Molecular model of TriBP1, a protein involved in nuclear import.

Further structural analysis will be performed in order to understand the biological properties and roles of TriBP1 and TriBP2.X-meeting 2007

Preliminary analysis of differentially expressed genes involved in meat tenderness in Angus and Nelore beef cattle.

ISCB-Latin America 2014. Pôster O10

Detecção de erros de montagens em regiões gênicas.

Muitos genomas ainda apresentam erros de montagem. Tais erros são particularmente graves se ocorrerem em regiões gênicas, pois muitos trabalhos científicos se concentram exatamente nessas regiões por razões óbvias. Uma forma de tentar identificar erros de montagens em regiões gênicas é utilizar sequencias adquiras de forma independente, como, por exemplo bases de ESTs ou bases de Full length cDNA (FlcDNA). O foco deste trabalho é propor uma metodologia de Bioinformática que utiliza bibliotecas de FlcDNA para detectar tais erros

Wheat transcriptome analysis targeting leaf rust resistance-related genes.

ISCB-Latin America 2014. Pôster D03

Laboratório avançado multiusuário de bioinformática da Embrapa.

Apresentamos aqui a proposta de implementação de um Laboratório Multiusuário de Bioinformática, reunindo diversas unidades e competências da Embrapa

De novo assembly of a Nelore (Bos indicus) bull genome based on short read sequences.

Zebu cattle breeds (Bos indicus) are widely used for milk and beef production in the tropics and show natural adaptations to biotic and abiotic stresses especially found in these regions. Advanced genomic tools will be essential to help unveil and explore the underlying genetic variations that distinguish taurine and indicine cattle and, at the same time, will facilitate the work of breeders striding towards incorporating genomic tools into breeding programs aiming to improve productivity and beef and milk quality.P554

2D maps of protein surface.

Short Abstract: In this work, we present 2DIM (Two Dimensional Interface Maps). It is a graphical interface that permits to visualize the protein-protein interfaces in 2D maps.ISMB, X-MEETING 2006. Poster B-63

Embrapa Bioinformatics Multi-Users Laboratory - LMB.

The Bioinformatics Multi-Users Laboratory of Embrapa provides an array of shared research resources and infra-structure to the Embrapa community and research collaborators The primary mission of the LMB is to address the increasing need of Embrapa investigators for support and solutions in Bioinformatics in a collaborative environment. To fulfill this mission, the LMB collaborates on research projects that require expertise in genome assembly, meta-genomics analysis to unravel candidate genes, molecular markers, differential gene expression, and structural bioinformatics, and assists in the implementation of computational solutions .X-MEETING 2012

Embrapa Bioinformatic Multi-user laboratory.

Recently Brazilian Agricultural Research Corporation (Embrapa) implemented the Embrapa Bioinformatic Multi-user Laboratory(LMB) that provides a central point of convergency for related bioinformatics issues in the organization, a high performance computing (HPC) infrastructure to be used by employees and partners on solution of computational intensive problems in bioinformatics, and principally, provides specialized collaborators to realize training, assist the elaboration of projects with bioinformatics components and in specific cases contribute to execute them. The importance of LMB is best understood when one takes into account the way Embrapa research centers are geographically located. The research centers are distributed among the several regions of the Brazil, and bioinformatic becames necessary in many of the projects developed all over the centers, most using considerable computational resources. How is inviable to replicate the HPC infrastructure in every locations, the practical solution is concentrate computational resources at a unique point and provide remote access to them. At human resources perspective, Embrapa has bioinformatics professionals working directly in the units, and is very important ensure they will communicate appropriately. LMB is a convergent point for bioinformaticians in the organization. Finally, The LMB has critical mass to explore complex problems in bioinformatics area. LMB´s infrastructure includes two HPC servers, each one with 512 GB RAM and 48 cores; one storage system and one tape library for backup. The users can execute their jobs by directly accessing the system through a ssh connection or using the Galaxy web system. LMB is also committed to education and training in bioinformatics by providing workshops and courses.Pôster 1017

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

Abstract. An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented