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emerging technologies
On this page, you will find useful references pertaining to emerging technologies.
Publications using information from UHNMAC printed microarrays can be found here.
- Next-Generation Sequencing
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Asmann YW et al. Transcriptome Profiling Using Next-Generation Sequencing. Gastroenterology 2008,
135(5):1466.
Chellappan P & Jin H. Discovery of Plant MicroRNAs and Short-Interfering RNAs by Deep Parallel Sequencing. Methods Molecular Biology 2009, 495:1-12
This chapter describes the methods for small RNA discovery in plants by small RNA cloning and deep parallel sequencing.
Choi M, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. PNAS 2009, 106:19096
Guyer M & Felsenfeld A. Future of Genome Sequencing: A white paper for the National Human Genome Research Institute. Posted January 28, 2009.
Ji H, et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nature Biotechnology 2008, 26(11):1293
Pan Q, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics 2008, 40:1413-1415
This paper describes the first analysis of alternative splicing complexity using mRNA-Seq, a method that uses NGS platforms to profile the transcriptome.
Park PJ. Epigenetics meets next-generation sequencing. Epigenetics 2008, 3(6):318-321
Petrone J. Cost, Data Analysis, and Throughput Keep Array Users from Switching to DGE, Some Say. GenomeWeb BioArray News, December 23, 2008
This online article discusses digital gene expression (DGE) applications performed on next-generation sequencing platforms and the impact this technology could have on microarrays.
Shah SP, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 2009 461:809
Tang F, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods, 2009 6:377
This paper describes a single-cell digital gene expression profiling assay. The mRNA-Seq assay was able to detect the expression of 75% more genes than microarray techniques for a single mouse blastomere.
- Multiplexed Gene Quantitation
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Geiss GK et al.
Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Technology 2008,
26(3):317-325
This paper describes the NanoString nCounter gene expression system which captures and counts individual mRNA transcripts.
Rai AJ et al. Analytical validation of the GeXP analyzer and design of a workflow for cancer-biomarker discovery using multiplexed gene-expression profiling. Analytical Bioanalytical Chemistry 2008, Oct 29, [Epub ahead of print]
Paper concludes that the GeXP genetic analysis system holds promise for rapidly identifying gene signatures from multiplexed reactions using small quantity samples.
- Carbohydrate Arrays
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Functional Glycomics Gateway
Disney MD & Seeberger PH. The Use of Carbohydrate Microarrays to Study Carbohydrate-Cell Interactions and to Detect Pathogens. Chem Biol 2004, 11(12):1701-1707
Huang CY, et al. Carbohydrate microarray for profiling the antibodies interacting with Globo H tumor antigen. PNAS, 2006, 103(1):15-20
Laurent N, et al. Glycoarrays - tools for determining protein-carbohydrate interactions and glycoenzyme specificity. Chem Comm 2008, 37:4400-4412
Liang CH, Wu CY. Glycan array: a powerful tool for glycomics studies.. Expert Rev Proteomics 2009, 6(6):631
Oyelaren O, et al. Profiling Human Serum Antibodies with a Carbohydrate Antigen Microarray. J Proteome Res 2009, 8(9):4301
Shin I, et al. Carbohydrate Microarrays: An Advanced Technology for Functional Studies of Glycans. Chem Eur J 2005, 11:2894-2901
Stevens J, et al. Glycan microarray technologies: tools to survey host specificity of influenza viruses. Nature Reviews Microbiology, 2006, 4:857-864
- Cell-Based Arrays
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Bailey SN, et al.
Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods 2006,
3(2):117-122
Carpenter AE & Sabatini DM. Systematic geneome-wide screens of gene function. Nature Reviews Genetics, 2004, 5:11-22
Palmer E & Freeman T. Cell-based microarrays: current progress, future prospects. Pharmacogenomics 2005, 6(5):527-534
Sturzl M, et al. High Throughput Screening of Gene Functions in Mammalian Cells Using Reversely Transfected Cell Arrays: Review And Protocol. Comb Chem High Throughput Screen. 2008, 11(2):159-172
Webb BL, et al. A reporter system for reverse transfection cell arrays. Journal of Biomolecular Screening, 2003, 8(6):620-623
Wheeler DB, et al. Cell microarrays and RNA interference chip away at gene function. Nature Genetics Supplement, 2005, 37:S25-S30
Ziauddin J & Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature, 2001, 411:107-110
- Lipid Arrays
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Fang Y. Spreading and Segregation of Lipids in Air-Stable Lipid Microarrays. J Am Chem Soc 2006,
128(10):3158
Feng L. Probing lipid-protein interactions using lipid microarrays. Prostaglandins & Other Lipid Mediators 2005, 77:158
Kanter JL, et al. Lipid microarrays identify key mediators of autoimmune brain inflammation. Nature Medicine, 2006, 12(1):138
Yamazaki V, et al. Cell membrane array fabrication and assay technology. BMC Biotechnology, 2005, 5:18
- Protein Arrays
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Berglund L, et al.
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies. Mol Cell Proteomics 2008,
7(10):2019-2027 (Review)
Bertone P & Snyder M. Advances in functional protein microarray technology. FEBS Journal, 2005, 272:5400-5411
Brembilla NC, et al. Profiling of T-cell receptor signaling complex assembly in human CD4 T-lymphocytes using RP protein arrays. Proteomics, 2009, 9(2):299
Chatterjee DK, et al. Protein Microarray On-Demand: A Novel Protein Microarray System. PLoS ONE 2008, 3(9):e3265
Coleman MA, et al. High-throughput, fluorescence-based screening for soluble protein expression. Journal of Proteome Research, 2004, 3:1024-1032
Gonzalez RM, et al. Development and Validation of Sandwich ELISA Microarrays with Minimal Assay Interference. J Proteome Res, 2008, 7(6):2406
LaBaer J & Ramachandran N. Protein microarrays as tools for functional proteomics. Current Opinion in Chemical Biology, 2005, 9:14-19
Lin J, et al. Development of a novel peptide microarray for large-scale epitope mapping of food allergens. J Allergy Clin Immunol, 2009, 124(2):315
Mathur, P. et al. Antibody-array technique reveals overexpression of important DNA-repair proteins during cardiac ischemic preconditioning. Journal of Molecular and Cellular Cardiology, 2005, 38:99-102.
Ramachandran N, et al Emerging tools for real-time label-free detection of interactions on functional protein microarrays. FEBS Journal, 2005, 272:5412-5425
Ramachandran N, et al Next-generation high-density self-assembling functional protein arrays. Nature Methods, 2008, 5:535
- Tissue Arrays
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Kononen J, et al.
Tissue Microarrays for high-throughput molecular profiling of tumor specimens. Nature Medicine, 1998,
4(7):844-847
Somers GR, et al. HER2 Amplification and Overexpression Is Not Present in Pediatric Osteosarcoma: A Tissue Microarray Study. Pediatric and Developmental Pathology, 2005, 8(5);525-532
Thomson TA, et al. Tissue microarray for routine analysis of breast biomarkers in the clinical laboratory. Am J Clin Pathol, 2009, 132(6):899
Torhorst J, et al. Tissue Microarrays for Rapid Linking of Molecular Changes to Clinical Endpoints. Am J Pathology, 2001, 159(6):2249-2256
Wan WH, Fortuna MB, Furmanski P. A rapid and efficient method for testing immunohistochemical reactivity of monoclonal antibodies against multiple tissue samples simultaneously. J. Immunol. Methods, 1987, 103(1):121-129