Science - 16
Co-authors Carlos Riveros, Pablo Moscato
2012 Arefin AS, Mathieson L, Johnstone DM, Berretta RE, Moscato PA, 'Unveiling clusters of RNA transcript pairs associated with markers of Alzheimer's disease progression', PLOS One, 7 1-25 (2012) [C1]
Citations Scopus - 17Web of Science - 16
Co-authors Pablo Moscato, Luke Mathieson
2012 Johnstone DM, Milward AE, Berretta RE, Moscato PA, 'Multivariate protein signatures of pre-clinical Alzheimer's disease in the Alzheimer's disease meuroimaging initiative (ADNI) plasma proteome dataset', PLoS One, 7 e34341 (2012) [C1]
Citations Scopus - 34Web of Science - 26
Co-authors Liz Milward, Pablo Moscato
2011 Inostroza-Ponta M, Berretta RE, Moscato PA, 'QAPgrid: A two level QAP-based approach for large-scale data analysis and visualization', PLoS ONE, 6 e14468 (2011) [C1]
DOI 10.1371/journal.pone.0014468
Citations Scopus - 13Web of Science - 12
Co-authors Pablo Moscato
2011 Rocha De Paula M, Gomez Ravetti M, Berretta RE, Moscato PA, 'Differences in abundances of cell-signalling proteins in blood reveal novel biomarkers for early detection of clinical alzheimer's disease', PLoS ONE, 6 e17481 (2011) [C1]
Citations Scopus - 19Web of Science - 12
Co-authors Pablo Moscato
2010 Berretta RE, Moscato PA, 'Cancer biomarker discovery: The entropic hallmark', Plos One, 5 e12262 (2010) [C1]
DOI 10.1371/journal.pone.0012262
Citations Scopus - 27Web of Science - 17
Co-authors Pablo Moscato
2010 Ravetti MG, Rosso OA, Berretta RE, Moscato PA, 'Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease', Plos One, 5 1-42 (2010) [C1]
DOI 10.1371/journal.pone.0010153
Citations Scopus - 64Web of Science - 53
Co-authors Pablo Moscato
2010 Riveros RC, Mellor D, Gandhi KS, McKay FC, Cox MB, Berretta RE, et al., 'A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis', Plos One, 5 1-28 (2010) [C1]
DOI 10.1371/journal.pone.0014176
Citations Scopus - 27Web of Science - 26
Co-authors Carlos Riveros, Rodney Scott, Pablo Moscato
2009 Rosso OA, Mendes ADS, Berretta RE, Rostas JA, Hunter M, Moscato PA, 'Distinguishing childhood absence epilepsy patients from controls by the analysis of their background brain electrical activity (II): A combinatorial optimization approach for electrode selection', Journal of Neuroscience Methods, 181 257-267 (2009) [C1]
DOI 10.1016/j.jneumeth.2009.04.028
Citations Scopus - 12Web of Science - 14
Co-authors Pablo Moscato, John Rostas, Alexandre Mendes, Mick Hunter
2007 De Oliveira LK, Berretta RE, 'An approach based on langranian relaxation and the taboo search for the multi-stage lot sizing problem', GEPROS: Gestao da Producao, Operacoes e Sistemas, 4 77-93 (2007) [C1]
2007 Berretta RE, Mendes ADS, Moscato PA, 'Selection of discriminative genes in microarray experiments using mathematical programming', Journal of Research and Practice in Information Technology, 39 287-299 (2007) [C1]
Citations Scopus - 12Web of Science - 9
Co-authors Pablo Moscato, Alexandre Mendes
2007 Moscato PA, Mendes ADS, Berretta RE, 'Benchmarking a Memetic Algorithm for Ordering Microarray Data', Biosystems, 88 56-75 (2007) [C1]
DOI 10.1016/j.biosystems.2006.04.005
Citations Scopus - 32Web of Science - 30
Co-authors Pablo Moscato, Alexandre Mendes
2005 Berretta RE, Franca PM, Armentano VA, 'Metaheuristic approaches for the multilevel resource-constrained lot-sizing problem with setup and lead times', Asia-Pacific Journal of Operational Research, 22 261-286 (2005) [C1]
DOI 10.1142/S0217595905000510
Citations Scopus - 18Web of Science - 14
2004 Berretta RE, Rodrigues LF, 'A memetic algorithm for a multistage capacitated lot-sizing problem', International journal of production economics, 87 67-81 (2004) [C1]
DOI 10.1016/S0925-5273(03)00093-8
Citations Scopus - 45Web of Science - 41
2001 Armentano VA, Berretta RE, Franca PM, 'Lot-sizing in capacitated multi-stage serial systems', PRODUCTION AND OPERATIONS MANAGEMENT, 10 68-86 (2001)
Citations Scopus - 5Web of Science - 2
1997 Franca PM, Armentano VA, Berretta RE, Clark AR, 'A heuristic method for lot-sizing in multi-stage systems', COMPUTERS & OPERATIONS RESEARCH, 24 861-874 (1997)
DOI 10.1016/S0305-0548(96)00097-4
Citations Scopus - 27Web of Science - 22
Show 23 more journal articles

