J Quackenbush

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. 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
  2. pmc Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis
    Elodie Ghedin
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Retrovirology 1:10. 2004
  3. pmc RESOURCERER: a database for annotating and linking microarray resources within and across species
    J Tsai
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Biol 2:SOFTWARE0002. 2001
  4. 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
  5. pmc The limits of log-ratios
    Vasily Sharov
    The Institute for Genomic Research, Rockville, MD, USA
    BMC Biotechnol 4:3. 2004
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
    J Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 29:159-64. 2001

Collaborators

Detail Information

Publications81

  1. 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."..
  2. pmc Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis
    Elodie Ghedin
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Retrovirology 1:10. 2004
    ..Therefore, a multi-virus array containing eight human viruses implicated in AIDS pathogenesis was developed and its efficacy in various applications was characterized...
  3. pmc RESOURCERER: a database for annotating and linking microarray resources within and across species
    J Tsai
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Biol 2:SOFTWARE0002. 2001
    ....
  4. 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...
  5. 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...
  6. 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...
  7. 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
    ....
  8. 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...
  9. 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
  10. pmc The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
    J Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 29:159-64. 2001
    ....
  11. ncbi request reprint Computational analysis of microarray data
    J Quackenbush
    The Institute for Genomic Research, 9, 712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Rev Genet 2:418-27. 2001
    ..A basic understanding of these computational tools is therefore required for optimal experimental design and meaningful data analysis...
  12. pmc The TIGR gene indices: reconstruction and representation of expressed gene sequences
    J Quackenbush
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Nucleic Acids Res 28:141-5. 2000
    ..The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes...
  13. pmc The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
    Y Lee
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 33:D71-4. 2005
    ....
  14. ncbi request reprint Enrichment of gene-coding sequences in maize by genome filtration
    C A Whitelaw
    The Institute for Genomic Research TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 302:2118-20. 2003
    ..Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library...
  15. 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...
  16. pmc Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species
    Q Yuan
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 125:1166-74. 2001
    ..In addition, we have used data from The Institute of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Projects to identify putative orthologues and paralogues among these nine genomes...
  17. ncbi request reprint 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
  18. 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...
  19. 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...
  20. 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...
  21. ncbi request reprint AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum
    Vishvanath Nene
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Int J Parasitol 32:1447-56. 2002
    ..The database may be accessed via the World Wide Web at http://www.tigr.org/tdb/tgi.shtml...
  22. 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
    ....
  23. ncbi request reprint Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva
    Vishvanath Nene
    Parasite Genomics Department, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Insect Biochem Mol Biol 34:1117-28. 2004
    ..The EST data will be a useful resource for construction of microarrays to probe vector biology, vector-host and vector-pathogen interactions and to underpin gene identification via proteomics approaches...
  24. ncbi request reprint Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002
    ..This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease...
  25. 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...
  26. 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
    ....
  27. ncbi request reprint Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses
    H Kim
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Biotechniques 33:924-30. 2002
    ..Our analysis demonstrates that while genomic DNA can serve as a reasonable reference source for microarray assays, a much greater correlation with direct measurements can be achieved using an RNA-based reference sample...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. ncbi request reprint Plant database resources at The Institute for Genomic Research
    Agnes P Chan
    The Institute for Genomic Research, Rockville, MD, USA
    Methods Mol Biol 406:113-36. 2007
    ..We present here an overview of the TIGR database resources for plant genomics and describe methods to access the data...
  34. ncbi request reprint The African trypanosome genome
    N M El-Sayed
    The Institute for Genomic Research TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Int J Parasitol 30:329-45. 2000
    ..brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite...
  35. ncbi request reprint Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray
    P Hegde
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Cancer Res 61:7792-7. 2001
    ..Northern analysis of a limited number of these genes validates the observed pattern of expression and suggests that further investigation and functional characterization of the identified genes is warranted...
