Research Topics
Species | Aron C EklundSummaryAffiliation: Center for Biological Sequence Analysis Country: Denmark Publications
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Detail Information
Publications
Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasetsCharles Swanton
Cancer Research UK London Research Institute, 44 Lincoln s Inn Fields, London, WC2A 3PX, UK
Genome Med 2:53. 2010....- Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridizationAron 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... - Correction of technical bias in clinical microarray data improves concordance with known biological informationAron 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... - Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy responseQiyuan 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... - Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER statusQiyuan Li
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
PLoS ONE 5:e15031. 2010.... - Paradoxical relationship between chromosomal instability and survival outcome in cancerNicolai 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... - Jetset: selecting the optimal microarray probe set to represent a geneQiyuan 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... 
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 trialsNicolai 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...- Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression dataPeng 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... - Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agentsNicolai J Birkbak
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
Cancer Discov 2:366-75. 2012..NtAI, a genomic measure of unfaithfully repaired DNA, may identify cancer patients likely to benefit from treatments targeting defective DNA repair... - Efficacy of neoadjuvant Cisplatin in triple-negative breast cancerDaniel 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... 
A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancersScott 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...- A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexesKasper 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... - Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurementsScott 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... - Molecular markers of early Parkinson's disease based on gene expression in bloodClemens 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... - The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsLeming 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... - Replacing cRNA targets with cDNA reduces microarray cross-hybridizationAron C Eklund
Nat Biotechnol 24:1071-3. 2006 - Reliability and reproducibility issues in DNA microarray measurementsSorin 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... - Spatiotemporal patterns of gene expression during fetal monkey brain developmentD 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...