Conference (40 outputs)

Year Citation Altmetrics Link
2016 Haque MN, Noman N, Berretta R, Moscato P, 'Optimising weights for heterogeneous ensemble of classifiers with differential evolution', Evolutionary Computation (CEC), 2016 IEEE Congress on (2016)
DOI 10.1109/CEC.2016.7743800
Co-authors Mohammad Haque, Pablo Moscato, Nasimul Noman
2015 Harris M, Berretta R, Inostroza-Ponta M, Moscato P, 'A Memetic Algorithm for the Quadratic Assignment Problem with parallel local search', 2015 IEEE Congress on Evolutionary Computation, CEC 2015 - Proceedings (2015) [E1]

© 2015 IEEE.The Quadratic Assignment Problem (QAP) is a well-studied, NP-Hard combinatorial optimization problem with practical applications in timetabling, scheduling, logistics... [more]

© 2015 IEEE.The Quadratic Assignment Problem (QAP) is a well-studied, NP-Hard combinatorial optimization problem with practical applications in timetabling, scheduling, logistics, circuit design and data visualisation, to name a few. In this paper a Memetic Algorithm is described, which utilises a ternary tree structure for its population and uses a Tabu Search as its local improvement strategy. The Tabu Search is also run in parallel, significantly reducing the running time of the algorithm. The ternary tree not only stores the individuals within the population, but the inherent structure within this tree also determines parent selection for crossover. A small number of rules, which include fitness and diversity-based rules, govern whether a newly produced solution remains within the population, or whether it is discarded. These key features are tested against a basic Memetic Algorithm using the instances from the QAP library, QAPLIB, and have shown to significantly improve the performance in terms of both time and solution quality. The best version of the Memetic Algorithm is shown to perform competitively with some of the state-of-the-art algorithms for the QAP from the literature, with grid-based and real-life instances shown to be solved very efficiently and effectively by the presented algorithms.

DOI 10.1109/CEC.2015.7256978
Co-authors Pablo Moscato
2015 Milioli H, Tishchenko I, Riveros C, Berretta R, Moscato P, 'BASAL-LIKE BREAST CANCER SUBGROUPS UNCOVERED BY GENOMIC AND TRANSCRIPTOMIC PROFILES AND OVERALL SURVIVAL OUTCOMES', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
Co-authors Pablo Moscato, Inna Tishchenko, Carlos Riveros
2015 Arefin AS, Riveros C, Berretta R, Moscato P, 'The MST-kNN with paracliques', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (2015) [E1]

© Springer International Publishing Switzerland 2015.In this work, we incorporate new edges from a paracliqueidentification approach to the output of theMST-kNN graph partitionin... [more]

© Springer International Publishing Switzerland 2015.In this work, we incorporate new edges from a paracliqueidentification approach to the output of theMST-kNN graph partitioning method. We present a statistical analysis of the results on a dataset originated from a computational linguistic study of 84 Indo-European languages. We also present results from a computational stylistic study of 168 plays of the Shakespearean era. For the latter, results of the Kruskal- Wallis test 1 (observed vs. all permutations) showed a p-value of a 1.62E- 11 and a Wilcoxon test a p-value of 8.1E-12. Overall, our results clearly show in both cases that the modified approach provides statistically more significant results than the use of the MST-kNN alone, thus providing a highly-scalable alternative and statistically sound approach for data clustering.

