Paul T Spellman

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Evidence for large domains of similarly expressed genes in the Drosophila genome
    Paul T Spellman
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3400, USA
    J Biol 1:5. 2002
  2. pmc A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047
    Wen Lin Kuo
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    BMC Med 7:77. 2009
  3. pmc Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition
    Olga K Mirzoeva
    Department of Medicine, Division of Gastroenterology, University of California, San Francisco, California 94115, USA
    Cancer Res 69:565-72. 2009
  4. pmc A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    Richard M Neve
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, USA
    Cancer Cell 10:515-27. 2006
  5. pmc Integrated analysis of breast cancer cell lines reveals unique signaling pathways
    Laura M Heiser
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 10:R31. 2009
  6. ncbi request reprint Final words: cell age and cell cycle are unlinked
    Paul T Spellman
    Lawrence Berkeley National Laboratory, Life Science Division, 1 Cyclotron Road, Building 84, Room 336, Berkeley, California 94720, USA
    Trends Biotechnol 22:277-8. 2004
  7. ncbi request reprint Reply: whole-culture synchronization - effective tools for cell cycle studies
    Paul T Spellman
    Lawrence Berkeley National Laboratory, Life Science Division, 1 Cyclotron Road, Building 84, Room 336, Berkeley, California 94720, USA
    Trends Biotechnol 22:270-3. 2004
  8. pmc The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression
    Paraic A Kenny
    Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    Mol Oncol 1:84-96. 2007
  9. pmc Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
    Steffen Durinck
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Nat Protoc 4:1184-91. 2009
  10. 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

Collaborators

Detail Information

Publications20

  1. pmc Evidence for large domains of similarly expressed genes in the Drosophila genome
    Paul T Spellman
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3400, USA
    J Biol 1:5. 2002
    ..Regulation of sets of adjacent genes by mechanisms operating at the level of chromosomal domains has been demonstrated in a number of cases, but the fraction of genes in the genome subject to regulation at this level is unknown...
  2. pmc A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047
    Wen Lin Kuo
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    BMC Med 7:77. 2009
    ....
  3. pmc Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition
    Olga K Mirzoeva
    Department of Medicine, Division of Gastroenterology, University of California, San Francisco, California 94115, USA
    Cancer Res 69:565-72. 2009
    ....
  4. pmc A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    Richard M Neve
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, USA
    Cancer Cell 10:515-27. 2006
    ..We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations...
  5. pmc Integrated analysis of breast cancer cell lines reveals unique signaling pathways
    Laura M Heiser
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 10:R31. 2009
    ..Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes...
  6. ncbi request reprint Final words: cell age and cell cycle are unlinked
    Paul T Spellman
    Lawrence Berkeley National Laboratory, Life Science Division, 1 Cyclotron Road, Building 84, Room 336, Berkeley, California 94720, USA
    Trends Biotechnol 22:277-8. 2004
    ..Unfortunately the corollaries of this law are rather suspect, drawing inferences from cell age to cell size to the cell cycle...
  7. ncbi request reprint Reply: whole-culture synchronization - effective tools for cell cycle studies
    Paul T Spellman
    Lawrence Berkeley National Laboratory, Life Science Division, 1 Cyclotron Road, Building 84, Room 336, Berkeley, California 94720, USA
    Trends Biotechnol 22:270-3. 2004
    ....
  8. pmc The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression
    Paraic A Kenny
    Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
    Mol Oncol 1:84-96. 2007
    ..We further demonstrate that consistent differences in genes encoding signal transduction proteins emerge when even tumor cells are cultured in 3D microenvironments...
  9. pmc Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
    Steffen Durinck
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Nat Protoc 4:1184-91. 2009
    ..We also discuss typical problems that are encountered in making gene-to-transcript-to-protein mappings. The approach provides a flexible, programmable and reproducible basis for state-of-the-art bioinformatic data integration...
  10. 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...
  11. pmc Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts
    J Graeme Hodgson
    Dept of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
    Neuro Oncol 11:477-87. 2009
    ....
  12. pmc GenomeGraphs: integrated genomic data visualization with R
    Steffen Durinck
    Life Sciences Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
    BMC Bioinformatics 10:2. 2009
    ..In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses...
  13. doi request reprint Amplification of 11q13 in ovarian carcinoma
    Lindsay A Brown
    Department of Pathology, Vancouver Coastal Health Research Institute, Genetic Pathology Evaluation Centre, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
    Genes Chromosomes Cancer 47:481-9. 2008
    ..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
  14. pmc The Toll and Imd pathways are the major regulators of the immune response in Drosophila
    Ennio De Gregorio
    Centre de Genetique Moleculaire, CNRS, F 91198 Gif sur Yvette, France
    EMBO J 21:2568-79. 2002
    ..Interestingly, we observed that some Drosophila immune-responsive genes are located in gene clusters, which often are transcriptionally co-regulated...
  15. ncbi request reprint Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
    Koei Chin
    Comprehensive Cancer Center, 2340 Sutter Street, University of California, San Francisco, San Francisco, California 94143
    Cancer Cell 10:529-41. 2006
    ..Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism...
  16. pmc Analysis of molecular inversion probe performance for allele copy number determination
    Yuker Wang
    Affymetrix Inc, Shoreline Blvd, South San Francisco, CA 94080, USA
    Genome Biol 8:R246. 2007
    ....
  17. 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...
  18. ncbi request reprint The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolism
    Lori A Pile
    NICHD, National Institutes of Health, Cell Biology and Metabolism Branch, Bethesda, Maryland 20892, USA
    J Biol Chem 278:37840-8. 2003
    ..Increased expression of mitochondrial proteins in SIN3-deficient cells is manifested in an increase in mitochondrial mass. Thus, SIN3 may play an important role in regulating mitochondrial respiratory activity...
  19. pmc Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities
    Joshua Z Press
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Cancer 8:17. 2008
    ..The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas...