Dr Carlos Riveros
Conjoint Senior Lecturer
School of Medicine and Public Health (Computer Science and Software Engineering)
- Email:carlos.riveros@newcastle.edu.au
- Phone:(02) 4042 0478
Career Summary
Biography
In my position as bioinformatician and health informatician at the Hunter Medical Research Institute, I provide data analysis services to researchers. Current areas of work include `omics' sequencing data analysis, integrative analysis, network-based analysis, business intelligence tools for health data. My current research interests are in multi-dimensional clustering and classification in large to very large datasets, integration of data from multiple domains. Application of high performance computing techniques, massively parallel systems (in particular GPUs), and heterogeneous distributed computing is central for the practical and efficient solution of these problems.
My background is more than thirty years of experience in computer science and data analysis in academic, scientific and industrial settings, with the last decade spent in research and development in Bioinformatics and Information-Based Medicine. I obtained my PhD in Physics in 1990 and have since worked in the public and private sectors for multinational companies and research institutions, and owned a small specialized software development company for almost eight years.
Qualifications
- PhD (Physics), Universidad Nacional de la Plata - Argentina
- Bachelor of Physics, Universidad Nacional de la Plata - Argentina
Keywords
- Algorithms
- Bioinformatics
- Health informatics
- Machine Learning
- Statistics
Languages
- English (Fluent)
- Spanish (Fluent)
Fields of Research
| Code | Description | Percentage |
|---|---|---|
| 010299 | Applied Mathematics not elsewhere classified | 35 |
| 060499 | Genetics not elsewhere classified | 35 |
| 080299 | Computation Theory and Mathematics not elsewhere classified | 30 |
Professional Experience
Academic appointment
| Dates | Title | Organisation / Department |
|---|---|---|
| 21/06/2018 - | Conjoint Senior Lecturer | School of Medicine & Public Health, Faculty of Health & Medicine, University of Newcastle | Australia Australia |
Professional appointment
| Dates | Title | Organisation / Department |
|---|---|---|
| 1/02/2016 - | HMRI Bioinformatics Fellow | Hunter Medical Research Institute (HMRI) Australia |
| 1/08/2006 - 1/01/2008 | I&C Senior Engineer / Chief of Engineering | Termoelectrica San Martin, Argentina Engineering Argentina |
| 1/08/2001 - 1/08/2006 | Contract Performance Manager | General Electric Argentina |
| 1/09/1994 - 1/08/2001 | CEO / Principal Software Engineer | VFlops Informatica, Argentina Industrial Software Development Argentina |
| 1/04/1992 - 1/08/1993 |
Visiting PostDoc Research Associate R&D in advanced geophysical data processing algorithms: multi-layer wave decomposition and propagation, experimental anisotropic wave propagation, cross-borehole and surface-to-borehole diffraction tomography for reservoir characterisation. Design and implementation of data management and conversion front-ends for large 3D geophysical exploration datasets for the Lab’s Convex supercomputer. |
University of Houston Allied Geophysical Labs United States |
| 1/01/1991 - 1/09/1994 |
Chief Geophysical Researcher Principal software architect and algorithm designer of a real-time 2D & 3D ruggedized geophysical array multiprocessor system. Development of active and passive sonar detection and ranging with hydrophone aperture arrays for military application. R&D of adaptive filtering and signal recognition algorithms for deep-well oil pump predictive maintenance characterisation. Development and vectorisation of geophysical data processing algorithms for geophysical prospecting. |
Sismos Geophysical Company Geophysics R&D Argentina |
Teaching
| Code | Course | Role | Duration |
|---|---|---|---|
| SENG3100 |
Personal Software Process Faculty of Engineering and Built Environment - The University of Newcastle (Australia) |
Lecturer | 1/03/2008 - 31/07/2008 |
| COMP3320 |
Computer Graphics Faculty of Engineering and Built Environment - The University of Newcastle (Australia) |
Lecturer | 1/08/2008 - 30/11/2008 |
| COMP3320 |
Computer Graphics Faculty of Engineering and Built Environment - The University of Newcastle (Australia) |
Tutorial demonstrator | 1/08/2008 - 30/11/2008 |
| SENG4800 A/B |
Final Year Project (Embedded Honors) Faculty of Engineering and Built Environment - The University of Newcastle (Australia) |
Teaching Assistant | 1/03/2012 - 30/11/2012 |
Publications
For publications that are currently unpublished or in-press, details are shown in italics.
