John Quackenbush

Personal Home Page

http://www.hsph.harvard.edu/faculty/john-quackenbush/

Articles in Scholarly Journals [Incomplete List]

  1. Functional classification analysis of somatically mutated genes in human breast and colorectal cancers
    Genomics, vol. 91, no. 6, pp. 508–511, 2008
  2. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Nature Biotechnology, vol. 26, no. 3, Article ID nbt1391, 7 pages, 2008
  3. High-throughput amplicon scanning of the TP53 gene in breast cancer using high-resolution fluorescent melting curve analyses and automatic mutation calling
    Human Mutation, vol. 29, no. 5, pp. 757–764, 2008
  4. ESR1 gene amplification in breast cancer: a common phenomenon?
    Nature Genetics, vol. 40, no. 7, Article ID ng0708-806, 1 pages, 2008
  5. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Nature Biotechnology, vol. 26, no. 8, Article ID nbt.1411, 7 pages, 2008
  6. Epithelial Progeny of Estrogen-Exposed Breast Progenitor Cells Display a Cancer-like Methylome
    Cancer Research, vol. 68, no. 6, pp. 1786–1796, 2008
  7. Seeded Bayesian Networks: Constructing genetic networks from microarray data
    BMC Systems Biology, vol. 2, no. 1, p. 57, 2008
  8. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
    BMC Genomics, vol. 9, no. 1, p. 285, 2008
  9. Correction: Statistical modeling for selecting housekeeper genes
    Genome Biology, vol. 9, no. 8, p. 405, 2008
  10. Extracting biology from high-dimensional biological data
    Journal of Experimental Biology, vol. 210, no. 9, pp. 1507–1517, 2007
  11. A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution
    BMC Genomics, vol. 8, no. 1, p. 109, 2007
  12. Agreement in Breast Cancer Classification between Microarray and Quantitative Reverse Transcription PCR from Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Tissues
    Clinical Chemistry, vol. 53, no. 7, pp. 1273–1279, 2007
  13. Genomics and proteomics of lung disease: conference summary
    AJP: Lung Cellular and Molecular Physiology, vol. 293, no. 1, pp. L45–L51, 2007
  14. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors
    Genome Biology, vol. 8, no. 5, p. R76, 2007
  15. Microarray blob-defect removal improves array analysis
    Bioinformatics, vol. 23, no. 8, pp. 966–971, 2007
  16. Genetic basis of murine antibacterial defense to streptococcal lung infection
    Immunogenetics, vol. 59, no. 9, pp. 713–724, 2007
  17. Top-down standards will not serve systems biology
    Nature, vol. 440, no. 7080, Article ID 440024a, 1 pages, 2006
  18. Physiogenomic resources for rat models of heart, lung and blood disorders
    Nature Genetics, vol. 38, no. 2, Article ID ng1693, 5 pages, 2006
  19. Weighing our measures of gene expression
    Molecular Systems Biology, vol. 2, Article ID msb4100096, 2006
  20. Response to Shields: ‘MIAME, we have a problem’
    Trends in Genetics, vol. 22, no. 9, pp. 471–472, 2006
  21. Microarray Analysis and Tumor Classification
    New England Journal of Medicine, vol. 354, no. 23, pp. 2463–2472, 2006
  22. Standardizing the standards
    Molecular Systems Biology, vol. 2, Article ID msb4100052, 2006
  23. Development of the Minimum Information Specification forIn SituHybridization and Immunohistochemistry Experiments (MISFISHIE)
    OMICS: A Journal of Integrative Biology, vol. 10, no. 2, pp. 205–208, 2006
  24. Wrestling with SUMO and bio-ontologies
    Nature Biotechnology, vol. 24, no. 1, Article ID nbt0106-21b, 1 pages, 2006
  25. Microarray Analysis and Tumor Classification
    New England Journal of Medicine, vol. 355, no. 9, pp. 960–960, 2006
  26. Data Standards: A Call to Action
    OMICS: A Journal of Integrative Biology, vol. 10, no. 2, pp. 94–99, 2006
  27. Sonic hedgehog promotes CD4+ T lymphocyte proliferation and modulates the expression of a subset of CD28-targeted genes
    International Immunology, vol. 18, no. 12, pp. 1627–1636, 2006
  28. It is time to end the patenting of software
    Bioinformatics, vol. 22, no. 12, pp. 1416–1417, 2006
  29. Marked Genomic Differences Characterize Primary and Secondary Glioblastoma Subtypes and Identify Two Distinct Molecular and Clinical Secondary Glioblastoma Entities
    Cancer Research, vol. 66, no. 23, pp. 11502–11513, 2006
  30. Breast Cancer Research, vol. 8, no. 2, p. R23, 2006
  31. BMC Genomics, vol. 7, no. 1, p. 96, 2006
  32. Multistrain Genetic Comparisons Reveal CCR5 as a Receptor Involved in Airway Hyperresponsiveness
