Transcript Posters Students 2 - Computer Vision Research Group

Posters Students 2
October 24, Wednesday
Fabrício Martins Lopes
Brazilian
• Ph.D. in Bioinformatics at USP
• Professor at UTFPR - Federal
University of Technology – Paraná
• Research interests: Bioinformatics,
pattern recognition and image
processing.
Current work
Biological Systems
GNs Inference
• Biological systems are
complex;
• Several physical
interactions;
• Components with different
behaviors (functions);
• Different interactions
(protein-protein, proteinDNA, etc.).
• Curse of dimensionality:
there are much more genes
than features;
• Expression data are only
part of the information.
A possible way:
• Data Integration
Gabriela Rodrigues Luiz
• Brazilian
• Bachelor in Biological Science
• Ph.D student in Bioinformatics
• UFMG (University of Minas Gerais)
Expression profile of blood and culture trypomastigotes of
Trypanosoma cruzi by RNA-Seq
• The parasite Trypanosoma cruzi is the etiologic agent of Chagas disease, a
neglected tropical disease.
• Trypomastigotes are the bloodstream circulating form that infect a wide variety
of nucleated host cells.
• Recent advances in high-throughput sequencing offers the ability to discover
new genes and transcripts and measure transcript expression in a single assay.
• However, even small RNA-seq experiments involving only a single sample
produce enormous volumes of raw sequencing reads.
• The volume and complexity of data from RNA-seq experiments requires
powerful computational tools: scalable, fast and mathematically principled
analysis.
• This methodology could reveal the real complexity of the dynamics of expression
of this parasite.
Junior Research Fellow,
Machine Intelligence Unit,
Nationality:
Application of Machine Learning Techniques and Graph Algorithms towards Analysis of
Protein-Protein Interaction Network
Introduction and Objective:
emergent properties of biological entities not readily explainable by the their constituent parts
components are best characterized as interaction networks; interaction patterns being non-trivial and irregular
Further comparison of networks inform us with the shared functional modules in species as well as change in functionality within a species over time
Data:
Interaction collected
from STRING database
for Plasmodium
Falciparum
Phases-sporozoite,
gametophyte
Identification of
connected
components on
perturbation,
and
Clustering
Centrality
Parameter
computation
•Node parameters
•Network parameters
Blast similarity
Topology similarity
Mapped Nodes
Conserved Interaction Edge
Current Scope of Improvement:
•Perturbation analysis
•Improvise on similarity score
including neighborhood, expression
data, gene ontology
• integrate tools into GUI
Acknowledgement
•Dr. Saikat Chakrabarti, Indian
institute of Chemical Biology, for
complete guidance and
computational source
•Prof. Ujjwal Maulik, Jadavpur
Univerisity for thesis supervision
Name: Geizecler Tomazetto
Nationality: Brazilian
Institution: Campinas University (UNICAMP)
PhD Student is supported by grants from FAPESP
Supervisor: Valéria Maia de Oliveira
Diversity analysis and bioprospection of microbial metagenome in
H2-producing biogas fermenter
Characterization of the diversity:
- Bacteria and Archaea Domains;
- FeFe-hydrogenases.
DNA extraction
Bioinformatic: analysis of the
community anaerobic, new
hydrogenases and enzymes for
Domestic sewage
treatment plant at
Water Supply and
Sanitation Company
(SANASA)
biotechnological application
Construction
fosmid library
Sequencing by
means 454pyrosequencing
- Cloning and expression of
hydrogenases
Gilb e r t o Z . Pa st or e llo
[email protected]
Post Doct oral Fellow
Depart m ent s of Eart h & At m ospheric Sciences and
Biological Sciences
Universit y of Albert a
Edm ont on, Albert a, Canada
background:
BSc, MSc, PhD in Com put er Science
Inst it ut e of Com put ing
Universit y of Cam pinas
Cam pinas, São Paulo, Brazil
http://isvm.eas.ualberta.ca
from:
Gamon et al. 2006
Glauco Vitor Pedrosa
I am a PhD student in Computer Science at University of São
Paulo (USP), Brazil. My research area is Image Processing and my
ongoing projects are concerning to feature detection and content
based image retrieval systems.
Glauco Vitor Pedrosa
My ongoing PhD project aims at studying and exploring the
Bag-of-Features approach to support content-based image retrieval
for medical systems, considering the specialists' point of view and
knowledge.
