Microarray Technology

Microarray technology, with its high-throughput advantage, has been applied to analyze various biomaterials, such as nucleic acids, proteins, glycans, peptides, and cells.

[1]  Eoin L Brodie,et al.  Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation , 2006, Applied and Environmental Microbiology.

[2]  Jizhong Zhou,et al.  Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.

[3]  K. Lam,et al.  Peptide and small molecule microarray for high throughput cell adhesion and functional assays. , 2001, Bioconjugate chemistry.

[4]  Henrik Bjørn Nielsen,et al.  OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes , 2005, Nucleic Acids Res..

[5]  Ronald T. Raines,et al.  Site-specific protein immobilization by Staudinger ligation. , 2003, Journal of the American Chemical Society.

[6]  M. Marra,et al.  Applications of new sequencing technologies for transcriptome analysis. , 2009, Annual review of genomics and human genetics.

[7]  Gary L. Andersen,et al.  High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment , 2007, Microbial Ecology.

[8]  T. Hazen,et al.  Advances in monitoring environmental microbes. , 2013, Current opinion in biotechnology.

[9]  Xiaowei Wang,et al.  Selection of Oligonucleotide Probes for Protein Coding Sequences , 2003, Bioinform..

[10]  Hamid Mohamadi,et al.  BOND: Basic OligoNucleotide Design , 2013, BMC Bioinformatics.

[11]  Eli J. Weinberg,et al.  In vitro analysis of a hepatic device with intrinsic microvascular-based channels , 2008, Biomedical microdevices.

[12]  I-Ming Hsing,et al.  A DNA biochip for on-the-spot multiplexed pathogen identification , 2006, Nucleic acids research.

[13]  Gary L. Andersen,et al.  High-Density Microarray of Small-Subunit Ribosomal DNA Probes , 2002, Applied and Environmental Microbiology.

[14]  J Christopher Love,et al.  Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. , 2012, Analytical chemistry.

[15]  Ying Xu,et al.  PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis , 2002, Bioinform..

[16]  Vadim Backman,et al.  Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data , 2006, Proceedings of the National Academy of Sciences.

[17]  Peter X Ma,et al.  Primary rat hepatocyte culture on 3D nanofibrous polymer scaffolds for toxicology and pharmaceutical research , 2011, Biotechnology and bioengineering.

[18]  Vincent Barra,et al.  PhylArray: phylogenetic probe design algorithm for microarray. , 2007, Bioinformatics.

[19]  R. Raines,et al.  Staudinger ligation: a peptide from a thioester and azide. , 2000, Organic letters.

[20]  R. McKay,et al.  Differentiation of Embryonic Stem Cells to Insulin-Secreting Structures Similar to Pancreatic Islets , 2001, Science.

[21]  L Gepstein,et al.  Human embryonic stem cells can differentiate into myocytes with structural and functional properties of cardiomyocytes. , 2001, The Journal of clinical investigation.

[22]  Xiaomin Ying,et al.  Mprobe 2.0: computer-aided probe design for oligonucleotide microarray. , 2006, Applied bioinformatics.

[23]  Hee‐Tae Jung,et al.  Application of supramolecular nanostamping to the replication of DNA nanoarrays. , 2007, Nano letters.

[24]  Donald Wlodkowic,et al.  Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells. , 2009, Lab on a chip.

[25]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[26]  K. Schleifer,et al.  Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment , 2002, Applied and Environmental Microbiology.

[27]  Jizhong Zhou.  Microarrays for bacterial detection and microbial community analysis. , 2003, Current opinion in microbiology.

[28]  Gary D. Stormo,et al.  Selection of optimal DNA oligos for gene expression arrays , 2001, Bioinform..

[29]  Wenxin Wang,et al.  Application of a microfluidic chip-based 3D co-culture to test drug sensitivity for individualized treatment of lung cancer. , 2013, Biomaterials.

[30]  Wenjun Yang,et al.  Nanoencapsulated microcrystalline particles for superamplified biochemical assays. , 2002, Analytical chemistry.

[31]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[32]  Douglas A. Lauffenburger,et al.  Polyfunctional responses by human T cells result from sequential release of cytokines , 2011, Proceedings of the National Academy of Sciences.

