J Quackenbush

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study
    Elena Fountzilas
    Division of Hematology Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
    BMC Genomics 13:332. 2012
  2. pmc Multiple-input multiple-output causal strategies for gene selection
    Gianluca Bontempi
    Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles, Belgium
    BMC Bioinformatics 12:458. 2011
  3. pmc Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old
    Dilek Colak
    Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
    Mol Cancer 9:146. 2010
  4. pmc Molecular processes during fat cell development revealed by gene expression profiling and functional annotation
    Hubert Hackl
    Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
    Genome Biol 6:R108. 2005
  5. pmc Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Huntington Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 7:R119. 2006
  6. pmc Seeded Bayesian Networks: constructing genetic networks from microarray data
    Amira Djebbari
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    BMC Syst Biol 2:57. 2008
  7. pmc A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution
    PATRICK D DANLEY
    Department of Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 8:109. 2007
  8. pmc Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
    Michael J Boedigheimer
    CDER, US FDA, Silver Spring, MD 20993, USA
    BMC Genomics 9:285. 2008
  9. pmc Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes
    Valerie W Hu
    The George Washington University Medical Center, Dept of Biochemistry and Molecular Biology, 2300 Eye St, N W Washington, DC 20037, USA
    BMC Genomics 7:118. 2006
  10. pmc A robust method for the amplification of RNA in the sense orientation
    Nicholas F Marko
    The George Washington University Medical Center, USA
    BMC Genomics 6:27. 2005

