[9] TM4 microarray software suite

AI Saeed, NK Bhagabati, JC Braisted, W Liang… - Methods in …, 2006 - Elsevier
Powerful specialized software is essential for managing, quantifying, and ultimately deriving
scientific insight from results of a microarray experiment. We have developed a suite of …

Bioinformatics applications for pathway analysis of microarray data

T Werner - Current opinion in biotechnology, 2008 - Elsevier
Changes in transcript levels are assessed by microarray analysis on an individual basis,
essentially resulting in long lists of genes that were found to have significantly changed …

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia

TJ Schuijt, JM Lankelma, BP Scicluna, FS e Melo… - Gut, 2016 - gut.bmj.com
Objective Pneumonia accounts for more deaths than any other infectious disease
worldwide. The intestinal microbiota supports local mucosal immunity and is increasingly …

The BioMart community portal: an innovative alternative to large, centralized data repositories

D Smedley, S Haider, S Durinck, L Pandini… - Nucleic acids …, 2015 - academic.oup.com
Abstract The BioMart Community Portal (www. biomart. org) is a community-driven effort to
provide a unified interface to biomedical databases that are distributed worldwide. The …

Global transcriptome analyses of human and murine terminal erythroid differentiation

X An, VP Schulz, J Li, K Wu, J Liu, F Xue… - Blood, The Journal …, 2014 - ashpublications.org
We recently developed fluorescence-activated cell sorting (FACS)-based methods to purify
morphologically and functionally discrete populations of cells, each representing specific …

Wnt signaling in triple negative breast cancer is associated with metastasis

N Dey, BG Barwick, CS Moreno, M Ordanic-Kodani… - BMC cancer, 2013 - Springer
Abstract Background Triple Negative subset of (TN) Breast Cancers (BC), a close associate
of the basal-like subtype (with limited discordance) is an aggressive form of the disease …

Circulating miR-378 and miR-451 in serum are potential biomarkers for renal cell carcinoma

M Redova, A Poprach, J Nekvindova, R Iliev… - Journal of translational …, 2012 - Springer
Background There is no standard serum biomarker used for diagnosis or early detection of
recurrence for renal cell carcinoma (RCC) patients. MicroRNAs (miRNAs) are abundant and …

OmicCircos: a simple-to-use R package for the circular visualization of multidimensional omics data

Y Hu, C Yan, CH Hsu, QR Chen, K Niu… - Cancer …, 2014 - journals.sagepub.com
OmicCircos is an R software package used to generate high-quality circular plots for
visualizing genomic variations, including mutation patterns, copy number variations (CNVs) …

Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis

WR Swindell, A Johnston, S Carbajal, G Han, C Wohn… - PloS one, 2011 - journals.plos.org
Development of a suitable mouse model would facilitate the investigation of
pathomechanisms underlying human psoriasis and would also assist in development of …

RNA-seq and microarray complement each other in transcriptome profiling

S Kogenaru, Q Yan, Y Guo, N Wang - BMC genomics, 2012 - Springer
Background RNA-seq and microarray are the two popular methods employed for genome-
wide transcriptome profiling. Current comparison studies have shown that transcriptome …