Stefano Calza

Summary

Affiliation: University of Brescia
Country: Italy

Publications

  1. pmc Secretoglobin expression in ovarian carcinoma: lipophilin B gene upregulation as an independent marker of better prognosis
    Eliana Bignotti
    Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
    J Transl Med 11:162. 2013
  2. pmc Molecular sampling of prostate cancer: a dilemma for predicting disease progression
    Andrea Sboner
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
    BMC Med Genomics 3:8. 2010
  3. pmc Mammaglobin B is an independent prognostic marker in epithelial ovarian cancer and its expression is associated with reduced risk of disease recurrence
    Renata A Tassi
    Division of Gynecologic Oncology, Department Materno Infantile e Tecnologie Biomediche, University of Brescia, Brescia, Italy
    BMC Cancer 9:253. 2009
  4. pmc Normalization of oligonucleotide arrays based on the least-variant set of genes
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Bioinformatics 9:140. 2008
  5. ncbi EPIC-Italy cohorts and multipurpose national surveys. A comparison of some socio-demographic and life-style characteristics
    Stefano Calza
    Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Italy
    Tumori 89:615-23. 2003
  6. pmc Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE 171 77 Stockholm, Sweden
    Breast Cancer Res 8:R34. 2006
  7. pmc Detecting differential expression in microarray data: comparison of optimal procedures
    Elena Perelman
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
    BMC Bioinformatics 8:28. 2007
  8. ncbi Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes
    Kristian Wennmalm
    Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
    Genes Chromosomes Cancer 46:87-97. 2007
  9. ncbi Estimation of false discovery proportion under general dependence
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 22:3025-31. 2006
  10. ncbi Multidimensional local false discovery rate for microarray studies
    Alexander Ploner
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
    Bioinformatics 22:556-65. 2006