[33]  Kyung-Jin Jang,et al.  Fluid-shear-stress-induced translocation of aquaporin-2 and reorganization of actin cytoskeleton in renal tubular epithelial cells. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[34]  Gianluca De Bellis,et al.  ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design , 2009, Nucleic acids research.

[35]  F. Cohen,et al.  Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray , 2003, Genome Biology.

[36]  Jiasen Lu,et al.  Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. , 2000, Nucleic acids research.

[37]  P. D’haeseleer,et al.  Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria , 2010, Science.

[38]  Loïc J Blum,et al.  Diazonium-protein adducts for graphite electrode microarrays modification: direct and addressed electrochemical immobilization. , 2005, Journal of the American Chemical Society.

[39]  Levente Bodrossy,et al.  Highly parallel microbial diagnostics using oligonucleotide microarrays. , 2006, Clinica chimica acta; international journal of clinical chemistry.

[40]  Jennifer Sturgis,et al.  'Living cantilever arrays' for characterization of mass of single live cells in fluids. , 2008, Lab on a chip.

[41]  Chen-Zen Lo,et al.  UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level , 2010, BMC Genomics.

[42]  David R. C. Hill,et al.  HiSpOD: probe design for functional DNA microarrays , 2011, Bioinform..

[43]  Luca Berdondini,et al.  Active pixel sensor array for high spatio-temporal resolution electrophysiological recordings from single cell to large scale neuronal networks. , 2009, Lab on a chip.

[44]  J. Jukes,et al.  Endochondral bone tissue engineering using embryonic stem cells , 2008, Proceedings of the National Academy of Sciences.

[45]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[46]  Matsuhiko Nishizawa,et al.  Multi-channel 3-D cell culture device integrated on a silicon chip for anticancer drug sensitivity test. , 2005, Biomaterials.

[47]  Daniela Loessner,et al.  Kallikrein-related peptidase 7 promotes multicellular aggregation via the alpha(5)beta(1) integrin pathway and paclitaxel chemoresistance in serous epithelial ovarian carcinoma. , 2010, Cancer research.

[48]  Eoin L. Brodie,et al.  Urban aerosols harbor diverse and dynamic bacterial populations , 2007, Proceedings of the National Academy of Sciences.

[49]  E. Dugat-Bony,et al.  Detecting unknown sequences with DNA microarrays: explorative probe design strategies. , 2012, Environmental microbiology.

[50]  Ali Khademhosseini,et al.  Microfluidic patterning for fabrication of contractile cardiac organoids , 2007, Biomedical microdevices.

[51]  Cheng-Hsien Liu,et al.  A microfluidic chip with a U-shaped microstructure array for multicellular spheroid formation, culturing and analysis , 2014, Biofabrication.

[52]  Eric Peyretaillade,et al.  KASpOD - a web service for highly specific and explorative oligonucleotide design , 2012, Bioinform..

[53]  Christian Grothoff,et al.  Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets , 2011, Bioinform..

[54]  Jizhong Zhou,et al.  Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation , 2005, Nucleic acids research.

[55]  J. Shively,et al.  Angiopoietins-1 and -2 play opposing roles in endothelial sprouting of embryoid bodies in 3D culture and their receptor Tie-2 associates with the cell-cell adhesion molecule PECAM1. , 2011, Experimental cell research.

[56]  M. Gerstein,et al.  Design optimization methods for genomic DNA tiling arrays. , 2005, Genome research.

[57]  Jeffery H. Fenton,et al.  A miniature integrated device for automated multistep genetic assays. , 2000, Nucleic acids research.

[58]  Gyan Bhanot,et al.  Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines , 2012, PloS one.

[59]  Shengzhong Feng,et al.  A fast and flexible approach to oligonucleotide probe design for genomes and gene families , 2007, Bioinform..

[60]  Sophie Lemoine,et al.  An evaluation of custom microarray applications: the oligonucleotide design challenge , 2009, Nucleic acids research.

[61]  Adam M. Phillippy,et al.  Efficient oligonucleotide probe selection for pan-genomic tiling arrays , 2009, BMC Bioinformatics.

[62]  Vanessa L. Horner,et al.  Microarray oligonucleotide probe designer (MOPeD): A web service. , 2010, Open access bioinformatics.

[63]  H. Kimura,et al.  An integrated microfluidic system for long-term perfusion culture and on-line monitoring of intestinal tissue models. , 2008, Lab on a chip.