Chapter (1 outputs)
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| 2015 |
Riveros C, Vimieiro R, Holliday EG, Oldmeadow C, Wang JJ, Mitchell P, et al., 'Identification of genome-wide SNP-SNP and SNP-clinical Boolean interactions in Age-related Macular Degeneration', Epistasis: Methods and Protocols, Springer, New York 217-255 (2015) [B1]
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Journal article (30 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2019 |
Lawson J, McGill A, Meares H, Coleman H, Riveros C, Martin A, 'Wound protectors for improved exposure in open hernia repair', Hernia, (2019) © 2019, Springer-Verlag France SAS, part of Springer Nature. Introduction: Achieving adequate surgical exposure is fundamental to good surgical practice. Traditionally, in the rep... [more] © 2019, Springer-Verlag France SAS, part of Springer Nature. Introduction: Achieving adequate surgical exposure is fundamental to good surgical practice. Traditionally, in the repair of ventral and open inguinal hernias, this has been accomplished with the aid of self-retaining retractors or by extending the incision length. We propose that using disposable wound protectors, surgical exposure will be improved for a given incision length in the repair of ventral and open inguinal hernias, compared to traditional methods. Method: Through the use of an animal tissue model, we compared incisions of varying lengths and measured the dimensions of the exposure achieved with disposable wound protectors (Alexis¿) and a Mollison self-retainer. We calculated the surface area and, therefore, exposure gained using the specified wound retraction devices and compared the results. Results: The average superficial surface area of wound with a self-retainer compared to the small and extra-small disposable wound protector was 2.65¿cm2 vs 2.27¿cm2 (small) and 2.2¿cm2 (extra-small) for 2¿cm incision length, 3.6¿cm2 vs 4.93¿cm2 and 4.2¿cm2 for 3¿cm incision length, 5.19¿cm2 vs 8.25¿cm2 and 6.27¿cm2 for 4¿cm incision length, 6.17¿cm2 vs 12.25¿cm2 and 9.07¿cm2 for 5¿cm incision length, and 8.75¿cm2 vs 16.73¿cm2 and 10.78¿cm2 for 6¿cm incision length [p = 0.038 (small) and p = 0.049 (extra-small)]. Our results show a statistically significant increase in surface area of a wound for each incision length when a disposable wound protector was used for exposure, compared to a self-retainer. Conclusion: Our results demonstrate that the use of disposable wound protectors provides superior surgical exposure for a given incision length compared to traditional techniques in the repair of ventral and open inguinal hernia repairs.
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| 2019 |
Revelas M, Thalamuthu A, Oldmeadow C, Evans T-J, Armstrong NJ, Riveros C, et al., 'Exceptional Longevity and Polygenic Risk for Cardiovascular Health', GENES, 10 (2019) [C1]
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| 2019 |
Hyde LL, Boyes AW, Mackenzie LJ, Leigh L, Oldmeadow C, Riveros C, Sanson-Fisher R, 'Electronic Health Literacy Among Magnetic Resonance Imaging and Computed Tomography Medical Imaging Outpatients: Cluster Analysis.', J Med Internet Res, 21 e13423 (2019)
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| 2019 |
Hendrickx W, Riveros C, Askim T, Bussmann JBJ, Callisaya ML, Chastin SFM, et al., 'Identifying factors associated with sedentary time after stroke. Secondary analysis of pooled data from nine primary studies.', Topics in Stroke Rehabilitation, 26 327-334 (2019) [C1] © 2019, © 2019 The Author(s). Published with license by Taylor & Francis Group, LLC. Background: High levels of sedentary time increases the risk of cardiovascular disease, ... [more] © 2019, © 2019 The Author(s). Published with license by Taylor & Francis Group, LLC. Background: High levels of sedentary time increases the risk of cardiovascular disease, including recurrent stroke. Objective: This study aimed to identify factors associated with high sedentary time in community-dwelling people with stroke. Methods: For this data pooling study, authors of published and ongoing trials that collected sedentary time data, using the activPAL monitor, in community-dwelling people with stroke were invited to contribute their raw data. The data was reprocessed, algorithms were created to identify sleep-wake time and determine the percentage of waking hours spent sedentary. We explored demographic and stroke-related factors associated with total sedentary time and time in uninterrupted sedentary bouts using unique, both univariable and multivariable, regression analyses. Results: The 274 included participants were from Australia, Canada, and the United Kingdom, and spent, on average, 69% (SD 12.4) of their waking hours sedentary. Of the demographic and stroke-related factors, slower walking speeds were significantly and independently associated with a higher percentage of waking hours spent sedentary (p = 0.001) and uninterrupted sedentary bouts of >30 and >60 min (p = 0.001 and p = 0.004, respectively). Regression models explained 11¿19% of the variance in total sedentary time and time in prolonged sedentary bouts. Conclusion: We found that variability in sedentary time of people with stroke was largely unaccounted for by demographic and stroke-related variables. Behavioral and environmental factors are likely to play an important role in sedentary behavior after stroke. Further work is required to develop and test effective interventions to address sedentary behavior after stroke.
