Igor Jurisica

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. pmc NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs
    Elize A Shirdel
    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 6:e17429. 2011
  2. pmc Protein crystallization analysis on the World Community Grid
    Christian A Cumbaa
    Division of Signaling Biology, Ontario Cancer Institute, University Health Network, Toronto Medical Discovery Tower, 9 305, 101 College Street, Toronto, ON, M5G 1L7, Canada
    J Struct Funct Genomics 11:61-9. 2010
  3. pmc NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
    Kevin R Brown
    Division of Signaling Biology, Ontario Cancer Institute and University Health Network, Toronto, ON
    Bioinformatics 25:3327-9. 2009
  4. pmc Integrative computational biology for cancer research
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
    Hum Genet 130:465-81. 2011
  5. pmc NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
    Nucleic Acids Res 41:D720-7. 2013
  6. pmc Visual data mining of biological networks: one size does not fit all
    Chiara Pastrello
    CRO Aviano, National Cancer Institute, Aviano, Italy
    PLoS Comput Biol 9:e1002833. 2013
  7. pmc Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
    Fatemeh Vafaee
    Ontario Cancer Institute and Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    BMC Syst Biol 7:22. 2013
  8. ncbi request reprint Cancer informatics in the post genomic era. Toward information-based medicine
    Igor Jurisica
    Ontario Cancer Institute, PMH UHN, Toronto Medical Discovery Tower, Division of Signaling Biology, Life Sciences Discovery Centre, Toronto, Ontario
    Cancer Treat Res 137:1-178. 2007
  9. pmc A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence
    Patricia P Reis
    Div, of Applied Molecular Oncology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
    BMC Cancer 11:437. 2011
  10. ncbi request reprint Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)
    Katharine L Sodek
    Cell and Systems Biology, University of Toronto, Toronto, Canada
    Mol Biosyst 4:762-73. 2008

Detail Information

Publications85

  1. pmc NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs
    Elize A Shirdel
    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 6:e17429. 2011
    ..We make this data freely available with a flexible user interface as our microRNA Data Integration Portal--mirDIP (http://ophid.utoronto.ca/mirDIP)...
  2. pmc Protein crystallization analysis on the World Community Grid
    Christian A Cumbaa
    Division of Signaling Biology, Ontario Cancer Institute, University Health Network, Toronto Medical Discovery Tower, 9 305, 101 College Street, Toronto, ON, M5G 1L7, Canada
    J Struct Funct Genomics 11:61-9. 2010
    ..The system successfully recognizes 80% of crystal-bearing images, 89% of precipitate images, and 98% of clear drops...
  3. pmc NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
    Kevin R Brown
    Division of Signaling Biology, Ontario Cancer Institute and University Health Network, Toronto, ON
    Bioinformatics 25:3327-9. 2009
    ..Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture...
  4. pmc Integrative computational biology for cancer research
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
    Hum Genet 130:465-81. 2011
    ..Here we discuss these challenges, and show how integrative computational biology can help diminish them by creating new software tools, analytical methods, and data standards...
  5. pmc NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
    Nucleic Acids Res 41:D720-7. 2013
    ..We demonstrate with use case examples how NetwoRx can be applied to target specific phenotypes, repurpose drugs using mode of action analysis, investigate bipartite networks and predict new drugs that affect yeast aging...
  6. pmc Visual data mining of biological networks: one size does not fit all
    Chiara Pastrello
    CRO Aviano, National Cancer Institute, Aviano, Italy
    PLoS Comput Biol 9:e1002833. 2013
    ..In this tutorial, we illustrate a workflow useful to integrate, analyze, and visualize data from different sources, and highlight important features of tools to support such analyses...
  7. pmc Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
    Fatemeh Vafaee
    Ontario Cancer Institute and Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    BMC Syst Biol 7:22. 2013
    ..The annotation information is incorporated from several public pathway databases, Gene Ontology annotations as well as drug and disease associations from the scientific literature...
