Andreas Keller

Summary

Affiliation: Saarland University
Country: Germany

Publications

  1. doi request reprint Toward the blood-borne miRNome of human diseases
    Andreas Keller
    Biomarker Discovery Center, Heidelberg, Germany
    Nat Methods 8:841-3. 2011
  2. doi request reprint Combining gene expression signatures and autoantibody profiles in human meningioma
    A Keller
    Center for Bioinformatics, Saarland University, Saarbrucken, Germany
    Gene Ther 16:184-9. 2009
  3. pmc A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E 1 1, Saarbrucken, Germany
    Bioinformatics 25:2787-94. 2009
  4. pmc SePaCS--a web-based application for classification of seroreactivity profiles
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E1 1, 66041 Saarbrucken, Germany
    Nucleic Acids Res 35:W683-7. 2007
  5. pmc Computation of significance scores of unweighted Gene Set Enrichment Analyses
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E1 1, 66804 Saarbrücken, Germany
    BMC Bioinformatics 8:290. 2007
  6. pmc GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
    Andreas Keller
    Center for Bioinformatics, Saarland University, Saarbrucken, Germany
    BMC Bioinformatics 9:552. 2008
  7. pmc A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building 3, 11, 66041 Saarbrucken, Germany
    BMC Bioinformatics 7:539. 2006
  8. doi request reprint Genome wide expression profiling identifies specific deregulated pathways in meningioma
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E 1 1, Saarbrücken 66041, Germany
    Int J Cancer 124:346-51. 2009
  9. doi request reprint Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%
    Nicole Ludwig
    Department of Human Genetics, Medical School, Saarland University, Homburg Saar, Germany
    Int J Cancer 128:1493-501. 2011
  10. ncbi request reprint NetworkTrail--a web service for identifying and visualizing deregulated subnetworks
    Daniel Stöckel
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    Bioinformatics 29:1702-3. 2013

