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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

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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

CodeDescriptionPercentage
060499Genetics not elsewhere classified20
080108Neural, Evolutionary and Fuzzy Computation40
080199Artificial Intelligence and Image Processing not elsewhere classified40

Professional Experience

UON Appointment

DatesTitleOrganisation / Department
1/07/2014 - Associate ProfessorUniversity of Newcastle
School of Elect Engineering and Computer Science
Australia

Academic appointment

DatesTitleOrganisation / Department
1/02/2003 - LecturerUniversity of Newcastle
Faculty of Engineering and Built Environment
Australia
1/07/1999 - LecturerSan Francisco University
United States

Invitations

Participant

YearTitle / Rationale
2006Combinatorial optimization models for finding genetic signature from gene expression
Organisation: 2006 Student Symposium in Bioinformatics Description: tutorial Auckland, 1115 July
2006Combinatorial 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 (6 outputs)

YearCitationAltmetricsLink
2014Lachiondo 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]
DOI10.1201/b15810-51Author URL
Co-authorsPablo Moscato
2012Berretta RE, Cotta C, Moscato PA, 'Memetic algorithms in bioinformatics', Handbook of Memetic Algorithms, Springer, Berlin, Germany 261-271 (2012) [B1]
Co-authorsPablo Moscato
2009Ravetti 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) [B1]
DOI10.1007/978-3-642-01536-6
Co-authorsPablo Moscato
2008Berretta RE, Costa WE, Moscato PA, 'Combinatorial optimization models for finding genetic signatures from gene expression datasets', Bioinformatics, Humana Press, New York 363-377 (2008) [B1]
DOI10.1007/978-1-60327-429-6
Co-authorsPablo Moscato
2008Hourani 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]
DOI10.1007/978-1-60327-429-6
Co-authorsPablo Moscato
2004Berretta 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]
CitationsWeb of Science - 5
Co-authorsPablo Moscato
Show 3 more chapters

Journal article (16 outputs)

YearCitationAltmetricsLink
2013Johnstone 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-authorsPablo Moscato, Rodney Scott, Liz Milward
2012Arefin 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]
CitationsScopus - 14Web of Science - 6
Co-authorsPablo Moscato, Ahmed Arefin
2012Arefin 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]
CitationsScopus - 14Web of Science - 10
Co-authorsAhmed Arefin, Pablo Moscato, Luke Mathieson
2012Johnstone 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]
CitationsScopus - 23Web of Science - 18
Co-authorsLiz Milward, Pablo Moscato
2011Inostroza-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]
DOI10.1371/journal.pone.0014468
CitationsScopus - 9Web of Science - 5
Co-authorsPablo Moscato
2011Rocha 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]
CitationsScopus - 14Web of Science - 10
Co-authorsPablo Moscato, Mateus Rochadepaula
2010Berretta RE, Moscato PA, 'Cancer biomarker discovery: The entropic hallmark', Plos One, 5 e12262 (2010) [C1]
DOI10.1371/journal.pone.0012262
CitationsScopus - 19Web of Science - 11
Co-authorsPablo Moscato
2010Ravetti 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]
DOI10.1371/journal.pone.0010153
CitationsScopus - 46Web of Science - 40
Co-authorsPablo Moscato
2010Riveros 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]
DOI10.1371/journal.pone.0014176
CitationsScopus - 18Web of Science - 18
Co-authorsPablo Moscato, Rodney Scott
2009Rosso 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]
DOI10.1016/j.jneumeth.2009.04.028
CitationsScopus - 9Web of Science - 9
Co-authorsPablo Moscato, John Rostas, Mick Hunter
2007Moscato PA, Mendes ADS, Berretta RE, 'Benchmarking a Memetic Algorithm for Ordering Microarray Data', Biosystems, 88 56-75 (2007) [C1]
DOI10.1016/j.biosystems.2006.04.005
CitationsScopus - 25Web of Science - 24
Co-authorsPablo Moscato
2007De 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]
2007Berretta 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]
CitationsScopus - 9Web of Science - 6
Co-authorsPablo Moscato
2004Berretta RE, Rodrigues LF, 'A memetic algorithm for a multistage capacitated lot-sizing problem', International journal of production economics, 87 67-81 (2004) [C1]
DOI10.1016/S0925-5273(03)00093-8
2001Armentano VA, Berretta RE, Franca PM, 'Lot-sizing in capacitated multi-stage serial systems', PRODUCTION AND OPERATIONS MANAGEMENT, 10 68-86 (2001)
Author URL
CitationsScopus - 5Web of Science - 2
1997Franca PM, Armentano VA, Berretta RE, Clark AR, 'A heuristic method for lot-sizing in multi-stage systems', COMPUTERS & OPERATIONS RESEARCH, 24 861-874 (1997)
DOI10.1016/S0305-0548(96)00097-4Author URL
CitationsScopus - 25Web of Science - 22
Show 13 more journal articles

Review (1 outputs)

YearCitationAltmetricsLink
2011Moscato PA, Berretta RE, Cotta C, 'Memetic algorithms', Wiley Encyclopedia of Operations Research and Management Science (2011) [D1]
Co-authorsPablo Moscato

Conference (23 outputs)

YearCitationAltmetricsLink
2014Riveros 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, Sydney, Australia (2014) [E3]
Co-authorsPablo Moscato
2014Prieto-Rodriguez E, Berretta R, 'Digital Technology Teachers' Perceptions of Computer Science: It Is Not All About Programming', 2014 IEEE Frontiers in Education Conference Proceedings, Madrid, Spain (2014) [E1]
DOI10.1109/FIE.2014.7044134
Co-authorsElena Prieto
2014Moslemi 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, Sydney (2014) [E1]
DOI10.1109/BDCloud.2014.83
Co-authorsNatalie Devries, Pablo Moscato, Ahmed Arefin
2014Lucas 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, Sydney (2014) [E1]
DOI10.1109/BDCloud.2014.56
Co-authorsJamie Carlson, Pablo Moscato, Ahmed Arefin, Natalie Devries
2014Jayasooriya S, Johnson SJ, Ong L, Berretta R, 'Optimization of graph based codes for belief propagation decoding', Information Theory Workshop (ITW), 2014 IEEE, Hobart, Tas (2014) [E1]
DOI10.1109/ITW.2014.6970873
Co-authorsSarah Johnson, Lawrence L Ong
2013Arefin 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), Adelaide (2013) [E1]
Co-authorsPablo Moscato, Ahmed Arefin
2012Arefin AS, Riveros RC, Berretta RE, Moscato PA, 'Computing large-scale distance matrices on GPU', Proceedings of 2012 7th International Conference on Computer Science & Education, Melbourne (2012) [E1]
Co-authorsPablo Moscato, Ahmed Arefin
2012Arefin 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, Melbourne (2012) [E1]
CitationsScopus - 6
Co-authorsAhmed Arefin, Pablo Moscato
2012Arefin 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, Salvador de Bahia, Brazil (2012) [E1]
CitationsScopus - 3Web of Science - 2
Co-authorsPablo Moscato, Ahmed Arefin
2011Arefin 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, Melbourne, Australia (2011) [E1]
DOI10.1007/978-3-642-24669-2_36
CitationsScopus - 4Web of Science - 3
Co-authorsPablo Moscato, Ahmed Arefin, Luke Mathieson
2010Arefin AS, Berretta RE, Moscato PA, 'An external memory approach for clustering of large-scale biological networks', Biomarker Discovery Conference, Shoal bay, NSW (2010) [E3]
Co-authorsAhmed Arefin, Pablo Moscato
2009Berretta 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, Beijing, China (2009) [E1]
DOI10.1109/iccsit.2009.5234460
Co-authorsHelen Giggins
2009Milward 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, Hobart, TAS (2009) [E3]
Co-authorsPablo Moscato, Rodney Scott, Liz Milward
2007Cox 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), Prague, Czech Republic (2007) [E3]
CitationsWeb of Science - 2
Co-authorsRodney Scott, Pablo Moscato, Nikola Bowden
2007Hourani 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, Gold Coast, QLD (2007) [E1]
CitationsScopus - 1Web of Science - 1
Co-authorsPablo Moscato
2007Tuga 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, Melbourne (2007) [E1]
DOI10.1109/icis.2007.25
CitationsScopus - 9Web of Science - 3
2007Inostroza-Ponta M, Mendes ADS, Berretta RE, Moscato PA, 'An integrated QAP-based approach to visualize patterns of gene expression similarity', Progress in Artificial Life, Gold Coast, QLD (2007) [E1]
DOI10.1007/978-3-540-76931-6_14
CitationsScopus - 2Web of Science - 7
Co-authorsPablo Moscato
2006Inostroza-Ponta M, Berretta RE, Mendes ADS, Moscato PA, 'An automatic graph layout procedure to visualize correlated data', Artificial Intelligence in Theory and Practice, Santiago, Chile (2006) [E1]
CitationsScopus - 7Web of Science - 6
Co-authorsPablo Moscato
2005Berretta 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, Newcastle, N.S.W (2005) [E1]
CitationsScopus - 1
Co-authorsPablo Moscato
2005Moscato 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, Newcastle, N.S.W (2005) [E1]
CitationsScopus - 1
Co-authorsLuke Mathieson, Pablo Moscato
2005Moscato 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, Lausanne, Switzerland (2005) [E1]
CitationsScopus - 6Web of Science - 9
Co-authorsPablo Moscato
2005Berretta 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, Granada, Spain (2005) [E2]
Co-authorsPablo Moscato
2005Moscato PA, Berretta RE, Mendes ADS, 'A New Memetic Algorithm for Ordering Datasets: Applications in Microarray Analysis', Proceedings of MIC2005, Vienna, Austria (2005) [E2]
Co-authorsPablo Moscato
Show 20 more conferences
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Grants and Funding