Citations Web of Science - 1
Co-authors Carlos Riveros, Pablo Moscato
2015 Zaher AA, Berretta RE, Arefin AS, Moscato P, 'FSMEC: A Feature Selection Method based on the Minimum Spanning Tree and Evolutionary Computation', Conferences in Research and Practice in Information Technology (CRPIT) (2015) [E1]
Co-authors Pablo Moscato
2015 Arefin AS, Berretta RE, Moscato P, 'On Ranking Nodes using kNN Graphs, Shortest-paths and GPUs', Conferences in Research and Practice in Information Technology (CRPIT) (2015) [E1]
Co-authors Pablo Moscato
2015 Milioli HH, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Molecular classification of basal-like breast cancer subtypes based on predictive survival markers', ANNALS OF ONCOLOGY (2015) [E3]
DOI 10.1093/annonc/mdv117.11
Co-authors Carlos Riveros, Inna Tishchenko, Pablo Moscato
2015 Milioli HH, Tishchenko I, Riveros C, Sakoff J, Berretta R, Moscato P, 'Consensus on breast cancer cell lines classification for an effective and efficient clinical decision-making', ANNALS OF ONCOLOGY (2015) [E3]
DOI 10.1093/annonc/mdv121.8
Co-authors Jennette Sakoff, Inna Tishchenko, Carlos Riveros, Pablo Moscato
2015 Milioli HH, Vimieiro R, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Refining the breast cancer molecular subtypes in the METABRIC data set' (2015) [O1]
Co-authors Inna Tishchenko, Pablo Moscato
2015 Puthiyedth N, Riveros C, Berretta R, Moscato P, 'A NOVEL COMBINATORIAL OPTIMISATION APPROACH FOR FEATURE SELECTION VIA INTEGRATION OF INFORMATION FROM MULTIPLE DATASETS', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
Co-authors Carlos Riveros, Pablo Moscato
2015 Moslemi Naeni L, Moscato PA, Berretta RE, 'MA-Net: A Reliable Memetic Algorithm for Community Detection by Modularity Optimization', Proceedings of the 18th Asia Pacific Symposium on Intelligent and Evolutionary Systems, Volume 1 (2015) [E1]
DOI 10.1007/978-3-319-13359-1_25
Citations Web of Science - 1
Co-authors Pablo Moscato
2014 Riveros C, Milioli H, Vimieiro R, Berretta R, Moscato P, 'Discovery of gene interactions by GPU-enabled computation of pairwise expression level metafeatures', International Conference in Bioinformatics InCoB2014 (2014) [E3]
Co-authors Pablo Moscato, Carlos Riveros
2014 Prieto-Rodriguez E, Berretta R, 'Digital Technology Teachers' Perceptions of Computer Science: It Is Not All About Programming', 2014 IEEE Frontiers in Education Conference Proceedings (2014) [E1]
DOI 10.1109/FIE.2014.7044134
Co-authors Elena Prieto
2014 Milioli HH, Vimieiro R, Riveros C, Berretta R, Moscato P, 'Meta-features as predictors of breast cancer intrinsic subtypes in the METABRIC gene expression dataset', International Conference in Bioinformatics InCoB2014 (2014)
Co-authors Pablo Moscato
2014 Moslemi Naeni L, de Vries N, Reis R, Arefin AS, Berretta R, Moscato P, 'Identifying Communities of Trust and Confidence in the Charity and Not-for-Profit Sector: A Memetic Algorithm Approach', Proceedings IEEE Fourth International Conference on Big Data and Cloud Computing (BdCloud) 2014 (2014) [E1]
DOI 10.1109/BDCloud.2014.83
Citations Scopus - 1
Co-authors Pablo Moscato, Natalie Devries
2014 Lucas B, Arefin AS, de Vries NJD, Berretta R, Carlson J, Moscato P, 'Engagement in Motion: Exploring Short Term Dynamics in Page-Level Social Media Metrics', Proceedings of the 2014 IEEE Fourth International Conference on Big Data and Cloud Computing (2014) [E1]
DOI 10.1109/BDCloud.2014.56
Co-authors Pablo Moscato, Natalie Devries, Jamie Carlson
2014 Jayasooriya S, Johnson SJ, Ong L, Berretta R, 'Optimization of graph based codes for belief propagation decoding', Information Theory Workshop (ITW), 2014 IEEE (2014) [E1]
DOI 10.1109/ITW.2014.6970873
Citations Scopus - 1
Co-authors Sarah Johnson, Lawrence Ong
2013 Arefin AS, Berretta R, Moscato P, 'A GPU-based Method for Computing Eigenvector Centrality of Gene-expression Networks', Proceedings of the Eleventh Australasian Symposium on Parallel and Distributed Computing (AusPDC 2013) (2013) [E1]
Co-authors Pablo Moscato
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'Computing large-scale distance matrices on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education (2012) [E1]
Co-authors Pablo Moscato, Carlos Riveros
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'kNN-MST-Agglomerative: A fast and scalable graph-based data clustering approach on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education (2012) [E1]
Citations Scopus - 8
Co-authors Carlos Riveros, Pablo Moscato
2012 Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'kNN-Boruvka-GPU: A fast and scalable MST construction from kNN graphs on GPU', Lecture Notes in Computer Science (2012) [E1]
Citations Scopus - 3Web of Science - 6
Co-authors Pablo Moscato, Carlos Riveros
2011 Arefin AS, Inostroza-Ponta M, Mathieson L, Berretta RE, Moscato PA, 'Clustering nodes in large-scale biological networks using external memory algorithms', Algorithms and Architectures for Parallel Processing (2011) [E1]
DOI 10.1007/978-3-642-24669-2_36
Citations Scopus - 4Web of Science - 6
Co-authors Pablo Moscato, Luke Mathieson
2010 Arefin AS, Berretta RE, Moscato PA, 'An external memory approach for clustering of large-scale biological networks', Biomarker Discovery Conference (2010) [E3]
Co-authors Pablo Moscato