  8. ncbi request reprint Cancer informatics in the post genomic era. Toward information-based medicine
    Igor Jurisica
    Ontario Cancer Institute, PMH UHN, Toronto Medical Discovery Tower, Division of Signaling Biology, Life Sciences Discovery Centre, Toronto, Ontario
    Cancer Treat Res 137:1-178. 2007
  9. pmc A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence
    Patricia P Reis
    Div, of Applied Molecular Oncology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
    BMC Cancer 11:437. 2011
    ..Therefore, molecular analysis of histologically normal resection margins and the corresponding OSCC may aid in identifying a gene signature predictive of recurrence...
  10. ncbi request reprint Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)
    Katharine L Sodek
    Cell and Systems Biology, University of Toronto, Toronto, Canada
    Mol Biosyst 4:762-73. 2008
    ....
  11. pmc Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology
    Brian Cox
    The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, Ontario, Canada
    Mol Syst Biol 5:279. 2009
    ..The entire data are available as a web-accessible database to guide the informed development of mouse models to study human disease...
  12. pmc mRNA transcript quantification in archival samples using multiplexed, color-coded probes
    Patricia P Reis
    Division of Applied Molecular Oncology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
    BMC Biotechnol 11:46. 2011
    ..We assessed the ability of this technology for mRNA expression quantification in archived formalin-fixed, paraffin-embedded (FFPE) oral carcinoma samples...
  13. pmc Dysregulation of the mevalonate pathway promotes transformation
    James W Clendening
    Ontario Cancer Institute, Toronto, ON, Canada
    Proc Natl Acad Sci U S A 107:15051-6. 2010
    ..Taken together, our results suggest that HMGCR is a candidate metabolic oncogene and provide a molecular rationale for further exploring the statin family of HMGCR inhibitors as anticancer agents...
  14. ncbi request reprint Three-gene prognostic classifier for early-stage non small-cell lung cancer
    Suzanne K Lau
    Princess Margaret Hospital, 610 University Ave, Toronto, Ontario, Canada
    J Clin Oncol 25:5562-9. 2007
    ..However, the prognostic gene lists reported to date overlap poorly across studies, and few have been validated independently using more quantitative assay methods...
  15. doi request reprint Prognostic gene expression signature for squamous cell carcinoma of lung
    Chang Qi Zhu
    Ontario Cancer Institute and Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
    Clin Cancer Res 16:5038-47. 2010
    ..This study aimed to identify and validate a gene expression signature for squamous cell carcinoma of the lung (SQCC)...
  16. pmc Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma
    Patricia P Reis
    Division of Applied Molecular Oncology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    Mol Cancer 9:238. 2010
    ..We also examined PDCD4 regulation by microRNA 21 (miR-21) in OSCC...
  17. pmc Stability and heterogeneity of expression profiles in lung cancer specimens harvested following surgical resection
    Fiona H Blackhall
    University Health Network, Ontario Cancer Institute Princess Margaret Hospital, Toronto General Hospital and University of Toronto, Toronto, Ontario, Canada M5G 2M9
    Neoplasia 6:761-7. 2004
    ..However, sampling and pooling from multiple sites of each tumor may be necessary for expression profiling studies to overcome the molecular heterogeneity present in tumor specimens...
  18. pmc Integrin alpha 11 regulates IGF2 expression in fibroblasts to enhance tumorigenicity of human non-small-cell lung cancer cells
    Chang Qi Zhu
    Ontario Cancer Institute and Princess Margaret Hospital, University Health Network, Toronto, ON, Canada M5G 2M9
    Proc Natl Acad Sci U S A 104:11754-9. 2007
    ....
