Cancer & Cancer Pathways

2010

• The Genetic Landscape of the Childhood Cancer Medulloblastoma
  ( 10.1126/science.1198056 )
  Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and ...
• Altered antisense-to-sense transcript ratios in breast cancer
  ( PNAS doi: 10.1073/pnas.1010559107 )
  Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in ...
• Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome
  ( BMC Cancer 2010, 10:506 )
  Background Osteosarcoma (OSA) spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in ...
• An "Omics" based survey of human colon cancer
  ( Mutation Research 693 (2010) 3–18 )
  Despite an increased understanding of the molecular pathogenesis of colorectal cancer (CRC) during the past two decades, reliable and robust biomarkers to enable screening, surveillance, and primary prevention of this ...
• ‘‘Topological Significance’’ Analysis of Gene Expression and Proteomic Profiles from Prostate Cancer Cells Reveals Key Mechanisms of Androgen Response
  ( PLoS ONE 5(6): e10936. doi:10.1371/journal.pone.0010936 )
• Integrative Genome Comparison of Primary and Metastatic Melanomas
  ( PLoS One. 2010; 5(5): e10770 )
  Abstract A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of ...
• Evidence of perturbations of cell cycle and DNA repair pathways as a consequence of human and murine NF1-haploinsufficiency
  ( BMC Genomics. 2010 Mar 22;11:194. )
  BACKGROUND: Neurofibromatosis type 1 (NF1) is a common monogenic tumor-predisposition disorder that arises secondary to mutations in the tumor suppressor gene NF1. Haploinsufficiency of NF1 fosters a permissive tumorigenic environment ...
• TCEAL7 Inhibition of c-Myc Activity in Alternative Lengthening of Telomeres Regulates hTERT Expression
  ( Neoplasia (2010) 12, 405–414 )
  Abstract Replicative senescence forms a major barrier to tumor progression. Cancer cells bypass this by using one of the two known telomere maintenance mechanisms: telomerase or the recombination-based alternative lengthening ...
• Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells
  ( Proteomics. 2010 Mar;10(5):914-29 )
  Certain antitumor agents have recently been extracted from the roots of Salvia miltiorrhiza Bunge. The diterpene derivative, tanshinone IIA, possesses cytotoxic activity against several human carcinoma cell lines. It also ...
• Bimodal gene expression patterns in breast cancer
  ( BMC Genomics. 2010; 11(Suppl 1): S8. )
  We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were ...
• Eight-plex iTRAQ analysis of variant metastatic human prostate cancer cells identifies candidate biomarkers of progression: An exploratory study.
  ( The Prostate )
  BACKGROUND: Due to the heterogeneity in the biological behaviour of prostate cancer, biomarkers that can reliably distinguish indolent from aggressive disease are urgently needed to inform treatment choices. METHODS: We ...
• Effect of training sample size and classification difficulty on the accuracy of genomic predictors
  ( Breast Cancer Research 2010, 12:R5 doi:10.1186/bcr2468 )
  Introduction: As part of the MicroArray Quality Control (MAQC)-II project, this analysis examines how the choice of univariate feature selection methods and classification algorithms may influence the performance of genomic ...
• Telomerase upregulation is a postcrisis event during senescence bypass and immortalization of two Nijmegen breakage syndrome T cell cultures
  ( Aging Cell (2010) 9, pp220–235 )
  Our knowledge on immortalization and telomere biology is mainly based on genetically manipulated cells analyzed before and many population doublings post growth crisis. The general view is that growth crisis ...

