[HTML][HTML] Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest

E Saka, BJ Harrison, K West, JC Petruska, EC Rouchka - BMC genomics, 2017 - Springer
Background Since the introduction of microarrays in 1995, researchers world-wide have
used both commercial and custom-designed microarrays for understanding differential …

[BOOK][B] Image registration and visualization of in situ gene expression images

E Saka - 2011 - search.proquest.com
In the age of high-throughput molecular biology techniques, scientists have incorporated the
methodology of in-situ hybridization to map spatial patterns of gene expression. In order to …

Region based gene expression via reanalysis of publicly available microarray data sets.

E Saka - 2018 - ir.library.louisville.edu
A DNA microarray is a high-throughput technology used to identify relative gene expression.
One of the most widely used platforms is the Affymetrix® GeneChip® technology which …

Region-based custom chip description formats for reanalysis of publicly available affymetrix® genechip® data sets

E Saka, BJ Harrison, K West, JC Petruska… - 2016 IEEE 6th …, 2016 - computer.org
Commercially developed microarrays, such as those from Agilent® and Affymetrix®, allow
for the analysis of differential gene expression changes on a genome-wide scale. Publicly …

Poster: Image registration and visualization tool for in-situ gene expression images

E Saka, E Rouchka - … on Computational Advances in Bio and …, 2012 - ieeexplore.ieee.org
In the age of high-throughput molecular biology techniques, scientists have incorporated the
methodology of in-situ hybridization to map spatial patterns of gene expression. In order to …

[BOOK][B] Swarm intellilgence for clustering dynamic data sets for web usage mining and personalization

E Saka - 2011 - search.proquest.com
… Most of all, I am so grateful to my family, in particular my mother Nuran, my father Erol, and
my sister Ernur for supporting me in every possible way unconditionally and selflessly. Sevgili …

[HTML][HTML] Salvaging Affymetrix probes after probe-level re-annotation

WC de Leeuw, H Rauwerda, MJ Jonker, TM Breit - BMC research notes, 2008 - Springer
Background Affymetrix GeneChips can be re-annotated at the probe-level by breaking up
the original probe-sets and recomposing new probe-sets based on up-to-date genomic …

[HTML][HTML] Alternative mapping of probes to genes for Affymetrix chips

L Gautier, M Møller, L Friis-Hansen, S Knudsen - BMC bioinformatics, 2004 - Springer
Background Short oligonucleotide arrays have several probes measuring the expression
level of each target transcript. Therefore the selection of probes is a key component for the …

[HTML][HTML] Novel definition files for human GeneChips based on GeneAnnot

F Ferrari, S Bortoluzzi, A Coppe, A Sirota, M Safran… - BMC …, 2007 - Springer
Background Improvements in genome sequence annotation revealed discrepancies in the
original probeset/gene assignment in Affymetrix microarray and the existence of differences …

[HTML][HTML] Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

MA Stalteri, AP Harrison - BMC bioinformatics, 2007 - Springer
Background Affymetrix GeneChip technology enables the parallel observations of tens of
thousands of genes. It is important that the probe set annotations are reliable so that biological …