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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

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 (6 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
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) [B1]
DOI 10.1007/978-3-642-01536-6
Co-authors Pablo Moscato
2008 Berretta 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]
DOI 10.1007/978-1-60327-429-6
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
Co-authors 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 - 5
Co-authors Pablo Moscato
Show 3 more chapters

Journal article (16 outputs)

Year Citation Altmetrics Link
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, Liz Milward, Pablo Moscato
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 - 14Web of Science - 6
Co-authors 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 - 14Web of Science - 10
Co-authors Luke Mathieson, Pablo Moscato
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 - 23Web of Science - 18
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 - 9Web of Science - 5
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 - 14Web of Science - 10
Co-authors Pablo Moscato, Mateus Rochadepaula
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 - 19Web of Science - 11
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 - 46Web of Science - 40
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 - 18Web of Science - 18
Co-authors Pablo Moscato, Rodney Scott
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 - 9Web of Science - 10
Co-authors Pablo Moscato, John Rostas, Alexandre Mendes, Mick Hunter
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 - 25Web of Science - 24
Co-authors Pablo Moscato, Alexandre Mendes
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 - 9Web of Science - 6
Co-authors Pablo Moscato, Alexandre Mendes
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
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 - 25Web of Science - 22
Show 13 more journal articles

Review (1 outputs)

Year Citation Altmetrics Link
2011 Moscato PA, Berretta RE, Cotta C, 'Memetic algorithms', Wiley Encyclopedia of Operations Research and Management Science (2011) [D1]
Co-authors Pablo Moscato

Conference (23 outputs)

Year Citation Altmetrics Link
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, Sydney, Australia (2014) [E3]
Co-authors Pablo Moscato
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, Madrid, Spain (2014) [E1]
DOI 10.1109/FIE.2014.7044134
Co-authors Elena Prieto
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, Sydney (2014) [E1]
DOI 10.1109/BDCloud.2014.83
Co-authors Natalie Devries, Pablo Moscato
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, Sydney (2014) [E1]
DOI 10.1109/BDCloud.2014.56
Co-authors Jamie Carlson, Pablo Moscato, Natalie Devries
2014 Jayasooriya 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]
DOI 10.1109/ITW.2014.6970873
Co-authors Sarah Johnson, Lawrence L 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), Adelaide (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, Melbourne (2012) [E1]
Co-authors Pablo Moscato
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, Melbourne (2012) [E1]
Citations Scopus - 6
Co-authors 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, Salvador de Bahia, Brazil (2012) [E1]
Citations Scopus - 3Web of Science - 2
Co-authors Pablo Moscato
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, Melbourne, Australia (2011) [E1]
DOI 10.1007/978-3-642-24669-2_36
Citations Scopus - 4Web of Science - 3
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, Shoal bay, NSW (2010) [E3]
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, Beijing, China (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, Hobart, TAS (2009) [E3]
Co-authors Pablo Moscato, Rodney Scott, 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), Prague, Czech Republic (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, Gold Coast, QLD (2007) [E1]
Citations Scopus - 1Web of Science - 1
Co-authors Pablo Moscato, Alexandre Mendes
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, Melbourne (2007) [E1]
DOI 10.1109/icis.2007.25
Citations Scopus - 9Web of Science - 3
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, Gold Coast, QLD (2007) [E1]
DOI 10.1007/978-3-540-76931-6_14
Citations Scopus - 2Web of Science - 7
Co-authors Pablo Moscato, Alexandre Mendes
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, Santiago, Chile (2006) [E1]
Citations Scopus - 7Web of Science - 6
Co-authors Alexandre Mendes, Pablo Moscato
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, Newcastle, N.S.W (2005) [E1]
Citations Scopus - 1
Co-authors Pablo Moscato, Alexandre Mendes
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, Newcastle, N.S.W (2005) [E1]
Citations Scopus - 1
Co-authors Luke Mathieson, Alexandre Mendes, Pablo Moscato
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, Lausanne, Switzerland (2005) [E1]
Citations Scopus - 6Web of Science - 9
Co-authors Pablo Moscato, Alexandre Mendes
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, Granada, Spain (2005) [E2]
Co-authors Alexandre Mendes, Pablo Moscato
2005 Moscato PA, Berretta RE, Mendes ADS, 'A New Memetic Algorithm for Ordering Datasets: Applications in Microarray Analysis', Proceedings of MIC2005, Vienna, Austria (2005) [E2]
Co-authors Pablo Moscato, Alexandre Mendes
Show 20 more conferences
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Grants and Funding

Summary

Number of grants 28
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 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

20149 grants / $2,870,865

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 John Golding, Doctor Simon Dunstall, Mrs Carlee McGowan, Mr Robert McMahon, Mr Robert Scoines, Mr Tim Norris, Doctor Christopher Scarlett
Scheme Industrial Transformation Training Centres
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1301004
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
UON Y

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

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 2014
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
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 Y

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 2014
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, 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
Scheme ARC IC Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1301129
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
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, 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
Scheme ARC IC Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1301130
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
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, 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
Scheme ARC IC Partner Funding
Role Investigator
Funding Start 2014
Funding Finish 2014
GNo G1301131
Type Of Funding Aust Competitive - Commonwealth
Category 1CS
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, Doctor 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

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 2014
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
Scheme Google CS4HS
Role Investigator
Funding Start 2013
Funding Finish 2013
GNo
Type Of Funding International - Competitive
Category 3IFA
UON Y

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 2012
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, Mr 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, Doctor 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, Mr 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

20071 grants / $20,000

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

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 2005
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

1 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
Scheme Donation
Role Investigator
Funding Start
Funding Finish
GNo G1400548
Type Of Funding Donation - Aust Non Government
Category 3AFD
UON Y
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Research Supervision

Number of supervisions

Completed10
Current7

Total current UON EFTSL

PhD3.2

Current Supervision

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

Past Supervision

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