Christian J Stoeckert

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. ncbi request reprint Microarray databases: standards and ontologies
    Christian J Stoeckert
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
    Nat Genet 32:469-73. 2002
  2. pmc EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
    Joan M Mazzarelli
    Department of Genetics, School of Medicine, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 35:D751-5. 2007
  3. pmc ToxoDB: an integrated Toxoplasma gondii database resource
    Bindu Gajria
    Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 36:D553-6. 2008
  4. pmc Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta
    Anthony G Passerini
    Institute for Medicine and Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 101:2482-7. 2004
  5. pmc PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    Amit Bahl
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 31:212-5. 2003
  6. pmc Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Physiol Heart Circ Physiol 298:H163-70. 2010
  7. pmc Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups
    Steve Fischer
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Curr Protoc Bioinformatics . 2011
  8. pmc Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha
    Rana K Gupta
    Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 21:756-69. 2007
  9. pmc ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
    Li Li
    Department of Biology, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 32:D326-8. 2004
  10. pmc Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis
    Mete Civelek
    Department of Bioengineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Circ Cardiovasc Genet 4:243-52. 2011

Research Grants

  1. Annotation-based meta-analysis of microarray experiments
    Christian Stoeckert; Fiscal Year: 2008

Collaborators

Detail Information

Publications65

  1. ncbi request reprint Microarray databases: standards and ontologies
    Christian J Stoeckert
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
    Nat Genet 32:469-73. 2002
    ..The adoption of common standards and ontologies for the management and sharing of microarray data is essential and will provide immediate benefit to the research community...
  2. pmc EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
    Joan M Mazzarelli
    Department of Genetics, School of Medicine, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 35:D751-5. 2007
    ..EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues...
  3. pmc ToxoDB: an integrated Toxoplasma gondii database resource
    Bindu Gajria
    Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 36:D553-6. 2008
    ..ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website...
  4. pmc Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta
    Anthony G Passerini
    Institute for Medicine and Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 101:2482-7. 2004
    ..The introduction of additional risk factors may shift this balance to favor lesion development...
  5. pmc PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    Amit Bahl
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 31:212-5. 2003
    ..The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org)...
  6. pmc Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Physiol Heart Circ Physiol 298:H163-70. 2010
    ..Both region-specific and ubiquitous (ABCA1) phenotype changes were identified as early prelesional responses of the endothelium to hypercholesterolemia...
  7. pmc Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups
    Steve Fischer
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Curr Protoc Bioinformatics . 2011
    ..This method maps the uploaded proteins to existing groups in OrthoMCL-DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install, and run the stand-alone OrthoMCL software...
  8. pmc Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha
    Rana K Gupta
    Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 21:756-69. 2007
    ..Together, these results indicate that HNF-4alpha is essential for the physiological expansion of adult beta-cell mass in response to increased metabolic demand...
  9. pmc ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
    Li Li
    Department of Biology, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 32:D326-8. 2004
    ....
  10. pmc Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis
    Mete Civelek
    Department of Bioengineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Circ Cardiovasc Genet 4:243-52. 2011
    ..Endothelial function is central to the localization of atherosclerosis. The in vivo endothelial phenotypic footprints of arterial bed identity and site-specific atherosusceptibility are addressed...
  11. pmc Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    Gregory R Grant
    Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 27:2518-28. 2011
    ..The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously...
  12. pmc Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays
    Mitchell Guttman
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS Genet 3:e143. 2007
    ..The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA...