  36. ncbi request reprint The complete genome sequence of the gastric pathogen Helicobacter pylori
    J F Tomb
    Institute for Genomic Research, Rockville, Maryland 20850, USA
    Nature 388:539-47. 1997
    ..pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH...
  37. ncbi request reprint Identification of Src transformation fingerprint in human colon cancer
    Renae L Malek
    Department of Functional Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, Maryland, MD 20850, USA
    Oncogene 21:7256-65. 2002
    ..Supportive Supplemental Data can be viewed at http://pga.tigr.org/PGApubs.shtml...
  38. pmc Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis
    Fenglong Liu
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Plant Physiol 137:1115-29. 2005
    ..This study represents one of the most comprehensive analyses conducted to date investigating hypoxia-responsive transcriptional networks in plants...
  39. 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
    ....
  40. pmc The TIGR Maize Database
    Agnes P Chan
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 34:D771-6. 2006
    ..All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads...
  41. pmc Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays
    Hong Ying Wang
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 4:R5. 2003
    ..The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear...
  42. pmc Comparative analyses of potato expressed sequence tag libraries
    Catherine M Ronning
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 131:419-29. 2003
    ....
  43. ncbi request reprint Standards for microarray data
    Catherine A Ball
    Science 298:539. 2002
  44. 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...
  45. ncbi request reprint Response to Shields: 'MIAME, we have a problem'
    John Quackenbush
    Trends Genet 22:471-2. 2006
  46. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  47. pmc It is time to end the patenting of software
    John Quackenbush
    Bioinformatics 22:1416-7. 2006
  48. 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
  49. 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
    ....
  50. 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
    ....
  51. 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...
  52. 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...
  53. 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
    ....
  54. 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...
  55. 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...
  56. 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...
  57. 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
  58. 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...
  59. 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...
  60. 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...
  61. ncbi request reprint Discrimination of non-protein-coding transcripts from protein-coding mRNA
    Martin C Frith
    Genome Exploration Research Group Genome Network Project Core Group, RIKEN Genomic Sciences Center GSC, RIKEN Yokohama Institute, Kanagawa, Japan
    RNA Biol 3:40-8. 2006
    ..Conversely and surprisingly, our analyses also provide evidence that as much as approximately 10% of entries in the manually curated protein database Swiss-Prot are erroneous translations of actually non-coding transcripts...
  62. ncbi request reprint The underlying principles of scientific publication
    Catherine A Ball
    Bioinformatics 18:1409. 2002
  63. ncbi request reprint The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences
    Joseph M Merrick
    Department of Microbiology, State University of New York, Buffalo, New York 14214, USA
    J Parasitol 89:261-9. 2003
    ..The utility of EST analysis is demonstrated by identifying new protease genes, which may be involved in hemoglobin degradation...
  64. ncbi request reprint An open letter on microarray data from the MGED Society
    Catherine Ball
    Stanford University, USA
    Microbiology 150:3522-4. 2004
  65. 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
    ....
  66. 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
  67. 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...
  68. 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...
  69. 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...
  70. ncbi request reprint The quest for the mechanisms of life
    Maria I Klapa
    Department of Chemical Engineering, University of Maryland, College Park, Maryland 20742, USA
    Biotechnol Bioeng 84:739-42. 2003
    ....
  71. ncbi request reprint Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells
    James P Abulencia
    Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, USA
    J Biol Chem 278:28388-94. 2003
    ..Hence, a biochemical pathway exists wherein fluid shear activates COX-2, via a JNK2/c-Jun-dependent pathway, which in turn elicits downstream EP2 and EP3a1 mRNA synthesis...
  72. 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...
  73. ncbi request reprint Wrestling with SUMO and bio-ontologies
    Christian Stoeckert
    Nat Biotechnol 24:21-2; author reply 23. 2006
  74. 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
  75. ncbi request reprint Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index
    Tad S Sonstegard
    USDA, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland 20705, USA
    Mamm Genome 13:373-9. 2002
    ..These results demonstrate that bovine sequence expression data serve as a resource for characterizing mammalian transcriptomes and identifying those genes potentially unique to ruminants...
  76. ncbi request reprint Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages
    Liwang Cui
    Department of Entomology, The Pennsylvania State University, 501 ASI, University Park, PA 16802, USA
    Mol Biochem Parasitol 144:1-9. 2005
    ..This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence...
  77. 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)...
  78. 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...
  79. 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)...
  80. 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
    ....
  81. 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...