Yudi Pawitan

Summary

Affiliation: Karolinska Institutet
Country: Sweden

Publications

  1. 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
  2. ncbi request reprint Genetic and shared environmental factors do not confound the association between birth weight and hypertension: a study among Swedish twins
    Niklas Bergvall
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE 171 77 Stockholm, Sweden
    Circulation 115:2931-8. 2007
  3. ncbi request reprint Covariance component models for multivariate binary traits in family data analysis
    Benjamin H Yip
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobelvgen 12, Stockholm, Sweden
    Stat Med 27:1086-105. 2008
  4. doi request reprint Unequal group variances in microarray data analyses
    Meaza Demissie
    Department of Statistics, University of Orebro, Sweden
    Bioinformatics 24:1168-74. 2008
  5. 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
  6. ncbi request reprint 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
  7. pmc Matched ascertainment of informative families for complex genetic modelling
    Benjamin H Yip
    Department of Psychiatry, University of Hong Kong, Hong Kong, China
    Behav Genet 40:404-14. 2010
  8. 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
  9. pmc Identification of recurrent regions of Copy-Number Variants across multiple individuals
    Teo Shu Mei
    Department of Epidemiology and Public Health, National University of Singapore, 16 Medical Drive, Singapore
    BMC Bioinformatics 11:147. 2010
  10. pmc Correlating gene and protein expression data using Correlated Factor Analysis
    Chuen Seng Tan
    Lewis Sigler Institute, Princeton University, New Jersey, USA
    BMC Bioinformatics 10:272. 2009

Collaborators

Detail Information

Publications77

  1. 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...
  2. ncbi request reprint Genetic and shared environmental factors do not confound the association between birth weight and hypertension: a study among Swedish twins
    Niklas Bergvall
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE 171 77 Stockholm, Sweden
    Circulation 115:2931-8. 2007
    ..Studies have found associations between low birth weight and increased risks of cardiovascular diseases in adulthood. However, these associations could be due to confounding by genetic or socioeconomic factors...
  3. ncbi request reprint Covariance component models for multivariate binary traits in family data analysis
    Benjamin H Yip
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobelvgen 12, Stockholm, Sweden
    Stat Med 27:1086-105. 2008
    ..We motivate our problem with real questions from psychiatric epidemiology and demonstrate how different substantive issues of comorbidity between two diseases can be put into the analytical framework...
  4. doi request reprint 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...
  5. 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...
  6. ncbi request reprint 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...
  7. pmc Matched ascertainment of informative families for complex genetic modelling
    Benjamin H Yip
    Department of Psychiatry, University of Hong Kong, Hong Kong, China
    Behav Genet 40:404-14. 2010
    ..The ascertainment-adjusted analysis, which we implement using a pseudo-likelihood approach, is shown to be efficient relative to the analysis of the whole cohort and robust to mis-specification of the random effect distribution...
  8. 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...
  9. pmc Identification of recurrent regions of Copy-Number Variants across multiple individuals
    Teo Shu Mei
    Department of Epidemiology and Public Health, National University of Singapore, 16 Medical Drive, Singapore
    BMC Bioinformatics 11:147. 2010
    ..General methodologies for identifying these recurrent regions, especially those directed at SNP arrays, are still needed...
  10. pmc Correlating gene and protein expression data using Correlated Factor Analysis
    Chuen Seng Tan
    Lewis Sigler Institute, Princeton University, New Jersey, USA
    BMC Bioinformatics 10:272. 2009
    ..The Generalized Singular Value Decomposition (gSVD) is another method which takes into account all available transcriptomic and proteomic data. Comparison is made between CFA and gSVD...
  11. ncbi request reprint 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
    ....
  12. pmc How many genetic variants remain to be discovered?
    Yudi Pawitan
    Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden
    PLoS ONE 4:e7969. 2009
    ..Under rare-variant with medium- to high-penetrance models (odds-ratios between 1.6 and 4.0), studies comparable in size to many existing studies are adequate provided the genotyping technology can interrogate more and rarer variants...
  13. ncbi request reprint The association between low birth weight and type 2 diabetes: contribution of genetic factors
    Stefan Johansson
    Departments of Medical Epidemiology, and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Epidemiology 19:659-65. 2008
    ..Poor fetal nutrition has been suggested to explain this association. Our objective was to determine whether genetic factors contribute to the association between low birth weight and subsequent risk of type 2 diabetes...
