João Carlos Setubal

Ph.D., Computer Science, University of Washington, 1992

Research summary

My research interests are in the area of computational tools for genome annotation and analysis. Since 1997 I have worked primarily on bioinformatics support and analysis of bacterial genome projects. I developed or helped develop tools of various kinds, such as a lipoprotein prediction tool, genome contig scaffolder, a bacterial genome annotation system, and database models for genomic data.

I'm also interested in general algorithmic development, especially for combinatorial optimization problems, in the history of science and philosophy, and hiking.

Active funded projects include:

• Development of Gene Ontology terms for host-microbe interaction processes and gene functions (PAMGO project) (NSF)
• Agrobacterium biovar type strain sequencing project (NSF)
• Genome sequence and analysis of Azotobacter vinelandii (NSF)
• PATRIC: PathoSystems Resource Integration Center for the National Instiutute of Allergic and Infectious Diseases (NIH)
• Genome sequencing of Xanthomonas axonopodis pathovars (FAPESP/Fundecitrus, Brazil)
• A study of genomic variability in Pseudomonas syringae. Joint with Boris Vinatzer (Plant Pathology and Weed Science, VTech).

Ongoing research topics

• in silico recognition of bacterial lipoproteins
• Detection of pseudogenes in bacterial genomes
• better automated genome annotation methods

Genome projects that I have worked on include:

• Xylella fastidiosa, citrus pathogen
• Xylella fastidiosa, grapevine pathogen
• Xanthomonas axonopodis pv. citri, citrus pathogen
• Xanthomonas campestris pv. campestris, brassica pathogen
• Agrobacterium tumefaciens C58, the famous natural genetic engineer
• Leptospira interrogans serovar Copenhageni, causative agent of the human disease leptospirosis
• Leifsonia xyli subsp. xyli, sugarcane pathogen

I have also worked on one EST project:

• Schistosoma mansoni, the causative agent of the human disease schistosomiasis

All of these projects were carried out through the Laboratory for Bioinformatics of the Institute of Computing of the University of Campinas, in Brazil.

Appointments

2005-present VBI deputy director Virginia Bioinformatics Institute, Virginia Tech 2004-present Associate Professor Virginia Bioinformatics Institute, Virginia Tech 2004-present Associate Professor Department of Computer Science, Virginia Tech 2000-2001 Visiting Research Scholar Department of Genome Sciences, University of Washington 1998-2004 Associate Professor Institute of Computing, University of Campinas, Brazil 1992-1998 Assistant Professor Institute of Computing, University of Campinas, Brazil

Publications