2010 Arefin AS, Berretta RE, Moscato P, 'A systematic analysis of 1,881,012 ratios and differences of the gene expression values on hippocampus in Alzheimer¿s Disease patients reveals pairs of protein-coding and noncoding RNAs that are highly correlated with the Mini-Mental State Examination values' (2010)
Co-authors Pablo Moscato
2010 Milward, Ravetti M, Rosso O, Berretta RE, Johnstone D, Moscato P, 'A new approach to tracking progression of molecular pathogenesis in Alzheimer¿s disease identifies hippocampla iron dyshomeostasis as a novel potential biomarker' (2010)
Co-authors Liz Milward, Pablo Moscato
2010 Dinger M, Arefin A, Berretta RE, Moscato P, 'The hippocampal expression of 31 noncoding RNAs is upregulated in Alzheimer¿s Disease patients and three positively correlate with MMSE results and other biomarkers of disease progression' (2010)
Co-authors Pablo Moscato
2010 Moscato P, Ravetti M, Rosso O, Berretta RE, 'Towards a multi-marker molecular signature that identifies biomarkers that correlate with cognitive decline in Alzheimer¿s Disease: The Entropic Perspective' (2010)
Co-authors Pablo Moscato
2009 Berretta RE, Giggins HP, 'Online support material for computer science honours program using Blackboard', Proceedings 2009 2nd IEEE International Conference on Computer Science and Information Technology (2009) [E1]
DOI 10.1109/iccsit.2009.5234460
Co-authors Helen Giggins
2009 Milward AE, Johnstone DM, Ravetti MG, Berretta RE, Hersey P, Scott R, Moscato PA, 'The relationship between Parkinson's disease and melanoma: Insights from microarray analysis of genome-wide gene expression changes in melanoma', ASMR National Scientific Conference 2009. Proceedings of The Australian Society for Medical Research, 48th National Scientific Conference (2009) [E3]
Co-authors Rodney Scott, Pablo Moscato, Liz Milward
2007 Cox M, Bowden NA, Moscato PA, Berretta RE, Scott R, 'Memetic algorithms as a new method to interpret gene expression profiles in multiple sclerosis', Multiple Sclerosis (Abstracts of the 23rd Congress of the European Committee for Treatment and Research in Multiple Sclerosis and the 12th Annual Conference of Rehabilitation in Multiple Sclerosis) (2007) [E3]
Citations Web of Science - 2
Co-authors Nikola Bowden, Rodney Scott, Pablo Moscato
2007 Hourani MA, Mendes ADS, Berretta RE, Moscato PA, 'Genetic biomarkers for brain hemisphere differentiation in Parkinson's Disease', Computational Models for Life Sciences (CMLS '07): 2007 International Symposium. Conference Proceedings (2007) [E1]
Citations Scopus - 2Web of Science - 2
Co-authors Alexandre Mendes, Pablo Moscato
2007 Tuga M, Berretta RE, Mendes ADS, 'A hybrid simulated annealing with kempe chain neighborhood for the university timetabling problem', Proceedings of the 6th IEEE/ACIS International Conference on Computer and Information Science (2007) [E1]
DOI 10.1109/icis.2007.25
Citations Scopus - 13Web of Science - 5
Co-authors Alexandre Mendes
2007 Inostroza-Ponta M, Mendes ADS, Berretta RE, Moscato PA, 'An integrated QAP-based approach to visualize patterns of gene expression similarity', Progress in Artificial Life (2007) [E1]
DOI 10.1007/978-3-540-76931-6_14
Citations Scopus - 2Web of Science - 11
Co-authors Alexandre Mendes, Pablo Moscato
2006 Inostroza-Ponta M, Berretta RE, Mendes ADS, Moscato PA, 'An automatic graph layout procedure to visualize correlated data', Artificial Intelligence in Theory and Practice (2006) [E1]
Citations Scopus - 7Web of Science - 9
Co-authors Pablo Moscato, Alexandre Mendes
2005 Berretta RE, Mendes ADS, Moscato PA, 'Integer Programming Models and Algorithms for Molecular Classification of Cancer from Microarray Data', Proceedings of the twenty eighth Australasian Computer Science Conference (ACSC 2005) Newcastle, Australia, January, 2005 (2005) [E1]
Citations Scopus - 1
Co-authors Alexandre Mendes, Pablo Moscato
2005 Moscato PA, Mathieson L, Mendes ADS, Berretta RE, 'The Electronic Primaries: Predicting the U.S. Presidency Using Feature Selection with Safe Data Reduction', Proceedings of the twenty eighth Australasian Computer Science Conference (ACSC 2005) Newcastle, Australia, January, 2005 (2005) [E1]
Citations Scopus - 1
Co-authors Pablo Moscato, Alexandre Mendes, Luke Mathieson
2005 Moscato PA, Berretta RE, Hourani MA, Mendes ADS, Cotta C, 'Genes related with Alzheimer's disease: A comparison of evolutionary search, statistical and integer programming approaches', Applications on Evolutionary Computing: EvoWorkkshops 2005: EvoBIO, EvoCOMNET, EvoHOT, EvoIASP, EvoMUSART, and EvoSTOC (2005) [E1]
Citations Scopus - 7Web of Science - 11
Co-authors Alexandre Mendes, Pablo Moscato
2005 Berretta RE, Cotta C, Hourani MA, Mendes ADS, Moscato PA, 'Hacia una Mejor Compresion del Perfil Genetico de la Enfermedad de Alzheimer a Traves de Metaheuristicas', Proceedings of the MAEB2005 (2005) [E2]
Co-authors Pablo Moscato, Alexandre Mendes
2005 Moscato PA, Berretta RE, Mendes ADS, 'A New Memetic Algorithm for Ordering Datasets: Applications in Microarray Analysis', Proceedings of MIC2005 (2005) [E2]
Co-authors Alexandre Mendes, Pablo Moscato
2001 Berretta RE, Moscato P, Cotta C, 'Forma Analysis and New Heuristic Ideas for the Number Partitioning Problem' (2001)
Co-authors Pablo Moscato
Show 37 more conferences
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Grants and Funding

