oligonucleotide array sequence analysis

Summary

Summary: Hybridization of a nucleic acid sample to a very large set of oligonucleotide probes, which are attached to a solid support, to determine sequence or to detect variations in a gene sequence or expression or for gene mapping.

Top Publications

  1. pdf DAVID: Database for Annotation, Visualization, and Integrated Discovery
    Glynn Dennis
    Science Applications International Corporation Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA
    Genome Biol 4:P3. 2003
  2. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
  3. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
  4. pmc edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    Mark D Robinson
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Bioinformatics 26:139-40. 2010
  5. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
  6. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
  7. ncbi Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 126:663-76. 2006
  8. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
  9. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
  10. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003

Detail Information

Publications248 found, 100 shown here

  1. pdf DAVID: Database for Annotation, Visualization, and Integrated Discovery
    Glynn Dennis
    Science Applications International Corporation Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA
    Genome Biol 4:P3. 2003
    ..A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information...
  2. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
    ..The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets...
  3. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available...
  4. pmc edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    Mark D Robinson
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Bioinformatics 26:139-40. 2010
    ..The software may have other applications beyond sequencing data, such as proteome peptide count data...
  5. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
    ..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
  6. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process...
  7. ncbi Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 126:663-76. 2006
    ..These data demonstrate that pluripotent stem cells can be directly generated from fibroblast cultures by the addition of only a few defined factors...
  8. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
    ..A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo...
  9. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
    ..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities...
  10. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
  11. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  12. ncbi Molecular portraits of human breast tumours
    C M Perou
    Department of Genetics, Stanford University School of Medicine, California 94305, USA
    Nature 406:747-52. 2000
    ..The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns...
  13. pmc Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    T Sørlie
    Department of Genetics, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    Proc Natl Acad Sci U S A 98:10869-74. 2001
    ....
  14. ncbi MicroRNA signatures in human cancers
    George A Calin
    Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
    Nat Rev Cancer 6:857-66. 2006
    ..In addition, profiling has been exploited to identify miRNA genes that might represent downstream targets of activated oncogenic pathways, or that target protein-coding genes involved in cancer...
  15. ncbi Induced pluripotent stem cell lines derived from human somatic cells
    Junying Yu
    Genome Center of Wisconsin, Madison, WI 53706 1580, USA
    Science 318:1917-20. 2007
    ....
  16. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
    ..Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations...
  17. pmc RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
    ..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
  18. pmc Significance analysis of microarrays applied to the ionizing radiation response
    V G Tusher
    Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA
    Proc Natl Acad Sci U S A 98:5116-21. 2001
    ..Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation...
  19. pmc A microRNA expression signature of human solid tumors defines cancer gene targets
    Stefano Volinia
    Department of Molecular Virology, Immunology, and Medical Genetics and Cancer Comprehensive Center, Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 103:2257-61. 2006
    ..Our results indicate that miRNAs are extensively involved in cancer pathogenesis of solid tumors and support their function as either dominant or recessive cancer genes...
  20. ncbi TM4 microarray software suite
    Alexander I Saeed
    Department of Bioinformatics, The Institute for Genomic Research, Rockville, MD, USA
    Methods Enzymol 411:134-93. 2006
    ..An integrated MIAME-compliant MySQL database is included. This chapter describes each component of the suite and includes a sample analysis walk-through...
  21. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
    ..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
  22. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    ..An applet version is also available that can be used on any website with no special server-side setup...
  23. pmc NCBI GEO: archive for functional genomics data sets--10 years on
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:D1005-10. 2011
    ..This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  24. ncbi lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
    ..The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data...
  25. pmc The impact of microRNAs on protein output
    Daehyun Baek
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 455:64-71. 2008
    ..The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output...
  26. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency...
  27. ncbi Adjusting batch effects in microarray expression data using empirical Bayes methods
    W Evan Johnson
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
    Biostatistics 8:118-27. 2007
    ..We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/...