  14. ncbi request reprint Importance of familial factors in associations between offspring birth weight and parental risk of type-2 diabetes
    Niklas Bergvall
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Int J Epidemiol 37:185-92. 2008
    ..It is hypothesized that associations found between birth weight and subsequent risk of type-2 diabetes are due to inherited genes affecting both fetal growth and metabolism of insulin...
  15. doi request reprint Maternal effects for preterm birth: a genetic epidemiologic study of 630,000 families
    Anna C Svensson
    Division of Public Health Epidemiology, Department of Public Health Sciences, Karolinska Institutet, Norrbacka, Fifth Floor, SE 171 76 Stockholm, Sweden
    Am J Epidemiol 170:1365-72. 2009
    ..The increased odds ratio between offspring of sisters was independent of maternal risk factors for preterm birth, suggesting that the relative importance of maternal effects is not explained by these well-known risk factors...
  16. ncbi request reprint 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...
  17. ncbi request reprint Quantitative proteomics profiling of primary lung adenocarcinoma tumors reveals functional perturbations in tumor metabolism
    Maria Pernemalm
    Cancer Proteomics Mass Spectrometry, Department of Oncology Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
    J Proteome Res 12:3934-43. 2013
    ..Overall, these findings show how in-depth analysis of clinical material can lead to an increased understanding of the molecular mechanisms behind tumor progression. ..
  18. pmc Advancing paternal age and offspring violent offending: a sibling-comparison study
    Ralf Kuja-Halkola
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, P O Box 281, Stockholm 171 77, Sweden
    Dev Psychopathol 24:739-53. 2012
    ..Life-course persistent criminality has been proposed to have a partly biological etiology; our results agree with a stronger biological effect (i.e., de novo mutations) on persistent violent offending...
  19. doi request reprint Genomic copy number variations in three Southeast Asian populations
    Chee Seng Ku
    Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    Hum Mutat 31:851-7. 2010
    ..Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer...
  20. doi request reprint Copy number polymorphisms in new HapMap III and Singapore populations
    Chee Seng Ku
    Centre for Molecular Epidemiology, Department of Epidemiology and Public Health MD3, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore
    J Hum Genet 56:552-60. 2011
    ..Additionally, we also found 5014 novel copy number loci that have not been reported previously by McCarroll et al. (2008) in the 10 populations...
  21. pmc Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study
    Paul Lichtenstein
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Lancet 373:234-9. 2009
    ..We aimed to assess genetic and environmental contributions to liability for schizophrenia, bipolar disorder, and their comorbidity...
  22. ncbi request reprint Tobacco use, body mass index, and the risk of leukemia and multiple myeloma: a nationwide cohort study in Sweden
    Pia Fernberg
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Cancer Res 67:5983-6. 2007
    ..Results on snuff use as well as BMI showed no association. This study confirms the role of smoking as a risk factor for AML and gives no support to the hypothesis of a role of snuff use or BMI level on the risk of leukemia or MM...
  23. ncbi request reprint 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...
  24. doi request reprint Proteomic data analysis workflow for discovery of candidate biomarker peaks predictive of clinical outcome for patients with acute myeloid leukemia
    Jenny Forshed
    Clinical Proteomics, Karolinska Biomics Center, Karolinska University Hospital, Stockholm, Sweden
    J Proteome Res 7:2332-41. 2008
    ..The framework of this methodology should be seen as general and could be used with other one-dimensional spectral omics data than SELDI MS including an adequate number of samples...
  25. pmc Strategies and issues in the detection of pathway enrichment in genome-wide association studies
    Mun Gwan Hong
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Hum Genet 126:289-301. 2009
    ..This has allowed us to identify at least one replicable case of pathway enrichment but also to highlight functional gene clustering as a potentially serious problem that may lead to spurious pathway findings if not corrected...
  26. pmc Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study
    Per Hall
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Med 4:16. 2006
    ..Postmenopausal hormone-replacement therapy (HRT) increases breast-cancer risk. The influence of HRT on the biology of the primary tumor, however, is not well understood...
  27. ncbi request reprint Etiology of familial aggregation in melanoma and squamous cell carcinoma of the skin
    Linda S Lindström
    Department of Medical Epidemiology and Biostatistics, Karolinska Institute, P O Box 281, Stockholm 17177, Sweden
    Cancer Epidemiol Biomarkers Prev 16:1639-43. 2007
    ..Because the malignancies are dependent on UV radiation, we did separate analyses for sun-covered and sun-exposed sites...
  28. pmc Correlation test to assess low-level processing of high-density oligonucleotide microarray data
    Alexander Ploner
    Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Bioinformatics 6:80. 2005
    ..The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data...