Summary

Number of grants 34
Total funding $5,226,867

Click on a grant title below to expand the full details for that specific grant.


20161 grants / $10,000

CS4HS Workshop$10,000

Funding body: Google Australia Pty Ltd

Funding body Google Australia Pty Ltd
Project Team Doctor Elena Prieto-Rodriguez, Associate Professor Regina Berretta, Mr Andrew Lyell
Scheme Donation
Role Investigator
Funding Start 2016
Funding Finish 2016
GNo G1600629
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON Y

20151 grants / $14,832

CS4HS workshop$14,832

Funding body: Google Australia Pty Ltd

Funding body Google Australia Pty Ltd
Project Team Doctor Elena Prieto-Rodriguez, Associate Professor Regina Berretta, Mr Andrew Lyell
Scheme Donation
Role Investigator
Funding Start 2015
Funding Finish 2015
GNo G1500616
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON Y

201410 grants / $2,897,839

Food & Beverage Supply Chain Optimisation Industrial Transformation Training Centre$2,119,872

Funding body: ARC (Australian Research Council)

Funding body ARC (Australian Research Council)
Project Team Professor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Tim Norris, Mr Robert Scoines, Associate Professor Christopher Scarlett
Scheme Industrial Transformation Training Centres
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1301004
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON Y

Unleashing the power of a supernetwork-driven approach for bioinformatics$364,974

Funding body: ARC (Australian Research Council)

Funding body ARC (Australian Research Council)
Project Team Professor Pablo Moscato, Associate Professor Regina Berretta
Scheme Discovery Projects
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1300392
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON Y

Aceleración en GPU del Procesamiento de Datos Genómicos e Imágenes Biomédicas de Alta Resolución$131,382

Funding body: Ciencia y Empleo de la Junta de Andalucia

Funding body Ciencia y Empleo de la Junta de Andalucia
Project Team

Manuel Ujaldón Martínez

Scheme Proyectos de Excelencia de la Consejería de Economía, Innovación
Role Investigator
Funding Start 2014
Funding Finish 2017
GNo
Type Of Funding Not Known
Category UNKN
UON N

Computational prediction and functional clarification of novel drug combination strategies for the treatment of brain tumours$100,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Professor Pablo Moscato, Associate Professor Regina Berretta
Scheme Project Grant
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1400454
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

Food & Beverage Supply Chain Optimisation Industrial Transformation Training Centre$90,000

Funding body: Coca Cola Amatil (Australia)

Funding body Coca Cola Amatil (Australia)
Project Team Professor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Associate Professor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
Scheme Industrial Transformation Training Centres Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1301129
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

Food & Beverage Supply Chain Optimisation Industrial Transformation Training Centre$30,000