  28. ncbi Unique microRNA molecular profiles in lung cancer diagnosis and prognosis
    Nozomu Yanaihara
    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Cell 9:189-98. 2006
    ..These results indicate that miRNA expression profiles are diagnostic and prognostic markers of lung cancer...
  29. pmc Summaries of Affymetrix GeneChip probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 31:e15. 2003
    ..In particular, improvements in the ability to detect differentially expressed genes are demonstrated...
  30. pmc Origins and functional impact of copy number variation in the human genome
    Donald F Conrad
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
    Nature 464:704-12. 2010
    ....
  31. ncbi The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    Justin Lamb
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Science 313:1929-35. 2006
    ..These results indicate the feasibility of the approach and suggest the value of a large-scale community Connectivity Map project...
  32. ncbi Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
    Heidi S Phillips
    Department of Tumor Biology and Angiogenesis, Genentech, Inc, South San Francisco, California 94080, USA
    Cancer Cell 9:157-73. 2006
    ..A robust two-gene prognostic model utilizing PTEN and DLL3 expression suggests that Akt and Notch signaling are hallmarks of poor prognosis versus better prognosis gliomas, respectively...
  33. pmc WGCNA: an R package for weighted correlation network analysis
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 9:559. 2008
    ..While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial...
  34. pmc The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Genet 41:178-86. 2009
    ....
  35. ncbi MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer
    Fanyin Meng
    Department of Internal Medicine, Scott and White Clinic, Texas A and M University System Health Science Center College of Medicine, Temple, Texas, USA
    Gastroenterology 133:647-58. 2007
    ..Although a role for aberrant miRNA expression in cancer has been postulated, the pathophysiologic role and relevance of aberrantly expressed miRNA to tumor biology has not been established...
  36. ncbi Gene expression profiling predicts clinical outcome of breast cancer
    Laura J van 't Veer
    Division of Diagnostic Oncology, The Netherlands Cancer Institute, 121 Plesmanlaan, 1066 CX Amsterdam, The Netherlands
    Nature 415:530-6. 2002
    ..This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy...
  37. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future...
  38. ncbi Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Lee P Lim
    Rosetta Inpharmatics, Merck and Co, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Nature 433:769-73. 2005
    ..Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans...
  39. ncbi Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    Adrian Alexa
    Max Planck Institute for Informatics Stuhlsatzenhausweg 85, D 66123 Saarbrucken, Germany
    Bioinformatics 22:1600-7. 2006
    ..g. based on Gene Ontology (GO). We develop methods that increase the explanatory power of this approach by integrating knowledge about relationships between the GO terms into the calculation of the statistical significance...
  40. ncbi PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    Vamsi K Mootha
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 34:267-73. 2003
    ..Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments...
  41. ncbi Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
    ..In addition, using RP can lead to a sharp reduction in the number of replicate experiments needed to obtain reproducible results...
  42. ncbi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008
    ..This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies...
  43. ncbi A gene-expression signature as a predictor of survival in breast cancer
    Marc J van de Vijver
    Division of Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
    N Engl J Med 347:1999-2009. 2002
    ..A more accurate means of prognostication in breast cancer will improve the selection of patients for adjuvant systemic therapy...
  44. pmc Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
    Alexander Marson
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 134:521-33. 2008
    ..These data reveal how key ES cell transcription factors promote the ES cell miRNA expression program and integrate miRNAs into the regulatory circuitry controlling ES cell identity...
  45. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter A C 't Hoen
    The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nucleic Acids Res 36:e141. 2008
    ..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies...
  46. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...
  47. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
    ..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
  48. ncbi A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia
    George Adrian Calin
    Department of Molecular Virology, Immunology, and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
    N Engl J Med 353:1793-801. 2005
    ..We investigated whether microRNA profiles are associated with known prognostic factors in CLL...
  49. ncbi Direct multiplexed measurement of gene expression with color-coded probe pairs
    Gary K Geiss
    NanoString Technologies Inc, 201 Elliott Ave West, Suite 300, Seattle, Washington 98119, USA
    Nat Biotechnol 26:317-25. 2008
    ..Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels...
