Posters Students 3
October 25, Thursday
Marcelo Mottalli
Computer Science Department
University of Buenos Aires (UBA)
Buenos Aires, Argentina
Research topics
• Iris recognition (and biometrics in general)
• Statistical analysis for biometric template
matching in large databases
• Large scale searching in biometric databases
using GPU
Who am I?
Márcio de Carvalho Saraiva
Brazilian
Master's degree
Federal University of Campina Grande - PB
Current work
Recommendation query database
- Classification database users using queries
log
Marcus Vinicius de Aragão Batista
Brazilian PhD Student
Federal University of Pernambuco - UFPE
Laboratory of Bioinformatics and
Evolutionary Biology – LABBE
http://www.bioinfo.ufpe.br/
Projects I have been engaged on…
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Bioinformatics Applied to Viral Genomics and Evolution.
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Development and Application of Novel Computational Methods to
Papillomavirus Genomic Diversity Studies.
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Comparative Transcriptomics of Sandflies (Diptera: Pscychodidae) of
Medical and Veterinary Importance.
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Transcriptomics of Leishmania chagasi.
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Database and Bioinformatics Tool Development.
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And others...
Maria Augusta C. Horta
pHD student at Molecular Biology and Genetic Engineering Center (CBMEG),
State University of Campinas (UNICAMP)
Brazil
Current work: Bioprospection of new enzymes for biomass
degradation
The main objective is to contribute to the development of enzymatic hydrolysis of
sugarcane bagasse for the production of cellulosic ethanol.
Through analysis of genomes of microorganisms with demonstrated hydrolytic
potential we expect to obtain genes and heterologous proteins for efficient
degradation of biomass and high conversion yields.
Third-year PhD Student
Myrids Team
IRISA / INRIA / University of Rennes I
Rennes, France
Advisors: Cédric Tedeschi and Thierry Priol
• Chemical Programming Model
– implicitly parallel and non-deterministic model
– higher order → on-the-fly modification of programs
– suitable for large-scale applications
• scientific workflows: enactment, execution, scheduling
• autonomic computing: self-* properties
• Runtime for Large-scale Platfroms
– fully decentralised
– efficient and scalable
– real-world prototype
• Questions? Comments?
– marko.obrovac@inria.fr
– http://www.irisa.fr/myriads/members/doorman
Matheus Silva Mota
mota@ic.unicamp.br
Laboratory of Information Systems - LIS
Institute of Computing - UNICAMP
Campinas, São Paulo
Shadow-driven document Representation (Master)
Attacked problem: Document is everywhere; but in different formats.
Our solution: Shadows - an interoperable descriptor that represents documents’
structure and content, regardless of formats.
Correlating Ontologies in a Multiscale Perspective (PhD)
Attacked problem: How to analyze (very) large knowledge bases?
Our solution: Multiscale(?)
Personal Information
Name : Mauricio Barrientos Somarribas
Nationality: Costa Rica
Studies:
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B.Sc. In Computer Science
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University of Costa Rica
2nd year M.Sc in Comp. & Systems Biology
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Kth Royal Institute of Technology, Sweden
Recent and Current Work
• Transposable Element Database
• Collaboration with Stanford University
• ChIP-seq online analysis platform
• Karolinska Institutet, Sweden
• Regulatory region annotation
• Oxford University
UNIVERSITY OF SAO PAULO
Inter-institutional Grad Program on Bioinformatics
Milton Yutaka Nishiyama Junior
PhD Student
Brazil
• Advisor: Dra. Glaucia M. Souza (Department of Biochemistry – IQ/USP)
• Co-Advisor: Dr. João E. Ferreira (Department of Computer Science – IME/USP)
Development of an environment based on metabolic pathways
for integration and analysis of functional genomics of Sugarcane
-Functional Annotation of Sugarcane Transcriptome
(SANGER, RNA-Seq)
- Development and Application of Metodologies and Tools for
cDNA Microarray Analysis
-Work on an Heterogeneous Database Integrating different
Sources
-Development of a Framework to Integrate Heterogeneous Data
from Sugarcane and other Grasses
Nils Murrugarra
Graphs, ensembles and Classification Tasks
Outlier Detection in Medical Records
Rafael Santos – Brazil
Technologist
INPE – Instituto Nacional de Pesquisas Espaciais
(the Brazilian National Institute for Space Research)
www.inpe.br
www.lac.inpe.br/~rafael.santos
rafael.santos@inpe.br
Rafael Santos – Brazil (rafael.santos@inpe.br)
R&D in Artificial Intelligence, Data Mining, Image Processing,
Distributed Information Systems.