Funding body: Sanitarium Health and Wellbeing Company

Funding body Sanitarium Health and Wellbeing Company
Project Team Professor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Associate Professor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
Scheme Industrial Transformation Training Centres Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1301130
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

Food & Beverage Supply Chain Optimisation Industrial Transformation Training Centre$30,000

Funding body: Sunrice

Funding body Sunrice
Project Team Professor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Associate Professor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
Scheme Industrial Transformation Training Centres Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2016
GNo G1301131
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

Applications of Feature Selection Methods for morphological characterization of images and subtypes of brain tumours $11,611

Funding body: University of Newcastle - Faculty of Engineering & Built Environment

Funding body University of Newcastle - Faculty of Engineering & Built Environment
Project Team Associate Professor Regina Berretta, Associate Professor Yuqing Lin, Associate Professor Stephan Chalup
Scheme Pilot Grant
Role Lead
Funding Start 2014
Funding Finish 2014
GNo G1400970
Type Of Funding Internal
Category INTE
UON Y

CS4HS workshop$10,000

Funding body: Google Australia Pty Ltd

Funding body Google Australia Pty Ltd
Project Team Doctor Elena Prieto-Rodriguez, Associate Professor Regina Berretta
Scheme Donation
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1400548
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON Y

An Investigation on the Consensus Between Different Genomic and Transcriptomic Results in Breast Cancer$10,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Ms Heloisa Milioli, Professor Pablo Moscato, Doctor Jennette Sakoff, Associate Professor Regina Berretta
Scheme Jennie Thomas Medical Research Travel Grant
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1401334
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON Y

20133 grants / $244,930

The integration of bioinformatics, chemoinformatics, and toxicogenomics methods: a new approach for the identification of combination tailored therapies and novel drug targets in breast cancer$210,000

Funding body: Cancer Institute NSW

Funding body Cancer Institute NSW
Project Team Professor Pablo Moscato, Doctor Jennette Sakoff, Associate Professor Regina Berretta
Scheme NSW Premier's Awards for Outstanding Cancer Research: "Big Data, Big Impact" Grant
Role Investigator
Funding Start 2013
Funding Finish 2015
GNo G1300826
Type Of Funding Other Public Sector - State
Category 2OPS
UON Y

Solving challenging combinatorial optimization problems in bioinformatics by designing high-performance metaheuristics in GPU-CPU supercomputers$20,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Professor Pablo Moscato, Associate Professor Regina Berretta, Associate Professor Carlos Cotta, Dr Michael Langston, Professor Fred Glover, Mr Manuel Ujaldon Martinez
Scheme Near Miss Grant
Role Investigator
Funding Start 2013
Funding Finish 2013
GNo G1300461
Type Of Funding Internal
Category INTE
UON Y

Educating, informing and preparing high school teachers to engage and inspire the next generation of computer scientists$14,930

Funding body: Google

Funding body Google
Project Team

Elena Prieto Rodriguez

Scheme Google CS4HS
Role Investigator
Funding Start 2013
Funding Finish 2013
GNo
Type Of Funding International - Competitive
Category 3IFA
UON N

20124 grants / $641,000

Memetic algorithms and adaptive memory metaheuristics for large scale combinatorial optimisation problems arising in biomarker discovery $320,000

Funding body: ARC (Australian Research Council)

Funding body ARC (Australian Research Council)
Project Team Professor Pablo Moscato, Associate Professor Regina Berretta, Associate Professor Carlos Cotta, Dr Michael Langston, Professor Fred Glover
Scheme Discovery Projects
Role Investigator
Funding Start 2012
Funding Finish 2014
GNo G1100292
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON Y

Project EVA: an environmentally responsible facility for interdisciplinary supercomputing applications$263,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Professor Pablo Moscato, Laureate Professor Jon Borwein, Conjoint Professor Keith Jones, Conjoint Professor Chris Levi, Professor Mark Parsons, Professor Michael Ostwald, Professor Hugh Craig, Conjoint Professor Peter Greer, Associate Professor Stephan Chalup, Associate Professor Regina Berretta
Scheme Equipment Grant
Role Investigator
Funding Start 2012
Funding Finish 2012
GNo G1100627
Type Of Funding Internal
Category INTE
UON Y

Teaching Relief - Berretta$50,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Professor Robert Betz, Associate Professor Regina Berretta
Scheme Career Enhancement Fellowship for Academic Women
Role Investigator
Funding Start 2012
Funding Finish 2012
GNo G1101203
Type Of Funding Internal
Category INTE
UON Y

