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We present single-molecule sequencing digital gene expression (smsDGE), a high-throughput, amplification-free method for accurate quantification of the full range of cellular polyadenylated RNA transcripts using a Helicos Genetic Analysis system. smsDGE involves a reverse-transcription and polyA-tailing sample preparation procedure followed by sequencing(More)
Satellite repeats in heterochromatin are transcribed into noncoding RNAs that have been linked to gene silencing and maintenance of chromosomal integrity. Using digital gene expression analysis, we showed that these transcripts are greatly overexpressed in mouse and human epithelial cancers. In 8 of 10 mouse pancreatic ductal adenocarcinomas (PDACs),(More)
COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support(More)
RNA Seq provides unparalleled levels of information about the transcriptome including precise expression levels over a wide dynamic range. It is essential to understand how technical variation impacts the quality and interpretability of results, how potential errors could be introduced by the protocol, how the source of RNA affects transcript detection, and(More)
The rapid adoption of high-throughput next generation sequence data in biological research is presenting a major challenge for sequence alignment tools—specifically, the efficient alignment of vast amounts of short reads to large references in the presence of differences arising from sequencing errors and biological sequence variations. To address this(More)
BACKGROUND The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known about interactions between higher order biological systems, such as biological pathways and processes. We propose a methodology for gleaning(More)
We describe in this document the OPM multidatabase query system (OPM*QS) that allows querying multiple databases that have an OPM interface, using the OPM multidatabase query language (OPM*QL). OPM is a data model that allows specifying database schemas in terms of objects and protocols (laboratory experiments). The OPM query language, OPM QL, allows(More)
  • William K Purves, Daniel Dermett, Larry Birnbaum, Margot Flowers, Larry Hnnter, Stan Letovsky +2 others
  • 2001
Alt,hough cognitive AI is not generally viewed as being " scieutific " in the same, strong sense as is physics, it shares a number of the properties of the natural sciences, especially biology Certain of the special themes of biology, notably the principles of bistoricity and of structure-function relations, are applicable in AI research From a biologist's(More)
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