Collaborators

Detail Information

Publications26

  1. pmc Secretoglobin expression in ovarian carcinoma: lipophilin B gene upregulation as an independent marker of better prognosis
    Eliana Bignotti
    Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
    J Transl Med 11:162. 2013
    ....
  2. pmc Molecular sampling of prostate cancer: a dilemma for predicting disease progression
    Andrea Sboner
    Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA
    BMC Med Genomics 3:8. 2010
    ..Hence, we sought to develop a molecular panel for prostate cancer progression by reasoning that molecular profiles might further improve current clinical models...
  3. pmc Mammaglobin B is an independent prognostic marker in epithelial ovarian cancer and its expression is associated with reduced risk of disease recurrence
    Renata A Tassi
    Division of Gynecologic Oncology, Department Materno Infantile e Tecnologie Biomediche, University of Brescia, Brescia, Italy
    BMC Cancer 9:253. 2009
    ....
  4. pmc Normalization of oligonucleotide arrays based on the least-variant set of genes
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Bioinformatics 9:140. 2008
    ..This means it is still important to develop a normalization method that is robust against violation of the standard assumptions..
  5. ncbi EPIC-Italy cohorts and multipurpose national surveys. A comparison of some socio-demographic and life-style characteristics
    Stefano Calza
    Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Italy
    Tumori 89:615-23. 2003
    ..Knowledge of the bias related to self-selected sampling is important for better directing the interpretation of the EPIC-Italy study results...
  6. pmc Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE 171 77 Stockholm, Sweden
    Breast Cancer Res 8:R34. 2006
    ..So far, however, they have not superseded routine histopathology and staging criteria, partly because the few studies performed on molecular subtyping have had little validation and limited clinical characterization...
  7. pmc Detecting differential expression in microarray data: comparison of optimal procedures
    Elena Perelman
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
    BMC Bioinformatics 8:28. 2007
    ..The relationship and relative performance of these methods in two-sample comparisons is currently unknown...
  8. ncbi Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes
    Kristian Wennmalm
    Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
    Genes Chromosomes Cancer 46:87-97. 2007
    ..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
  9. ncbi Estimation of false discovery proportion under general dependence
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 22:3025-31. 2006
    ....
  10. ncbi Multidimensional local false discovery rate for microarray studies
    Alexander Ploner
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
    Bioinformatics 22:556-65. 2006
    ..It is desirable to have an fdr-controlling procedure that automatically accounts for gene variability...
  11. pmc Filtering genes to improve sensitivity in oligonucleotide microarray data analysis
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics Karolinska Institute, Stockholm, Sweden
    Nucleic Acids Res 35:e102. 2007
    ..A freely-available package called FLUSH implements the procedures and graphical displays described in the article...
  12. doi Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data
    Chen Suo
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, Department of Molecular and Translational Medicine, University of Brescia, Italy and Department of Mathematics and Statistics, La Trobe University, Australia
    Bioinformatics 30:506-13. 2014
    ..The problem is that, without strong assumptions, the read intensity pattern is not identifiable from data observed in a single sample...
  13. doi Normalization of gene-expression microarray data
    Stefano Calza
    Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
    Methods Mol Biol 673:37-52. 2010
    ..In this chapter, we introduce the basic concepts and methods, and illustrate them using data from three commonly used commercial platforms...
  14. doi Antiangiogenic activity of a neutralizing human single-chain antibody fragment against fibroblast growth factor receptor 1
    Roberto Ronca
    Unit of General Pathology and Immunology, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
    Mol Cancer Ther 9:3244-53. 2010
    ..Taken together, the data show that scFv RR-C2 recognizes and neutralizes FGFR-1 activity in different animal species, including humans, thus representing a novel tool for the development of antiangiogenic/antineoplastic therapies...
  15. ncbi Application of a latent variable model for a multicenter study on early effects due to mercury exposure
    Roberto Lucchini
    Institute of Occupational Health and Industrial Hygiene, University of Brescia, Brescia, Italy
    Neurotoxicology 24:605-16. 2003
    ..On the contrary, dental amalgams and small-size fish consumption do not seem to be associated to any adverse health effect at these exposure levels...
  16. doi Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival
    Chen Suo
    School of Life Sciences, Peking University, Beijing, China, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 31:2607-13. 2015
    ..Clinical validation, particularly based on patient outcomes such as survival, is important for assessing the relevance of the integrated information and for comparing different procedures...
  17. pmc Integrated molecular portrait of non-small cell lung cancers
    Vladimir Lazar
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Med Genomics 6:53. 2013
    ..The objectives of this study were to utilize integrated genomic data including copy-number alteration, mRNA, microRNA expression and candidate-gene full sequencing data to characterize the molecular distinctions between AC and SCC...
  18. pmc Obesity and prevalence of chronic diseases in the 1999-2000 Italian National Health Survey
    Stefano Calza
    Section of Medical Statistics and Biometry, Department of Biotechnologies and Biomedical Sciences, University of Brescia, Italy
    BMC Public Health 8:140. 2008
    ..We investigated the prevalence of overweight and obesity and their relationship with 14 groups of chronic diseases in a Mediterranean population using data from the Italian National Survey collected in 1999-2000...
  19. ncbi Identification of differentially expressed genes and false discovery rate in microarray studies
    Arief Gusnanto
    Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, UK
    Curr Opin Lipidol 18:187-93. 2007
    ..To highlight the development in microarray data analysis for the identification of differentially expressed genes, particularly via control of false discovery rate...
  20. doi Unequal group variances in microarray data analyses
    Meaza Demissie
    Department of Statistics, University of Orebro, Sweden
    Bioinformatics 24:1168-74. 2008
    ..The problem arises in the small-sample setting, where the approximately valid Welch test lacks sensitivity, while the more sensitive moderated t-test assumes equal variance...
  21. ncbi Fetal DNA detection in maternal plasma throughout gestation
    Silvia Galbiati
    Unit of Genomics for Diagnosis of Human Pathologies, IRCCS H San Raffaele, Via Olgettina 58, 20132 Milan, Italy
    Hum Genet 117:243-8. 2005
    ..No SRY amplification was obtained in seven out of the 246 (2.8%) male-bearing pregnancies. Fetal DNA from maternal plasma seems to be an adequate and reliable source of genetic material for a noninvasive prenatal diagnostic approach...
  22. ncbi Differential gene expression profiles between tumor biopsies and short-term primary cultures of ovarian serous carcinomas: identification of novel molecular biomarkers for early diagnosis and therapy
    Eliana Bignotti
    Division of Gynecologic Oncology, University of Brescia, Brescia, Italy
    Gynecol Oncol 103:405-16. 2006
    ..To compare the genetic fingerprints of flash-frozen ovarian serous carcinomas to those of matched highly purified primary tumor cell cultures...
  23. ncbi Gail model for prediction of absolute risk of invasive breast cancer: independent evaluation in the Florence-European Prospective Investigation Into Cancer and Nutrition cohort
    Adriano Decarli
    Medical Statistics and Biometry Institute, University of Milan, Via Venezian 1, 20133 Milan, Italy
    J Natl Cancer Inst 98:1686-93. 2006
    ..Although the GM has been validated in US populations, its performance in other populations is unclear because of the wide variation in international breast cancer rates...
  24. ncbi Gene expression profile of ovarian serous papillary carcinomas: identification of metastasis-associated genes
    Eliana Bignotti
    Division of Gynecologic Oncology, University of Brescia Medical School, Brescia, Italy
    Am J Obstet Gynecol 196:245.e1-11. 2007
    ..The purpose of this study was to identify genes that are highly differentially expressed in metastatic serous papillary ovarian tumors (MET) when compared with primary ovarian serous carcinomas (OSPC)...
  25. pmc Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer
    Sunita R Setlur
    Department of Pathology, Brigham and Women s Hospital, Boston, MA, USA
    J Natl Cancer Inst 100:815-25. 2008
    ....
  26. ncbi Overexpression of mammaglobin B in epithelial ovarian carcinomas
    Renata A Tassi
    Division of Gynecologic Oncology, University of Brescia, Brescia, Italy
    Gynecol Oncol 105:578-85. 2007
    ..In order to evaluate its potential as a novel ovarian cancer biomarker, in this study we quantified and compared Mammaglobin B expression in various histologic types of epithelial ovarian carcinomas (EOC)...