Summary

Number of grants28
Total funding$4,783,893

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


20151 grants / $14,832

CS4HS workshop$14,832

Funding body: Google Australia Pty Ltd

Funding bodyGoogle Australia Pty Ltd
Project TeamDoctor Elena Prieto-Rodriguez, Associate Professor Regina Berretta, Mr Andrew Lyell
SchemeDonation
RoleInvestigator
Funding Start2015
Funding Finish2015
GNoG1500616
Type Of FundingDonation - Aust Non Government
Category3AFD
UONY

20149 grants / $2,870,865

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

Funding body: ARC (Australian Research Council)

Funding bodyARC (Australian Research Council)
Project TeamProfessor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Doctor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor John Golding, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
SchemeIndustrial Transformation Training Centres
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1301004
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

Unleashing the power of a supernetwork-driven approach for bioinformatics$348,000

Funding body: ARC (Australian Research Council)

Funding bodyARC (Australian Research Council)
Project TeamProfessor Pablo Moscato, Associate Professor Regina Berretta
SchemeDiscovery Projects
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1300392
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

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 bodyCiencia y Empleo de la Junta de Andalucia
Project Team
SchemeProyectos de Excelencia de la Consejería de Economía, Innovación
RoleInvestigator
Funding Start2014
Funding Finish2017
GNo
Type Of FundingNot Known
CategoryUNKN
UONY

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 bodyHunter Medical Research Institute
Project TeamProfessor Pablo Moscato, Associate Professor Regina Berretta
SchemeProject Grant
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1400454
Type Of FundingGrant - Aust Non Government
Category3AFG
UONY

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

Funding body: Coca Cola Amatil (Australia)

Funding bodyCoca Cola Amatil (Australia)
Project TeamProfessor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Doctor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor John Golding, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
SchemeARC IC Partner Funding
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1301129
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

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

Funding body: Sanitarium Health and Wellbeing Company

Funding bodySanitarium Health and Wellbeing Company
Project TeamProfessor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Doctor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor John Golding, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
SchemeARC IC Partner Funding
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1301130
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

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

Funding body: Sunrice

Funding bodySunrice
Project TeamProfessor Rick Middleton, Associate Professor Regina Berretta, Associate Professor Michael Bowyer, Doctor Ali Eshragh, Doctor Christopher Scarlett, Doctor Masoud Talebian, Associate Professor Behnam Fahimnia, Professor Mathieu Savelsbergh, Professor Natashia Boland, Dr Costas Stathopoulos, Professor John Bartholdi, Doctor John Golding, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris
SchemeARC IC Partner Funding
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1301131
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

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 bodyUniversity of Newcastle - Faculty of Engineering & Built Environment
Project TeamAssociate Professor Regina Berretta, Doctor Yuqing Lin, Associate Professor Stephan Chalup
SchemePilot Grant
RoleLead
Funding Start2014
Funding Finish2014
GNoG1400970
Type Of FundingInternal
CategoryINTE
UONY

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

Funding body: Hunter Medical Research Institute

Funding bodyHunter Medical Research Institute
Project TeamMs Heloisa Milioli, Professor Pablo Moscato, Doctor Jennette Sakoff, Associate Professor Regina Berretta
SchemeJennie Thomas Medical Research Travel Grant
RoleInvestigator
Funding Start2014
Funding Finish2014
GNoG1401334
Type Of FundingGrant - Aust Non Government
Category3AFG
UONY

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 bodyCancer Institute NSW
Project TeamProfessor Pablo Moscato, Doctor Jennette Sakoff, Associate Professor Regina Berretta
SchemeNSW Premier's Awards for Outstanding Cancer Research: "Big Data, Big Impact" Grant
RoleInvestigator
Funding Start2013
Funding Finish2014
GNoG1300826
Type Of FundingOther Public Sector - State
Category2OPS
UONY

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

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamProfessor Pablo Moscato, Associate Professor Regina Berretta, Associate Professor Carlos Cotta, Dr Michael Langston, Professor Fred Glover, Mr Manuel Ujaldon Martinez
SchemeNear Miss Grant
RoleInvestigator
Funding Start2013
Funding Finish2013
GNoG1300461
Type Of FundingInternal
CategoryINTE
UONY

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

Funding body: Google

Funding bodyGoogle
Project Team
SchemeGoogle CS4HS
RoleInvestigator
Funding Start2013
Funding Finish2013
GNo
Type Of FundingInternational - Competitive
Category3IFA
UONY

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 bodyARC (Australian Research Council)
Project TeamProfessor Pablo Moscato, Associate Professor Regina Berretta, Associate Professor Carlos Cotta, Dr Michael Langston, Professor Fred Glover
SchemeDiscovery Projects
RoleInvestigator
Funding Start2012
Funding Finish2012
GNoG1100292
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

Teaching Relief - Berretta$50,000

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamProfessor Robert Betz, Associate Professor Regina Berretta
SchemeCareer Enhancement Fellowship for Academic Women
RoleInvestigator
Funding Start2012
Funding Finish2012
GNoG1101203
Type Of FundingInternal
CategoryINTE
UONY

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

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamAssociate Professor Regina Berretta
SchemeCareer Enhancement Fellowship for Academic Women
RoleLead
Funding Start2012
Funding Finish2012
GNoG1100996
Type Of FundingInternal
CategoryINTE
UONY

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 bodyMaitland Cancer Appeal Committee
Project TeamProfessor Pablo Moscato, Mr Dan Johnstone, Associate Professor Regina Berretta, Doctor Luke Mathieson, Professor Manuel Graeber, Doctor Jennette Sakoff
SchemeResearch Project
RoleInvestigator
Funding Start2011
Funding Finish2011
GNoG1100275
Type Of FundingDonation - Aust Non Government
Category3AFD
UONY

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

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

Funding bodyNHMRC (National Health & Medical Research Council)
Project TeamProfessor Pablo Moscato, Conjoint Professor Peter Greer, Associate Professor Regina Berretta, Doctor Carlos Riveros
SchemeEquipment Grant
RoleInvestigator
Funding Start2011
Funding Finish2011
GNoG1100032
Type Of FundingOther Public Sector - Commonwealth
Category2OPC
UONY

20102 grants / $46,998

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

Funding body: Hunter Medical Research Institute

Funding bodyHunter Medical Research Institute
Project TeamProfessor Pablo Moscato, Associate Professor Liz Milward, Doctor Martin Ravetti, Mr Dan Johnstone, Dr M Guillemin, Associate Professor Regina Berretta
SchemeProject Grant
RoleInvestigator
Funding Start2010
Funding Finish2010
GNoG0900149
Type Of FundingContract - Aust Non Government
Category3AFC
UONY

Sir Ronald Fisher GPU computing cluster $22,000

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

Funding bodyNHMRC (National Health & Medical Research Council)
Project TeamProfessor Pablo Moscato, Conjoint Professor Chris Levi, Associate Professor Regina Berretta
SchemeEquipment Grant
RoleInvestigator
Funding Start2010
Funding Finish2010
GNoG1000054
Type Of FundingOther Public Sector - Commonwealth
Category2OPC
UONY

