John O'Brien

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Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for(More)
In mouse brain cDNA libraries generated from small RNA molecules we have identified a total of 201 different expressed RNA sequences potentially encoding novel small non-messenger RNA species (snmRNAs). Based on sequence and structural motifs, 113 of these RNAs can be assigned to the C/D box or H/ACA box subclass of small nucleolar RNAs (snoRNAs), known as(More)
MOTIVATION Image analysis is a major part of data evaluation for array hybridization experiments in molecular biology. The program presented here is designed to analyze automatically images from hybridization experiments with various arrangements: different kinds of probes (oligonucleotides or complex probes), different supports (nylon filters or glass(More)
Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods(More)
Use cases are a powerful and widely recognised tool for the elicitation and specification of functional software requirements. However, major problems and gaps still exist; practitioners frequently encounter these. One of these is the specification of alternative use case interaction courses. Experience shows that practitioners do not only need to specify(More)
Use cases are a powerful and widely recognised tool for functional requirements elicitation and specification of prospective software applications. However, there still are major problems and misunderstandings about the use case approach. One of these is the troublesome notion of use case interleaving which is discussed in this work. Interleaving is still(More)
Calmodulin is an essential regulator of intracellular processes in response to extracellular stimuli mediated by a rise in Ca(2+) ion concentration. To profile protein-protein interactions of calmodulin in human brain, we probed a high content human protein array with fluorophore-labeled calmodulin in the presence of Ca(2+). This protein array contains(More)
This article is the second work in a series of papers on advancing specification and modelling techniques for goal-based use cases. In this article we highlight major and remaining problems associated with the true semantics of extension points and rejoin points, which are used as branching and return locations for a use case’s alternative interaction(More)
We have used oligonucleotide-fingerprinting data on 60,000 cDNA clones from two different mouse embryonic stages to establish a normalized cDNA clone set. The normalized set of 5,376 clones represents different clusters and therefore, in almost all cases, different genes. The inserts of the cDNA clones were amplified by PCR and spotted on glass slides. The(More)
UNLABELLED Xdigitise is a software system for visualization of hybridization experiments giving the user facilities to analyze the corresponding images manually or automatically. Images of the high-density DNA arrays are displayed as well as the results of an external image analysis bundled with Xdigitise, e.g. the spot locations are marked and the(More)