Education phD, Electrical Engineering / Automation




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CURRICULUM VITAE




Name: Professor PABLO MOSCATO


Positions: Founding Co-Director

Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine (2006-current)

Funding Director

Newcastle Bioinformatics Initiative (2002)


Deputy Director of the Information-based Medicine Program and

Strategic Research Advisory Panel Member

Hunter Medical Research Institute


Professor

School of Electrical Engineering and Computer Science

The University of Newcastle


Work address: Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine

The University of Newcastle

University Drive

Callaghan, 2308, New South Wales

AUSTRALIA

Telephone: +61 2 4921 6056

FAX: +61 2 4921 6929

Email: Pablo.Moscato@newcastle.edu.au


Home address: 173 Park Avenue Home phone number +61 2 4952 4320

Kotara, NSW, 2289

AUSTRALIA

EDUCATION




PhD, Electrical Engineering / Automation,

Universidade Estadual de Campinas,

Faculdade de Engenharia Elétrica e de Computação, Campinas, Brazil,

Dissertation Title: “NP Optimization Problems, Approximability and Evolutionary Computation: From Practice to Theory”, April 2001.

Full-time Visiting Graduate Student, Physics,

California Institute of Technology, Pasadena, California, USA, Sept. 1988 – Oct. 1989.

Licenciado en Física (a five-year degree in Physics, with final Research Degree Thesis).

Universidad Nacional de La Plata, Department of Physics, La Plata, Argentina, Dec. 1987.



RESEARCH INTEREST


Computational Systems Biology in Health and Disease – Reverse Engineering of biological systems –Applied Computer Science – Application and development of state-of-the-art mathematical models and computer algorithms for the most challenging problems in biology and biotechnology research with emphasis on uncovering the molecular basis of different cellular phenotypes and diseases.

ACHIEVEMENTS


My papers have been cited more than 2,700 times, this number has been approximately doubling every twelve months, corresponding to an H-index of 20. My first 20 most cited manuscripts have been cited 2,204 times, and my 49 most cited manuscripts have been cited more than 49 times on average. My work has been highly influential in many scientific and technological fields (data from Google Scholar, January 2010; H-index=20, G-Index=49). It has been obtained using “Publish and Perish”, software available online for free download at http://www.harzing.com/pop.htm


Measures of impact include:


Life Sciences – Molecular and Clinical Biomarker Discovery


  • Introduced a unifying hallmark of cancer based on the changes of Information Theory quantifiers (Cancer Biomarker Discovery: The Entropic Hallmark”, PLoS ONE 5(8): e12262. doi:10.1371/journal.pone.0012262). We say in the conclusions “We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.” This manuscript analyses datasets in prostate cancer and melanoma and has more than 800 references linking our results with the literature information.




  • We proved the validity of our argumentation about the power of our Information Theory driven methodology by applying the technique to the identification of Alzheimer’s Disease biomarkers. This resulted in the publication of: “Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus' Gene Expression Profiles in Alzheimer's Disease”, PLoS ONE 5(4): e10153. doi:10.1371/journal.pone.0010153.




  • Identified new Multiple Sclerosis susceptibility loci on chromosomes 12 and 20 (Nature Genetics 41, 824 - 828 (2009)) the GWAS supported by an ARC Linkage and Multiple Sclerosis Research Australia, and in collaboration with the Australian–New Zealand Multiple Sclerosis Genetics Consortium that I co-founded.




  • Led the team that developed the first transcription factor map that can explain most of the gene expression variation observed in the gene expression molecular signatures for Relapse Remitting, Primary Progressive, and Secondary Progressive Multiple Sclerosis (this study was completed in a 65-pages manuscript describing the method and results have been accepted in October in PLoS ONE, to appear).




  • Developed a novel mathematical model, and an associated solution procedure based on combinatorial optimization techniques, to identify optimal drug combinations for cancer therapeutics (PLoS ONE 5(10): e13055. doi:10.1371/journal.pone.0013055)




  • Using a panel of abundances of 120 signalling proteins on archived plasma samples, developed a novel mathematical method for biomarker discovery that led to the 5-protein biomarker molecular signature for clinical Alzheimer’s disease. Developed classifiers that predicted with 96% total accuracy the onset of the illness (results published in PLoS ONE 3(9): e3111. doi:10.1371/journal.pone.0003111).