Teach at the Graduate Program in Applied CS at INPE, Summer
and Winter schools.
Present R&D projects: data organization, federation,
provenance, distribution / virtual laboratories & observatories
/ “data salvage” / collaborative systems.
Ricardo Cerri, Ph.D. candidate
Nationality: Brazilian
Field: Computer Science
Institution:
Institute of Mathematics and Computer Science
University of São Paulo at São Carlos
ICMC – USP – São Carlos – São Paulo – Brazil
Current Work
• Hierarchical Multi-Label Classification
• Protein and gene function prediction
• Neural Networks and Genetic Algorithms
• Identification of Transposable Elements
• Hidden Markov Models
• Decision Trees
Name:
Roberto Hirochi Herai
Nationality:
Brazilian
Institution:
School of Medicine,
University of California San Diego,
Ca, USA
Current work
-Bioinformatics approaches for autism spectrum disorders,
based on:
→ Induced pluripotent stem cell technology;
→ Neuron cell diferentiation;
→ High throughput sequencing extraction;
Pos-Doc position at
Dr. Ronaldo Júnio de Oliveira
Sup: Vitor B. P. Leite
Theoretical Models for Protein Studies
Protein Folding
Bioethanol Enzymes
PNAS (2007, 2012)
About me
Who: Santiago Videla - santiago.videla@[irisa.fr | gmail.com]
From: Buenos Aires / Cordoba, Argentina
Institutions:
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France: CNRS, IRISA – INRIA Rennes, University of Rennes 1
Germany: Institute for Computer Science, University of Potsdam
About my work: Qualitative modeling in Systems Biology
Approach: Answer Set Programming
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Declarative problem solving paradigm
Good for solving combinatorial search problems in NP(-hard)
Knowledge Representation and Reasoning, Databases, Constraint Solving and
Logic Programming
Shayan Shahand
s.shahand@amc.uva.nl
Born in Isfahan, Iran
Bachelor: Computer Eng.,
SBU, Tehran, Iran
Master: Computer Eng.,
NTU, Singapore
PhD candidate: Medical informatics (e-bioscience)
UvA, AMC, Amsterdam, Netherlands
Front-ends to biomedical data analysis on
e-infrastructure
Front-end
CLI
Desktop
App
Web
App
Mobile
App
middleware
Back-end
API /
CLI Tools
API /
CLI Tools
Cluster
Grid
s.shahand@amc.uva.nl
…
API /
CLI Tools
Cloud
e-infrastructure
Spencer Angus Thomas
British
University of Surrey
Guildford, Surrey
GU2 7XH, UK
Current Research
1. Synthesis and analysis of gene regulatory networks (GRNs)
a) Optimising GRNs with evolutionary algorithms (EAs)
b) Producing functional dynamics from GRNs
• Genetic oscillators and switches
• The effect of objective set up: multiobjectivization
c) Evolutionary mechanism
• Coupling small motifs
• Gene duplication and deletion
2. Reconstruction of biological networks
a) Modelling bacteria that produce antibiotics
b) Experimental data and correlations to identify genes
c) EAs to build model and reproduce gene expression
Teresa Sousa
• Portuguese
• University of Coimbra – Portugal
• Doctoral Program in Biomedical Engineering
• Host institutions:
 Biomedical Institute for Research in Light and Image (IBILI), Faculty of
Medicine, Coimbra University
 Institute for Systems and Robotics (ISR), Faculty of Sciences and
Technology, Coimbra University
 Brain Imaging Center, Department of Cognitive Neuroscience,
Maastricht University
From parametric decoding of simple mental states to neurofeedback:
insights into the neuroscience of cognitive control
Speed 1
Speed 2
Speed 3
Speed 4
Identification of brain areas which
respond to parametric stimulus
Developing a brain reading
technique to automatically
detect the parametric levels of
brain activation
BCI applications: manipulating target
parameters such object position and
velocity
New neurofeedback approach with
more precision allowing understand the
neurocorrelates of cognitive control
Transfer the new technique to EEG
VELIMIR GAYEVSKIY
PhD Student – Second Year
Supervised by Dr. Matthew Goddard
The University of Auckland, New Zealand
http://goddardlab.auckland.ac.nz
OUR RESEARCH
Microbial Ecology Wine Science
Population Genetics Experimental Evolution
The Diversity, Origins and Ancestry of
Saccharomyces cerevisiae
in New Zealand
WHOLE GENOME SEQUENCING
Phylogenetics Phylogeography
Divergence Dating
Wissam A. A. Albukhanajer
PhD Student
Nationality: Iraq
Permanent Resident: United Kingdom
University of Surrey
Faculty of Engineering and Physical Science
Department of Computing
Nature Inspired Computing and Engineering Group
Current work involves fast and robust Invariant feature extraction
and Image recognition using Bio-Inspired and Computational
Intelligence
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Dealing with massive image data on the web or local database.
