Pedro R Romero*

Biography and Interests

He was a Post Doctorate Fellow in the Bioinformatics Research Group in the AIC.

Current Projects

	EcoCyc: Encyclopedia of Escherichia coli Genes and Metabolism EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli.
	MetaCyc: Metabolic Pathway Database MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1800 pathways from more than 2200 different organisms (circa 2012). The MetaCyc data were curated from more than 33,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.
	Pathway Tools Pathway Tools is a systems biology software system that supports several use cases: Development of organism-specific database that integrate many bioinformatics datatypes, from genomes to pathways. Development of metabolic-flux models using flux-balance analysis. Scientific visualization, web publishing, and querying of organism-specific databases. Analysis of omics datasets. Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons. Comparative analyses.

Past Projects

A System for Representing Textbook Knowledge The goal of the project is to demonstrate the current state-of-the-art in knowledge representation by attempting to answer the questions in an advance placement test in chemistry.

Publications

The following are in reverse chronological order of publication.
[View All]

• Barker, K. and Chaudhri, V., Chaw, Sha Yi and Clark, Peter E. and Fan, James and Israel, David and Mishra, Sunil and Porter, Bruce and Romero, Pedro and Tecuci, Dan and Yeh, Peter. A Question Answering System for AP Chemistry: Assessing KR Technologies, in Proceedings of the 9th International Conference on Knowledge Representation and Reasoning, June 2-4 2004.  [PDF, Details]

• Barker, K. and Chaudhri V. and Clark, P. and Israel, D. and Porter, B. and Romero, P. Halo Pilot Project, Technical Report . SRI International, May 2003.  [Details]

• Karp, P.D. and Paley, S. and Romero, P. The Pathway Tools Software. Bioinformatics, vol. 18, pp. S225-S232, 2002.  [Details]

• Romero, P. and Karp, P.D. Nutrient-related Analysis of Pathway/Genome Databases, in Proceedings of the Pacific Symposium on Biocomputing, World Scientific, Singapore, pp. 471-482, 2001.  [PDF, Details]