Informatics Training Grant

A new training grant was awarded - go to the project web site

 

 

Informatics training - Brazilian vector/parasitic disease

Grant number: 5D43TW007012-03.
Financial support: FOGARTY INTERNATIONAL CENTER

Link to the project web site at CRISP-NIH.

Principal investigators

In the US – Jessica Kissinger – Web – Email
In Brazil – Guilherme Oliveira – Web – Email

Trainers

Rodrigo Corrêa-Oliveira (Brazil) – Email
Rick Tarleton (US) – Web – Email
Alberto D’Ávila (Brazil) – Web – Email
Bruno Sobral (US) – Web – Email
João Setúbal (US) – Web – Email

Facilitators

José Ribeiro dos Santos – Web – Email
Chuong Huynh – Email
Martin Embley – Web – Email

Project summary

This proposal represents a collaborative training partnership between researchers at the University of Georgia, the Centro de Pesquisas Rene Rachou - FIOCRUZ in Belo Horizonte, Brazil, the George Washington University, and the Instituto Oswaldo Cruz-FIOCRUZ in Rio de Janeiro, Brazil. The CPqRR currently has 15 laboratories and 3 funded NIH grants (A training grant in emerging and re-emerging diseases, an ICIDR grant on host genetic correlates in schistosomiasis and a grant on the genetic architecture of heart disease in rural Brazil". The goal of this training proposal is to establish a sustainable core infrastructure at the CPqRR in the areas of ioinformatics, epidemiology and molecular evolution that will complement existing NIH funded research and facilitate research conducted in other laboratories. The focus of research at the CPqRR is tropical parasites, their vectors and their hosts. These organisms include: Plasmodium falciparum, Trypanosoma cruzi, Toxoplasma gondii, Schistosoma mansoni, Anopheles, Biomphalaria and Humans. This proposal is designed to meet the needs of the CPqRR by initiating a 5-year targeted training program that involves pre-and post-doctoral students from many of the 15 laboratories at the CPqRR. Advanced training will be conducted via workshops, courses, short- and long-term training both within Brazil and abroad. Training will involve collaborative research projects originating from the needs of the CPqRR and focusing on several aspects of schistosomiasis. The unifying project for this training will be the creation of a Schistosoma genome relational database housed and served from the CPqRR. This database will house the transcriptome data and epidemiological data being generated by the CPqRR. Molecular evolution training will focus on the Schistosome vector, Biomphalaria and epidemiological/ biostatistical data will be derived and analyzed from existing funded projects. The technology and knowledge acquired from this training and implementation exercise will be directly applicable to research on other parasitic organisms. We will proactively seek out well qualified candidates for training that have a strong desire to return and contribute their newly acquired expertise to the continuation of a local training center of excellence.

Training opportunities

In Brazil

  Yr 1 Yr 2 Yr 3 Yr 4 Yr 5
MSc 1 1 2 2 2
PhD 1 2 2 2 3
Post-Doc 1 2 2 2 2

In US

  Yr 1 Yr 2 Yr 3 Yr 4 Yr 5
PhD 1 1 1 2 1
Post-Doc 1 2 2 2 1

Courses

From year 2 on there will be opportunities for short courses and workshop in Brasil and abroad.

English courses for the students traveling abroad.

Course opportunities

Project activities

08/31/2004 - Centro de Pesquisas René Rachou – FIOCRUZ
Description of the Project to the CPqRR-FIOCRUZ community

02/21-25/2005 - Centro de Pesquisas René Rachou – FIOCRUZ
GUS course - Link

04/25-29/2005 - Centro de Pesquisas René Rachou – FIOCRUZ
Introduction to bioinformatics tools - Link

10/4-7/2005 - X-meeting. Brazilian Association of Bioinformatics and Computational Biology. - Link

10/10/2005 - Centro de Pesquisas René Rachou – FIOCRUZ / Universidade Federal de Minas Gerais, Department of Biochemistry Proteomics - Peter Roepstorff and Adriano Pimenta

10/4-30/2005 - Advances in Genome Technology and Bioinformatics. Link to the course web page

11/2-8/2005 - Computational Genomics Course - Cold Spring Harbor.
Link to the course web page

11/10-11/2005 - International Workshop on Genomic Databases (IWGD´05). - Link

06/5-6/2006 - Web design. - Link

29/1-4/2/2007 - PERL programing. - Link

04/8-14/2007 - EMBO World Practical Course on Comparative Genomics. - Link

04/24-26/2007 - Liquid chromatography coupled to mass spectrometry. International Chromatography Association. São Carlos, São Paulo, Brazil. Link

07/21/2007 - Genomic data fusion for gene prioritization and function prediction. Part of ISMB 2007, Vienna, Austria.- Link

07/21/2007 - Systems biology of host-pathogen interactions and microbial communities. Part of ISMB 2007, Vienna, Austria.- Link

5/24 to 12/14/2007 - Bioinformatics Course. - Link

7/2-6/2007 - Workshop on genomic databases. - Link

7/1-5/2007 - Workshop on bioinformatics. Teresina, PI, Brazil.

7/14-18/2007 - Web design for biologists. Centro de Pesquisas René Rachou, FIOCRUZ, Belo Horizonte, Brazil.

9/6-13/2007 and 1/9-16/2008 - Microarray analysis workshop. USP, São Paulo, Brazil.

9/21-27/2007 - Immunoinformatics. Teresina, PI, Brazil. - Link

11/1/2007 - Immunoinformatics. Part of the X-Meeting of the Brazilian Association for Bioinformatics and Computational Biology. - Link

10/31 to 11/28/2007 - Statistical Analysis of Microarray Data with R. Online course. - Link

12/9-14/2007 - Workshop on the kinome of schistosomes. International Symposium - 150 years of microbiology. Institute Pasteur, Lille, France.