    American Journal of Respiratory Cell and Molecular Biology, vol. 34, no. 6, pp. 711–718, 2006
  33. BMC Bioinformatics, vol. 7, no. 1, p. 489, 2006
  34. BMC Genomics, vol. 7, no. 1, p. 118, 2006
  35. Uneven chromosome contraction and expansion in the maize genome
    Genome Research, vol. 16, no. 10, pp. 1241–1251, 2006
  36. From 'omes to biology
    Animal Genetics, vol. 37, no. s1, pp. 48–56, 2006
  37. Genome Biology, vol. 7, no. 12, p. R119, 2006
  38. Molecular Staging for Survival Prediction of Colorectal Cancer Patients
    Journal of Clinical Oncology, vol. 23, no. 15, pp. 3526–3535, 2005
  39. Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication
    Infection and Immunity, vol. 73, no. 2, pp. 1069–1080, 2005
  40. BMC Genomics, vol. 6, no. 1, p. 27, 2005
  41. CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
    Bioinformatics, vol. 21, no. 15, pp. 3308–3311, 2005
  42. MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms
    Bioinformatics, vol. 21, no. 15, pp. 3324–3326, 2005
  43. Global Transcription Profiling Reveals Comprehensive Insights into Hypoxic Response in Arabidopsis
    PLANT PHYSIOLOGY, vol. 137, no. 3, pp. 1115–1129, 2005
  44. Corrigendum: Multiple-laboratory comparison of microarray platforms
    Nature Methods, vol. 2, no. 6, Article ID nmeth0605-477b, 1 pages, 2005
  45. Multiple-laboratory comparison of microarray platforms
    Nature Methods, vol. 2, no. 5, Article ID nmeth756, 5 pages, 2005
  46. Independence and reproducibility across microarray platforms
    Nature Methods, vol. 2, no. 5, Article ID nmeth757, 7 pages, 2005
  47. Gene discovery in through sequencing of ESTs from mixed blood stages
    Molecular and Biochemical Parasitology, vol. 144, no. 1, pp. 1–9, 2005
  48. Synchronous global assessment of gene and protein expression in colorectal cancer progression
    Genomics, vol. 86, no. 2, pp. 142–158, 2005
  49. Extracting meaning from functional genomics experiments
    Toxicology and Applied Pharmacology, vol. 207, no. 2, pp. 195–199, 2005
  50. Genetic regulation of endotoxin-induced airway disease
    Genomics, vol. 83, no. 6, pp. 961–969, 2004
  51. Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies
    Drug Discovery Today: TARGETS, vol. 3, no. 4, pp. 159–164, 2004
  52. Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva*1
    Insect Biochemistry and Molecular Biology, vol. 34, no. 10, pp. 1117–1128, 2004
  53. Data standards for 'omic' science
    Nature Biotechnology, vol. 22, no. 5, Article ID nbt0504-613, 1 pages, 2004
  54. The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D71–D74, 2004
  55. Submission of Microarray Data to Public Repositories
    PLoS Biology, vol. 2, no. 9, p. e317, 2004
  56. Cardiac transcriptional response to acute and chronic angiotensin II treatments
    Physiological Genomics, vol. 18, no. 2, pp. 152–166, 2004
  57. BMC Biotechnology, vol. 4, no. 1, p. 3, 2004
  58. Universal RNA Reference Materials for Gene Expression
    Clinical Chemistry, vol. 50, no. 8, pp. 1464–1471, 2004
  59. Genome Biology, vol. 4, no. 9, p. 336, 2003
  60. Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
    Genome Research, vol. 13, no. 3, pp. 327–340, 2003
  61. THE SCHISTOSOMA MANSONI GENE INDEX: GENE DISCOVERY AND BIOLOGY BY RECONSTRUCTION AND ANALYSIS OF EXPRESSED GENE SEQUENCES
    Journal of Parasitology, vol. 89, no. 2, p. 261, 2003
  62. Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
    Science, vol. 302, no. 5653, pp. 2118–2120, 2003
  63. Comparative Analyses of Potato Expressed Sequence Tag Libraries
    PLANT PHYSIOLOGY, vol. 131, no. 2, pp. 419–429, 2003
  64. GENOMICS: Microarrays--Guilt by Association
    Science, vol. 302, no. 5643, pp. 240–241, 2003
  65. Shear-induced Cyclooxygenase-2 via a JNK2/c-Jun-dependent Pathway Regulates Prostaglandin Receptor Expression in Chondrocytic Cells
    Journal of Biological Chemistry, vol. 278, no. 31, pp. 28388–28394, 2003
  66. Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
    Genome Research, vol. 13, no. 6, pp. 1542–1551, 2003
  67. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
    Nucleic Acids Research, vol. 31, no. 1, pp. 229–233, 2003
  68. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Bioinformatics, vol. 19, no. 5, pp. 651–652, 2003
  69. Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
    Genome Research, vol. 13, no. 6, pp. 1360–1365, 2003
  70. Osteopontin identified as colon cancer tumor progression marker
