@proceedings {38218,
	title = {Dynamic querying for pattern identification in microarray and genomic data},
	volume = {3},
	year = {2003},
	month = {2003},
	publisher = {IEEE},
	type = {10.1109/ICME.2003.1221346},
	abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.},
	keywords = {Bioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher},
	isbn = {0-7803-7965-9},
	author = {Hochheiser, H. and Baehrecke, E. H. and Stephen M. Mount and Shneiderman, Ben}
}
@article {38115,
	title = {Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray},
	journal = {Molecular and Biochemical ParasitologyMolecular and Biochemical Parasitology},
	volume = {123},
	year = {2002},
	type = {16/S0166-6851(02)00138-X},
	abstract = {A microarray comprising 21[punctuation space]024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75\% of the genomic fragments produced a signal and about 2\% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.},
	keywords = {Expression, Gene, Microarray, Regulation, Trypanosoma brucei},
	isbn = {0166-6851},
	author = {Diehl, Susanne and Diehl, Frank and Najib M. El-Sayed and Clayton, Christine and Hoheisel, J{\"o}rg D.}
}