  50. pmc Core transcriptional regulatory circuitry in human embryonic stem cells
    Laurie A Boyer
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Cell 122:947-56. 2005
    ..These results provide new insights into the transcriptional regulation of stem cells and reveal how OCT4, SOX2, and NANOG contribute to pluripotency and self-renewal...
  51. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
    ..This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  52. ncbi A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function
    John D Cahoy
    Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305, USA
    J Neurosci 28:264-78. 2008
    ....
  53. pmc Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  54. ncbi A comparison of background correction methods for two-colour microarrays
    Matthew E Ritchie
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Bioinformatics 23:2700-7. 2007
    ..Different estimators of background, and various model-based processing methods, are compared in this study in search of the best option for differential expression analyses of small microarray experiments...
  55. pmc Genomic expression programs in the response of yeast cells to environmental changes
    A P Gasch
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5428, USA
    Mol Biol Cell 11:4241-57. 2000
    ..Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell...
  56. ncbi High density DNA methylation array with single CpG site resolution
    Marina Bibikova
    Illumina, Inc 9885 Towne Centre Drive, San Diego, CA 92121, USA
    Genomics 98:288-95. 2011
    ..Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research...
  57. pmc ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    Adam A Margolin
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
    BMC Bioinformatics 7:S7. 2006
    ..This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods...
  58. pmc Requirement of bic/microRNA-155 for normal immune function
    Antony Rodriguez
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Science 316:608-11. 2007
    ..Our work suggests that bic/microRNA-155 plays a key role in the homeostasis and function of the immune system...
  59. pmc ONCOMINE: a cancer microarray database and integrated data-mining platform
    Daniel R Rhodes
    Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Neoplasia 6:1-6. 2004
    ..Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets...
  60. ncbi Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Motoaki Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant J 31:279-92. 2002
    ....
  61. ncbi Use of within-array replicate spots for assessing differential expression in microarray experiments
    Gordon K Smyth
    Walter and Eliza Hall Institute of Medical Research, Melbourne, Vic, Australia
    Bioinformatics 21:2067-75. 2005
    ..The usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This results in the loss of valuable information about genewise variability...
  62. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    ....
  63. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  64. pmc Epigenome-wide association studies for common human diseases
    Vardhman K Rakyan
    Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
    Nat Rev Genet 12:529-41. 2011
    ..We also discuss how integration of EWASs with GWASs can help to dissect complex GWAS haplotypes for functional analysis...
  65. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
  66. ncbi The polycomb group protein EZH2 is involved in progression of prostate cancer
    Sooryanarayana Varambally
    Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Nature 419:624-9. 2002
    ..Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal progression...
  67. pmc Microarrays, deep sequencing and the true measure of the transcriptome
    John H Malone
    Laboratory of Cellular and Developmental Biology, National Institute of Digestive, Diabetes, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Biol 9:34. 2011
    ..We conclude that microarrays remain useful and accurate tools for measuring expression levels, and RNA-Seq complements and extends microarray measurements...
  68. pmc Development of the human infant intestinal microbiota
    Chana Palmer
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Biol 5:e177. 2007
    ..By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract...
  69. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
    ..With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists...
  70. pmc Epigenetic differences arise during the lifetime of monozygotic twins
    Mario F Fraga
    Epigenetics Laboratory, Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 102:10604-9. 2005
    ..These findings indicate how an appreciation of epigenetics is missing from our understanding of how different phenotypes can be originated from the same genotype...
  71. pmc XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
    Ann Hwee Lee
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Mol Cell Biol 23:7448-59. 2003
    ..Further, our observations suggest the existence of additional, as-yet-unknown, key regulators of the UPR...
  72. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  73. ncbi Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
    Juan Sandoval
    Cancer Epigenetics and Biology Program PEBC, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute IDIBELL, Spain
    Epigenetics 6:692-702. 2011
    ..The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects...