Research Grants

Detail Information

Publications76

  1. pmc A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study
    Elena Fountzilas
    Division of Hematology Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
    BMC Genomics 13:332. 2012
    ..In this study we integrate multiple gene expression datasets to determine miRNA activity patterns associated with cancer phenotypes and oncogenic pathways in mesenchymal tumors - a very heterogeneous class of malignancies...
  2. pmc Multiple-input multiple-output causal strategies for gene selection
    Gianluca Bontempi
    Machine Learning Group, Computer Science Department, Universite Libre de Bruxelles, Belgium
    BMC Bioinformatics 12:458. 2011
    ..In this study, we show how to efficiently incorporate causal information into gene selection by moving from a single-input single-output to a multiple-input multiple-output setting...
  3. pmc Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old
    Dilek Colak
    Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
    Mol Cancer 9:146. 2010
    ....
  4. pmc Molecular processes during fat cell development revealed by gene expression profiling and functional annotation
    Hubert Hackl
    Institute for Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
    Genome Biol 6:R108. 2005
    ..We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development...
  5. pmc Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, Huntington Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 7:R119. 2006
    ..However, the starting point for all cellular gene expression, the transcription of RNA, has not been described and measured in a population of living cells...
  6. pmc Seeded Bayesian Networks: constructing genetic networks from microarray data
    Amira Djebbari
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    BMC Syst Biol 2:57. 2008
    ..Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results...
  7. pmc A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution
    PATRICK D DANLEY
    Department of Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 8:109. 2007
    ..Here we report the development of expressed sequence tags (EST's) in an orthopteroid insect, a model for the study of neurobiology, speciation, and evolution...
  8. pmc Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
    Michael J Boedigheimer
    CDER, US FDA, Silver Spring, MD 20993, USA
    BMC Genomics 9:285. 2008
    ....
  9. pmc Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes
    Valerie W Hu
    The George Washington University Medical Center, Dept of Biochemistry and Molecular Biology, 2300 Eye St, N W Washington, DC 20037, USA
    BMC Genomics 7:118. 2006
    ....
  10. pmc A robust method for the amplification of RNA in the sense orientation
    Nicholas F Marko
    The George Washington University Medical Center, USA
    BMC Genomics 6:27. 2005
    ..Alternatives lack extensive validation and are often confounded by problems with bias or yield attributable to their greater biological and technical complexity...
  11. pmc GCOD - GeneChip Oncology Database
    Fenglong Liu
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    BMC Bioinformatics 12:46. 2011
    ..With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data...
  12. pmc Data-driven normalization strategies for high-throughput quantitative RT-PCR
    Jessica C Mar
    Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 10:110. 2009
    ..The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline...
  13. pmc An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
    Martin J Aryee
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA
    BMC Bioinformatics 10:409. 2009
    ..Therefore they do not make full use of the information intrinsic to the data, leading to a loss of power...
  14. pmc A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
    Tim F Rayner
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 7:489. 2006
    ..However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support...
  15. ncbi request reprint From 'omes to biology
    J Quackenbush
    Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Anim Genet 37:48-56. 2006
    ..Here we outline the general approach and provide three examples from published studies of the way in which we have applied this strategy...
  16. ncbi request reprint Extracting biology from high-dimensional biological data
    John Quackenbush
    Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
    J Exp Biol 210:1507-17. 2007
    ..Recently, we have used a similar approach to trying to understand the biological networks that underlie the phenotypic responses we observe and starting us on the road to developing a predictive biology...
  17. ncbi request reprint Microarray analysis and tumor classification
    John Quackenbush
    Dana Farber Cancer Institute and Harvard School of Public Health, Boston, USA
    N Engl J Med 354:2463-72. 2006
  18. pmc GeneSigDB--a curated database of gene expression signatures
    Aedin C Culhane
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Nucleic Acids Res 38:D716-25. 2010
    ..The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats...
  19. ncbi request reprint Extracting meaning from functional genomics experiments
    John Quackenbush
    Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02030, USA
    Toxicol Appl Pharmacol 207:195-9. 2005
    ....
  20. doi request reprint Using the DFCI gene index databases for biological discovery
    Corina Antonescu
    Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Curr Protoc Bioinformatics . 2010
    ..This protocol provides guidance for using the Gene Index Databases to extract information...
  21. ncbi request reprint Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities
    Elizabeth A Maher
    Center for Neuro Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Cancer Res 66:11502-13. 2006
    ..We conclude that glioblastoma is composed of at least three distinct molecular subtypes, including novel subgroups of secondary glioblastoma, which may benefit from different therapeutic strategies...
  22. pmc Functional classification analysis of somatically mutated genes in human breast and colorectal cancers
    Thomas W Chittenden
    Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115 6084, USA
    Genomics 91:508-11. 2008
    ....
  23. ncbi request reprint Microarray blob-defect removal improves array analysis
    Jun S Song
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA
    Bioinformatics 23:966-71. 2007
    ....
  24. pmc HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition
    Karin Hellner
    Infectious Diseases Division, The Channing Laboratories, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
    Virology 391:57-63. 2009
    ..Hence, HPV16 oncoproteins may contribute to malignant progression through EMT induction...
  25. pmc Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample
    Katsuhiko Nosho
    Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
    PLoS ONE 3:e3698. 2008