  19. doi request reprint Allelic loss of the loci containing the androgen synthesis gene, StAR, is prognostic for relapse in intermediate-risk prostate cancer
    Jennifer A Locke
    Department of Radiation Oncology, Medical Biophysics, Laboratory Medicine and Pathology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
    Prostate 72:1295-305. 2012
    ..In this hypothesis generating study, we conducted an array comparative genomic hybridization (aCGH) analysis of 33 androgen synthesis genes to identify potential prognostic factors for radiotherapy outcome...
  20. doi request reprint L1 cell adhesion molecule promotes tumorigenicity and metastatic potential in non-small cell lung cancer
    Josephine Hai
    Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
    Clin Cancer Res 18:1914-24. 2012
    ..However, there is little information on the biologic function of L1CAM in lung cancer cells. This study investigates the functional and prognostic role of L1CAM in NSCLC...
  21. pmc Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer
    Roya Navab
    The Campbell Family Institute for Cancer Research, Ontario Cancer Institute at Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
    Proc Natl Acad Sci U S A 108:7160-5. 2011
    ..Six of these 14 genes could be induced by TGF-β1 in NF. The results establish the prognostic impact of CAF-associated gene-expression changes in NSCLC patients...
  22. pmc Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma
    Nikolina Radulovich
    Ontario Cancer Institute and Princess Margaret Hospital, University Health Network, Toronto, Ontario M5G 2M9, Canada
    Mol Cancer 9:24. 2010
    ..The cyclin D1 (CCND1) and cyclin D3 (CCND3) are frequently co-overexpressed in pancreatic ductal adenocarcinoma (PDAC). Here we examine their differential roles in PDAC...
  23. ncbi request reprint The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells
    Julia Petschnigg
    Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Nat Methods 11:585-92. 2014
    ..MaMTH is a powerful tool for investigating the dynamic interactomes of human integral membrane proteins. ..
  24. ncbi request reprint Validating the prognostic value of marker genes derived from a non-small cell lung cancer microarray study
    Fiona H Blackhall
    Division of Cellular and Molecular Biology, University Health Network, Ontario Cancer Institute, Princess Margaret Hospital and University of Toronto, Toronto, Ontario, Canada M5G 2M9
    Lung Cancer 46:197-204. 2004
    ....
  25. pmc Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features
    Sarit Aviel-Ronen
    University Health Network, Ontario Cancer Institute and Princess Margaret Hospital Site, Toronto, ON, Canada
    Proc Natl Acad Sci U S A 105:10155-60. 2008
    ..We identified candidate genes that may be responsible for and are potential markers for malignant progression in AWBF...
  26. pmc Prognostic gene signatures for non-small-cell lung cancer
    Paul C Boutros
    Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
    Proc Natl Acad Sci U S A 106:2824-8. 2009
    ..This result appears to rationalize the observed lack of overlap among reported NSCLC prognostic signatures...
  27. ncbi request reprint Understanding prognostic gene expression signatures in lung cancer
    Chang Qi Zhu
    University Health Network, Ontario Cancer Institute Princess Margaret Hospital, Ontario, Canada
    Clin Lung Cancer 10:331-40. 2009
    ..This review discusses the concepts and methodologies involved in these analytical steps, primarily to facilitate the understanding of reports on large dataset gene expression studies that focus on prognostic signatures in NSCLC...
  28. doi request reprint Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas
    Angela B Y Hui
    Division of Applied Molecular Oncology, Ontario Cancer Institute, University of Toronto, Toronto, Ontario, Canada
    Clin Cancer Res 16:1129-39. 2010
    ..The objective of this study is to investigate the significance of microRNAs (miRNA) in patients with locally advanced head and neck squamous cell carcinoma (HNSCC)...
  29. pmc Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes
    Brian Cox
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 3:109. 2007
    ..These targets are evidence that Nmyc is a regulator of genes involved in mRNA processing and a repressor of the imprinted gene Igf2r in the developing lung...
