Microarrays Research Today is a free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software. | ||||||
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Feature Selection with Conjunctions of Decision Stumps and Learning from Microarray Data.Shah M, Marchand M, Corbeil J Accenture Technology Labs, Chicago. One of the objectives of designing feature selection learning algorithms is to obtain classifiers that depend on a small number of attributes and have verifiable future performance guarantees. There are few, if any, approaches that successfully address the two goals simultaneously. To the best of our knowledge, such algorithms that give theoretical bounds on the future performance have not been proposed so far in the context of the classification of gene expression data. In this work, we investigate the premise of learning a conjunction (or disjunction) of decision stumps in Occam's Razor, Sample Compression, and PAC-Bayes learning settings for identifying a small subset of attributes that can be used to perform reliable classification tasks. We apply the proposed approaches for gene identification from DNA microarray data and compare our results to those of the well known successful approaches proposed for the task. We show that our algorithm not only finds hypotheses with much smaller number of genes while giving competitive classification accuracy but also have tight risk guarantees on future performance unlike other approaches. The proposed approaches are general and extensible in terms of both designing novel algorithms and application to other domains. Published 17 May 2011 in IEEE Trans Pattern Anal Mach Intell. Articles on Microarrays published 17 May 2011: Preprocessing differential methylation hybridization microarray data. BioData Min, 4(1): 13. ABSTRACT: BACKGROUND: DNA methylation plays a very important role in the silencing of tumor suppressor genes in various tumor types. In order to gain a genome-wide understanding of how changes in methylation affect tumor growth, the differential methylation hybridization (DMH) protocol has been developed and large amounts of DMH microarray data have been generated. However, it is still unclear how to preprocess this type of microarray data and how different background correction and ... [Abstract] [Full-text] Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma. BMC Med Genomics, 4: 33. Articles on Microarrays published 16 May 2011: The improvement of riboflavin production in Ashbya gossypii via disparity mutagenesis and DNA microarray analysis. Appl Microbiol Biotechnol. We generated a high riboflavin-producing mutant strain of Ashbya gossypii by disparity mutagenesis using mutation of DNA polymerase δ in the lagging strand, resulting in loss of DNA repair function by the polymerase. Among 1,353 colonies generated in the first screen, 26 mutants produced more than 3 g/L of riboflavin. By the second screen and single-colony isolation, nine strains that produced more than 5.2 g/L of riboflavin were selected as high riboflavin-producing strains. These mutants ... [Abstract] [Full-text] The extracellular matrix (ECM) provides an essential structural framework for cell attachment, proliferation, and differentiation, and undergoes progressive changes during senescence. To investigate changes in protein expression in the extracellular matrix between young and senescent fibroblasts, we compared proteomic data (LTQ-FT) with cDNA microarray results. The peptide counts from the proteomics analysis were used to evaluate the level of ECM protein expression by young cells and senescent ... [Abstract] [Full-text] Microarray-Based Analysis of Differential Gene Expression between Infective and Noninfective Larvae of Strongyloides stercoralis. PLoS Negl Trop Dis, 5(5): e1039. Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assay. J Immunol Methods. Cytokines are secreted immunomodulating proteins involved in pancreatic stellate cell activation and propagation of fibrosis in chronic pancreatitis. We aim to show that cytokines can be identified from pancreatic fluid by (1) collecting pancreatic fluid with the ePFT method, (2) processing the fluid for cytokine-targeted microarray analysis, and (3) comparing cytokine profiles in pancreatic fluid of chronic pancreatitis (CP) patients and of chronic abdominal pain (CAP) controls. We ... [Abstract] [Full-text] Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics, 12(1): 234. ABSTRACT: BACKGROUND: The Manila clam, Ruditapes philippinarum, is one of the major aquaculture species in the world and a potential sentinel organism for monitoring the status of marine ecosystems. However, genomic resources for R. philippinarum are still extremely limited. Global analysis of gene expression profiles is increasingly used to evaluate the biological effects of various environmental stressors on aquatic animals under either artificial conditions or in the wild. Here, we report on ... [Abstract] [Full-text] Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources. BMC Genomics, 12(1): 225. ABSTRACT: BACKGROUND: Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland ... [Abstract] [Full-text] © 2004-2011 Microarrays Research Today. All Rights Reserved. |
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