[64]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[65]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[66]  Jeffrey R. Morgan,et al.  Pannexin1 Drives Multicellular Aggregate Compaction via a Signaling Cascade That Remodels the Actin Cytoskeleton* , 2012, The Journal of Biological Chemistry.

[67]  Kia Peyvan,et al.  Fully integrated miniature device for automated gene expression DNA microarray processing. , 2006, Analytical chemistry.

[68]  Herbert Waldmann,et al.  Staudinger ligation: a new immobilization strategy for the preparation of small-molecule arrays. , 2003, Angewandte Chemie.

[69]  Arum Han,et al.  Microfluidic compartmentalized co-culture platform for CNS axon myelination research , 2009, Biomedical microdevices.

[70]  Julie C. Mitchell,et al.  chipD: a web tool to design oligonucleotide probes for high-density tiling arrays , 2010, Nucleic Acids Res..

[71]  Donald Wlodkowic,et al.  Microfluidic single-cell array cytometry for the analysis of tumor apoptosis. , 2009, Analytical chemistry.

[72]  Michael B. Eisen,et al.  Rapid quantitative profiling of complex microbial populations , 2006, Nucleic acids research.

[73]  Roman K Truckenmüller,et al.  Tissue deformation spatially modulates VEGF signaling and angiogenesis , 2012, Proceedings of the National Academy of Sciences.

[74]  Yong Tae Kim,et al.  An integrated allele-specific polymerase chain reaction-microarray chip for multiplex single nucleotide polymorphism typing. , 2012, Lab on a chip.

[75]  Steven Russell,et al.  MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays , 2006, Bioinform..

[76]  Jizhong Zhou,et al.  Development and application of functional gene arrays for microbial community analysis , 2008 .

[77]  Tomoyuki Yasukawa,et al.  A multicellular spheroid array to realize spheroid formation, culture, and viability assay on a chip. , 2007, Biomaterials.

[78]  M. Zuker,et al.  OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. , 2003, Nucleic acids research.

[79]  Michael Leiss,et al.  Formation and activation of fibroblast spheroids depend on fibronectin-integrin interaction. , 2008, Experimental cell research.

[80]  Robin H. Liu,et al.  Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. , 2004, Analytical chemistry.

[81]  Richard Simon,et al.  Lost in translation: problems and pitfalls in translating laboratory observations to clinical utility. , 2008, European journal of cancer.

[82]  D. Kent,et al.  High-throughput analysis of single hematopoietic stem cell proliferation in microfluidic cell culture arrays , 2011, Nature Methods.

[83]  C. Bertozzi,et al.  Cell surface engineering by a modified Staudinger reaction. , 2000, Science.

[84]  Shuichi Takayama,et al.  Microfluidic system for formation of PC-3 prostate cancer co-culture spheroids. , 2009, Biomaterials.

[85]  I-Ming Hsing,et al.  Microfabricated PCR-electrochemical device for simultaneous DNA amplification and detection. , 2003, Lab on a chip.

[86]  Michael Wagner,et al.  Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions , 2007, Microbial Ecology.

[87]  Fredj Tekaia,et al.  A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization , 2003, BMC Genomics.

[88]  O. Gascuel,et al.  SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. , 2010, Molecular biology and evolution.

[89]  Hiroyuki Kishi,et al.  A rapid and efficient single-cell manipulation method for screening antigen-specific antibody–secreting cells from human peripheral blood , 2009, Nature Medicine.

[90]  Jun Li,et al.  3D PLGA scaffolds improve differentiation and function of bone marrow mesenchymal stem cell-derived hepatocytes. , 2010, Stem cells and development.

[91]  R. Ismagilov,et al.  Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics. , 2008, Lab on a chip.

[92]  Patrick S. Schnable,et al.  Picky: oligo microarray design for large genomes , 2004, Bioinform..

[93]  R. J. Tonucci,et al.  Towards environmental toxicogenomics -- development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment. , 2001, The Science of the total environment.

[94]  Andreas Hierlemann,et al.  Reconfigurable microfluidic hanging drop network for multi-tissue interaction and analysis , 2014, Nature Communications.

[95]  Jeroen Rouwkema,et al.  Endothelial cells assemble into a 3-dimensional prevascular network in a bone tissue engineering construct. , 2006, Tissue engineering.