An integrated plan for leadership development in research teaching and learning and service$8,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Associate Professor Regina Berretta
Scheme Career Enhancement Fellowship for Academic Women
Role Lead
Funding Start 2012
Funding Finish 2012
GNo G1100996
Type Of Funding Internal
Category INTE
UON Y

20112 grants / $77,000

Computational prediction and functional clarification of novel drug combination strategies for the treatment of brain tumours$50,000

Funding body: Maitland Cancer Appeal Committee

Funding body Maitland Cancer Appeal Committee
Project Team Professor Pablo Moscato, Dr DAN Johnstone, Associate Professor Regina Berretta, Doctor Luke Mathieson, Professor Manuel Graeber, Doctor Jennette Sakoff
Scheme Research Project
Role Investigator
Funding Start 2011
Funding Finish 2011
GNo G1100275
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON Y

The Pierre and Marie Curie GPU computing servers$27,000

Funding body: NHMRC (National Health & Medical Research Council)

Funding body NHMRC (National Health & Medical Research Council)
Project Team Professor Pablo Moscato, Conjoint Professor Peter Greer, Associate Professor Regina Berretta, Dr CARLOS Riveros
Scheme Equipment Grant
Role Investigator
Funding Start 2011
Funding Finish 2011
GNo G1100032
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

20102 grants / $46,998

Identification of novel biomarkers for pre-clinical Alzheimer's disease$24,998

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Professor Pablo Moscato, Associate Professor Liz Milward, Doctor Martin Ravetti, Dr DAN Johnstone, Dr M Guillemin, Associate Professor Regina Berretta
Scheme Project Grant
Role Investigator
Funding Start 2010
Funding Finish 2010
GNo G0900149
Type Of Funding Contract - Aust Non Government
Category 3AFC
UON Y

Sir Ronald Fisher GPU computing cluster $22,000

Funding body: NHMRC (National Health & Medical Research Council)

Funding body NHMRC (National Health & Medical Research Council)
Project Team Professor Pablo Moscato, Conjoint Professor Chris Levi, Associate Professor Regina Berretta
Scheme Equipment Grant
Role Investigator
Funding Start 2010
Funding Finish 2010
GNo G1000054
Type Of Funding Other Public Sector - Commonwealth
Category 2OPC
UON Y

20072 grants / $40,000

Healthy Airways and Obstructive Lung Disease (HAROLD)$20,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Conjoint Professor Wayne Smith, Associate Professor Lisa Wood, Professor John Attia, Associate Professor Regina Berretta, Professor Pablo Moscato
Scheme Project Grant
Role Investigator
Funding Start 2007
Funding Finish 2007
GNo G0187246
Type Of Funding Contract - Aust Non Government
Category 3AFC
UON Y

Online support material for Computer Science Honours degree using Blackboard$20,000

Funding body: Centre for Teaching and Learning, The University of Newcastle

Funding body Centre for Teaching and Learning, The University of Newcastle
Project Team

A/Prof R Berretta

Scheme Teaching and Learning fellowship
Role Lead
Funding Start 2007
Funding Finish 2008
GNo
Type Of Funding Other Public Sector - Local
Category 2OPL
UON N

20061 grants / $621,143

20052 grants / $221,000

Evolutionary algorithms for problems in functional genomics data analysis$218,000

Funding body: ARC (Australian Research Council)

Funding body ARC (Australian Research Council)
Project Team Professor Pablo Moscato, Professor Rodney Scott, Associate Professor Regina Berretta
Scheme Discovery Projects
Role Investigator
Funding Start 2005
Funding Finish 2007
GNo G0184416
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON Y

Australasian Computer Science Week (ACSW'05)$3,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Associate Professor Regina Berretta, Doctor Michael Hannaford, Associate Professor Frans Henskens, Professor Pablo Moscato, Dr Richard Webber
Scheme Conference Establishment Grant
Role Lead
Funding Start 2005
Funding Finish 2005
GNo G0184971
Type Of Funding Internal
Category INTE
UON Y

20041 grants / $12,000

Feature selection problems arising in Bioinformatics$12,000

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Associate Professor Regina Berretta
Scheme New Staff Grant
Role Lead
Funding Start 2004
Funding Finish 2004
GNo G0183765
Type Of Funding Internal
Category INTE
UON Y

20031 grants / $4,125

Visit by Dr Guiseppe Lancia 13/08/03 to 24/09/03$4,125

Funding body: University of Newcastle

Funding body University of Newcastle
Project Team Associate Professor Regina Berretta
Scheme Visitor Grant
Role Lead
Funding Start 2003
Funding Finish 2003
GNo G0183278
Type Of Funding Internal
Category INTE
UON Y