  13. pmc Discovery approaches to UPR in athero-susceptible endothelium in vivo
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    Methods Enzymol 489:109-26. 2011
    ..Here, we outline global genomic profiling, pathway analyses, and gene connectivity approaches to the identification of UPR and associated pathways as discrete markers of athero-susceptibility in arterial endothelium...
  14. ncbi request reprint The Plasmodium genome database
    Jessica C Kissinger
    Department of Biology and Genetics, Center for Bioinformatics and Genomics Institute, University of Pennsylvania, Philadelphia, 19104 6018, USA
    Nature 419:490-2. 2002
  15. ncbi request reprint Novel genes identified by manual annotation and microarray expression analysis in the pancreas
    Joan M Mazzarelli
    Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genomics 88:752-61. 2006
    ..Interestingly, when we investigated the novel transcripts for their overlap with noncoding microRNAs, we found that 1 of the novel transcripts overlapped a known microRNA gene...
  16. ncbi request reprint The MGED Ontology: a resource for semantics-based description of microarray experiments
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, USA
    Bioinformatics 22:866-73. 2006
    ....
  17. ncbi request reprint PlasmoDB v5: new looks, new genomes
    Christian J Stoeckert
    Department of Genetics, 1415 Blockley Hall, Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA 19104, USA
    Trends Parasitol 22:543-6. 2006
    ..This new release includes additional Plasmodium genomes and a newly designed website. The new site reflects the status of PlasmoDB as a member of a linked family of Apicomplexan databases...
  18. ncbi request reprint Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet
    Anthony G Passerini
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
    Biochem Biophys Res Commun 332:142-8. 2005
    ..The results implicate regional hemodynamics as a predominant epigenetic determinant of endothelial phenotypic heterogeneity underlying atherosusceptibility in vivo...
  19. pmc Conservation and divergence of known apicomplexan transcriptional regulons
    Kobby Essien
    Department of Bioengineering, University of Pennsylvania, 240 SkirkanichHall, Philadelphia, Pennsylvania 19104, USA
    BMC Genomics 11:147. 2010
    ..Even less is known about how regulon systems, consisting of transcription factors and target genes together with their associated biological process, evolve in these diverse parasites...
  20. pmc Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity
    Kobby Essien
    Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 3:e3122. 2008
    ..The genetic bases of phenotypic differences between parasites can be understood, in part, by investigating constraints on gene expression and genic sequences, both coding and regulatory...
  21. pmc The Strategies WDK: a graphical search interface and web development kit for functional genomics databases
    Steve Fischer
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Database (Oxford) 2011:bar027. 2011
    ..The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org...
  22. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
    ..cbil.upenn.edu/gene-family). Analysis of clusters incorporating P. falciparum genes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome...
  23. pmc Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, 1010 Vagelos Laboratories, 3340 Smith Walk, Philadelphia, PA 19104, USA
    Circ Res 105:453-61. 2009
    ....
  24. pmc Propagation of adipogenic signals through an epigenomic transition state
    David J Steger
    Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 24:1035-44. 2010
    ..Thus, the conversion of preadipocyte to adipocyte involves the formation of an epigenomic transition state that is not observed in cells at the beginning or end of the differentiation process...
  25. pmc Clustering of genes into regulons using integrated modeling-COGRIM
    Guang Chen
    Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Biol 8:R4. 2007
    ..In these applications, we demonstrate the ability to predict gene-transcription factor interactions with reduced numbers of false-positive findings and to make predictions beyond what is obtained when single types of data are considered...
  26. pmc Development of FuGO: an ontology for functional genomics investigations
    Patricia L Whetzel
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    OMICS 10:199-204. 2006
    ....
  27. ncbi request reprint Transcriptional program of the endocrine pancreas in mice and humans
    Klaus H Kaestner
    Department of Genetics, University of Pennsylvania, Philadelphia 19104, USA
    Diabetes 52:1604-10. 2003
    ..We show that this PancChip is highly enriched for genes expressed in the endocrine pancreas. The mouse and human clone sets and corresponding arrays will be important resources for diabetes research...
  28. pmc Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database
    Li Li
    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:443-54. 2003
    ..These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets...
  29. ncbi request reprint Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA
    Denise C Polacek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia 19104, USA
    Physiol Genomics 13:147-56. 2003
    ....
  30. pmc PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale
    Martina I Lefterova
    Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 22:2941-52. 2008
    ..Thus, PPARgamma and C/EBP factors cooperatively orchestrate adipocyte biology by adjacent binding on an unanticipated scale...
  31. pmc OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
    Feng Chen
    Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104 6018, USA
    Nucleic Acids Res 34:D363-8. 2006
    ..OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be updated and expanded as additional genome sequence data become available...
  32. ncbi request reprint Analysis and management of microarray gene expression data
    Gregory R Grant
    University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
    Curr Protoc Mol Biol . 2007
    ....
  33. ncbi request reprint Functional genomics databases on the web
    Christian J Stoeckert
    Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell Microbiol 7:1053-9. 2005
    ..Functional genomic databases are not yet very common; however, there are a few focused on microbial genomes and a couple integrative systems are available for setting up functional genomics databases...
  34. pmc EuPathDB: the eukaryotic pathogen database
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
    Nucleic Acids Res 41:D684-91. 2013
    ..The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010...
  35. pmc Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale
    Shailesh V Date
    Center for Bioinformatics, Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 16:542-9. 2006
    ..falciparum; for instance, a deficit of nearly 26% in terms of predicted interactions is observed against P. yoelii, because of missing ortholog partners in pairs of functionally linked proteins...
  36. ncbi request reprint Using ontologies to annotate microarray experiments
    Patricia L Whetzel
    Department of Genetics, Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Methods Enzymol 411:325-39. 2006
    ..The MO is freely available and has been incorporated into the annotation systems of several public microarray database systems...
  37. pmc AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments
    Jie Zheng
    Department of Genetics, Center for Bioinformatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
    Database (Oxford) 2011:bar045. 2011
    ..Nonetheless, tools such as AnnotCompute may provide an incentive for richer annotations of experiments. Database URL: http://www.cbil.upenn.edu/annotCompute/..
  38. ncbi request reprint Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents
    Olga T Hardy
    Department of Genetics, University of Pennsylvania School of Medicine, 415 Curie Boulevard, 560 Clinical Research Building, Philadelphia, Pennsylvania 19104, USA
    Mol Endocrinol 21:765-73. 2007
    ..Our results suggest a molecular explanation for the hyperinsulinemia hypoglycemic seen in patients with SCHAD deficiency...
  39. pmc PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
    Amit Bahl
    Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104 6018, USA
    Nucleic Acids Res 30:87-90. 2002
    ..g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community...
  40. pmc Ontodog: a web-based ontology community view generation tool
    Jie Zheng
    Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 30:1340-2. 2014
    ..We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology...
  41. pmc Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis
    Emily Greenfest-Allen
    Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA stoec
    BMC Syst Biol 7:38. 2013
    ..Inferred networks are strongly connected and do not fit a scale-free model, making it difficult to identify essential regulators using the hub-essentiality standard...
  42. ncbi request reprint A practical false discovery rate approach to identifying patterns of differential expression in microarray data
    Gregory R Grant
    Center for Bioinformatics, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
    Bioinformatics 21:2684-90. 2005
    ..For example, the log transform can both help and hurt at the same time, depending on the gene. We examine issues surrounding the SAM 'fudge factor' parameter, and how to handle these issues by optimizing with respect to power...
  43. ncbi request reprint Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury
    Paolo G Marciano
    Departments of Neuroscience, Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    J Neurosci 24:2866-76. 2004
    ....
  44. pmc Promoter features related to tissue specificity as measured by Shannon entropy
    Jonathan Schug
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Biol 6:R33. 2005
    ..A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms...
  45. ncbi request reprint Common objects: think global, act local
    Christian J Stoeckert
    Department of Genetics and Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    OMICS 7:103-4. 2003
  46. ncbi request reprint Comparison of different labeling methods for two-channel high-density microarray experiments
