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Peter D Karp - Developer of bioinformatics software and databases
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Open to new opportunities

Peter D Karp

Developer of bioinformatics software and databases
SRI International • Menlo Park • United States of America

Skills and expertise

Fields of interest
  • RNA-seq analysis
  • MS-based untargeted metabolomics
  • Protein interaction analysis
Languages
  • English
Programming languages
  • Lisp

TOOLS MAINTAINED

MetaCyc

Dataset

MetaCyc

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Collects metabolic pathways, biochemical reactions, enzymes, genes and chemical compounds from various organisms. MetaCyc is a database, part of the BioCyc PGDB collection, containing over 2 600…

PseudoCyc

Dataset

PseudoCyc

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Provides a pathway-genome database (PGDB) for Pseudomonas aeruginosa, strain PAO1. PseudoCyc is a manually curated repository that gathers more than 800 biochemical reactions and over 700 enzymes. It…

Omics Dashboard

Dataset

Omics Dashboard

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Enhances the interpretation of omics data to reduce analysis time and to make omics data more accessible. Omics Dashboard is a customizable visualization tool that enables user to quickly survey…

CCO

Terminology

CCO / Cell Component Ontology

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Intends to describe the cellular architecture of a unicellular organism, or a cell type from a multicellular organism as well as the particular cellular components from which a specific type of cell…

YeastCyc

Dataset

YeastCyc

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A Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae S288c. YeastCyc contains, in addition to genomic information, metabolic pathway, reaction, enzyme, and compound information,…

HumanCyc

Dataset

HumanCyc

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Provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The…

BioCyc

Dataset

BioCyc

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Allows users to search information about pathway/genomes. BioCyc is a database that mixes thousands of genomes with additional information curated from the biomedical literature by biologist…

EcoCyc

Dataset

EcoCyc

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Hosts experimental data for Escherichia coli K-12. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.…

Fields of interest

RNA-seq analysis
Evaluates RNA-seq alignment results. RNAseqEval is a package that can be used…
Models associated risk-dependence between long intergenic noncoding RNAs…
Enables genotyping and variant annotation of resequencing data produced by…
MS-based untargeted metabolomics
Provides a package for metabolic modeling of microbial communities. Micom…
Consists of a filtering approach for the linear noise approximation (LNA) in…
Allows to simulate the effects of reaction inhibition across different stages…
Protein interaction analysis
Performs multivariate pathway enrichment analysis. ActivePathways is a…
Assesses the native-likeness of designed or predicted protein-ligand…
Predicts protein cavity and allows functional analyses. CavityPlus can…