  30. doi request reprint MicroRNA signature obtained from the comparison of aggressive with indolent non-Hodgkin lymphomas: potential prognostic value in mantle-cell lymphoma
    Rashmi S Goswami
    Ontario Cancer Institute, University Health Network
    J Clin Oncol 31:2903-11. 2013
    ..MicroRNAs (miRs) are useful in prognostic assessment of cancer. We determined an miR signature defining aggressiveness in B-cell non-Hodgkin lymphomas (NHL) and assessed whether this signature aids in MCL prognosis...
  31. ncbi request reprint Molecular classification of oral cancer by cDNA microarrays identifies overexpressed genes correlated with nodal metastasis
    Giles C Warner
    Department of Cellular and Molecular Biology, Princess Margaret Hospital, Ontario Cancer Institute, University Health Network, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
    Int J Cancer 110:857-68. 2004
    ..Application of this methodology represents an advance in the classification of oral cavity tumors and may ultimately aid in the development of more tailored therapies for oral carcinoma...
  32. pmc Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples
    Rashmi S Goswami
    Division of Applied Molecular Oncology, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
    BMC Biotechnol 10:47. 2010
    ..miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE) tissue...
  33. doi request reprint Identification of a microRNA signature associated with progression of leukoplakia to oral carcinoma
    Nilva K Cervigne
    Division of Applied Molecular Oncology, Toronto General Hospital, Ontario Cancer Institute, The University Health Network, Toronto, ON, Canada
    Hum Mol Genet 18:4818-29. 2009
    ..Our study provides the first evidence of an miR signature potentially useful for identifying leukoplakias at risk of malignant transformation...
  34. doi request reprint In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry
    Sarah Elschenbroich
    Ontario Cancer Institute, University Health Network, Toronto, Canada
    J Proteome Res 10:2286-99. 2011
    ....
  35. pmc Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer
    Chang Qi Zhu
    University Health Network, Ontario Cancer Institute and Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
    J Clin Oncol 28:4417-24. 2010
    ..10 trial demonstrated benefit from adjuvant cisplatin/vinorelbine (ACT) in early-stage non-small-cell lung cancer (NSCLC). We hypothesized that expression profiling may identify stage-independent subgroups who might benefit from ACT...
  36. doi request reprint Primary tumor xenografts of human lung adeno and squamous cell carcinoma express distinct proteomic signatures
    Yuhong Wei
    Program in Molecular Structure and Function, Hospital for Sick Children, University Health Network, Ontario Cancer Institute Princess Margaret Hospital, Toronto, Canada
    J Proteome Res 10:161-74. 2011
    ..These findings illustrate the potential to develop a comprehensive MS-based platform in oncologic pathology for better classification and potentially treatment of NSCLC patients...
  37. ncbi request reprint Exploiting the mevalonate pathway to distinguish statin-sensitive multiple myeloma
    James W Clendening
    Ontario Cancer Institute Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, ON, Canada
    Blood 115:4787-97. 2010
    ..This determinant of sensitivity further provides molecular rationale for the significant therapeutic index of statins on these tumor cells...
  38. ncbi request reprint Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity
    Barbara Bachtiary
    Department of Radiation Oncology, Clinical Study Coordination and Biostatistics, Division of Cancer Genomics and Proteomics, Princess Margaret Hospital, Toronto, Ontario, Canada
    Clin Cancer Res 12:5632-40. 2006
    ..To explore intratumor heterogeneity in gene expression profiles from patients with cervical cancer...
  39. pmc Characterization of the apoptotic response of human leukemia cells to organosulfur compounds
    W Wei Lynn Wong
    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, Toronto M5G2M1, Canada
    BMC Cancer 10:351. 2010
    ..We have previously shown that synthesized relatives of dysoxysulfone, a natural OSC derived from the Fijian medicinal plant, Dysoxylum richi, possess tumor-specific antiproliferative effects and are thus promising lead candidates...
  40. ncbi request reprint Online predicted human interaction database
    Kevin R Brown
    Division of Cancer Informatics, Ontario Cancer Institute, University of Toronto, Canada
    Bioinformatics 21:2076-82. 2005
    ....
