Timothy E. Allen

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The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to(More)
The genome-wide location of RNA polymerase binding sites was determined in Escherichia coli using chromatin immunoprecipitation and microarrays (chIP-chip). Cross-linked chromatin was isolated in triplicate from rifampin-treated cells, and DNA bound to RNA polymerase was precipitated with an antibody specific for the beta' subunit. The DNA was amplified and(More)
Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial(More)
Alain T. Drooz, MD, Curtis A. Lewis, MD, Timothy E. Allen, MD, Steven J. Citron, MD, Patricia E. Cole, PhD, MD, Neil J. Freeman, MD, James W. Husted, MD, Patrick C. Malloy, MD, Louis G. Martin, MD, A. Van Moore, MD, Calvin D. Neithamer, MD, Anne C. Roberts, MD, David Sacks, MD, Orestes Sanchez, MD, Anthony C. Venbrux, MD, Curtis W. Bakal, MD, MPH, for the(More)
Curtis A. Lewis, MD, Timothy E. Allen, MD, Dana R. Burke, MD, John F. Cardella, MD, Steven J. Citron, MD, Patricia E. Cole, MD, PhD, Alain T. Drooz, MD, Elizabeth A. Drucker, MD, JD, Ziv J. Haskal, MD, Louis G. Martin, MD, A. Van Moore, MD, Calvin D. Neithamer, MD, Steven B. Oglevie, MD, Kenneth S. Rholl, MD, Anne C. Roberts, MD, David Sacks, MD, Orestes(More)
Prenatal factors known to be associated with delivery of an infant with low birth weight (LBW) were studied in 165 women who were delivered of infants of 25,000 gm or less, as well as 154 women who were delivered of term infants with normal birth weights (greater than 2,500 gm). Data included information related to th clinical course of the pregnancy(More)
Constraints-based models for microbial metabolism can currently be constructed on a genome-scale. These models do not account for RNA and protein synthesis. A scalable formalism to describe translation and transcription that can be integrated with the existing metabolic models is thus needed. Here, we developed such a formalism. The fundamental protein(More)