Robustness to general image deformation (Invariance), such as rotation, scale, noise
etc.
High performance algorithms and parallel computation are essential.
(Published) W. A. Albukhanajer, Y. Jin, J. A. Briffa and G. Williams "Evolutionary MultiObjective Optimization of Trace Transform for Invariant Feature Extraction" IEEE
Congress on Evolutionary Computation CEC, Brisbane, Australia, June 10-15,
2012. Digital Object Identifier : 10.1109/CEC.2012.6256160
(Submitted) W. A. Albukhanajer, Y. Jin, J. A. Briffa and G. Williams “A comparative Study
of Multi-Objective Evolutionary Trace Transform Algorithms for Robust Feature
Extraction " 7th International conference on Evolutionary Multi-Criterion Optimization.
EMO 2013, Sheffield UK, 19-22 March 2013
Yingchao Piao
Ph.D. student, Advisor: Prof. Baoping Yan
General Group for Advancing e-Science Applications
Computer Network Information Center, Chinese
Academy of Sciences (CNIC, CAS), China.
Email: pyc@cnic.cn
MSN: piaoyingchao@live.cn
Current Work
• Change Detection in Remote Sensing Time Series
 Using wavelet transform method
 Seeded region growing algorithm for detailed analysis
• Massive data processing algorithm
 Problem found during former work (OOM in transformation)
 Accelerate the remote sensing image processing algorithm
Yuwei Wang
Ph.D. student, Advisor: Prof. Baoping Yan
General Group for Advancing e-Science Applications
Computer Network Information Center, Chinese
Academy of Sciences (CNIC, CAS), China
Email: ahwangyuwei@cnic.cn
Current Work
• Spatial and Temporal Visualization and Visual Analysis
of Movement Data of Migratory Birds
• Data Mining on GPS data of Wild Birds
• 3D Visualization Platform of Bird Migration
• Network Video Monitoring System for Qinghai Lake
Talita Perciano Costa Leite
1.
Bachelor’s degree in Computer Science from Federal University of Alagoas - Brazil
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Master’s degree in Computer Science from Federal University of São Carlos –
Brazil
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3.
Advisor: Alejandro C. Frery
Data mining, computational statistics, R software, image processing
Advisor: Nelson D. A. Mascarenhas
Image restoration, ultrasound, vibro-acoustography (collaboration with Mayo Clinic)
PhD degree in Computer Science from University of São Paulo – Brazil (1 year
and 3 months stage at ENST Paris with Florence Tupin)
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Advisors: Roberto Hirata Jr. and Roberto M. Cesar Jr.
Title: Detection of thin and ramified structures in images using Markov random fields and
perceptual information
Image segmentation, thin and ramified structures, Markov random fields
Blood vessels, plant root images, satellite images (image fusion)
Current work
USP e-Science Research Network
Roberto M. Cesar Jr.
• Setting up an e-Science infrastructure:
 The infrastructure for data acquisition and treatment will be organized as
a network
 Hardware and software to support the main research steps: data capture,
storage, maintenance, analysis and visualization.
 Data stored in databases distributed and integrated to other bases
available at Internet
 Computational statistical and mathematical analysis tools and data
visualization techniques => data interpretation