  41. doi request reprint Validation of a histology-independent prognostic gene signature for early-stage, non-small-cell lung cancer including stage IA patients
    Sandy D Der
    Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada and Departments of Computer Science, Medical Biophysics, Medicine, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
    J Thorac Oncol 9:59-64. 2014
    ..A 15-gene prognostic classifier for NSCLC was identified from mRNA expression profiling of tumor samples from the NCIC CTG JBR.10 trial. In this study, we assessed its value in an independent set of cases...
  42. doi request reprint Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues
    Angela B Y Hui
    Division of Applied Molecular Oncology, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
    Lab Invest 89:597-606. 2009
    ....
  43. ncbi request reprint Impaired tRNA nuclear export links DNA damage and cell-cycle checkpoint
    Ata Ghavidel
    Ontario Cancer Institute, Division of Signaling Biology, Toronto, Ontario M5G 1L7, Canada
    Cell 131:915-26. 2007
    ....
  44. ncbi request reprint A proteome resource of ovarian cancer ascites: integrated proteomic and bioinformatic analyses to identify putative biomarkers
    Limor Gortzak-Uzan
    Ontario Cancer Institute, Division of Cancer Genomics and Proteomics, Canada
    J Proteome Res 7:339-51. 2008
    ..utoronto.ca/i2d) resulted in a short-list of 80 putative biomarkers. The presented proteomics analysis provides a significant resource for ovarian cancer research, and a framework for biomarker discovery...
  45. pmc Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, M5G 2M9, Canada
    Genome Biol 11:R13. 2010
    ..We apply these modular biomarkers to assign novel aging-related functions to poorly characterized longevity genes...
  46. pmc Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies
    Romina Ponzielli
    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, ON, Canada
    Nucleic Acids Res 36:e144. 2008
    ..Increased sensitivity and decreased noise in ChIP-chip assays will enable wider use of this methodology to accurately and affordably elucidate transcriptional networks...
  47. ncbi request reprint Automatic classification and pattern discovery in high-throughput protein crystallization trials
    Christian Cumbaa
    Ontario Cancer Institute, Northeast Structural Genomics Consortium, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
    J Struct Funct Genomics 6:195-202. 2005
    ..We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins...
  48. doi request reprint In silico drug screen in mouse liver identifies candidate calorie restriction mimetics
    Kristen Fortney
    Department of Medical Biophysics, University of Toronto, Ontario, Canada
    Rejuvenation Res 15:148-52. 2012
    ..Here we integrate these data with gene expression signatures of CR in mouse liver to generate a prioritized list of candidate CR mimetics. We identify 14 drugs that reproduce the effects of CR at the transcriptional level...
  49. ncbi request reprint Modeling of lung cancer by an orthotopically growing H460SM variant cell line reveals novel candidate genes for systemic metastasis
    Jiang Liu
    Division of Thoracic Surgery, University Health Network, Princess Margaret Hospital and Ontario Cancer Institute, Ontario, Canada M5G 2M9
    Oncogene 23:6316-24. 2004
    ..The model identifies additional novel candidate genes for the progression of lung cancer to systemic metastases and poor prognosis...
  50. ncbi request reprint Inhibition of the sodium/potassium ATPase impairs N-glycan expression and function
    Reza Beheshti Zavareh
    Ontario Cancer Institute, Princess Margaret Hospital, Canada
    Cancer Res 68:6688-97. 2008
    ..These molecules can be used as tools to better understand the role of N-glycans in normal and malignant cells. Moreover, these results may partly explain the anticancer effect of CGs in cardiovascular patients...