Detail Information

Publications53

  1. doi request reprint Toward the blood-borne miRNome of human diseases
    Andreas Keller
    Biomarker Discovery Center, Heidelberg, Germany
    Nat Methods 8:841-3. 2011
    ..We observed significant correlations (P = 0.004) between the genomic location of disease-associated genetic variants and deregulated microRNAs...
  2. doi request reprint Combining gene expression signatures and autoantibody profiles in human meningioma
    A Keller
    Center for Bioinformatics, Saarland University, Saarbrucken, Germany
    Gene Ther 16:184-9. 2009
    ....
  3. pmc A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E 1 1, Saarbrucken, Germany
    Bioinformatics 25:2787-94. 2009
    ....
  4. pmc SePaCS--a web-based application for classification of seroreactivity profiles
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E1 1, 66041 Saarbrucken, Germany
    Nucleic Acids Res 35:W683-7. 2007
    ..As a second example, we evaluated SePaCS on glioma, a malignant brain tumor. SePaCS is freely available at http://www.bioinf.uni-sb.de/sepacs...
  5. pmc Computation of significance scores of unweighted Gene Set Enrichment Analyses
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E1 1, 66804 Saarbrücken, Germany
    BMC Bioinformatics 8:290. 2007
    ..Usually, significance scores (p-values) of GSEA are computed by nonparametric permutation tests, a time consuming procedure that yields only estimates of the p-values...
  6. pmc GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
    Andreas Keller
    Center for Bioinformatics, Saarland University, Saarbrucken, Germany
    BMC Bioinformatics 9:552. 2008
    ..While a variety of tools for normalizing, analysing, or visualizing expression profiles has been developed in the last years, most of these tools offer only functionality for accomplishing certain steps of the evaluation pipeline...
  7. pmc A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building 3, 11, 66041 Saarbrucken, Germany
    BMC Bioinformatics 7:539. 2006
    ..For validation purposes we choose the intracranial meningioma tumors as model system since they occur very frequently, are mostly benign, and are genetically stable...
  8. doi request reprint Genome wide expression profiling identifies specific deregulated pathways in meningioma
    Andreas Keller
    Center for Bioinformatics, Saarland University, Building E 1 1, Saarbrücken 66041, Germany
    Int J Cancer 124:346-51. 2009
    ..0001). Pathways with increased expression included several metabolic pathways. Extended expression profiling by a novel statistical gene set enrichment identified pathways that have previously not been associated with meningioma...
  9. doi request reprint Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%
    Nicole Ludwig
    Department of Human Genetics, Medical School, Saarland University, Homburg Saar, Germany
    Int J Cancer 128:1493-501. 2011
    ..normal sera as shown by their AUC values. These results demonstrate that the accuracy of a serum-based diagnostic can be readily and considerably improved by screening extended sets of proteins...
  10. ncbi request reprint NetworkTrail--a web service for identifying and visualizing deregulated subnetworks
    Daniel Stöckel
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    Bioinformatics 29:1702-3. 2013
    ..By providing an accessible interface to otherwise hard-to-use command line tools, the new web service enables non-experts to quickly and reliably carry out this type of network analyses...
  11. pmc Treatment-independent miRNA signature in blood of Wilms tumor patients
    Jana Schmitt
    Department of Human Genetics, Saarland University, 66421 Homburg Saar, Germany
    BMC Genomics 13:379. 2012
    ..Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001...
  12. pmc miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases
    Cedric Laczny
    Center for Bioinformatics, Saarland University, Campus E2 1, 66041 Saarbrucken, Germany
    BMC Bioinformatics 13:36. 2012
    ..To understand the regulatory processes of miRNAs on genes, integrative computer-aided approaches are essential, especially in the light of complex human diseases as cancer...
  13. pmc miRNAs in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments
    Andreas Keller
    febit biomed gmbh, Heidelberg, Germany
    BMC Cancer 9:353. 2009
    ..Here we addressed the question whether there is a sufficient number of miRNAs deregulated in blood cells of cancer patients to be able to distinguish between cancer patients and controls...
  14. doi request reprint Is there a general autoantibody signature for cancer?
    Nicole Ludwig
    Department of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Saar, Germany
    Eur J Cancer 48:2451-61. 2012
    ..Here we address the question whether cancer specific signatures exist...
  15. doi request reprint Multicenter study identified molecular blood-born protein signatures for Wilms Tumor
    Jana Schmitt
    Department of Human Genetics, Medical School, Saarland University, 66421 Homburg, Germany
    Int J Cancer 131:673-82. 2012
    ..We present the first multicenter study of autoantibody signatures in patients with WT. We established an autoantibody signature that separates patients with WT from controls...
  16. pmc High-throughput miRNA profiling of human melanoma blood samples
    Petra Leidinger
    Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Saar, Germany
    BMC Cancer 10:262. 2010
    ..MicroRNA (miRNA) signatures are not only found in cancer tissue but also in blood of cancer patients. Specifically, miRNA detection in blood offers the prospect of a non-invasive analysis tool...
  17. pmc Identification of lung cancer with high sensitivity and specificity by blood testing
    Petra Leidinger
    Department of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Saar, Germany
    Respir Res 11:18. 2010
    ..Cytological analysis and chest X-ray failed to reduce mortality, and CT screenings are still controversially discussed. Recent studies provided first evidence for the potential usefulness of autoantigens as markers for lung cancer...
  18. pmc Alterations in cardiac DNA methylation in human dilated cardiomyopathy
    Jan Haas
    Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
    EMBO Mol Med 5:413-29. 2013
    ..In vivo studies of orthologous ly75 and adora2a in zebrafish demonstrate a functional role of these genes in adaptive or maladaptive pathways in heart failure...