  • Developed a new method for clustering that helped, in a different application, to identify seven well-defined clusters of symptoms that categorized longitudinal radiation-induced rectal toxicity data. The result is a collaboration with one of the largest prostate cancer clinical trials in the area (results published in Radiother. Oncol. 2009 (Mar.), 90(3): 400-07; Epub 24 Oct. 2008).




  • Developed the first method to distinguish childhood absence eplilepsy from controls by the analysis of their background EEG (J Neurosci Methods, 13 May 2009).




  • Transformed The University of Newcastle from an inactive institution in research in bioinformatics to being a leader in NSW and in Australia in translational and clinical bioinformatics (via the establishment of the Newcastle Bioinformatics Initiative in 2002 and the creation of the Priority Research Centre in 2006), two ARC Discovery Projects (as first named Chief Investigator) and by leading the Newcastle node of the ARC Centre of Excelence in Bioinformatics since 2004).


Basic Mathematics


  • In a collaboration with M.G. Norman (CEO, Scapatech), discovered 0.714782700791294…one of the 164 fundamental mathematical constants. From more than 215000000 mathematical constants calculated with more than 2 billion digits, our constant (named “TSP constant” in the link that follows) http://pi.lacim.uqam.ca/eng/table_en.html has been selected as “essential” for Simon Plouffe’s Inverter (see http://pi.lacim.uqam.ca/eng/ for the latest version), establishing one important opening conjecture in Computer Science— http://mathworld.wolfram.com/TravelingSalesmanConstants.html—that our constant may indeed be the elusive “TSP constant” introduced by Beardwood, Halton and Hammersley in 1959 (first proposed in Proc. of the Cambridge Philosophical Society).


Computer Science and Applied Mathematics


  • “Memetic algorithms”, the field I have championed in the computing literature since my collaboration with M.G. Norman (Caltech Concurrent Computation Program Report 826, 1989), has expanded rapidly and gained worldwide reputation. A web search on Google with “memetic (algorithms OR algorithm)” returns 80 500 hits with pages containing information that refers to this subject.




  • I have been invited to be an author of Scholarpedia (http://www.scholarpedia.org). I was elected by peers around the world and subsequently invited to write an article on Memetic Algorithms. Scholarpedia is “a peer-reviewed open-access encyclopedia written by scholars written by the leading experts in their respective fields. It does not publish "research" or "position" papers, but rather "living reviews" that will be maintained by the future generation of experts via the process of curatorship”. At present, eighteen Nobel Laureates and five Field Medalists have already contributed to this endeavour.



  • “Memetic algorithms”, the field I have championed in the computing literature since my collaboration with M.G. Norman (Caltech Concurrent Computation Program Report 826, 1989), has expanded rapidly and gained worldwide reputation. A web search on Google with “memetic (algorithms OR algorithm)” returns 80 500 hits with pages containing information that refers to this subject.







  • Searching with the web search engine Google, in July 2006, a total of 4,763 hits could be found of people/websites/publications that recommend my web pages.




  • My research output has been influential in Computer Science. My papers have been cited in a variety of journals and publications including:



Lecture Notes in Computer Science

Lecture Notes in Artificial Intelligence

Information Processing Letters

Discrete Applied Mathematics

BMC Bioinformatics

Engineering Applications of Artificial Intelligence

Artificial Intelligence Review

Journal of Heuristics

Artificial Life

Neurocomputing

NETWORK-Computation in Neural Systems

Journal of Computer Science and Technology

Applied Mathematics and Computation

Computational Statistics & Data Analysis

Evolutionary Computation

Artificial Intelligence In Medicine

Applied Intelligence

Future Generation Computer Systems

IEEE Transactions on Systems Man and Cybernetics, Part B-Cybernetics

Biol. Cybernetics

Applied Intelligence

BT Technol. Journal

Pattern Recognition

Concurrency – Practice and Experience,

IEEE Transactions on Parall. Distr.

OR SPEKTRUM

Neural Computation

Network: Computation in Neural Systems

Revue de Intelligence Artificielle

Artificial Immune Systems

ACM Computing Surveys

ACM Transactions on Mathematical Software

Mathematics And Computers In Simulation

Computer Communications

Handbook of Applied Optimization (book)

Knowledge-based Systems

Journal of Combinatorial Optimization

IEEE Transactions on Evolutionary Computation

Parallel Computing

and also in proceedings, books, contributed/edited books, and PhD theses in Asia, Europe, North America and South America.