  51. ncbi request reprint Integration, visualization and analysis of human interactome
    Chiara Pastrello
    Princess Margaret Cancer Centre, University Health Network and TECHNA Institute for the Advancement of Technology for Health, TMDT, Room 11 314, 101 College Street, Toronto, ON M5G 1L7, Canada
    Biochem Biophys Res Commun 445:757-73. 2014
    ..Finally, we present an example integration to demonstrate the value of the network approach in cancer research, and highlight the importance of dynamic data in the specific context of signaling pathways...
  52. doi request reprint Identifying Myc interactors
    Romina Ponzielli
    Ontario Cancer Institute, The Campbell Family Institute for Cancer Research, Toronto, ON, Canada
    Methods Mol Biol 1012:51-64. 2013
    ..We also discuss methods used to screen for Myc interactors and provide an in silico strategy to help prioritize hits for further validation using the described Co-IP and in vitro pull-down assays. ..
  53. ncbi request reprint High-throughput mapping of a dynamic signaling network in mammalian cells
    Miriam Barrios-Rodiles
    Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
    Science 307:1621-5. 2005
    ..We show that Occludin regulates TGFbeta type I receptor localization for efficient TGFbeta-dependent dissolution of tight junctions during epithelial-to-mesenchymal transitions...
  54. doi request reprint Network-based characterization of drug-regulated genes, drug targets, and toxicity
    Max Kotlyar
    The Campbell Family Institute for Cancer Research, Ontario Cancer Institute, University Health Network, IBM Life Sciences Discovery Centre, Toronto Medical Discovery Tower, 9 305, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
    Methods 57:499-507. 2012
    ..Finally, network centrality of a drug's differentially regulated genes correlated significantly with drug toxicity...
  55. doi request reprint Algorithms for systematic identification of small subgraphs
    Joseph Geraci
    Ontario Cancer Institute UHN, Toronto, ON, Canada
    Methods Mol Biol 804:219-44. 2012
    ..After a brief introduction, we concentrate on methods based on the analysis of subnetworks, namely, graph motifs and graphlets...
  56. pmc Making sense of lung-cancer gene-expression profiles
    Dennis A Wigle
    Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Genome Biol 5:309. 2004
  57. ncbi request reprint Current applications of microarrays in head and neck cancer research
    Giles C Warner
    Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
    Laryngoscope 114:241-8. 2004
    ..The objective was to introduce microarray technology and its applications in cancer research to the head and neck clinician...
  58. ncbi request reprint Multiple dysregulated pathways in nasopharyngeal carcinoma revealed by gene expression profiling
    Wei Shi
    Division of Applied Molecular Oncology, Ontario Cancer Institute, Toronto, Canada
    Int J Cancer 119:2467-75. 2006
    ..The role of survivin in resisting apoptosis in NPC was confirmed by RNA interference. Our data provide novel insights into the development and progression of NPC, and suggest survivin as a novel therapeutic target for NPC...
  59. ncbi request reprint CUL7 is a novel antiapoptotic oncogene
    Sam S Kim
    Division of Cancer Genomics, Ontario Cancer Institute and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
    Cancer Res 67:9616-22. 2007
    ..We provide experimental evidence to show CUL7 is a new oncogene that cooperates with Myc in transformation by blocking Myc-induced apoptosis in a p53-dependent manner...
  60. pmc Understanding biology through intelligent systems
    Igor Jurisica
    Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
    Genome Biol 3:reports4036. 2002
    ..A report on the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Edmonton, Canada, 3-7 August 2002...
  61. pmc TAp73 knockout shows genomic instability with infertility and tumor suppressor functions
    Richard Tomasini
    The Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, Toronto, Ontario M5G 2C1, Canada
    Genes Dev 22:2677-91. 2008
    ..Hence, TAp73 isoforms exert tumor-suppressive functions and indicate an emerging role for Trp73 in the maintenance of genomic stability...
  62. pmc The murine caecal microRNA signature depends on the presence of the endogenous microbiota
    Natasha Singh
    Department of Nutritional Sciences, University of Toronto, Ontario, Canada
    Int J Biol Sci 8:171-86. 2012
    ..In this perspective, abnormally expressed microRNAs could be considered as novel therapeutic targets...