  74. ncbi Stromal gene expression predicts clinical outcome in breast cancer
    Greg Finak
    McGill Centre for Bioinformatics, 3775 University Street, McGill University, Quebec H3A 2B4, Canada
    Nat Med 14:518-27. 2008
    ..Genes represented in the SDPP reveal the strong prognostic capacity of differential immune responses as well as angiogenic and hypoxic responses, highlighting the importance of stromal biology in tumor progression...
  75. pmc MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma
    Aaron J Schetter
    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    JAMA 299:425-36. 2008
    ..MicroRNAs have potential as diagnostic biomarkers and therapeutic targets in cancer. No study has evaluated the association between microRNA expression patterns and colon cancer prognosis or therapeutic outcome...
  76. pmc GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    Qi Zheng
    State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of the Chinese Academy of Sciences, Beijing 100101, China
    Nucleic Acids Res 36:W358-63. 2008
    ..GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/..
  77. ncbi Evaluation of the Infinium Methylation 450K technology
    Sarah Dedeurwaerder
    Laboratory of Cancer Epigenetics, Universite Libre de Bruxelles, Faculty of Medicine, Brussels, Belgium
    Epigenomics 3:771-84. 2011
    ..In particular, we compare the methylation values of the Infinium I and Infinium II assays...
  78. ncbi Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis
    Christos Sotiriou
    Functional Genomics and Translational Research Unit, Universite Libre de Bruxelles, Brussels, Belgium
    J Natl Cancer Inst 98:262-72. 2006
    ..We examined whether histologic grade was associated with gene expression profiles of breast cancers and whether such profiles could be used to improve histologic grading...
  79. ncbi Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
    Coleen T Murphy
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
    Nature 424:277-83. 2003
    ....
  80. pmc A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    Serge Saxonov
    Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:1412-7. 2006
    ....
  81. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  82. ncbi Next-generation sequencing transforms today's biology
    Stephan C Schuster
    Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
    Nat Methods 5:16-8. 2008
    ..However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years...
  83. pmc Population analysis of large copy number variants and hotspots of human genetic disease
    Andy Itsara
    Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 84:148-61. 2009
    ..g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease...
  84. ncbi MicroRNA expression profiles in serous ovarian carcinoma
    Eun Ji Nam
    Women s Cancer Clinic, Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Korea
    Clin Cancer Res 14:2690-5. 2008
    ..We assessed the expression of microRNA and the association between microRNA expression and the prognosis of serous ovarian carcinoma...
  85. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  86. pmc Global variation in copy number in the human genome
    Richard Redon
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 444:444-54. 2006
    ..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
  87. ncbi Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
    Yixin Wang
    Veridex LLC, a Johnson and Johnson Company, San Diego, CA, USA
    Lancet 365:671-9. 2005
    ....
  88. pmc The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Nat Biotechnol 28:827-38. 2010
    ..The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis...
  89. ncbi Normalization of cDNA microarray data
    Gordon K Smyth
    Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC 3050, Australia
    Methods 31:265-73. 2003
    ..Variations on loess normalization include global loess normalization and two-dimensional normalization. Detailed commands are given to implement the normalization techniques using freely available software...
  90. ncbi Genesis: cluster analysis of microarray data
    Alexander Sturn
    Institute of Biomedical Engineering, Graz University of Technology, Krenngasse 37, 8010 Graz, Austria
    Bioinformatics 18:207-8. 2002
    ..Additionally, mapping of gene expression data onto chromosomal sequences was implemented to enhance promoter analysis and investigation of transcriptional control mechanisms...
  91. ncbi A multigenic program mediating breast cancer metastasis to bone
    Yibin Kang
    Cell Biology Program and Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Cancer Cell 3:537-49. 2003
    ....
  92. pmc Transcript length bias in RNA-seq data confounds systems biology
    Alicia Oshlack
    Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia
    Biol Direct 4:14. 2009
    ..As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data...
  93. ncbi A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    Marc Sultan
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Science 321:956-60. 2008
    ..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
  94. pmc Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Jason I Herschkowitz
    Lineberger Comprehensive Cancer Center
    Genome Biol 8:R76. 2007
    ..To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors...