  29. ncbi request reprint False discovery rate, sensitivity and sample size for microarray studies
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet 17177 Stockholm, Sweden
    Bioinformatics 21:3017-24. 2005
    ....
  30. pmc Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
    Andrey Alexeyenko
    School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
    BMC Bioinformatics 13:226. 2012
    ....
  31. ncbi request reprint Bias in the estimation of false discovery rate in microarray studies
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Bioinformatics 21:3865-72. 2005
    ..In most microarray studies, many genes have small effects not easily separable from non-DE genes. As a result, current methods often overestimate pi(0) and FDR, leading to unnecessary loss of power in the overall analysis...
  32. ncbi request reprint Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers
    Chuen Seng Tan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Proteomics 6:6124-33. 2006
    ..In conclusion, we find that ARS alleviates the main problems in the preprocessing of SELDI-TOF spectra. The R-package ProSpect that implements ARS is freely available for academic use at http://www.meb.ki.se/ yudpaw...
  33. ncbi request reprint Familial aggregation of small-for-gestational-age births: the importance of fetal genetic effects
    Anna C Svensson
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Am J Obstet Gynecol 194:475-9. 2006
    ..This study was undertaken to disentangle the maternal genetic, fetal genetic, and environmental effects for the risk of having small-for-gestational-age (SGA) offspring...
  34. doi request reprint Multi-platform segmentation for joint detection of copy number variants
    Shu Mei Teo
    Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore
    Bioinformatics 27:1555-61. 2011
    ..Currently, there is still a relative lack of procedures for combining information from different platforms...
  35. ncbi request reprint 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...
  36. pmc Is the association between general cognitive ability and violent crime caused by family-level confounders?
    Thomas Frisell
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    PLoS ONE 7:e41783. 2012
    ..Socioeconomic differences are notoriously difficult to quantify, however, and it is possible that the association between intelligence and delinquency suffer substantial residual confounding...
  37. 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...
  38. doi request reprint Heritability, assortative mating and gender differences in violent crime: results from a total population sample using twin, adoption, and sibling models
    Thomas Frisell
    Department of Medical Epidemiology and Biostatistics, Karolinska Institute, PO Box 281, 171 77, Stockholm, Sweden
    Behav Genet 42:3-18. 2012
    ..4), appeared to result from both phenotypic assortment and social homogamy, but had only minor effect on variance components. Finally, we found significant gender differences in the etiology of violent crime...
  39. pmc Incidence, mortality and survival patterns of prostate cancer among residents in Singapore from 1968 to 2002
    Sin Eng Chia
    Centre for Molecular Epidemiology, National University of Singapore, Singapore
    BMC Cancer 8:368. 2008
    ..From 1968 to 2002, Singapore experienced an almost four-fold increase in prostate cancer incidence. This paper examines the incidence, mortality and survival patterns for prostate cancer among all residents in Singapore from 1968 to 2002...
  40. 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..
  41. ncbi request reprint The discovery of human genetic variations and their use as disease markers: past, present and future
    Chee Seng Ku
    Department of Epidemiology and Public Health, Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    J Hum Genet 55:403-15. 2010
    ..Finally, we also discuss the future directions in the field and their impacts on next generation genome-wide association studies...
  42. ncbi request reprint Maternal and fetal genetic factors account for most of familial aggregation of preeclampsia: a population-based Swedish cohort study
    Sven Cnattingius
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
    Am J Med Genet A 130:365-71. 2004
    ..4-0.9). Genetic factors account for more than half of the liability of preeclampsia, and maternal genes contribute more than fetal genes. We suggest that the couple effect is due to a genetic interaction between mother and father...
  43. doi request reprint Regions of homozygosity in three Southeast Asian populations
    Shu Mei Teo
    Centre for Molecular Epidemiology, National University of Singapore, Singapore
    J Hum Genet 57:101-8. 2012
    ....
  44. pmc Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Breast Cancer Res 7:R953-64. 2005
    ..Breast cancer expression profiling has so far mainly been used to identify women with a poor prognosis as candidates for adjuvant therapy but without demonstrated value for therapy prediction...
  45. doi request reprint Regions of homozygosity and their impact on complex diseases and traits
    Chee Seng Ku
    Department of Epidemiology and Public Health, Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
    Hum Genet 129:1-15. 2011
    ..The homozygosity association approach holds great promise in identifying genetic susceptibility loci harboring recessive variants for complex diseases and traits...
  46. doi request reprint The pursuit of genome-wide association studies: where are we now?
    Chee Seng Ku
    Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, Centre for Molecular Epidemiology, National University of Singapore, Singapore
    J Hum Genet 55:195-206. 2010
    ..This review will focus on GWAS of SNPs association for complex diseases but not studies of copy number variations...