02/12-18/2008 - Mining for protein-protein interactions. UFRJ, Rio de Janeiro, Brazil.

02/23-05/31/2008 - CISCO CCNA (Cisco Certified Network Associate). Belo Horizonte, Brazil.- Link

03/17-19/2008 - Workshop on systems biology. UNB, Brasília, Brazil.

05/05/2008 - II Curso Internacional "Informática en Salud Global: Avances en Salud Pública y Genómica", Joint activity with ITGH Fogarty Grant 5D43TW007551-04. Link to grant. Link to course

06/29 to 07/04/08 - Practical aspects of small molecule drug discovery. Wellcome Trust course. Link to course web page

08/01/08 - Brucella genome comparison. Seminar by João Setúbal, Virginia Bioinformatics Institute.

08/21/2008 - Demonstration of SchistoDB at the International Symposium on Schistosomiasis. Link to the event web site.

09/14-16/2008 - Python for bioinformatics. Course given during the X-Meeting. Link to the web site.

09/14-16/2008 - Complex network and biological applications. Course given during the X-Meeting. Link to the web site.

09/10-10/03/2008 - Microarray data analysis using R and bioconductor.  Gulbekian Institute, Oeiras, Portugal.  Link to course web page.

10/13-17/2008 - Comparative genomics and phylogenomics course. Toni Gabaldon. Center for Genomic Regulation, Barcelona, Spain. Link to course web page

11/5-11/2008 - Computational & Comparative Genomics. Cold Spring Harbour Laboratory, USA. Link to course web page

11/3-13/2008 - Red Hat Linux Networking & Security. Link to course information

02/2-13/2009 - Genomic mapping and annotation. 5th bioinformatics course at USP.  Link to course information

3/2-6/2009 -  Working with pathogen genomes.  Wellcome Trust Sanger Institute, UK.  Link to course web page

05/25-28/2009 - MySQL for beginners.  MySQL.  Link to course web page

Trainees at the end of the funding period

. Anderson Dominitini – Systems management / Bioinformatics, training with Dr. Guilherme Oliveira, CPqRR-FIOCRUZ.

. Ricardo José de Paula Souza - GIS/GPS, PhD, training with Dr. Omar dos Santos Carvalho, CPqRR-FIOCRUZ/Santa Casa BH.

. Ronaldo Scholte - Statistics, GIS/GPS, Ph.D, training with Dr. Omar dos Santos Carvalho, CPqRR-FIOCRUZ/Santa Casa BH.

. Larissa Lopes Silva - Phylogenomics, MSc, training with Dr. Guilherme Oliveira, CPqRR-FIOCRUZ/Genetics UFMG.

. Leandro Scott Rocha Zambrano Jacques - Bioinformatics, training with Dr. Guilherme Oliveira, CPqRR-FIOCRUZ.

. Laila Nahum - Phylogenetics, training with Dr. Guilherme Oliveira, CPqRR-FIOCRUZ.

Former trainees (as of April, 2010)

. Talita Armborst (MSc) – Currently at the Ministry of Health, Brasília

. Adhemar Zelotini Neto (Systems Manager) – Currently enrolled in the PhD program in Bioinformatics at UFMG and training at University or Georgia with Dr. Jessica Kissinger.

. Cristiana Gomes de Oliveira (Post Doc) - Currently at the Bioprocess Engineering Lab Division of Chemical Engineering Department The University of Queensland Brisbane.

. Alberto Idelfonso - Bioinformatics (Post Doc) - Currently working in the private sector.

. Ronaldo Scholte - Statistics, GIS (Ph.d) - Previously training at Purdue Univerisity with Dr. Dennis Minchella and Dr. Melba Kraft.

. Jerônimo Ruiz - Bioinformatics (Post-Doc) - Currently staff bioinformatician at the Laboratory of Cellular and Molecular Parasitology, Centro de Pesquisas René Rachou - FIOCRUZ.

. Luiza Freire de Andrade e Almeida - Currently enrolled in the PhD program at CPqRR-FIOCRUZ.

. Adriana Oliveira - Currently in the private sector.

. Jean Gabriel Nguema Ngomo - Currently in the private sector.

. Paula Fernandes dos Santos - Enrolled in medical school.

. Luciana Oliveira - M.Sc at Universidade Federal de Ouro Preto.

. Fernanda Ludolf Ribeiro - Currently enrolled in the PhD program at CPqRR-FIOCRUZ.

. Lívia Amaral - Currently enrolled in the Genetics PhD program at UFMG.

. Luiza Freire de Andrade e Almeida - Currently enrolled in the PhD program at CPqRR-FIOCRUZ.

. Adhemar Zerlotini - Currently a post-doctoral fellow at CEBio, CPqRR-FIOCRUZ.

. Rômulo Lucio Vale de Moraes - Bioinformatics, Ph.D., training with Dr. Guilherme Oliveira, CPqRR-FIOCRUZ/Bioinformatics UFMG.

Photos

Click here

Links to activites that received NIH-Fogarty funding

 

The Project in the news

University of Georgia - Link
Fundação Oswaldo Cruz - Link
Jornal da Ciência - Link
Estado de Minas - PDF
Terra Notícias - Link
Saúde Business web - Link
Associação Brasileira das Empresas de Biotecnologia - Link
Federação Nacional dos Médicos - Link
Jornal da Ciência SBPC - Link