    Elisabetta Manduchi
    Center for Bioinformatics, Univ of Pennsylvania, Philadelphia, Pennsylvania 19104 6021, USA
    Physiol Genomics 10:169-79. 2002
    ..These findings are helping to guide our decisions on what labeling method to use for subsequent studies, based on the purpose of a specific study and its limitations in terms of available material...
  47. ncbi request reprint Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research
    L Marie Scearce
    Department of Genetics, University of Pennsylvania, 415 Curie Boulevard, Philadephia, PA 19104, USA
    Diabetes 51:1997-2004. 2002
    ..5 through adulthood in mice. The clone set and corresponding array are useful resources for diabetes research...
  48. pmc Predicting gene ontology functions from ProDom and CDD protein domains
    Jonathan Schug
    Center for Bioinformatics, Computational Biology and Informatics Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
    Genome Res 12:648-55. 2002
    ..The domain-function associations and function assignments are available from our website http://www.cbil.upenn.edu/GO...
  49. 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...
  50. ncbi request reprint Standards for microarray data
    Catherine A Ball
    Science 298:539. 2002
  51. pmc A molecular profile of a hematopoietic stem cell niche
    Jason A Hackney
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544 Laboratoire d Hematopoi├Ęse, Faculte de Medecine, Universite de Tours, 37041 Tours Cedex 1, France
    Proc Natl Acad Sci U S A 99:13061-6. 2002
    ..The data have been assembled into a biological process oriented database, and represent a molecular profile of a candidate stem cell niche...
  52. pmc Design and implementation of microarray gene expression markup language (MAGE-ML)
    Paul T Spellman
    Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720 3206, USA
    Genome Biol 3:RESEARCH0046. 2002
    ..Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies...
  53. pmc ApiDB: integrated resources for the apicomplexan bioinformatics resource center
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, Athens, GA, USA
    Nucleic Acids Res 35:D427-30. 2007
    ..Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases...
  54. ncbi request reprint The underlying principles of scientific publication
    Catherine A Ball
    Bioinformatics 18:1409. 2002
  55. ncbi request reprint An object model and database for functional genomics
    Andrew Jones
    Department of Computing Science, University of Glasgow, Glasgow, UK
    Bioinformatics 20:1583-90. 2004
    ..We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics...
  56. 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...
  57. pmc STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
    Sharon J Diskin
    Division of Oncology, Children s Hospital of Philadelphia, Pennsylvania 19104, USA
    Genome Res 16:1149-58. 2006
    ..We conclude that STAC is a powerful tool for identifying nonrandom genomic amplifications and deletions across multiple experiments. A Java version of STAC is freely available for download at http://cbil.upenn.edu/STAC...
  58. ncbi request reprint The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  59. pmc Defining the mammalian CArGome
    Qiang Sun
    Cardiovascular Research Institute, University of Rochester School of Medicine, Rochester, NY 14642, USA
    Genome Res 16:197-207. 2006
    ..We suggest one function of SRF is that of an ancient master regulator of the actin cytoskeleton...
  60. ncbi request reprint Plasmodium research in the postgenomic era
    Manoj Duraisingh
    Department of Immunology and Infectious Diseases, Harvard School of Public Health Building I, Room 715, 665 Huntington Avenue, Boston, MA 02115, USA
    Trends Parasitol 22:1-4. 2006
    ....
  61. pmc Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status
    Bin Yan
    Head and Neck Surgery Branch, NIDCD, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 9:R53. 2008
    ..However, how NF-kappaB acts as a key regulatory node to modulate global gene expression, and contributes to the malignant heterogeneity of head and neck cancer, is not well understood...
  62. pmc Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    Jane M Carlton
    The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
    Nature 455:757-63. 2008
    ..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
  63. 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...
  64. ncbi request reprint Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, Seattle, Washington 98103, USA
    OMICS 10:205-8. 2006
    ..The full specification will soon be published as a version 1.0 proposal to the community, upon which a more full discussion must take place so that the final specification may be achieved with the involvement of the whole community...
  65. 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

Research Grants1

  1. Annotation-based meta-analysis of microarray experiments
    Christian Stoeckert; Fiscal Year: 2008
    ..This can further facilitate integration of data of different types to address a scientific question of interest. These benefits may encourage better annotation of experiments and use of standards. ..