  47. ncbi request reprint Analysis of p53 mutation status in human cancer cell lines: a paradigm for cell line cross-contamination
    Hanna Berglind
    Karolinska Institute, Department of Oncology Pathology, Cancer Center Karolinska CCK, Stockholm, Sweden
    Cancer Biol Ther 7:699-708. 2008
    ..The p53 web site has been updated with new sections describing the p53 status in the majority of cell lines and a special section devoted to cell lines with controversial p53 status...
  48. ncbi request reprint Risk and protective factors for Parkinson's disease: a study in Swedish twins
    Karin Wirdefeldt
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE 181 77 Stockholm, Sweden
    Ann Neurol 57:27-33. 2005
    ..We confirm the protective effect of smoking on Parkinson's disease and establish that the association is only partially explained by genetic and familial environmental factors...
  49. pmc Super-sparse principal component analyses for high-throughput genomic data
    Donghwan Lee
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    BMC Bioinformatics 11:296. 2010
    ....
  50. ncbi request reprint A genome-wide assessment of variability in human serum metabolism
    Mun Gwan Hong
    Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
    Hum Mutat 34:515-24. 2013
    ..mQTL SNPs and mQTL-harboring genes were over-represented across GWASs conducted to date, suggesting that these data may have utility in tracing the molecular basis of some complex disease associations...
  51. doi request reprint Statistical challenges associated with detecting copy number variations with next-generation sequencing
    Shu Mei Teo
    Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597
    Bioinformatics 28:2711-8. 2012
    ..However, because of the complexity of the genome and the short read lengths from NGS technology, there are still many challenges associated with the analysis of NGS data for CNVs, no matter which method or algorithm is used...
  52. ncbi request reprint Finding regions of significance in SELDI measurements for identifying protein biomarkers
    Chuen Seng Tan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet Stockholm, Sweden
    Bioinformatics 22:1515-23. 2006
    ..The pre-processing of the raw data, however, is still problematic...
  53. ncbi request reprint Tobacco use, body mass index and the risk of malignant lymphomas--a nationwide cohort study in Sweden
    Pia Fernberg
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
    Int J Cancer 118:2298-302. 2006
    ..6-24.9). We conclude that tobacco smoking and high BMI do not entail an increased risk of NHL and HD. Our findings of a relation between the duration of snuff dipping and HD need further investigation...
  54. doi request reprint Genetic analysis of age-at-onset traits based on case-control family data
    Benjamin H Yip
    Department of Psychiatry, The University of Hong Kong, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong
    Stat Med 29:3258-66. 2010
    ..A pseudo-h-likelihood approach is used to analyse the ascertained data. We study the performance of the method using simulated data, and provide an illustration with analysis of melanoma in the Swedish population...
  55. ncbi request reprint Profound changes in breast cancer incidence may reflect changes into a Westernized lifestyle: a comparative population-based study in Singapore and Sweden
    Kee Seng Chia
    Center for Molecular Epidemiology, Faculty of Medicine, National University of Singapore, 16 Medical Drive, 117597, Singapore
    Int J Cancer 113:302-6. 2005
    ..The incidence of breast cancer in postmenopausal women in Singapore will probably continue to rise in the coming decades to match the current Swedish rates...
  56. doi request reprint 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...
  57. doi request reprint A population-based study of copy number variants and regions of homozygosity in healthy Swedish individuals
    Shu Mei Teo
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    J Hum Genet 56:524-33. 2011
    ..This study found many CNV loci that warrant further investigation, and also highlighted the abundance and importance of investigating ROHs for their associations with complex diseases and traits...
  58. ncbi request reprint Parental age and risk of childhood cancers: a population-based cohort study from Sweden
    Benjamin H Yip
    Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 171 77 Stockholm, Sweden
    Int J Epidemiol 35:1495-503. 2006
    ..A population-based cohort study of parental ages and other prenatal risk factors for five main childhood cancers was performed with the use of a linkage between several national-based registries...
  59. doi request reprint Sparse partial least-squares regression for high-throughput survival data analysis
    Donghwan Lee
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
    Stat Med 32:5340-52. 2013
    ..Through the numerical studies, we find that our SPLS method generally performs better than the standard PLS and sparse Cox regression methods in variable selection and prediction...
  60. doi request reprint Revisiting Mendelian disorders through exome sequencing
    Chee Seng Ku
    Department of Epidemiology and Public Health, Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
    Hum Genet 129:351-70. 2011
    ....
  61. doi request reprint Between-within models for survival analysis
    Arvid Sjölander
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm
    Stat Med 32:3067-76. 2013
    ....
  62. ncbi request reprint Modelling infectious disease transmission with complex exposure pattern and sparse outcome data
    Marie Reilly
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Stat Med 23:3013-32. 2004
    ..Finally, we discuss other problems where the model is applicable...
  63. pmc Human genetics and genomics a decade after the release of the draft sequence of the human genome
    Nasheen Naidoo
    Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    Hum Genomics 5:577-622. 2011
    ..This paper reviews these major developments in human genetics and genomics over the past decade...
  64. doi request reprint Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data
    Arief Gusnanto
    Department of Statistics, University of Leeds, Leeds LS2 9JT, UK
    Bioinformatics 28:40-7. 2012
    ..Here we provide a method that corrects contamination with normal cells and adjusts for genomes of different sizes so that the actual copy number of each region can be estimated...
  65. ncbi request reprint Analysis and prediction of the BSE incidence in Ireland
    Yudi Pawitan
    Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, P O Box 281, 17177 Stockholm, Sweden
    Prev Vet Med 62:267-83. 2004
    ..The trough in the propagation risk in 1990 coincided with a ban of the use of meat-and-bone meal for ruminant feed. Excluding the newly adopted active surveillance method in 2001, the predicted and observed data were comparable...
  66. ncbi request reprint Improved grading of breast adenocarcinomas based on genomic instability
    Ulrike Kronenwett
    Division of Cellular and Molecular Analysis, Department of Oncology and Pathology, Karolinska Institute and Hospital, Stockholm, Sweden
    Cancer Res 64:904-9. 2004
    ....
  67. ncbi request reprint Case-cohort methods for survival data on families from routine registers
    Tron Anders Moger
    Institute of Basic Medical Sciences, Department of Biostatistics, University of Oslo, Blindern, 0317 Oslo, Norway
    Stat Med 27:1062-74. 2008
    ..We also provide an application to survival data from the Medical Birth Registry of Norway...
  68. ncbi request reprint Genetic mixed linear models for twin survival data
    Il Do Ha
    Department of Asset Management, Daegu Haany University, Gyeongsan 712 715, Korea
    Behav Genet 37:621-30. 2007
    ..We also propose a simple and fast computation method for dealing with large data sets. The method is illustrated by the survival data from the Swedish Twin Registry. Finally, a simulation study is carried out to evaluate its performance...
  69. ncbi request reprint [Cancer researchers need statistical uncertainty!]
    Paul Dickman
    Lakartidningen 101:1842. 2004
  70. 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
    ....
  71. pmc An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    Lance D Miller
    Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
    Proc Natl Acad Sci U S A 102:13550-5. 2005
    ..Our results show the primary importance of p53 functional status in predicting clinical breast cancer behavior...
  72. doi request reprint Nine-gene molecular signature is not associated with prostate cancer death in a watchful waiting cohort
    Lorelei A Mucci
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
    Cancer Epidemiol Biomarkers Prev 17:249-51. 2008
    ..We quantified protein expression of the nine genes in tumors to classify progression risk. Accounting for clinical prognostic factors, the nine-gene model did not provide discrimination to predict lethal and indolent prostate cancer...
  73. ncbi request reprint 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...
  74. ncbi request reprint Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer
    Anna V Ivshina
    Genome Institute of Singapore, Singapore
    Cancer Res 66:10292-301. 2006
    ....
  75. ncbi request reprint Robust smooth segmentation approach for array CGH data analysis
    Jian Huang
    Statistical Laboratory, Department of Statistics, University College Cork, Ireland
    Bioinformatics 23:2463-9. 2007
    ..To take this into account, we propose a smooth segmentation (smoothseg) approach...
  76. ncbi request reprint Genomic instability and prognosis in breast carcinomas
    Ulrike Kronenwett
    Department of Medical Epidemiology and Biostatistics Karolinska Institutet, Box 281, 17176 Stockholm, Sweden
    Cancer Epidemiol Biomarkers Prev 15:1630-5. 2006
    ..The aim of the present study was to survey the clinical correlates and the prognostic value of the SSI in a consecutive series of 890 breast cancer patients...
  77. ncbi request reprint Robust ascertainment-adjusted parameter estimation
    Maengseok Noh
    Department of Statistics, Seoul University, Seoul, Republic of Korea
    Genet Epidemiol 29:68-75. 2005
    ..We revisit and extend the previous simulation, and show that the resulting estimator is efficient and robust against misspecification of the distribution of latent variables...