20071 grants / $20,000

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

Funding body: Hunter Medical Research Institute

Funding bodyHunter Medical Research Institute
Project TeamConjoint Professor Wayne Smith, Associate Professor Lisa Wood, Professor John Attia, Associate Professor Regina Berretta, Professor Pablo Moscato
SchemeProject Grant
RoleInvestigator
Funding Start2007
Funding Finish2007
GNoG0187246
Type Of FundingContract - Aust Non Government
Category3AFC
UONY

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 bodyARC (Australian Research Council)
Project TeamProfessor Pablo Moscato, Professor Rodney Scott, Associate Professor Regina Berretta
SchemeDiscovery Projects
RoleInvestigator
Funding Start2005
Funding Finish2005
GNoG0184416
Type Of FundingAust Competitive - Commonwealth
Category1CS
UONY

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

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamAssociate Professor Regina Berretta, Doctor Michael Hannaford, Associate Professor Frans Henskens, Professor Pablo Moscato, Dr Richard Webber
SchemeConference Establishment Grant
RoleLead
Funding Start2005
Funding Finish2005
GNoG0184971
Type Of FundingInternal
CategoryINTE
UONY

20041 grants / $12,000

Feature selection problems arising in Bioinformatics$12,000

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamAssociate Professor Regina Berretta
SchemeNew Staff Grant
RoleLead
Funding Start2004
Funding Finish2004
GNoG0183765
Type Of FundingInternal
CategoryINTE
UONY

20031 grants / $4,125

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

Funding body: University of Newcastle

Funding bodyUniversity of Newcastle
Project TeamAssociate Professor Regina Berretta
SchemeVisitor Grant
RoleLead
Funding Start2003
Funding Finish2003
GNoG0183278
Type Of FundingInternal
CategoryINTE
UONY

1 grants / $10,000

CS4HS workshop$10,000

Funding body: Google Australia Pty Ltd

Funding bodyGoogle Australia Pty Ltd
Project TeamDoctor Elena Prieto-Rodriguez, Associate Professor Regina Berretta
SchemeDonation
RoleInvestigator
Funding Start
Funding Finish
GNoG1400548
Type Of FundingDonation - Aust Non Government
Category3AFD
UONY
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Research Supervision

Current Supervision

CommencedResearch Title / Program / Supervisor Type
2015A New Feature Selection Approach Based on Minimum Spanning Tree Using Evolutionary Computation
Computer Science, Faculty of Engineering and Built Environment
Principal Supervisor
2015A Novel Approach to Detect Communities in Large Dynamic Complex Networks
Computer Science, Faculty of Engineering and Built Environment
Principal Supervisor
2013Biomarker Discovery in Breast Cancer
Biological Sciences, Faculty of Science and Information Technology
Co-Supervisor
2012Combinatorial Optimization Methods for Selecting Features with Applications in Bioinformatics
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2012Community Detection in Large-Scale Biological Networks
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2012Combinational Meta-Analysis of Microarray Gene Expression Data and Applications to Prostate Cancer
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2012Genetic Algorithm-Based Ensemble Method for Large-Scale Biological Data Classification
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor

Past Supervision

YearResearch Title / Program / Supervisor Type
2013An Integrated, Fast and Scalable Approach for Large-Scale Biological Network Analysis
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2013Efficient Methods of Feature Selection Based on Combinatorial Optimization Motivated by the Analysis of Large Biological Datasets
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2012Mining Disjunctive Patterns in Biomedical Data Sets
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2008An Integrated and Scalable Approach Based on Combinatorial Optimization Techniques for the Analysis of Microarray Data
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
2007Simulated Annealing-Based Hybrid Heuristics for Educational Timetabling Problems
Computer Science, Faculty of Engineering and Built Environment
Principal Supervisor
2001Evaluation of Metaheuristics for The Quadratic Assignment Problem
Computer Science, Unknown
Sole Supervisor
2000Tabu Search for Single Machine Scheduling
Computer Science, Unknown
Sole Supervisor
2000Metaheuristics For The Multilevel Resource-Constrained Lot-Sizing Problem
Computer Science, Unknown
Sole Supervisor
2000Introduction to Metaheuristics applied to Integer Programming Problems
Computer Science, Unknown
Sole Supervisor
2000Lagrangian 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

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

Office

RoomES229
BuildingEngineering Science - D.W. George
LocationCallaghan
University Drive
Callaghan, NSW 2308
Australia
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