  63. doi request reprint A comprehensive catalogue of functional genetic variations in the EGFR pathway: protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research
    Sevtap Savas
    Division of Applied Molecular Oncology, Department of Medical Biophysics, Ontario Cancer Institute, Toronto, Ontario, Canada
    Int J Cancer 125:1257-65. 2009
    ..The genes and their SNPs identified in the network-based analysis represent potential candidates for gene-gene and SNP-SNP interaction studies in cancer research...
  64. doi request reprint Stem cell gene expression programs influence clinical outcome in human leukemia
    Kolja Eppert
    Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research, Ontario Cancer Institute, University Health Network and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    Nat Med 17:1086-93. 2011
    ..Thus, determinants of stemness influence the clinical outcome of AML, establishing that LSCs are clinically relevant and not artifacts of xenotransplantation...
  65. doi request reprint Advances in ovarian cancer proteomics: the quest for biomarkers and improved therapeutic interventions
    Andrea Jurisicova
    Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON M5G 1X5, Canada
    Expert Rev Proteomics 5:551-60. 2008
    ..Recent proteomics work on ovarian cancer cells and tissues will be discussed in light of obtaining new insights into fundamental biological processes, as well as their potential integration with ongoing biomarker discovery pipelines...
  66. pmc Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D
    Yun Niu
    Ontario Cancer Institute, UHN, 101 College Street, Toronto, Ontario M5G1L7, Canada
    Bioinformatics 26:111-9. 2010
    ..More accurate PPI detection will also improve the ability to extract experimental data related to PPIs and provide multiple evidence for each interaction...
  67. doi request reprint A tree-based approach for motif discovery and sequence classification
    Rui Yan
    Department of Computer Science, University of Toronto, Toronto, Canada M5S 3G4
    Bioinformatics 27:2054-61. 2011
    ..We introduce an algorithm optimized to exploit spatial information in sparse-but-populous datasets...
  68. doi request reprint Hypoxia predicts aggressive growth and spontaneous metastasis formation from orthotopically grown primary xenografts of human pancreatic cancer
    Qing Chang
    Ontario Cancer Institute Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
    Cancer Res 71:3110-20. 2011
    ....
  69. ncbi request reprint The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis
    Dalia Barsyte-Lovejoy
    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute Princess Margaret Hospital, University of Toronto, Toronto, Canada
    Cancer Res 66:5330-7. 2006
    ..In addition, c-Myc and H19 expression shows strong association in primary breast and lung carcinomas. This work indicates that c-Myc induction of the H19 gene product holds an important role in transformation...
  70. doi request reprint NKX3.1 haploinsufficiency is prognostic for prostate cancer relapse following surgery or image-guided radiotherapy
    Jennifer A Locke
    Department of Radiation Oncology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
    Clin Cancer Res 18:308-16. 2012
    ..We tested the role of the NKX3.1 gene as a determinant of treatment outcome given its reported roles in tumor initiating cell (TIC) renewal, the DNA damage response, and cooperation with c-MYC during prostate cancer progression...
  71. pmc Role of Pirh2 in mediating the regulation of p53 and c-Myc
    Anne Hakem
    Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Canada
    PLoS Genet 7:e1002360. 2011
    ..Collectively, our data reveal the in vivo roles of Pirh2 in the regulation of p53 and c-Myc stability and support its role as a tumor suppressor...
  72. pmc Unequal evolutionary conservation of human protein interactions in interologous networks
    Kevin R Brown
    Department of Medical Biophysics, University of Toronto, Toronto, Canada M5G 1L7
    Genome Biol 8:R95. 2007
    ..However, the conservation of various network components has not been fully explored. Unequal conservation of certain network components may limit the ability to fully expand the target interactomes using interologs...