The Bag-of-Features approach represents the image as an collection of local features. For this, first
the image local features are extracted, and then they are assigned to their nearest matching term
from a visual vocabulary. The image feature vector is represented by a histogram of features
detected in the image.
Govinda Murali
4th year Undergraduate Student
Department of Physics & Meteorology
Indian Institute of Technology Kharagpur
India
Direct laser pruning of Nanostructures and study of their optical and
electrical properties
Under Dr. Sow Chorng Haur, Nanomaterials Research lab, National University of Singapore
Practical Applications
• Photodetectors - Image sensing
• Biophysics – optical tweezers used for
study of extension and twisting of
DNA & blood cells
General Information
• Name: Guilherme da Silva Pereira
• City: Campina Grande – State: Paraíba (Northeast of Brazil)
• Graduate in Biology
• State University of Paraíba (UEPB), Campina Grande, Paraíba
• Master’s degree in Genetics and Plant Breeding
• University of São Paulo (USP), College of Agriculture “Luiz de Queiroz”
(ESALQ), Piracicaba, São Paulo
• PhD student in Genetics and Plant Breeding – USP/ESALQ
Current Work
• Title: QTL mapping in sweet sorghum and synteny with sugarcane
• Objectives:
• To found QTL related to production and bioenergy characters in sorghum
• To compare genomes (synteny) and QTL locations between both species
• Data:
• Sorghum population: 225 RIL (recombinant inbred lines) individuals
•
Genotyping-by-sequencing (GBS) – Illumina
• Sugarcane population: 200 F1 individuals
•
Genotyping by iPLEX MassARRAY – Sequenom
• Phenotypes: e.g. production, sugar and fiber contents, ethanol production
Lic. Inti Anabela Pagnuco
• Ph.D. student in Electronic Engineering.
Argentina
• School of Engineering, Mar del Plata National University,
Argentina.
• National Council of Scientific and Technical Research,
CONICET, Argentina.
Current work:
• Supervised classification techniques applied to high
density genetic data.
•Advantages of balanced
microarray data classification
classifier
design
on
•Decision Making for the Semi-automatic Clustering of
large Protein Superfamilies
Email: [email protected]
Ivo Koga
[email protected]
LIS-IC-UNICAMP
BRAZIL
Ivo Koga – LIS – IC – UNICAMP - BRAZIL
•Problem - heterogeneity and data deluge from
environmental monitoring scenarios
•Objective – use Enterprise Service Bus (ESB) and
Complex Event Processing (CEP) to integrate and
process events from sensor data
Thanks!
Ivo Koga
[email protected]
Advisor: Claudia Bauzer Medeiros
[email protected]
JAYANTA KUMAR PAL
JUNIOR RESEARCH FELLOW
INDIAN
CENTER FOR SOFT COMPUTING RESEARCH
INDIAN STATISTICAL INSTITUTE
KOLKATA, INDIA
Current Research Area
• MiRNA and its role on cancer
– Computational Approaches for Identifying
Cancerous miRNA Expressions
– miRNA selection for cancer classification
THANK YOU
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Name: Joana E. Gonzales Malaverri
Advisor: Claudia M. Bauzer Medeiros
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Nationality: Peruvian
Academic institution: Institute of Computing, UNICAMP
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A Provenance-Based Approach: helping to measure the
quality of data
Goal: Present an approach based on the use of provenance
that help on the measurement of the quality of a data
product.
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Laboratory of Information System (LIS)
www.lis.ic.unicamp.br
Subcritical hydrolysis with water/CO2 of agricultural residues for
the production of fermentable sugars
Sugarcane bagasse
Pressed palm fiber
Coconut husk
Defatted grape seed
Eng. Julio César Santos dos Anjos
Master in Computer Science at UFRGS/2012
PhD Student at UFRGS
GPPD Member
MapReduce Research Group Member
Nationality: Brazilian
MapReduce on Heterogeneous Environments +
Volatility
+
Stochastic Schedulers
=
MR-S++
MapReduce with Tasks Stochastic Scheduler
Jurandy Almeida
REasoning for COmplex Data – RECOD Lab
Institute of Computing, University of Campinas – UNICAMP
Campinas, SP – Brazil
[email protected]
e-phenology
e-phenology: The application of new
technologies to monitor plant phenology and
track climate changes in the tropics*
Patrícia Morellato
Phenology Laboratory
Dept. of Botany
UNESP, Rio Claro, SP
Ricardo Torres
RECOD Lab
Institute of Computing
UNICAMP, Campinas, SP
(a) use of new technologies of environmental
monitoring - remote phenology monitoring
systems
(b) provide models, methods, and algorithms to
support management, integration, and analysis of
remote phenology data
(c) create a protocol for a future Brazilian Network long term phenology monitoring program
*Supported
by the FAPESP-Microsoft Research Virtual Institute
Sílvia Cristina Dias Pinto
PostDoc
Institute of Mathematics and Statistics – IME
University of São Paulo – USP
Brazil
• 3D Shape Analysis using Wavelets
– 3D Facial Expression (ICIP 2011)
– Supra-orbital Margin
Submitted to IEEE Transactions on Information Forensics and Security
Kartick Chandra MONDAL
Nationality: INDIAN
4th Year PhD Student
I3S Laboratory (CNRS/UNSA UMR-7271)
University of Nice Sophia-Antipolis,
Nice, France
https://sites.google.com/site/mrkartickchandramondal/
Supervised by: Nicolas PASQUIER
Head of KEIA Team,
Pole GLC, Laboratory I3S, UNSA
Current research interest:
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Developing new closure based approaches for frequent pattern mining,
association rule mining and biclustering in one run.
Analyzing images using our own closure based approaches.
Finding unknown Protein Interactions from HIV-Human Protein Interaction
Data.
Using different data mining task, finding the relationships between
ontological terms and gene annotation from integrated gene expression
data.
Finding biclusters and ranking genes from gene expression data using multiobject methods.
Thank you for your kind interest!!!
Katti Faceli
Associate professor – Department of Computing
Federal University of São Carlos (UFSCar) at Sorocaba
Brazil
Main research project:
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An hybrid intelligent system for clusters’ identification,
which integrates ensembles, multiobjective optimization and
model selection strategies
Other current works:
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Complexity of gene expression data and model selection
for clustering
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Visualization of a set of clustering solutions
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Classification of e-tongue sensor data
Name: Leonardo Galindo Gonzalez
Nationality: Colombia
Institution: University of Alberta, Canada
Flax genome sequencing
and annotation
Transposable element
studies
Reverse genetics to find
mutations in fiber
development genes
Lucas Antiqueira
PhD Computational Physics, MSc/BSc Computer Science
Post-doctoral associate at:
Instituto de Ciências Matemáticas e de Computação (ICMC)
Universidade de São Paulo (USP), São Carlos, Brazil
Current work
Complex networks
– Neuroinformatics
• Brain sampling through functional networks
– Bioinformatics
• Integrated analysis (transcriptome + metabolome +
proteome)
– Natural language processing
• Text analysis for, e.g., authorship identification and
automatic summarization
Declarative queries for Information Retrieval over
graph databases
Luiz Gomes – UNICAMP (Brazil)
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Defining GIRDBs – Graph Information Retrieval DataBases
Representing structured (e.g. relational) and unstructured
(e.g. documents) data as graphs
Mapping IR metrics (relevance, reputation, similarity, etc.)
into graph analysis tasks
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Integrating the metrics in a declarative query language
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Optimizing/Processing queries
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Applying the framework to CMSs, e-health, biodiversity,
recommendation systems, etc.
Industrial Engineering and Operation Research
University of California, Berkeley
I am originally from China.
Focusing on data analysis research.
On-going research project
Berkeley Architecture Department Building
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Data of every plug load in the 4th floor for each minute
Analysis
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Applying clustering to detect the pattern.
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Time Series Analysis
Maiana de Oliveira Cerqueira e Costa
 M.Sc. in Computational Modeling at Laboratório
Nacional de Computação Científica (Petrópolis,
Brazil).
 B.Sc. in Biological Sciences at Universidade Federal da
Bahia (Salvador, BA).
Current work and interests
 Comparative genomics of
Staphylococcus aureus ST239
clinical isolates.
Previous works
 Participated in the annotation of a database dedicated to type
IV secretion systems (http://www.t4ss.lncc.br);
 Performed phylogenetic studies on the
evolution of Gymnotiformes.