Optimization, Operations Research and Management Science


  • My work in heuristic optimization has translated into a large number of applications in Computer Science, Operations Research (production planning, management science), Finance and Economics, Civil Engineering, Physics and Chemistry, Bioinformatics, design of experiments, and even into the design of interplanetary trajectories for spacecrafts. Articles that cite my contributions have appeared in the journals:


Discrete Applied Mathematics

AI EDAM-Artificial Intelligence for Engineering Design Analysis and Manufacturing Inverse Problems

Asia-Pacific Journal of Operational Research

European Journal of Operational Research

Journal of the Operational Research Society

International Journal of Advanced Manufacturing Technology


  • In recognition of my research outputs and trajectory I was invited to publish a chapter on “Memetic Algorithms” for the planned Encyclopedia of Operations Research and Management Science, published by Wiley (to appear in 2009).




  • I was also invited in 2001 to contribute a chapter on Memetic Algorithms for the Handbook of Applied Optimization (the book was runner-up (Honorable Mention) for the Association of American Publishers “Outstanding Professional and Scholarly Titles of 2002 in Computer Science”).


Physics, Engineering and Technology


  • My research output has been markedly influential in disciplines outside Computer Science. My skills allow me to collaborate with researchers in a truly interdisciplinary way. Aside from the obvious links of my research activities with the Life and Health Sciences, my research results have been cited in journals in a variety of fields, illustrating the wide impact of my research. These include:


Journal of the Astronautical Science

Physics Letters A

Physical Review E

Physical Review Letters

Applied Mathematics Letters

Journal of Computational Physics

Comp. Phys. Commun.

ACM Transactions on Mathematical Software

Chemometrics and Intelligent Laboratory Systems

Computers & Chemical Engineering

Computers and Industrial Engineering

Microwave and Optical Technology Letters

Microprocess. Microsy.

IEEE Transactions on Magnetics

IEEE Transactions on Power Systems

IEEE Transactions on Electronics Packaging Manufacturing

IEEE Transactions on Instrumentation and Measurement

IEEE Transactions on Geoscience and Remote Sensing

Journal of Water Resources Planning and Management – ACSE

Research in Engineering Design-Theory Applications and Concurrent Engineering

Control and Cybernetics

Computers & Structures

Experimental Mechanics

Journal of Mechanical Design

Engineering Fracture Mechanics

Advanced Engineering Informatics

International Journal of Advanced Manufacturing Technology


ACADEMIC AND PROFESSIONAL EXPERIENCE


Funding Co-Director Centre for Bioinformatics, Biomarker Discovery and Information-based Medicine (a Priority Research Centre of The University of Newcastle),

July 2006 – present.


  • Successfully bid for, guided and coordinated activities of the most multidisciplinary University Centre. This has been a very successful enterprise. In 2008, collectively, the Centre members have successfully attracted research funds in excess to A$ 9,000,000.

  • Supervised and guided PhD students’ thesis work (three students have successfully completed their PhD; currently directing four PhD students).

  • Supervised job performance of five post-doctoral research fellows and a Centre Manager.

  • Conducted and led Centre meetings.

  • Managed the Centre’s budget of more than A$500 000 yearly, including salary, equipment, travel, discretionary, supplies and miscellaneous expenses.

  • Participate in the recruiting and hiring of new professionals for the Centre.


Funding Director Newcastle Bioinformatics Initiative, The University of Newcastle,

Dec. 2002 – June 2006.


  • Led a new initiative for the University and established bioinformatics biomedical research, which did not previously exist (managed an initial budget of A$500 000).

  • Recruited and supervised two post-doctoral research fellows.

  • Collaborated as an Associate Investigator and led the activities of the ARC Centre of Bioinformatics at the Newcastle node from 2004 to June 2006.

  • Created in 2002, expanded and finally achieved financial self-support of the Newcastle Bioinformatics Initiative (NBI). When I moved to Newcastle (Sept. 2002) there was no full-time research associates employed in our discipline as a result of external grants being funded. By June 2006, under my guidance, the NBI had a staff composed of three lecturers, three post-docs and four PhD students. Because of the NBI, proven excellence in research in Bioinformatics and leadership in NSW was obtained. As a direct consequence of my research, the University is now describing itself as having strong expertise in Bioinformatics in its publicity material: Individual areas of research excellence include materials handling, reproductive biology, health economics, control systems and bioinformaticswww.biospace.com/company_profile.cfm?CompanyID=827220 www.irua.edu.au (see the information listed under “Member Universities”).
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