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| 2017 |
Dudding-Byth T, Baxter A, Holliday EG, Hackett A, O'Donnell S, White SM, et al., 'Computer face-matching technology using two-dimensional photographs accurately matches the facial gestalt of unrelated individuals with the same syndromic form of intellectual disability', BMC Biotechnology, 17 (2017) [C1]
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| 2017 |
Milioli HH, Tishchenko I, Riveros C, Berretta R, Moscato P, 'Basal-like breast cancer: molecular profiles, clinical features and survival outcomes', BMC MEDICAL GENOMICS, 10 (2017) [C1]
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| 2016 |
Tishchenko I, Riveros C, Moscato P, 'Alzheimer s disease patient groups derived from a multivariate analysis of cognitive test outcomes in the Coalition Against Major Diseases dataset', Future Science OA, 2 FSO140-FSO140 (2016) [C1]
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| 2016 |
Tishchenko I, Milioli HH, Riveros C, Moscato P, 'Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers', PLOS ONE, 11 (2016) [C1]
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| 2016 |
Casanova R, Varma S, Simpson B, Kim M, An Y, Saldana S, et al., 'Blood metabolite markers of preclinical Alzheimer's disease in two longitudinally followed cohorts of older individuals', ALZHEIMERS & DEMENTIA, 12 815-822 (2016) [C1]
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| 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 (2016) [C1]
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| 2016 |
Riveros C, Ujaldón M, Moscato P, 'GPU Acceleration of an Entropy-based Model to Quantify Epistatic Interactions Between SNPs', Current Bioinformatics, 11 396-407 (2016) [C1]
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| 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]
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| 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]
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| 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]
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| 2014 |
Arefin AS, Vimieiro R, Riveros C, Craig H, Moscato P, 'An information theoretic clustering approach for unveiling authorship affinities in Shakespearean era plays and poems.', PloS one, 9 e111445 (2014) [C1]
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| 2014 |
Milward EA, Moscato P, Riveros C, Johnstone DM, 'Beyond Statistics: A New Combinatorial Approach to Identifying Biomarker Panels for the Early Detection and Diagnosis of Alzheimer's Disease', JOURNAL OF ALZHEIMERS DISEASE, 39 211-217 (2014) [C1]
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| 2014 |
Mate K, Riveros C, Weidenhofer J, Goldie B, Scott J, Moscato P, et al., 'Strategies for Enhancing Communication between Students, Academics and Researchers participating in Large-Scale Undergraduate Research Projects', International Journal of Innovation in Science and Mathematics Education, 22 14-29 (2014) [C1]
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| 2013 |
Mendes A, Boland N, Guiney P, Riveros C, 'Switch and Tap-Changer Reconfiguration of Distribution Networks Using Evolutionary Algorithms', IEEE TRANSACTIONS ON POWER SYSTEMS, 28 85-92 (2013) [C1]
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| 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]
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| 2012 |
Johnstone DM, Graham RM, Trinder D, Delima RD, Riveros RC, Olynyk JK, et al., 'Brain transcriptome perturbations in the Hfe(-/-) mouse model of genetic iron loading', Brain Research, 1448 144-152 (2012) [C1]
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| 2012 |
Ravetti MG, Riveros RC, Mendes ADS, Resende MGC, Pardalos PM, 'Parallel hybrid heuristics for the permutation flow shop problem', Annals of Operations Research, 199 269-284 (2012) [C1]
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| 2012 |
Johnstone DM, Graham RM, Trinder D, Riveros RC, Olynyk JK, Scott R, et al., 'Changes in brain transcripts related to Alzheimer's disease in a model of HFE hemochromatosis are not consistent with increased Alzheimer's disease risk', Journal of Alzheimers Disease, 30 791-803 (2012) [C1]
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| 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 (2012) [C1]
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| 2011 |
Oldmeadow CJ, Riveros RC, Holliday EG, Scott R, Moscato PA, Wang JJ, et al., 'Sifting the wheat from the chaff: Prioritizing GWAS results by identifying consistency across analytical methods', Genetic Epidemiology, 35 745-754 (2011) [C1]
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| 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]
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| 2010 |
Gandhi KS, McKay FC, Cox MB, Riveros RC, Armstrong N, Heard RN, et al., 'The multiple sclerosis whole blood mRNA transcriptome and genetic associations indicate dysregulation of specific T cell pathways in pathogenesis', Human Molecular Genetics, 19 2134-2143 (2010) [C1]
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| 2009 |
