Aron C Eklund

Summary

Affiliation: Center for Biological Sequence Analysis
Country: Denmark

Publications

  1. pmc Biasogram: visualization of confounding technical bias in gene expression data
    Marcin Krzystanek
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 8:e61872. 2013
  2. pmc Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples
    Balazs Gyorffy
    Hungarian Academy of Sciences and Semmelweis University Budapest, Budapest, Hungary
    PLoS ONE 4:e5645. 2009
  3. pmc Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets
    Charles Swanton
    Cancer Research UK London Research Institute, 44 Lincoln s Inn Fields, London, WC2A 3PX, UK
    Genome Med 2:53. 2010
  4. pmc Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
    Aron C Eklund
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 38:e27. 2010
  5. pmc Correction of technical bias in clinical microarray data improves concordance with known biological information
    Aron C Eklund
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 9:R26. 2008
  6. pmc Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
    Qiyuan Li
    Center for Biological Sequence Analysis, Department of Systems Biolology, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 12:310. 2011
  7. pmc Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status
    Qiyuan Li
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 5:e15031. 2010
  8. pmc Jetset: selecting the optimal microarray probe set to represent a gene
    Qiyuan Li
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 12:474. 2011
  9. pmc The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer
    Attila Marcell Szasz
    2nd Department of Pathology, Semmelweis University, Budapest, Hungary
    PLoS ONE 8:e56707. 2013
  10. doi An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
    Balazs Gyorffy
    Joint Research Laboratory of the Hungarian Academy of Sciences and the Semmelweis University, Semmelweis University 1st Department of Pediatrics, Bókay u 53 54, 1083, Budapest, Hungary
    Breast Cancer Res Treat 123:725-31. 2010

