Thomas W. Blackwell

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HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base(More)
The MYC genes encode nuclear sequence specific-binding DNA-binding proteins that are pleiotropic regulators of cellular function, and the c-MYC proto-oncogene is deregulated and/or mutated in most human cancers. Experimental studies of MYC binding to the genome are not fully consistent. While many c-MYC recognition sites can be identified in c-MYC(More)
BACKGROUND Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to(More)
MOTIVATION Current methods for identifying sequence specific binding sites in DNA sequence using position specific weight matrices are limited in both sensitivity and specificity. Double strand DNA helix exhibits sequence dependent variations in conformation. Interactions between macromolecules result from complementarity of the two tertiary structures. We(More)
The pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and(More)
The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this(More)
Double strand DNA exhibits sequence dependent variations in three-dimensional conformation. Crystallographic studies have shown that regulatory proteins bind to DNA and may use these structural effects to indirectly recognize binding sites in a sequence specific manner. In this paper we describe a sequence similarity scoring measure based on the energetics(More)
UNLABELLED Physical map assembly is the inference of genome structure from experimental data. Map assembly depends on the integration of diverse data including sequence tagged site (STS) marker content, clone sizing, and restriction digest fingerprints (RDF). As experimentally measured data, these are uncertain and error prone. Physical map assembly from(More)
In the course of our efforts to build extended regions of human genomic sequence by assembling individual BAC sequences, we have encountered several instances where a region of the genome has been sequenced independently using reagents derived from two different individuals. Comparing these sequences allows us to analyze the frequency and distribution of(More)
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