Center for Bioinformatics &
Genome Biology

Projects Supported by Microsoft Sponsored Research

Collaboration with Microsoft Research Redmond

A collaboration has been established between the Fundación Ciencia (FCV) para la Vida and senior scientists Drs. David Heckerman and Nebosja Jojic at Microsoft Research (MR), Redmond. The objectives are to provide hands on training to advanced graduate students at the FCV in cutting edge bioinformatics approaches being developed at MR and to introduce the students to problems of interest at MR. The students bring novel insights to the problems using expertise they have developed during their training at the FCV. The collaboration has involved the participation of two FCV students at MR for two months each per year since 2007. One project involves the exploration of the potential role of antisense proteins in the life of the HIV virus. Research into the biology of HIV and the possibility of developing vaccines is an active area of investigation at MR and the bioinformatic prediction of alternate (usually antisense) genes is a major area of interest at the FCV. Another project has involved the use of a program for predicting MHC binding energy, developed by scientists at Microsoft Research (reference) , to search for patterns in the way HIV mutates during its evasion of the human immune system, taking into account proteins derived from sense and antisense genes.

AlterORF

Is an open source searchable, relational database created with Microsoft SQL Server 2008. The database is housed in the 132 CPUs computer cluster at the Center for Bioinformatics and Genome Biology, FCV. The database is housed and managed in an HP ProLiant DL320 Server, having 132 Opteron64 CPUs, 1 TB storage, Microsoft Windows Server 2008 and Microsoft HPC Server 2008. The alterORF database warehouses all annotated genes and the alternate open reading frames (ORFs) derived from these genes for all publicly available microbial (Archaea and Eubacteria) genomes (774 genomes, March 5, 2009). This amounts to over 2.5 million annotated genes and nearly 10 million alternate ORFs.

The database can be used:

(1) to improve gene annotation by identifying alternate ORFs that have better hits to known protein motifs, domains etc than the existing annotated genes, suggesting that the wrong ORF had been annotated. We have found hundreds of such cases and are collaborating with the Swiss Institute of Bioinformatics and the of Virginia Bioinformatics Institute to depurate gene annotations associated with pathogenic microorganisms.

(2) to search for examples of genes that potentially encode more than one protein.

(3) to search for examples of molecular fossils, where the remains of ancient genes can be found embedded in existing genes, or where novel ORFs await capture and expression as proteins.

Read More

Go to AlterORF Database

Publications

Genomics of Bioleaching Microorganisms

Bioleaching involves the solubilization of metals from sulfide ores using microorganisms in acidic conditions (pH 1-3) (read more). In Chile, copper is the principal metal recovered by bioleaching and accounts for about 10% of Chile’s total production. Bioleaching has particular advantages as an industrial process when the metal concentration in the ore is very low and for small or remote mining operations. It is considered less polluting than conventional pyrometallurgical processes that can generate airborne sulfur dioxide emissions with heavy metal contamination, although acid mine drainage that results from bioleaching has to be confronted as a potential environmental contaminant.

Microsoft is helping to support the training of graduate students and a postdoc who are working on the genomics of microorganisms involved in bioleaching. The objective is to advance our understanding of fundamental biological processes in extremely acidic environments and to capture usable knowledge that can be applied to bioleaching. A major thrust is to understand how microorganisms interact in space and time in a bioleaching operation (ecophysiology) and this involves computationally demanding comparative genomics studies. These studies have been facilitated by the use of a Microsoft Research sponsored 132 CPU computer cluster running Microsoft Windows Server 2008, housed in the Center for Bioinformatics and Genome Biology (CBGB).

Pictures

Publications

--Papers

--Talks, posters at congresses, workshops

--Download ppt presentations

Networking and e-science

Microsoft Sponsored Research has promoted the ability of the FCV to carry out data intensive national and international collaborations in an e-science environment. These include:

1) Collaboration with the Centre for Bioinformatics at the Pontifia Universidad Católica, Santiago and the Center for Bioinformatics and Molecular Simulation, Universidad de Talca, Chile to modeling proteins from acidic environments (more information).

2) Collaboration with the Swiss Institute of Bioinformatics and the Virginia Bioinformatics Institute, Virginia Tech, using AlterORF to improve gene annotation of pathogenic microorganisms (more information)

3) Collaboration with the Bioechnology Center, Universidad Católica del Norte, Antofagasta, Chile and BHP Billiton, the world’s largest mining company to carry out fundamental investigations into the genomics and ecophysiology of microorganisms involved in copper solubilization during bioleaching (more information).

4) Collaboration within the Iberoamerican Bioinformatics Network (RIB) (Red Iberoamericana de Bioinformatica).

5) Collaborations with Dr. Violaine Bonnefoy, CNRS, Marseille, France, Dr. Mark Dopson , University of Umea, Sweden and Dr. Barrie Johnson, University of Bangor, UK regarding the genomics and proteomics of bioleaching microorganisms.

6) Collaboration with Dr. Ehmke Pohl , University of Durham, UK and Dr. Danilo Gonzalez, University of Talca, Chile to carry out molecular modeling and crystal structure analysis of the transcriptional regulator Fur of Acidithiobacillus ferrooxidans.

7) Collaboration with Dr. Gisela Storz, NIH, USA to predict and experimentally validate small regulatory RNAs (srRNAs) in Acidithiobacillus ferrooxidans and other bioleaching microorganisms.

8) Collaboration with Dr. Jonathan Eisen, UC Davis Genome Center, USA to study the genomics of Acidithiobacillus ferrooxidans.

Outreach

The outreach project, “Collaborative Learning Based on Grid Infrastructure” (SACGRID), has recently been approved by the Chilean Govt. Funding is expected to begin in March, 2008 (read abstract). The project is partially supported by Microsoft Research who facilitated the necessary high speed internet access required by the project. The project also involves the Microsoft School of the Future. The principal investigator is Dr. Tomás Perez, Centre for Bioinformatics, Pontificia Universidad Católica, Santiago. Coinvestigators are Dr. Danilo Gonzalez, Center for Bioinformatics and Molecular Simulation, Universidad de Talca and Dr. David S. Holmes, Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Santiago, Chile.