  95. pmc Interferon and granulopoiesis signatures in systemic lupus erythematosus blood
    Lynda Bennett
    Baylor Institute for Immunology Research, Dallas, TX 75204, USA
    J Exp Med 197:711-23. 2003
    ..Therefore, while the IFN signature confirms the central role of this cytokine in SLE, microarray analysis of blood cells reveals that immature granulocytes may be involved in SLE pathogenesis...
  96. ncbi mRNA-Seq whole-transcriptome analysis of a single cell
    Fuchou Tang
    Wellcome Trust Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
    Nat Methods 6:377-82. 2009
    ..Finally, for Dicer1(-/-) and Ago2(-/-) (Eif2c2(-/-)) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common...
  97. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  98. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
    ..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
  99. ncbi Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus
    Darwyn Kobasa
    Respiratory Viruses, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
    Nature 445:319-23. 2007
    ..The ability of influenza viruses to modulate host immune responses, such as that demonstrated for the avian H5N1 influenza viruses, may be a feature shared by the virulent influenza viruses...
  100. pmc Model-based variance-stabilizing transformation for Illumina microarray data
    Simon M Lin
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
    Nucleic Acids Res 36:e11. 2008
    ..The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org...
  101. ncbi Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration
    Sebastian Bauer
    Institute of Medical Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
    Bioinformatics 24:1650-1. 2008
    ....

Research Grants63

  1. NOVEL FACTORS THAT REGULATE GNRH NEURONAL DEVELOPMENT
    Margaret E Wierman; Fiscal Year: 2010
    ....
  2. BMP signaling in vertebrate development
    Ken W Y Cho; Fiscal Year: 2013
    ..g., juvenile polyposis syndrome, primary pulmonary hypertension, Cowden's syndrome) and developmental abnormalities. Identification of candidate genes and signaling components will aid in developing new diagnosis and treatments. ..
  3. Inflammation and Repair in Cardiac Ischemia-Reperfusion
    Lewis C Becker; Fiscal Year: 2011
    ..abstract_text> ..
  4. Identification of Novel Genes for Congenital Diaphragmatic Hernia
    Wendy K Chung; Fiscal Year: 2012
    ..We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information for patients and families with CDH. ..
  5. Excitotoxicity in Circulatory Arrest ? Brain Injury
    WILLIAM ANTHONY BAUMGARTNER; Fiscal Year: 2012
    ....
  6. Regulation and Function of MGAT in Hepatic TAG Synthesis and Metabolic Disease
    ANGELA MARIE HALL; Fiscal Year: 2013
    ....
  7. Role of miRNA-375 in Invasive Phenotype of Head and Neck Squamous Cell Carcinoma
    Lizandra Jimenez; Fiscal Year: 2013
    ..Functional validation of the phenotypic effects of the down-regulation of putative targets of miR-375 will be performed by siRNA knockdown and rescue of the targets in the transductant cells. ..
  8. REGULATION OF CYCLIN D1 EXPRESSION
    Richard G Pestell; Fiscal Year: 2010
    ..Together these three integrated Aims will determine the role of cyclin D1-regulated functions in cellular migration, invasion and tumorigenesis. ..
  9. Sex, sex steroids and dry eye syndromes
    David A Sullivan; Fiscal Year: 2013
    ..abstract_text> ..
  10. Gene Expression and Regulatory Networks in Human Leukocytes
    Diane J Mathis; Fiscal Year: 2010
    ..These results will provide an invaluable reference benchmark for the interpretation of genetic and immunological studies. ..
  11. IL-1?? as a mediator of maternal infection-induced effects on offspring neuroinfl
    Heping Zhou; Fiscal Year: 2010
    ..Our results may also contribute to the finding of new diagnostic or therapeutic targets for mitigating maternal infection-induced defects in the offspring. ..
  12. Effects of developmental stage and of KLF2 on mouse erythroid genetic profiles
    Joyce A Lloyd; Fiscal Year: 2011
    ..In Aim 3, the hypotheses generated about genes controlling primitive erythropoiesis will be tested using existing knockout mice and knockdowns in erythroid cell lines. ..
  13. Precursor cell-niche interactions and the genesis of brainstem gliomas
    MICHELLE MONJE-DEISSEROTH; Fiscal Year: 2012
    ..We will test the functional significance of the findings about the normal brainstem in brainstem tumor cells, which may ultimately result in new therapies for this tragic disease. ..
  14. Elucidating the molecular mechanisms that shape the hair bundle
    BRIAN MICHAEL MCDERMOTT; Fiscal Year: 2013
    ..Using the molecular-biological techniques applicable to the zebrafish, we have begun to investigate the roles that some of these genes'products play in hair-bundle development. ..
  15. STRUCTURE AND REPLICATION OF HEPATITIS DELTA VIRUS
    John Taylor; Fiscal Year: 2009
    ..abstract_text> ..
  16. Sensitive and multiplexed analysis of cancer biomarkers with QD barcodes
    Xiaohu Gao; Fiscal Year: 2012
    ..We will further carry out experiments to detect mutations on both DNA and RNA level as well as the profiles of protein cancer biomarkers, which can be isolated from serum or homogenized cell and tissue specimens. ..
  17. The Role of DNA Methylation in Tumor Maintenance
    Peter W Laird; Fiscal Year: 2013
    ....
  18. Cancer Genome Characterization using Gene Expression and DNA Copy Number Analysis
    Charles Perou; Fiscal Year: 2009
    ..Importantly, we have also developed new data mining techniques that have allowed for integration and cross-validation of these comprehensive genomic data sets. ..
  19. Markers of Early Pancreatic Cancer
    Michael G Goggins; Fiscal Year: 2010
    ..We will also determine the diagnostic utility of combining the results of the markers derived from these 3 Aims. ..
  20. Targeting IKK beta and aurora kinases in melanoma
    Ann Richmond; Fiscal Year: 2013
    ..The data derived from this proposal will provide key insights for better design of clinical trials for melanoma patients which should positively impact our Veteran population. ..
  21. Localizing Maternal and Fetal Message in Translation of Preeclampsia Candidate Ge
    Sandra A Founds; Fiscal Year: 2013
    ..Validated candidates could be relevant to the prediction and early detection of later life preeclampsia-associated cardiovascular disease in mothers and offspring who survive this pregnancy complication. ..
  22. Molecular approaches to gene identification in congenital heart disease
    Dorothy P Warburton; Fiscal Year: 2013
    ....
  23. Genomic Approaches to Improve Transfusion Therapy in SCD Patients
    Marion E Reid; Fiscal Year: 2010
    ..We believe that data generated from this project will have an immediate impact in improving the transfusion of patients with SCD. (End of Abstract) ..
  24. Low cost custom synthesis microarray
    Erdogan Gulari; Fiscal Year: 2011
    ....
  25. LEAP Image Scanning Cytometer/Sorter/Optoinjection Shared Instrument
    James F Leary; Fiscal Year: 2010
    ..But there will also be a considerable expertise available from the PI's lab including a trained technician ready to either assist or run samples for each user. ..
  26. MATRIX REGULATION OF CELL FUNCTION DURING WOUND HEALING
    Livingston Van De Water; Fiscal Year: 2010
    ..Findings obtained from this work will fill important gaps in understanding pathogenic myofibroblast regulation and suggest new therapeutic strategies to modulate fibrosis following serious burn or traumatic injury. ..
  27. From human keratinocytes to biological pacemakers
    Ira S Cohen; Fiscal Year: 2013
    ..If the HFKT-pacemaker functions well in the canine heart, a future goal would be to advance this novel autologous, cellular approach towards clinical deployment. ..
  28. Genomewide Association Study of Cocaine Dependence in two Populations
    Joel Gelernter; Fiscal Year: 2010
    ..A secondary goal is to identify risk genes and variants for nicotine dependence. Finding these risk genes will aid in understanding, prevention, and eventually, treatment, of these disorders. ..
  29. Development of a Highly Automated Microarray Data Analysis System That Allows
    Yuerong Zhu; Fiscal Year: 2009
    ....
