Howard Tripp

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The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first(More)
The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the >1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments(More)
During the last decade the Internet has faced an architectural stagnation due to lack of wide scale adoption of new communication protocols. A significant reason for non-adoption is that the conflicting interests of networked stakeholders involved in the diffusion process are not understood or taken into account during the protocol development. This paper(More)
Since dynamic wireless networks evolve over time, optimal routing computations need to be performed frequently on time-varying network topologies. However, it is often infeasible or expensive to gather the current state of links for the entire network all the time. We provide a thorough analytical characterization of the effect of various link-state(More)
The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis(More)
Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5' enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased(More)
BACKGROUND In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, 1,004,576 peptides were collected from various publicly available resources, and were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an(More)
I am broadly interested in the field of computer networking. My research encompasses various aspects of wireless networks including mobile ad-hoc networks, sensor networks and 3G/4G networks. My research methodology combines modeling, optimization, analysis and trace-based performance evaluation of networks. – Modeling and exploiting channel variability of(More)