2009

• A Gene Expression Model of Intrinsic Tumor Radiosensitivity: Prediction of Response and Prognosis after Chemoradiation
  ( International Journal of Radiation Oncology, Biology, Physics (volume 75 issue 2 Pages 489-496) )
  Purpose: Development of a radiosensitivity predictive assay is a central goal of radiation oncology. We reasoned a gene expression model could be developed to predict intrinsic radiosensitivity and treatment response ...
• Systems Biology Modeling of the Radiation Sensitivity Network: A Biomarker Discovery Platform
  ( International Journal of Radiation Oncology, Biology, Physics (volume 75 issue 2 Pages 497-505) )
  Purpose: The discovery of effective biomarkers is a fundamental goal of molecular medicine. Developing a systems-biology understanding of radiosensitivity can enhance our ability of identifying radiation-specific biomarkers. Methods and Materials: ...
• MICRORNA PROFILING IN CANCER: A Bioinformatics Perspective
  ( Pan Stanford Publishing )
• A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT
  ( Oncogene (2009), 1–10 )
• Dynamic Telomerase Gene Suppression via Network Effects of GSK3 Inhibition
  ( PLoS ONE July 2009 | Volume 4 | Issue 7 | e6459 )
• Pathway analysis of senescence-associated miRNA targets reveals common processes to different senescence induction mechanisms
  ( Biochim. Biophys. Acta (2009), doi:10.1016/j.bbadis.2009.02.003 )
• MicroRNA deregulation and pathway alterations in nasopharyngeal carcinoma
  ( British Journal of Cancer (2009) 100, 1002 – 1011 )

2008

• Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer
  ( AACR Publications Cancer Res 2008; 68: (22) )
• Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers
  ( PNAS, vol. 105, no. 42, 16224–16229 )
• Establishment of Patient-Derived Non-Small Cell Lung Cancer Xenografts asModels for the Identification of Predictive Biomarkers
  ( Clin Cancer Res 2008;14(20) )
• Proteomic profiling of the effect of prostate-specific antigen on prostate cancer cells
  ( Prostate. 2008 Oct 1;68(14):1531-45 )
• Cell type-specific DNA methylation patterns n the human breast
  ( PNAS vol. 105 no. 37 )
• Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
  ( Sciencexpress 10.1126 science.1164368 )
• An Integrated Genomic Analysis of Human Glioblastoma Multiforme
  ( Sciencexpress 10.1126 science.1164382 )
• Identification and functional analysis of SKA2 interaction with the glucocorticoid receptor
  ( Journal of Endocrinology (2008) 198, 499–509 )
• BMI-1 Promotes Ewing Sarcoma Tumorigenicity Independent of CDKN2A Repression
  ( Cancer Res 2008; 68: (16) )
• Systems biology approach to identification of biomarkers for metastatic progression in cancer
  ( BMC Bioinformatics 2008, 9(Suppl 9):S8 )
• Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas
  ( Carcinogenesis vol.29 no.10 pp.1901–1910, 2008 )
• The Fibroblast Growth Factor–Inducible 14 Receptor Is Highly Expressed in HER2-Positive Breast Tumors and Regulates Breast Cancer Cell Invasive Capacity
  ( Mol Cancer Res 2008;6(5) )

2007

• The Genomic Landscapes of Human Breast and Colorectal Cancers
  ( Science 318, 1108 (2007) )
• Seeding drug discovery: integrating telomerase cancer biology and cellular senescence to uncover new therapeutic opportunities in targeting cancer stem cells
  ( Drug Discovery Today, Volume 12, Numbers 15/16, August 2007 )
• Transcriptional network governing the angiogenic switch in human pancreatic cancer
  ( PNAS, July 31, 2007, vol. 104, no. 31 )
• Functional Network Analysis of the Transcriptomes of Mesenchymal Stem Cells Derived from Amniotic Fluid, Amniotic Membrane, Cord Blood, and Bone Marrow
  ( Stem Cells 2007;25;2511-2523 )
• Quantitative proteomic analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer
  ( Mol Cell Proteomics 12 May 2007 )
• Molecular Definition of Breast Tumor Heterogeneity
  ( Cancer Cell 11, 259-273, March 2007 )

2006

• Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction
  ( Cancer Informatics. Libertas Academica )
• Pathway Analyses of Chondrosarcoma
  ( Pathway Analysis for Target and Compound Evaluation San Francisco, CA )

2005

• Differential Protein Expression Profiling by iTRAQ-2DLC-MS/MS of Lung Cancer Cells Undergoing Epithelial-Mesenchymal Transition Reveals a Migratory/Invasive Phenotype
  ( Journal of Proteome Research )