  30. Endodermal progenitor cell characterization
    PAUL J GADUE; Fiscal Year: 2013
    ..This information may make generating EP cells more efficient and may lead to a better understanding of the mechanisms controlling stem cell populations in general. ..
  31. Pharmacogenomics in Autism Treatment
    ROBERT LEE HENDREN; Fiscal Year: 2009
    ....
  32. In Vivo Selection of Tumor-Specific RNA Binding Motifs
    Bryan M Clary; Fiscal Year: 2013
    ..The relevance of the aptamers to a broad spectrum of patients with mCRC will be explored via cDNA arrays and IHC of resected tumors and through in vivo trafficking studies in mice bearing xenotransplants. ..
  33. Program Project,Restoration of Endocrine Pancreas Funct*
    JOEL HABENER; Fiscal Year: 2004
    ..This PPA proposes the initial studies on the way to providing a cure for diabetes via the approaches for regenerative medicine. ..
  34. Large-scale expression analysis of natural antisense transcripts
    Xijin Ge; Fiscal Year: 2012
    ..Such large-scale analysis of antisense expression will critically evaluate whether antisense transcription is a highly regulated process. ..
  35. DNA REPAIR AND SUSCEPTIBILITY TO ENVIRONMENTAL AGENTS
    Ivan Rusyn; Fiscal Year: 2004
    ..These experiments will also provide crucial mechanistic insights into possible differences in species- and tissue-specific responses to DNA damage induced by environmental agents. ..
  36. Biophysical Optimization of Oligonucleotide Microarrays
    Cynthia Gibas; Fiscal Year: 2009
    ..We will provide a well-designed and tested oligonucleotide microarray with the necessary probes for discrimination among three biovars of Brucelia (abortus, melitensis, and suis). ..
  37. Intestinal Iron Transport in Iron Deficiency/Anemia
    James Collins; Fiscal Year: 2005
    ..abstract_text> ..
  38. Differential Gene Expression Induced by Antioxidants
    Jeri Kim; Fiscal Year: 2004
    ..Once characterized, these SBs will widen the scope and enhance the feasibility of prostate cancer trials, creating broader opportunities for advances toward successful prevention, effective treatment, and eventual cure. ..
  39. MULTI-ANALYTE WAVEGUIDE IMMUNOSENSING
    JAMES HERRON; Fiscal Year: 2002
    ..Moreover, data acquisition in real time enables us monitoring hybridization kinetics, which is essential for identifying point mutations. ..
  40. Comprehensive Mutational Analysis of the Cancer Genome
    Dennis Ballinger; Fiscal Year: 2004
    ..abstract_text> ..
  41. Global Responses to Aflatoxin B1 & Alkylating Agents
    Leona Samson; Fiscal Year: 2006
    ..The investigators anticipate that this research will uncover a myriad of hitherto unknown ways in which cells respond to environmental agents. ..
  42. Novel Fluid Management System for Microfluidic Devices
    ALAN CISAR; Fiscal Year: 2009
    ..Cost effective next generation health care products and diagnostics will allow physicians to provide improved and more individualized patient treatment and care. ..
  43. MOLEC PATHOPHYS OF CLIN VARIATION IN SPINAL CORD DISEASE
    Eric Hoffman; Fiscal Year: 2001
    ..Our findings should have significance for the progression of inherited forms of spastic paraplegia but also more broadly for spinal cord injury and CNS homeostasis. ..
  44. MESSENGER RNA PROFILING BY SINGLE MOLECULE COUNTING
    Paul Lizardi; Fiscal Year: 2001
    ..abstract_text> ..
  45. INSTABILITY OF TUMOR PROMOTION IN HEPATOCARCINOGENESIS
    HENRY PITOT JR; Fiscal Year: 2006
    ..abstract_text> ..
  46. Genomics: Esophageal Metaplasia-Associated Malignancy
    Stephen Meltzer; Fiscal Year: 2006
    ..Potential biomarkers identified in Aims 1-3 will be studied individually for expression at the protein level in all stages of Barrett's neoplasia, using tissue microarrays. [unreadable] [unreadable] [unreadable]..