    ..In stratified analyses, the relations of CIMP-high with poor differentiation, KRAS mutation and LINE-1 hypomethylation significantly differed according to MSI status...
  26. doi request reprint An optimized predictive strategy for interactome mapping
    Martin J A Aryee
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA
    J Proteome Res 7:4089-94. 2008
    ..The approach is iterative as additional data allows one to refine predictions directing the next stage of experimentation...
  27. pmc E(mu)-TCL1 mice represent a model for immunotherapeutic reversal of chronic lymphocytic leukemia-induced T-cell dysfunction
    Gullu Gorgun
    Department of Medical Oncology, The Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 106:6250-5. 2009
    ..These results further demonstrate the utility of this animal model of CLL and define a versatile model to investigate both the molecular mechanisms of cancer-induced immune suppression and immunotherapeutic repair strategies...
  28. ncbi request reprint Physiogenomic resources for rat models of heart, lung and blood disorders
    Renae L Malek
    TREX, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Genet 38:234-9. 2006
    ..We performed a variety of data-mining manipulations on the profiles and used complementary physiological data from the PhysGen resource to demonstrate how TREX can be used by the cardiovascular community for hypothesis generation...
  29. ncbi request reprint An open letter on microarray data from the MGED Society
    Catherine Ball
    Stanford University, USA
    Microbiology 150:3522-4. 2004
  30. ncbi request reprint Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  31. pmc Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness
    Julia K L Walker
    Department of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
    Am J Respir Cell Mol Biol 34:711-8. 2006
    ..In addition, gene expression profiling data have revealed other potential novel targets for therapeutics-based research and has enhanced the understanding of the molecular mechanisms underlying the etiology of "asthma."..
  32. 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...
  33. doi request reprint Using the TIGR gene index databases for biological discovery
    Yuandan Lee
    The Institute for Genomic Research, Rockville, Maryland, USA
    Curr Protoc Bioinformatics . 2003
    ..This protocol provides guidance for using the Gene Index Databases to extract information...
  34. pmc The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags
    Helena Brentani
    Laboratório de Genética Molecular do Câncer, Departmento de Radiologia, Universidade de Sao Paulo, Travessa da Rua Dr Ovídeo Pires de Campos S N, 4deg, Brazil
    Proc Natl Acad Sci U S A 100:13418-23. 2003
    ....
  35. ncbi request reprint MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms
    Amira Djebbari
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 21:3324-6. 2005
    ..AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study...
  36. ncbi request reprint CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
    Adam A Margolin
    Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 21:3308-11. 2005
    ..It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com)...
  37. ncbi request reprint 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...
  38. ncbi request reprint John Quackenbush talks about the clinical promise of genetic microarrays. Interviewed by Brian Vastag
    John Quackenbush
    JAMA 289:159-60, 163. 2003
  39. ncbi request reprint TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  40. ncbi request reprint Data standards for 'omic' science
    John Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Biotechnol 22:613-4. 2004
  41. ncbi request reprint Open source software for the analysis of microarray data
    Sandrine Dudoit
    University of California, Berkeley, CA, USA
    Biotechniques . 2003
    ..bioconductor.org), the Java-based TM4 software system available from The Institute for Genomic Research (http://www.tigr.org/software), and BASE, the Web-based system developed at Lund University (http://base.thep.lu.se)...
  42. pmc Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage
    Christine A Wells
    Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
    Genome Res 13:1360-5. 2003
    ....
  43. pmc Multi-platform, multi-site, microarray-based human tumor classification
    Greg Bloom
    H Lee Moffitt Cancer Center, University of South Florida, Tampa, Florida 33612 9497, USA
    Am J Pathol 164:9-16. 2004
    ..These cDNA- and oligonucleotide-based classifiers provide a first proof of principle that data derived from multiple platforms and performance sites can be exploited to build multi-tissue tumor classifiers...
  44. pmc Development and evaluation of an automated annotation pipeline and cDNA annotation system
    Takeya Kasukawa
    Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Genome Res 13:1542-51. 2003
    ....
  45. ncbi request reprint Genomics. Microarrays--guilt by association
    John Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 302:240-1. 2003
    ..In his Perspective, Quackenbush discusses new work (Stuart et al.) that uses evolutionary conservation of gene expression patterns in yeast, worm, fruit fly, and human in an attempt to identify functionally related groups of genes...
  46. pmc Orthologous gene-expression profiling in multi-species models: search for candidate genes
    Dmitry N Grigoryev
    Center for Translational Respiratory Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, East Monument Street, Baltimore, MD 21287, USA
    Genome Biol 5:R34. 2004
    ..The results suggest that this approach may be a useful tool in the evaluation of biological processes of interest and selection of process-related candidate genes...
  47. ncbi request reprint Universal RNA reference materials for gene expression
    Maureen Cronin
    Genomic Health, Inc, Redwood City, CA, USA
    Clin Chem 50:1464-71. 2004
    ..Work is underway at NIST and among members of the gene expression array community to further define these materials and make them available...
  48. ncbi request reprint Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling
    Deepak Agrawal
    Department of Cell Biology, Interdisciplinary Oncology, H Lee Moffitt Cancer Center, University of South Florida, Tampa 33612, USA
    J Natl Cancer Inst 94:513-21. 2002
    ..Gene expression profiling techniques offer the opportunity to discover such markers. We investigated the feasibility of sample pooling strategy in combination with a novel analysis algorithm to identify markers...
  49. ncbi request reprint Standards for microarray data
    Catherine A Ball
    Science 298:539. 2002
  50. ncbi request reprint The underlying principles of scientific publication
    Catherine A Ball
    Bioinformatics 18:1409. 2002
  51. pmc Open-source software accelerates bioinformatics
    John Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 4:336. 2003
    ..A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003...
