Research Topics
| J QuackenbushSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
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Detail Information
Publications
Multiple-input multiple-output causal strategies for gene selectionGianluca 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...- Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and oldDilek Colak
Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
Mol Cancer 9:146. 2010.... - Molecular processes during fat cell development revealed by gene expression profiling and functional annotationHubert 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... - Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samplesJessica C Mar
Department of Biostatistics, Harvard School of Public Health, Huntington Avenue, Boston, Massachusetts 02115, USA
Genome Biol 7:R119. 2006.... - Seeded Bayesian Networks: constructing genetic networks from microarray dataAmira 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... - A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolutionPATRICK 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... - Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratoriesMichael J Boedigheimer
CDER, US FDA, Silver Spring, MD 20993, USA
BMC Genomics 9:285. 2008.... - Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genesValerie 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.... - A robust method for the amplification of RNA in the sense orientationNicholas 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... - GCOD - GeneChip Oncology DatabaseFenglong 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... - Data-driven normalization strategies for high-throughput quantitative RT-PCRJessica 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... - 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... - A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TABTim 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... 
Microarray analysis and tumor classificationJohn Quackenbush
Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, USA
N Engl J Med 354:2463-72. 2006- From 'omes to biologyJ 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... - Extracting meaning from functional genomics experimentsJohn Quackenbush
Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02030, USA
Toxicol Appl Pharmacol 207:195-9. 2005.... - Extracting biology from high-dimensional biological dataJohn 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... - GeneSigDB--a curated database of gene expression signaturesAedin 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... 
Using the DFCI gene index databases for biological discoveryCorina 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...- Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entitiesElizabeth 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... - Functional classification analysis of somatically mutated genes in human breast and colorectal cancersThomas 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.... - HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transitionKarin 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... - Microarray blob-defect removal improves array analysisJun 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.... - An optimized predictive strategy for interactome mappingMartin 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... - Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sampleKatsuhiko Nosho
Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
PLoS ONE 3:e3698. 2008..CIMP-high is independently associated with clinical and key molecular features in colorectal cancer. Our data also suggest that KRAS mutation is related with a random CpG island methylation pattern which may lead to CIMP-low tumors... - E(mu)-TCL1 mice represent a model for immunotherapeutic reversal of chronic lymphocytic leukemia-induced T-cell dysfunctionGullu 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... - MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH termsAmira 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... - The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tagsHelena Brentani
, Departmento de Radiologia, , , 4deg, Brazil
Proc Natl Acad Sci U S A 100:13418-23. 2003.... - Wrestling with SUMO and bio-ontologiesChristian Stoeckert
Nat Biotechnol 24:21-2; author reply 23. 2006 - Physiogenomic resources for rat models of heart, lung and blood disordersRenae 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... - Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumorsJason 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... - Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsivenessJulia 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.".. - Using the TIGR gene index databases for biological discoveryYuandan 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... - CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number dataAdam 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)... - Submission of microarray data to public repositoriesCatherine A Ball
Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
PLoS Biol 2:E317. 2004 - Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineageChristine 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.... - John Quackenbush talks about the clinical promise of genetic microarrays. Interviewed by Brian VastagJohn Quackenbush
JAMA 289:159-60, 163. 2003 - Genomics. Microarrays--guilt by associationJohn 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... - The underlying principles of scientific publicationCatherine A Ball
Bioinformatics 18:1409. 2002 - Multi-platform, multi-site, microarray-based human tumor classificationGreg 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... - TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsGeo 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... - Open-source software accelerates bioinformaticsJohn 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... - Open source software for the analysis of microarray dataSandrine 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)... - Development and evaluation of an automated annotation pipeline and cDNA annotation systemTakeya 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.... - Data standards for 'omic' scienceJohn Quackenbush
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Biotechnol 22:613-4. 2004 - Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profilingDeepak 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..We identified osteopontin as a clinically useful marker of tumor progression by use of gene expression profiling on pooled samples... - Standards for microarray dataCatherine A Ball
Science 298:539. 2002 - Orthologous gene-expression profiling in multi-species models: search for candidate genesDmitry 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... - Universal RNA reference materials for gene expressionMaureen 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... - Genesis: cluster analysis of microarray dataAlexander 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... - Genetic regulation of endotoxin-induced airway diseaseDonald 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... - An open letter on microarray data from the MGED SocietyCatherine Ball
Stanford University, USA
Microbiology 150:3522-4. 2004 - Genomics and proteomics of lung disease: conference summaryJ 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 - 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... - Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) databaseYunxia 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... - The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologistsQiaoping 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... - Synchronous global assessment of gene and protein expression in colorectal cancer progressionKa 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... - Microarray data normalization and transformationJohn Quackenbush
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Genet 32:496-501. 2002.... - Within the fold: assessing differential expression measures and reproducibility in microarray assaysIvana V Yang
The Institute for Genomic Research, Rockville, MD 20850, USA
Genome Biol 3:research0062. 2002..We show that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines... - TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injuryEra 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... - 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... - Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxicationNicholas 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... - Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genomeH Stanley Kim
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Plant J 41:212-20. 2005.... - Multiple-laboratory comparison of microarray platformsRafael 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... - Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAsNorihiro Maeda
Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
PLoS Genet 2:e62. 2006.... - Cardiac transcriptional response to acute and chronic angiotensin II treatmentsJennie E Larkin
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Physiol Genomics 18:152-66. 2004.... - Standards for microarray data: an open letterCatherine Ball
Environ Health Perspect 112:A666-7. 2004 - Data standards: a call to actionCath Brooksbank
EMBL European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
OMICS 10:94-9. 2006.... - Uneven chromosome contraction and expansion in the maize genomeRemy 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... - The limits of log-ratiosVasily 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... - Integrative annotation of 21,037 human genes validated by full-length cDNA clonesTadashi 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... - Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarrayHeenam 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... - TM4 microarray software suiteAlexander 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... - Regulation of caspase expression and apoptosis by adenomatous polyposis coliTingan 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... - Independence and reproducibility across microarray platformsJennie E Larkin
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Methods 2:337-44. 2005....
Research Grants
- EXPRESSION PROFILING OF RODENT MODELS OF HUMAN DISEASEJohn Quackenbush; Fiscal Year: 2004..abstract_text> ..
- TM4: Software for High-Dimensional Data AnalysisJohn Quackenbush; Fiscal Year: 2007....
- TM4: Software for High-Dimensional Data AnalysisJohn Quackenbush; Fiscal Year: 2009....
- Integrated approaches to deriving predictive networks from public data sourcesJohn 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. ..