  73. ncbi request reprint Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates
    Christian A Cumbaa
    Ontario Cancer Institute, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada
    Acta Crystallogr D Biol Crystallogr 59:1619-27. 2003
    ..Many images falsely classified as crystal-negative variously contain very fine crystal features or dendrites lacking straight edges. Characterization of these misclassifications suggests directions for improving the method...
  74. doi request reprint Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment
    Faiyaz Notta
    Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research Ontario Cancer Institute, Toronto, Ontario, Canada
    Science 333:218-21. 2011
    ..The demarcation of human HSCs and MPPs will enable the investigation of the molecular determinants of HSCs, with a goal of developing stem cell-based therapeutics...
  75. pmc Automated microinjection of recombinant BCL-X into mouse zygotes enhances embryo development
    Xinyu Liu
    Department of Mechanical and Industrial Engineering and Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 6:e21687. 2011
    ..This approach may lead to a possible treatment option for patients with repeated in vitro fertilization (IVF) failure due to poor embryo quality...
  76. ncbi request reprint Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent
    Melissa M Brierley
    Department of Cell and Molecular Biology, Toronto General Research Institute, University Health Network, University of Toronto, ON, Canada
    FEBS J 273:1569-81. 2006
    ..This report is the first analysis of the contribution of the STAT2 DNA binding domain to IFN responses on a global basis, and shows that STAT2 is required for the IFN-inducible activation of the full spectrum of GAS target genes...
  77. ncbi request reprint Molecular evidence of placental hypoxia in preeclampsia
    Nima Soleymanlou
    Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
    J Clin Endocrinol Metab 90:4299-308. 2005
    ..Insufficient uteroplacental oxygenation in preeclampsia is believed to be responsible for the molecular events leading to the clinical manifestations of this disease...
  78. ncbi request reprint Molecular profiling of non-small cell lung cancer and correlation with disease-free survival
    Dennis A Wigle
    Thoracic Oncology Site Group, Princess Margaret Hospital, Samuel Lunenfeld Research Institute of Mount Sinai Hospital, University of Toronto, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Cancer Res 62:3005-8. 2002
    ..The results provide evidence that molecular subtyping of NSCLC can identify distinct profiles of gene expression correlating with disease-free survival...
  79. pmc Phenotypic and transcriptional plasticity directed by a yeast mitogen-activated protein kinase network
    Ashton Breitkreutz
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
    Genetics 165:997-1015. 2003
    ..This systems-level robustness may also account for the observed diversity of signals that trigger invasive growth...
  80. ncbi request reprint Determinants of sensitivity to lovastatin-induced apoptosis in multiple myeloma
    W Wei Lynn Wong
    Departments of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
    Mol Cancer Ther 6:1886-97. 2007
    ..003). These results suggest that statins may be a useful molecular targeted therapy in the treatment of a subset of MM...
  81. ncbi request reprint Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening
    Chenggang Wu
    Department of Biochemistry and the Siebens Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
    Proteomics 7:1775-85. 2007
    ....
  82. ncbi request reprint Loss of coordinated androgen regulation in nonmalignant ovarian epithelial cells with BRCA1/2 mutations and ovarian cancer cells
    Andreas Evangelou
    Cancer and Blood Research Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X5, Canada
    Cancer Res 63:2416-24. 2003
    ..These findings raise the possibility that by modulating steroid receptor coactivator expression, androgen might affect other hormonal responses and contribute to the initiation of ovarian cancer...
  83. pmc CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome
    Lawrence E Heisler
    Department of Laboratory Medicine and Pathobiology, Program in Proteomics and Bioinformatics, University of Toronto Toronto, ON M5S 1A8, Canada
    Nucleic Acids Res 33:2952-61. 2005
    ..A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements...
  84. pmc Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study
    Kerby Shedden
    Department of Statistics, 1085 South University, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nat Med 14:822-7. 2008
    ..This study also provides the largest available set of microarray data with extensive pathological and clinical annotation for lung adenocarcinomas...