Research Topics
| Paul T SpellmanSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
| Collaborators
|
Detail Information
Publications
Evidence for large domains of similarly expressed genes in the Drosophila genomePaul 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...- A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047Wen Lin Kuo
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
BMC Med 7:77. 2009.... - Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibitionOlga K Mirzoeva
Department of Medicine, Division of Gastroenterology, University of California, San Francisco, California 94115, USA
Cancer Res 69:565-72. 2009.... - A collection of breast cancer cell lines for the study of functionally distinct cancer subtypesRichard 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... - Integrated analysis of breast cancer cell lines reveals unique signaling pathwaysLaura 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... - Final words: cell age and cell cycle are unlinkedPaul 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... - Reply: whole-culture synchronization - effective tools for cell cycle studiesPaul 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.... - The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expressionParaic 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... - Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRtSteffen 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... - 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... - Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenograftsJ Graeme Hodgson
Dept of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
Neuro Oncol 11:477-87. 2009.... - GenomeGraphs: integrated genomic data visualization with RSteffen 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... - Amplification of 11q13 in ovarian carcinomaLindsay 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... - The Toll and Imd pathways are the major regulators of the immune response in DrosophilaEnnio De Gregorio
, 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... - Genomic and transcriptional aberrations linked to breast cancer pathophysiologiesKoei 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... - Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysRoger McLendon
Nature 455:1061-8. 2008..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer... - Analysis of molecular inversion probe performance for allele copy number determinationYuker Wang
Affymetrix Inc, Shoreline Blvd, South San Francisco, CA 94080, USA
Genome Biol 8:R246. 2007.... - 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... - The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolismLori 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... - Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalitiesJoshua 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...