Patrick K. O'Neill

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The authors are with the Itek Corporation, Lexington, Massachusetts 02173. Received 25 September 1973. In this letter an interferometric method of measuring plotter distortion is described. A common method of measuring plotter distortion is to draw a known pattern, such as straight lines, and scan this pattern with a microdensitometer. This is a precise(More)
Codon usage bias (CUB) results from the complex interplay between translational selection and mutational biases. Current methods for CUB analysis apply heuristics to integrate both components, limiting the depth and scope of CUB analysis as a technique to probe into the evolution and optimization of protein-coding genes. Here we introduce a self-consistent(More)
Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be leveraged to characterize population-wide transcriptional regulatory networks, or meta-regulons, providing insights into how bacterial populations(More)
The application of laser technology has been extended to optical shop testing by incorporating a cw, helium-neon gas laser in a package that houses a modified Twyman-Green interferometer. This modification provides for optical testing over large path differences with an auxiliary set of lenses used in the long path and a small reference flat used in the(More)
Transcription factors (TFs) regulate transcription by binding to specific sites in promoter regions. Information theory provides a useful mathematical framework to analyze the binding motifs associated with TFs but imposes several assumptions that limit their applicability to specific regulatory scenarios. Explicit simulations of the co-evolution of TFs and(More)
The information-theoretic concept of Shannon entropy can be used to quantify the information provided by a diagnostic test. We hypothesized that in tumor types with stereotyped mutational profiles, the results of NGS testing would yield lower average information than in tumors with more diverse mutations. To test this hypothesis, we estimated the entropy of(More)
Activation of CD4+ T cells requires the recognition of peptides that are presented by HLA class II molecules and can be assessed experimentally using the ELISpot assay. However, even given an individual's HLA class II genotype, identifying which class II molecule is responsible for a positive ELISpot response to a given peptide is not trivial. The two main(More)
Biological sequence motifs drive the specific interactions of proteins and nucleic acids. Accordingly, the effective computational discovery and analysis of such motifs is a central theme in bioinformatics. Many practical questions about the properties of motifs can be recast as random sampling problems. In this light, the task is to determine for a given(More)
MOTIVATION Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. RESULTS We combine well-established in silico and(More)
The quantity ω, incorrectly defined in the paper by Degnan and Klein in the sentence containing Eq. (16), corre­ sponds to the radius to the 1/e (not 1/e) intensity point in the Gaussian local oscillator distribution. Please note that the latter definition is at variance with the more com­ mon definition of ω as the radius to the 1/e field (l/e in­ tensity)(More)
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