Ikin A, Riveros RC, Moscato PA, Mendes ADS, 'The Gene Interaction Miner: A new tool for data mining contextual information for protein-protein interaction analysis', Bioinformatics, 26 283-284 (2009) [C1]
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Conference (28 outputs)
| Year | Citation | Altmetrics | Link | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2019 |
Enjeti AK, Ariyarajah A, D'Crus A, Riveros C, Seldon M, Lincz LF, 'Circulating microvesicles are less procoagulant and carry different miRNA cargo in myelodysplasia', BLOOD CELLS MOLECULES AND DISEASES (2019)
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| 2018 |
Hyde L, Boyes A, Mackenzie L, Leigh L, Oldmeadow C, Riveros C, Sanson-Fisher R, 'Identifying Classes of eHealth Literacy Among Magnetic Resonance Imaging and Computed Tomography Outpatients', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2018)
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| 2017 |
English C, Hendrickx W, Riveros C, 'Slow walking speed is associated with high sitting time in stroke survivors: a data pooling study', INTERNATIONAL JOURNAL OF STROKE (2017)
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| 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]
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| 2015 |
Tishchenko I, Milioli H, Riveros C, Moscato P, 'HOW INTRINSIC ARE LUMINAL BREAST CANCER SUBTYPES?', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 2015 |
Tishchenko I, Riveros C, Moscato P, 'REVISION OF MOLECULAR BREAST CANCER SUBTYPES', ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2015) [E3]
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| 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.
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| 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, Brussels, BELGIUM (2015) [E3]
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| 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, Brussels, BELGIUM (2015) [E3]
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| 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]
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| 2014 |
Riveros C, Ujaldon M, Moscato P, 'Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs', PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, Granada, SPAIN (2014) [E1]
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| 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]
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| 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]
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| 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]
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| 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]
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| 2010 |
Mendes ADS, Boland NL, Guiney P, Riveros RC, '(N-1) contingency planning in radial distribution networks using genetic algorithms', 2010 IEEE/PES Transmission and Distribution. Proceedings, San Paulo, Brazil (2010) [E1]
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| 2009 |
Johnstone DM, Ravetti MG, Riveros C, Moscato PA, Hersey P, Scott R, Milward AE, 'Genome-wide microarray analysis of melanoma reveals unexpected anomalies in iron-related gene expression', 2009 International Biolron Society Meeting: Program Book, Porto, Portugal (2009) [E3]
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Report (1 outputs)
| Year | Citation | Altmetrics | Link | ||
|---|---|---|---|---|---|
| 1989 |
Moscato PA, Riveros C, 't-expansion and the Mathieu equation', . (1989)
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Thesis / Dissertation (1 outputs)
| Year | Citation | Altmetrics | Link |
|---|---|---|---|
| 1990 | Riveros C, El principio de equivalencia, su verificación experimental y su relación con las fuerzas fundamentales - Facultad de Ciencias Exactas - Tesis de Postgrado - ARG-UNLP-TPG-0000000079 - Departamento de Física, SeDiCI - Universidad Nacional de La Plata, (1990) |
Grants and Funding
Summary
| Number of grants | 1 |
|---|---|
| Total funding | $27,000 |
Click on a grant title below to expand the full details for that specific grant.
20111 grants / $27,000
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, 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 |
Research Supervision
Number of supervisions
Current Supervision
| Commenced | Level of Study | Research Title | Program | Supervisor Type |
|---|---|---|---|---|
| 2019 | PhD | Epigenetic Heterogeneity in Haematological Malignancies | PhD (Medical Genetics), Faculty of Health and Medicine, 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 |
Dr Carlos Riveros
Position
Conjoint Senior Lecturer
School of Medicine and Public Health
Faculty of Health and Medicine
Focus area
Computer Science and Software Engineering
Contact Details
| carlos.riveros@newcastle.edu.au | |
| Phone | (02) 4042 0478 |
| Fax | (02) 4042 0037 |
Office
| Room | Level 3 Pod - 3020 |
|---|---|
| Building | HMRI Building |
| Location | Lot 1, Kookaburra Circuit New Lambton Heights, NSW 2305 , |
Research Networks
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