Collaborators

Detail Information

Publications25

  1. pmc Biasogram: visualization of confounding technical bias in gene expression data
    Marcin Krzystanek
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 8:e61872. 2013
    ..This approach can be used as a quality control step to identify data sets that are likely to yield false positive results...
  2. pmc Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples
    Balazs Gyorffy
    Hungarian Academy of Sciences and Semmelweis University Budapest, Budapest, Hungary
    PLoS ONE 4:e5645. 2009
    ..However, a comprehensive comparison of preprocessing algorithms on samples taken under research conditions has not been performed...
  3. pmc Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets
    Charles Swanton
    Cancer Research UK London Research Institute, 44 Lincoln s Inn Fields, London, WC2A 3PX, UK
    Genome Med 2:53. 2010
    ....
  4. pmc Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
    Aron C Eklund
    Center for Biological Sequence Analysis, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 38:e27. 2010
    ..This optimized matrix may be useful in the design of microarray probes, and in other BLASTN-based searches for hybridization partners...
  5. pmc Correction of technical bias in clinical microarray data improves concordance with known biological information
    Aron C Eklund
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 9:R26. 2008
    ..We developed a method to correct for technical bias in clinical microarray data, which increased concordance with known biological relationships in multiple data sets...
  6. pmc Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
    Qiyuan Li
    Center for Biological Sequence Analysis, Department of Systems Biolology, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 12:310. 2011
    ..However, identification of clinically predictive or prognostic classifiers can be challenging when a large number of genes are measured in a small number of tumors...
  7. pmc Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status
    Qiyuan Li
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 5:e15031. 2010
    ....
  8. pmc Jetset: selecting the optimal microarray probe set to represent a gene
    Qiyuan Li
    Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
    BMC Bioinformatics 12:474. 2011
    ..Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task...
  9. pmc The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer
    Attila Marcell Szasz
    2nd Department of Pathology, Semmelweis University, Budapest, Hungary
    PLoS ONE 8:e56707. 2013
    ....
  10. doi An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
    Balazs Gyorffy
    Joint Research Laboratory of the Hungarian Academy of Sciences and the Semmelweis University, Semmelweis University 1st Department of Pediatrics, Bókay u 53 54, 1083, Budapest, Hungary
    Breast Cancer Res Treat 123:725-31. 2010
    ..The tool is highly valuable for the preliminary assessment of biomarkers, especially for research groups with limited bioinformatic resources...
  11. pmc Paradoxical relationship between chromosomal instability and survival outcome in cancer
    Nicolai J Birkbak
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Cancer Res 71:3447-52. 2011
    ..Inclusion of a surrogate measurement of CIN may improve cancer risk stratification and future therapeutic approaches...
  12. pmc Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations
    Nicolai Juul Birkbak
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 8:e80023. 2013
    ..The significance of these genome-wide mutations is unknown. We hypothesize genome-wide mutation burden mirrors deficiencies in DNA repair and is associated with treatment outcome in ovarian cancer...
  13. ncbi Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials
    Nicolai Juul
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Lancet Oncol 11:358-65. 2010
    ..Here, we assess these genes as a predictor of pCR to paclitaxel combination chemotherapy in triple-negative breast cancer...
  14. ncbi Evaluation of microarray preprocessing algorithms based on concordance with rt-PCR in clinical samples
    Balazs Gyorffy
    Hungarian Academy of Sciences and Semmelweis University Budapest, Budapest, Hungary
    PLoS ONE 4:e5645. 2009
    ..CONCLUSIONS/SIGNIFICANCE: Our results support the choice of PLIER+16 for the preprocessing of clinical Affymetrix microarray data. However, other algorithms performed similarly and are probably also good choices...
  15. pmc Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents
    Nicolai J Birkbak
    Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
    Cancer Discov 2:366-75. 2012
    ..Thus, accumulation of telomeric allelic imbalance is a marker of platinum sensitivity and suggests impaired DNA repair...
  16. doi Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression data
    Peng Wan
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Bldg 208, DK 2800 Kgs Lyngby, Denmark
    Bioorg Med Chem 20:167-76. 2012
    ..Our study demonstrates that the combined data sets, which provide comprehensive information on drug activity and gene expression profiles of tumor cell lines studied, are useful for identifying potential new active compounds...
  17. pmc Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer
    Daniel P Silver
    Dana Farber Cancer Institute, Department of Medical Oncology, Smith 209, 1 Jimmy Fund Way, Boston, MA 02115, USA
    J Clin Oncol 28:1145-53. 2010
    ..CONCLUSION Single-agent cisplatin induced response in a subset of patients with TNBC. Decreased BRCA1 expression may identify subsets of TNBCs that are cisplatin sensitive. Other biomarkers show promise in predicting cisplatin response...
  18. ncbi A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
    Scott L Carter
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:1043-8. 2006
    ..These results provide a means to assess the potential role of chromosomal instability in determining malignant potential over a broad range of tumors...
  19. pmc A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
    Kasper Lage
    Center for Biological Sequence Analysis, Kemitorvet building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Proc Natl Acad Sci U S A 105:20870-5. 2008
    ..Our method represents a conceptual scaffold for organism-spanning analyses and reveals an extensive list of tissue-specific draft molecular pathways, both known and unexpected, that might be disrupted in disease...
  20. pmc Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    Scott L Carter
    Children s Hospital Informatics Program, Harvard Medical School, Boston, MA 02115 USA
    BMC Bioinformatics 6:107. 2005
    ..The NCI-60 gene expression profiles produced by Affymetrix HuFL platform were recalculated using these redefined probe sets and compared to previously published cDNA measurements of the same panel of RNA samples...
  21. pmc Reliability and reproducibility issues in DNA microarray measurements
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Trends Genet 22:101-9. 2006
    ..The main problems seem to be the sub-optimal design or choice of probes and some incorrect probe annotations. Well-designed data-analysis approaches can rectify some of these problems...
  22. ncbi Replacing cRNA targets with cDNA reduces microarray cross-hybridization
    Aron C Eklund
    Nat Biotechnol 24:1071-3. 2006
  23. pmc The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1151-61. 2006
    ..This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings...
  24. pmc Molecular markers of early Parkinson's disease based on gene expression in blood
    Clemens R Scherzer
    Center for Neurologic Diseases, Brigham and Women s Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 104:955-60. 2007
    ..59 +/- 0.05) than in controls (0.96 +/- 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD...
  25. ncbi Spatiotemporal patterns of gene expression during fetal monkey brain development
    D Eugene Redmond
    Department of Psychiatry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
    Brain Res Dev Brain Res 146:99-106. 2003
    ..These results may lead to new understanding of brain development and new strategies for treating and repairing disorders of brain function...