19984 grants / $396,000

Production Planning and Control in Manufacturing Systems$250,000

Funding body: Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP

Funding body Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP
Project Team

Prof P Franca, A/Prof R Berretta et al. (academics and researchers from USP, UFSCAR, ENCAMP and IMPE)

Scheme projeto tematico
Role Lead
Funding Start 1998
Funding Finish 2001
GNo
Type Of Funding Other Public Sector - State
Category 2OPS
UON N

Heuristics and Meta-Heuristics in Production Planning Problems$90,000

Funding body: Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP

Funding body Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP
Project Team

A/Prof R Berretta

Scheme Young researcher fellowship
Role Lead
Funding Start 1998
Funding Finish 1999
GNo
Type Of Funding Other Public Sector - State
Category 2OPS
UON N

Evolutionary Meta-heuristics for Capacitated Lot-sizing Problems in Multistage Systems $28,000

Funding body: Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP

Funding body Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP
Project Team

A/Prof R Berretta

Scheme master student scholarship
Role Lead
Funding Start 1998
Funding Finish 2000
GNo
Type Of Funding Other Public Sector - State
Category 2OPS
UON N

Heuristics based on Lagrangian Relaxation for Capacitated Lot-sizing Problems in Multistage Systems$28,000

Funding body: Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP

Funding body Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP
Project Team

A/Prof R Berretta

Scheme master student scholarship
Role Lead
Funding Start 1998
Funding Finish 2000
GNo
Type Of Funding Other Public Sector - State
Category 2OPS
UON N
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Research Supervision

Number of supervisions

Completed11
Current10

Total current UON EFTSL

PhD4.6

Current Supervision

Commenced Level of Study Research Title / Program / Supervisor Type
2016 PhD Food Supply Chain Optimisation
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Principal Supervisor
2016 PhD Food Supply Chain Optimisation
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Principal Supervisor
2015 PhD A New Feature Selection Approach Based on Minimum Spanning Tree Using Evolutionary Computation
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Principal Supervisor
2015 PhD MADOC - Memetic Algorithm for Detecting Overlapping Communities
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Principal Supervisor
2014 PhD Multiobjective Quadratic Assignment Problem for Functional Genomics Analysis in Oncology and Neuroscience
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2014 PhD The Multiobjective (a,B)-k-Feature Set Problem Using Memetic Algorithms
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2013 PhD Breast Cancer Intrinsic Subtypes: A Critical Conception in Bioinformatics
PhD (Biological Sciences), Faculty of Science and Information Technology, The University of Newcastle
Co-Supervisor
2012 PhD Combinatorial Optimization Methods for Selecting Features with Applications in Bioinformatics
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2012 PhD Memetic Algorithms for Community Detection in Complex Networks
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2012 PhD Genetic Algorithm-Based Ensemble Method for Large-Scale Biological Data Classification
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor

Past Supervision

Year Level of Study Research Title / Program / Supervisor Type
2016 PhD A Novel Feature Selection Approach for Data Integration Analysis: Applications to Transcriptomics Study
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2013 PhD An Integrated, Fast and Scalable Approach for Large-Scale Biological Network Analysis
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2013 PhD Efficient Methods of Feature Selection Based on Combinatorial Optimization Motivated by the Analysis of Large Biological Datasets
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2012 PhD Mining Disjunctive Patterns in Biomedical Data Sets
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2008 PhD An Integrated and Scalable Approach Based on Combinatorial Optimization Techniques for the Analysis of Microarray Data
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Co-Supervisor
2007 PhD Simulated Annealing-Based Hybrid Heuristics for Educational Timetabling Problems
PhD (Computer Science), Faculty of Engineering and Built Environment, The University of Newcastle
Principal Supervisor
2001 Masters Evaluation of Metaheuristics for The Quadratic Assignment Problem
Computer Science, Unknown
Sole Supervisor
2000 Honours Tabu Search for Single Machine Scheduling
Computer Science, Unknown
Sole Supervisor
2000 Masters Metaheuristics For The Multilevel Resource-Constrained Lot-Sizing Problem
Computer Science, Unknown
Sole Supervisor
2000 Honours Introduction to Metaheuristics applied to Integer Programming Problems
Computer Science, Unknown
Sole Supervisor
2000 Masters Lagrangian heuristics for Multistage Capacitated Lot-Sizing Problem
Computer Science, Unknown
Sole Supervisor
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Associate Professor Regina Berretta

Position

Associate Professor
School of Elect Engineering and Computer Science
Faculty of Engineering and Built Environment

Focus area

Computer Science and Software Engineering

Contact Details

Email regina.berretta@newcastle.edu.au
Phone (02) 4921 8975
Fax (02) 4921 6929

Office

Room ES229
Building Engineering Science - D.W. George
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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