  52. pmc Submission of microarray data to public repositories
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E317. 2004
  53. ncbi request reprint Genetic regulation of endotoxin-induced airway disease
    Donald N Cook
    Department of Medicine, Duke University Medical Center, P O Box 2629, and the Durham VAMC, Durham, NC 27710, USA
    Genomics 83:961-9. 2004
    ..Functional studies of these genes are expected to reveal important molecular mechanisms regulating the magnitude of biologic responses to LPS...
  54. ncbi request reprint Microarray data normalization and transformation
    John Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Genet 32:496-501. 2002
    ....
  55. pmc Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database
    Yunxia Zhu
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Genome Biol 4:R16. 2003
    ..We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database...
  56. pmc The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
    Qiaoping Yuan
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    Nucleic Acids Res 31:229-33. 2003
    ..All of the data is available through web-based interfaces, FTP downloads, and a Distributed Annotation System...
  57. ncbi request reprint Regulation of caspase expression and apoptosis by adenomatous polyposis coli
    Tingan Chen
    Department of Interdisciplinary Oncology and Surgery, University of South Florida, Tampa, FL 33612, USA
    Cancer Res 63:4368-74. 2003
    ..These data provide support for the hypothesis that one of the functions of APC is the regulation of caspase activity and other apoptotic proteins by controlling their expression levels in the cell...
  58. pmc Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)
    Yuandan Lee
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 12:493-502. 2002
    ..TOGA provides an important new resource for the analysis of gene function in eukaryotes. In addition, an analysis of the most widely represented sequences can begin to provide insight into eukaryotic biological processes...
  59. pmc Within the fold: assessing differential expression measures and reproducibility in microarray assays
    Ivana V Yang
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Biol 3:research0062. 2002
    ..Further, the analysis of a large number of expression profiles is facilitated by a common reference sample, the construction of which must be carefully addressed...
  60. pmc TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury
    Era Taoufik
    Laboratory of Molecular Genetics, Hellenic Pasteur Institute, 11521 Athens, Greece
    Proc Natl Acad Sci U S A 105:6185-90. 2008
    ..Our results identify cross-talk between tissue protective cytokines, specifically that TNFRI is necessary for constitutive and GD-induced expression of EPOR and VEGF and for EPO-mediated neuroprotection...
  61. doi request reprint Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
    ..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...
  62. ncbi request reprint Synchronous global assessment of gene and protein expression in colorectal cancer progression
    Ka Yin Kwong
    Mammalian Genomics, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genomics 86:142-58. 2005
    ..This is potentially important as clinical staging is widely used as a prognostic indicator and used in the decision to pursue adjuvant therapies...
  63. ncbi request reprint Independence and reproducibility across microarray platforms
    Jennie E Larkin
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Methods 2:337-44. 2005
    ....
  64. pmc Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication
    Nicholas H Bergman
    Bioinformatics Program, and Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Med Sci II, Ann Arbor, MI 48109 0620, USA
    Infect Immun 73:1069-80. 2005
    ..These data provide insights into B. anthracis pathogenesis as well as potential leads for the development of new diagnostic and therapeutic options...
  65. ncbi request reprint Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome
    H Stanley Kim
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant J 41:212-20. 2005
    ....
  66. pmc Standards for microarray data: an open letter
    Catherine Ball
    Environ Health Perspect 112:A666-7. 2004
  67. pmc Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs
    Norihiro Maeda
    Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
    PLoS Genet 2:e62. 2006
    ....
  68. ncbi request reprint Data standards: a call to action
    Cath Brooksbank
    EMBL European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    OMICS 10:94-9. 2006
    ....
  69. pmc Uneven chromosome contraction and expansion in the maize genome
    Remy Bruggmann
    Munich Information Center for Protein Sequences MIPS, Institute for Bioinformatics, GSF Research Center for Environment and Health, D 85764 Neuherberg, Germany
    Genome Res 16:1241-51. 2006
    ..In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species...
  70. ncbi request reprint 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...
  71. ncbi request reprint Cardiac transcriptional response to acute and chronic angiotensin II treatments
    Jennie E Larkin
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Physiol Genomics 18:152-66. 2004
    ....
  72. pmc The limits of log-ratios
    Vasily Sharov
    The Institute for Genomic Research, Rockville, MD, USA
    BMC Biotechnol 4:3. 2004
    ..DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured expression levels for the two samples...
  73. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  74. pmc Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray
    Heenam Kim
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Res 13:327-40. 2003
    ..Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region...
  75. ncbi request reprint Genomics and proteomics of lung disease: conference summary
    J Usha Raj
    Division of Neonatology, Harbor UCLA Medical Center, Geffen School of Medicine at University of California, and Los Angeles Biomedical Research Institute, Los Angeles, California, USA
    Am J Physiol Lung Cell Mol Physiol 293:L45-51. 2007
  76. ncbi request reprint Multiple-laboratory comparison of microarray platforms
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Methods 2:345-50. 2005
    ..We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well...

Research Grants8

  1. EXPRESSION PROFILING OF RODENT MODELS OF HUMAN DISEASE
    John Quackenbush; Fiscal Year: 2004
    ..abstract_text> ..
  2. TM4: Software for High-Dimensional Data Analysis
    John Quackenbush; Fiscal Year: 2007
    ....
  3. TM4: Software for High-Dimensional Data Analysis
    John Quackenbush; Fiscal Year: 2009
    ....
  4. Integrated approaches to deriving predictive networks from public data sources
    John Quackenbush; Fiscal Year: 2010
    ..The end goals will not only be to create the framework for creating such predictive models, but to develop software and tools to allow others in the community to create models for their own systems of interest. ..