CURRICULUM VITAE
ANASTASIOS OULAS
Date of Birth:
Nationality:
E-mail Address:
19 September 1979
Greek
a_oulas@hotmail.com , oulas@imbb.forth.gr
EDUCATION
2003 - 2007
Institute of Molecular Biology and Biotechnology (IMBB),
Foundation for Research and Technology Hellas (FORTH),
Affiliated with The University Of Crete.
Department of Bioinformatics.
PHD in Computational Analysis of Microarray Data.
Course Description:
Our lab work in this area focuses on processing issues for gene/protein
expression data, mainly resulting from microarray experiments. We develop a
number of normalization methods for microarray data standardization so that inputs
from different arrays, experimental conditions or platforms can be compared to each
other. We investigate the performance of implemented noise removal techniques and
provide guidelines about the suitability of each method to various data categories.
We also develop feature extraction techniques for the identification of most
important input features (genes or samples) in terms of discriminatory power
between the categories of interest in the data set. These include information theoretic
approaches, multidimensional scaling, signal-to-noise statistical and neural network
methods as well as ad hoc algorithms. We develop new and modify existing
clustering (k-NN, hierarchical, SOM) and classification (SVM, Bayesian networks,
ANN) algorithms for the categorization of expression data. We aim to study the
complexity and performance of these algorithms on microarray data as functions of
the type of input data, size of input set, degree of correlation between input features,
number of categories, signal-to-noise ratio in data etc. We mainly focus on applying
and extending our current expertise in developing novel, biologically inspired neural
network architectures and learning rules for supervised classification tasks.
Furthermore, we are in the process of compiling a user-friendly, software
package incorporating a set of efficient and reliable computational methods
addressing all stages of microarray data analysis from normalization to
categorization and identification of marker features.
2001 – 2002
Imperial College of Science, Technology and
Medicine.
Department: School of Biological Sciences.
MSc in Computational Genetics and Bioinformatics.
MSc was completed with a distinction.
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Courses taken:
First Term:
Bioinformatics I (Genetics and Genomics): Allowed me to obtain a clear
view on current issues involving Genetics and Genomics and the possible
intervention of Bioinformatics in the fields. Includes: Linkage Analysis, Sequencing
Genomes, Single Nucleotide Polymorphisms, Complex locus disease genetics and
the genetics of model organisms.
Statistic for Bioinformaticians: Review of issues relevant to a statistical
geneticist, probabilistic models for Biological Sequences (Stochastic Processes,
Hidden Markov Models), Sequence Comparisons and the statistics of BLAST. The
course also involved practice in using the statistical package S+.
Computing: Involving practice in programming using high-level
languages such as C++ and Perl. Involved three short assignments in Perl whereby
Perl scripts where written for the retrieval of biological information from on-line
databases and performing typical file processing tasks. Perl modules such as FTP
(File Transport Protocol) and the LWP module for web access were also used. The
aspect of system calls to run programs outside the Perl script was also introduced.
Second Term:
Bioinformatics II: Practice in using computational tools and databases
available on the Web for the annotation of protein sequences, the analysis of DNA
sequences and the use of computational tools for determining linkage and linkage
disequilibrium. Includes concepts of pair-wise alignments, multiple sequence
alignments, database searching for similar sequences, protein structure prediction
(protein family analysis, relationships to known structures, 3D-comparitive
modelling).
Molecular Basis of Disease: This course allowed me to update my
knowledge on molecular issues relevant to diseases, and the use of Bioinformatics in
the analysis of complex and simple diseases.
Databases: Involving the creation and analysis of databases (i.e. mySQL
databases) using query languages such as SQL.
Computing: Programming in Java. Involved a mini project whereby EST
data was retrieved from an on-line database and sorted into stringency classes
according to length and homology.
Third Term Project:
Project Title: Computational Validation of Microarray Data using
Hierarchical Clustering. The high-level language Java was used to implement a
program for the rapid large-scale validation of H-clustering data.
1998 – 2001
University of Sussex.
Department: School of Biological Sciences.
BSc. Molecular Genetics in Biotechnology.
Degree class: 2.1 honours.
Subjects studied.
Final Year:
Membrane and Organelle Biochemistry;
Molecular
Biochemistry of cell Regulation; Biotechnology and Innovation.
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Genetics;
Second Year:
Arts/Science course (Italian); Computational, Analytical and Practical
Skills; Clinical Aspects of Biochemistry; Developmental Biology; Energy
Transducing Systems; Eukaryotic Genetics; Introduction to Cell Regulation;
Statistics for Biologists; Structural Molecular Biology.
First Year:
Biological Chemistry; Cellular Biochemistry; Computing Skills for
Biologists; Evolution; Introduction to Data Handling; Introduction to Molecular
Genetics; Physiology and Behaviour of Animals; Preliminary Chemistry; Research
Methods in Biochemistry.
Final Year Project:
Title of project: “The Detection of Suppressors of the Ypt5 gene in S.
Pombe yeast cells ”. Yeast Genomics, practical applications in using plasmid vectors
to insert foreign DNA in yeast cells, and the efficient detection of the transformed
yeast cells. Techniques used involve PCR, transformation, plating cells on agar
plates, inoculation, etc.
Other Skills:
I have significantly evaluated my practical and laboratory skills and I am
now experienced with official laboratory conditions.
1991 – 1998
The Campion School of Athens
‘A’ levels – Maths (C), Biology (D) , Chemistry (D)
GCSEs – 1 (A), 4 (B)s , 3 (C)s and a (D).
WORK EXPERIENCE
1/02/03 – 30/09/03
Research assistant at the Department of Bioinformatics, Institute of Molecular
Biology and Biotechnology, Foundation for Research and Technology Hellas, under
the supervision of Dr Yiota Poirazi.
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Summer 1998
Computational Analysis of Microarray data.
Using supervised machine-learning techniques such as Neural Networks.
Matlab is used as a working environment.
Training in an IVF (In Vitro Fertilisation) Unit , Maroussi ,Athens
under the supervision of Doctor Giles Palmer.
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I became aware of the IVF technique and its importance
Viewed the inside of the laboratory and discussed relative issues with the geneticists.
Witnessed the actual embryo-transfer, semi–surgical technique performed by one of the
clinic’s doctors
Filed clinical information about individual patients.
INTERESTS AND ACTIVITIES
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On my free time I practice the guitar and I enjoy playing for the entertainment of
friends or family.
OTHER SKILLS AND EXPERIENCE
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Familiar with Windows and Linux environments.
Fluent in Greek and English.
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REFERNCES
Dr Yiota Poirazi
IMBB
FORTH
Dr J. Armstrong
Third year Project supervisor
at Sussex University
porazi@imbb.forth.gr
j.armstrong@sussex.ac.uk
Tel(2810391139)
Tel(UK)01273 678576
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Dr G. Palmer
Supervisor at IVF
gpalme@otenet.g r
Tel(Gr)003010 6196082
Mr Moustafa Ghanem
Project supervisor at
Imperial College
m.ghanem@imperial.ac.uk