Michelle L.
Green, Ph.D.
E-mail:
Phone: 650-859-5669
Fax: 650-859-3735
Bioinformatics Scientist
Bioinformatics Research Group
Artificial Intelligence Center
SRI International
333 Ravenswood Ave.
Menlo Park, CA 94025
Curriculum
vitae
Resume
Research
PHFiller (Pathway
Hole Filler)
A
Description of PHFiller
PHFiller
is a tool developed by the Bioinformatics Research Group at SRI for
identifying and evaluating candidates enzymes for filling pathway holes
in Pathway/Genome Databases (PGDBs). A pathway hole is a reaction in a
predicted pathway
for which no enzyme has been identified in the organism's genome
annotation. PHFiller uses BLAST to identify candidate enzymes to fill
pathway holes
and a Bayesian classifier to determine the probability that each
candidate
has the function required to fill a particular pathway hole.
Validated
PHFiller Predictions
Predictions
of protein function made by PHFiller for which experimental
confirmation
have been independently made. In some cases, our predictions were used
to
identify hypotheses for testing and these predictions were subsequently
confirmed. In other cases, the function was experimentally verified
prior to our prediction, but was not included in the genome annotation
(or in the development of
our prediction).
Publications
Green, ML and
Karp, PD. The Outcomes of Pathway Database Computations Depend on
Pathway Ontology.
Nucleic Acids Research 2006,
34:13, 3687-3697.
Green, ML and
Karp, PD. Genome Annotation Errors in Pathway Databases Due to Semantic
Ambiguity in Partial EC Numbers. Nucleic Acids Research 2005, 33:13,
4035-4039.
Romero, P,
Wagg, J, Green, ML, Kaiser, D, Krummenacker, M, and Karp, PD.
Computational prediction of human metabolic pathways from the complete
human genome. Genome Biology 2004,
6:R2.
Green, ML and
Karp, PD. A Bayesian method for identifying missing enzymes in
predicted
metabolic pathway databases. BMC
Bioinformatics 2004, 5:76.
Green, ML
2003. A Bayesian Method for Identifying Missing Enzymes in
Pathway/Genome
Databases. Biomedical Informatics Program. Stanford, CA, Stanford
University:
22.
Green,
ML and Klein, TE. A Multidomain
TIGR/Olfactomedin Protein Family with Conserved Structural Similarity
in the N-terminal Region and Conserved Motifs in the C-terminal Region.
Mol Cell Proteomics 2002 1:394-403.
Michelle L.
Green <
>
Last modified:
20-Jun-06