  47. Microarrays in Fathead Minnows and Bass
    Barbara Carter; Fiscal Year: 2007
    ..unreadable] [unreadable]..
  48. GENE EXPRESSION PROFILING, OXIDATIVE STRESS AND AGING
    Richard Weindruch; Fiscal Year: 2005
    ....
  49. Role of 12/15-lipoxygenase pathway in implantation
    MILAN BAGCHI; Fiscal Year: 2006
    ..Collectively, the proposed experiments will test the hypothesis that a novel signaling pathway, involving 12/15-LOX-derived lipid mediators, PPARgamma, and its downstream target genes, regulates critical events during implantation. ..
  50. Molecular Epidemiology and Gene-Environment Interaction
    Zuo Feng Zhang; Fiscal Year: 2004
    ..abstract_text> ..
  51. Functional Cloning of Hutchinson-Gliford progeria gene
    Junko Oshima; Fiscal Year: 2004
    ..Once the putative HGPS gene is identified in this manner, the complete sequence of the gene will be determined in normal and HGPS cells to ascertain the nature of the mutational change. ..
  52. Site-directed Covalently Bound Fusion Protein Microarray
    Bryce Nelson; Fiscal Year: 2004
    ..abstract_text> ..
  53. GENE EXPRESSION BASED CLASSIFICATION OF GLIAL TUMORS
    Stanley Nelson; Fiscal Year: 2004
    ..3)To develop a set of genes with prognostic importance in low grade astrocytomas. 4)To validate the importance of the genes from specific aims 2 and 3 in the prognosis of low grade astrocytomas. ..
  54. HIGH SENSITIVITY, ULTRA-LOW BACKGROUND DNA CHIPS
    Mary Anne Watt; Fiscal Year: 2002
    ..Successful development of this technology will result in two highly optimized product lines for use in the DNA chip market (i.e. low background DNA chips and nucleic acid labeling reagents for chip applications). ..
  55. Identifying Molecular Signatures of Cancer
    Subha Srinivasan; Fiscal Year: 2004
    ..abstract_text> ..
  56. Molecular Approach in Predicting 5-Fluorouracil Efficacy
    Robert Diasio; Fiscal Year: 2005
    ..abstract_text> ..
  57. Microarray Center for Research on the Nervous System
    Dietrich Stephan; Fiscal Year: 2004
    ..abstract_text> ..
  58. Computationally Optimized Self-assembly of Multiple Genes from DNA Chips
    She pin Hung; Fiscal Year: 2006
    ..These studies will also provide the preliminary information for the design of DNA chips to produce gene libraries of proteins and protein variants for drug discovery studies. [unreadable] [unreadable]..
  59. ACQUISITION OF MIRCOARRAY SPOTTER, READER, SOFTWARE
    Alan Buckpitt; Fiscal Year: 2001
    ..abstract_text> ..
  60. Low-cost custom microarray synthesis
    Erdogan Gulari; Fiscal Year: 2006
    ..In this project, our goal is to produce microarrays that are much cheaper, as well as easier to use so that they can be used worldwide in tracking viruses, or disease diagnostics. [unreadable] [unreadable] [unreadable]..
  61. Gene Expression Profiling of the Development Inner Ear
    Michael Lovett; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  62. Expression Analysis to Study Disease Pathogenesis
    Mark Geraci; Fiscal Year: 2005
    ..Specific Aim 3 is designed to provide NHLBI researchers with a user-friendly, powerful Internet-based analysis tool. This tool will be specific for the needs of researchers in heart, lung, blood and sleep-related fields. ..
  63. Dysregulation of Type I interferon in human SLE
    Lynda Bennett; Fiscal Year: 2005
    ..Thus, the studies proposed here will provide insights into mechanisms of IFN action in SLE as well as invaluable information necessary for developing tools to block the excess of type 1 IFN as novel therapy in SLE. ..