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DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter(More)
All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first(More)
This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Hewlett-Packard Company products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new(More)
1. Abstract Prototypes are invaluable for studying special purpose parallel architectures and custom computing. This paper describes a new FPGA, called Plasma— the heart of a configur-able custom computing engine (Teramac) that can execute synchronous logic designs up to one million gates at rates up to one megahertz. Plasma FPGA's using 0.8 micron CMOS are(More)
This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Hewlett-Packard Company products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new(More)
Random number generators (RNGs) based upon neighborhood-of-four cellular automata (CA) with asymmetrical, non-local connections are explored. A number of RNGs that pass Marsaglia's rigorous Diehard suite of random number tests have been discovered. A neighborhood size of four allows a single CA cell to be implemented with a four-input lookup table and a(More)
Accelerating a genetic algorithm (GA) by implementing it in a reconfigurable field programm-able gate array (FPGA) is described. The implemented GA features: random parent selection, which conserves selection circuitry; a steady-state memory model, which conserves chip area; survival of fitter child chromosomes over their less-fit parent chromosomes, which(More)
BACKGROUND Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies(More)
It is difficult to exploit the massive, fine-grained parallelism of configurable hardware with a conventional application programðming language such as C, Pascal or Java. The difficulty arises from the mismatch between the synchronous, concurrent processing capability of the hardware and the expressiveness of the lanðguage-the so-called "semantic gap." We(More)