Author: Paul O’Maille
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The Comparative Genome Dashboard
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.
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Emergence of terpene chemical communication in insects: Evolutionary recruitment of isoprenoid metabolism
We present the first structural and mechanistic model for the evolutionary emergence of TPS function in insects. Through identifying key mechanistic differences between IDS and TPS enzymes, we hypothesize that the loss of isopentenyl diphosphate (IPP) binding motifs strongly correlates with the gain of the TPS function.
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Ancient origin and conserved gene function in terpene pheromone and defense evolution of stink bugs and hemipteran insects
The origin of enzymes involved in terpene biosynthesis and their evolution in insect genomes is still poorly understood. We addressed this question by investigating the evolution of isoprenyl diphosphate synthase (IDS)-like genes with terpene synthase function in the family of stink bugs.
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Sparse epistatic patterns in the evolution of terpene synthases
We explore sequence determinants of enzyme activity and specificity in a major enzyme family of terpene synthases.
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Resources to discover and use short linear motifs in viral proteins
We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery.
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Using pathway covering to explore connections among metabolites
Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites in the list.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.
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Emergence of terpene cyclization in Artemisia annua
Here we report the first discovery of an epistatic network of residues that controls the onset of terpene cyclization in Artemisia annua.