    Comptes Rendus Biologies, vol. 326, no. 10-11, pp. 1041–1043, 2003
  71. The quest for the mechanisms of life
    Biotechnology and Bioengineering, vol. 84, no. 7, pp. 739–742, 2003
  72. A guide to microarray experiments-an open letter to the scientific journals
    The Lancet, vol. 360, no. 9338, pp. 1019–1019, 2002
  73. Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly
    Mammalian Genome, vol. 13, no. 8, pp. 475–478, 2002
  74. Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index
    Mammalian Genome, vol. 13, no. 7, pp. 373–379, 2002
  75. AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum
    International Journal for Parasitology, vol. 32, no. 12, pp. 1447–1456, 2002
  76. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    Nature, vol. 420, no. 6915, Article ID nature01266, 10 pages, 2002
  77. Microarray data normalization and transformation
    Nature Genetics, vol. 32, no. Supp, Article ID ng1032, 5 pages, 2002
  78. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Nature, vol. 419, no. 6906, Article ID nature01099, 7 pages, 2002
  79. Identification of Src transformation fingerprint in human colon cancer
    Oncogene, vol. 21, no. 47, Article ID 1205900, 9 pages, 2002
  80. An open letter to the scientific journals
    Bioinformatics, vol. 18, no. 11, pp. 1409–1409, 2002
  81. Osteopontin Identified as Lead Marker of Colon Cancer Progression, Using Pooled Sample Expression Profiling
    CancerSpectrum Knowledge Environment, vol. 94, no. 7, pp. 513–521, 2002
  82. Genesis: cluster analysis of microarray data
    Bioinformatics, vol. 18, no. 1, pp. 207–208, 2002
  83. Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
    Genome Research, vol. 12, no. 3, pp. 493–502, 2002
  84. Microarray Analysis of the in Vivo Effects of Hypophysectomy and Growth Hormone Treatment on Gene Expression in the Rat
    Endocrinology, vol. 142, no. 7, pp. 3163–3176, 2001
  85. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
    Nucleic Acids Research, vol. 29, no. 1, pp. 159–164, 2001
  86. Exploring the transcriptome of the malaria sporozoite stage
    Proceedings of the National Academy of Sciences, vol. 98, no. 17, pp. 9895–9900, 2001
  87. Rice Bioinformatics. Analysis of Rice Sequence Data and Leveraging the Data to Other Plant Species
    PLANT PHYSIOLOGY, vol. 125, no. 3, pp. 1166–1174, 2001
  88. Sequence Evaluation of Four Pooled-Tissue Normalized Bovine cDNA Libraries and Construction of a Gene Index for Cattle
    Genome Research, vol. 11, no. 4, pp. 626–630, 2001
  89. Nature Genetics, vol. 29, no. 4, pp. 365–371, 2001
  90. Effects of Ischemia on Gene Expression,
    Journal of Surgical Research, vol. 99, no. 2, pp. 222–227, 2001
  91. COMPUTATIONAL GENETICS: COMPUTATIONAL ANALYSIS OF MICROARRAY DATA
    Nature Reviews Genetics, vol. 2, no. 6, Article ID 35076576, 9 pages, 2001
  92. Characterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA
    Microbial Pathogenesis, vol. 31, no. 6, pp. 295–307, 2001
  93. The African trypanosome genome
    International Journal for Parasitology, vol. 30, no. 4, pp. 329–345, 2000
  94. Nature Genetics, vol. 25, no. 2, pp. 239–240, 2000
  95. Nature Genetics, vol. 26, no. 3, pp. 255–256, 2000
  96. The TIGR Gene Indices: reconstruction and representation of expressed gene sequences
    Nucleic Acids Research, vol. 28, no. 1, pp. 141–145, 2000
  97. Anchoring of rice BAC clones to the rice genetic map in silico
    Nucleic Acids Research, vol. 28, no. 18, pp. 3636–3641, 2000
  98. An optimized protocol for analysis of EST sequences
    Nucleic Acids Research, vol. 28, no. 18, pp. 3657–3665, 2000
  99. A nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro.
    Journal of Clinical Investigation, vol. 99, no. 7, pp. 1786–1797, 1997
  100. Nature, vol. 388, no. 6642, pp. 539–547, 1997
  101. Nature, vol. 390, no. 6658, pp. 364–370, 1997
  102. Nature, vol. 390, no. 6660, pp. 580–586, 1997
  103. A Gene Map of the Human Genome
    Science, vol. 274, no. 5287, pp. 540–546, 1996
  104. An STS Content Map of Human Chromosome 11: Localization of 910 YAC Clones and 109 Islands
    Genomics, vol. 29, no. 2, pp. 512–525, 1995
  105. Physical Mapping of Complex Genomes by Sampled Sequencing: A Theoretical Analysis
    Genomics, vol. 27, no. 1, pp. 90–100, 1995
  106. Yeast Artificial Chromosome Cloning of 3.2 Megabases within Chromosomal Band 11q24 Closely Linking c-ets 1 and Fli-1 and Encompassing the Ewing Sarcoma Breakpoint
    Genomics, vol. 22, no. 1, pp. 137–147, 1994