  19. doi request reprint MicroRNA expression changes after lung cancer resection: a follow-up study
    Petra Leidinger
    Institute of Human Genetics, Saarland University, Medical School, Homburg, Germany
    RNA Biol 9:900-10. 2012
    ..Our data underline the importance of studies that follow the fate of miRNAs over time, both to further our understanding of the biology of miRNA signatures and to establish these signatures as biomarkers...
  20. ncbi request reprint Pattern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ
    Nicole Ludwig
    Department of Human Genetics, Medical School, Saarland University, Homburg Saar, Germany
    Clin Cancer Res 14:4767-74. 2008
    ..One of the major challenges toward this goal is to prove that seroreactivity profiles do not only allow for identifying a tumor but also allow for distinguishing tumors from other pathologies of the same organ...
  21. pmc Improving seroreactivity-based detection of glioma
    Nicole Ludwig
    Department of Human Genetics, Medical School, Saarland University, Building 60, Homburg Saar, Germany
    Neoplasia 11:1383-9. 2009
    ..In the future, autoantibody signatures in glioma not only may prove useful for diagnosis but also offer the prospect for a personalized immune-based therapy...
  22. doi request reprint Specific peripheral miRNA profiles for distinguishing lung cancer from COPD
    Petra Leidinger
    Institute of Human Genetics, Saarland University, Medical School, Homburg, Germany
    Lung Cancer 74:41-7. 2011
    ..In conclusion, we showed that blood miRNA signatures are suitable to distinguish lung cancer from COPD...
  23. pmc Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls
    Andreas Keller
    febit biomed gmbh, Heidelberg, Germany
    PLoS ONE 4:e7440. 2009
    ..The implications of our study are twofold. The miRNA expression profiles in blood cells may serve as a biomarker for MS, and deregulation of miRNA expression may play a role in the pathogenesis of MS...
  24. pmc GeneTrail--advanced gene set enrichment analysis
    Christina Backes
    Center for Bioinformatics, Saarland University, Building E1 1, 66041 Saarbrucken, Germany
    Nucleic Acids Res 35:W186-92. 2007
    ..GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de...
  25. doi request reprint A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma
    Ulrike Fischer
    Department of Human Genetics, Saarland University, 66421 Homburg Saar, Germany
    Mol Cancer Res 6:576-84. 2008
    ..Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time...
  26. ncbi request reprint Toward an early diagnosis of lung cancer: an autoantibody signature for squamous cell lung carcinoma
    Petra Leidinger
    Department of Human Genetics, Medical School, Saarland University, 66421 Homburg Saar, Germany
    Int J Cancer 123:1631-6. 2008
    ....
  27. doi request reprint Refining diagnostic microRNA signatures by whole-miRNome kinetic analysis in acute myocardial infarction
    Britta Vogel
    Department of Internal Medicine, University of Heidelberg, Heidelberg, Germany
    Clin Chem 59:410-8. 2013
    ..However, the kinetics of the time-dependent sensitivity of these novel miRNA biomarkers remained unknown...
  28. doi request reprint GAS41 amplification results in overexpression of a new spindle pole protein
    Jana Schmitt
    Department of Human Genetics, Saarland University, Medical School, Homburg, Germany
    Genes Chromosomes Cancer 51:868-80. 2012
    ..We propose that GAS41 amplification may have an effect on the highly altered karyotype of glioblastoma via its role during spindle pole formation...
  29. pmc An integer linear programming approach for finding deregulated subgraphs in regulatory networks
    Christina Backes
    Department of Human Genetics, Saarland University, 66421 Homburg Saar, Germany
    Nucleic Acids Res 40:e43. 2012
    ..In summary, our approach opens new avenues for the elucidation of pathogenic mechanisms and for the detection of molecular key players...
  30. pmc Immunogenicity of autoantigens
    Christina Backes
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    BMC Genomics 12:340. 2011
    ..To this end, we have carried out the most comprehensive in-silicio study of different groups of autoantigens including large antigen sets identified by our groups combined with publicly available antigen sets...
  31. pmc A dictionary on microRNAs and their putative target pathways
    Christina Backes
    Center for Bioinformatics, Saarland University, Germany
    Nucleic Acids Res 38:4476-86. 2010
    ..Our target pathways analysis provides a 'miRNA-target pathway' dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs...
  32. doi request reprint MicroRNA expression profiles in human testicular tissues of infertile men with different histopathologic patterns
    Masood Abu-Halima
    Department of Human Genetics, Saarland University, Saar, Germany Department of Obstetrics and Gynecology, IVF and Andrology Laboratory, Saarland University, Saar, Germany Electronic address
    Fertil Steril 101:78-86.e2. 2014
    ..To investigate the expression profiles of microRNA (miRNA) in human testes showing different histopathological patterns...
  33. pmc Novel autoantigens immunogenic in COPD patients
    Petra Leidinger
    Department of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Saar, Germany
    Respir Res 10:20. 2009
    ..In this study we analyze the complexity of the autoantibody response and reveal the nature of the antigens that are recognized by autoantibodies in COPD patients...
  34. ncbi request reprint Amplicons on chromosome 12q13-21 in glioblastoma recurrences
    Ulrike Fischer
    Department of Human Genetics, Saarland University, 66421 Homburg Saar, Germany
    Int J Cancer 126:2594-602. 2010
    ..We recognized a significant longer survival time in glioblastoma patients that lack amplifications of either CDK4, CYP27B1, XRCC6BP1 (KUB3), or MDM2...
  35. ncbi request reprint Stable serum miRNA profiles as potential tool for non-invasive lung cancer diagnosis
    Andreas Keller
    Biomarker Discovery Center Heidelberg, Heidelberg, Germany
    RNA Biol 8:506-16. 2011
    ..Our findings support the idea that a developing lung cancer might be detectable years prior to diagnosis through a specific miRNA signature and that this signature changes during tumor development...
  36. ncbi request reprint Frequent overexpression of the genes FXR1, CLAPM1 and EIF4G located on amplicon 3q26-27 in squamous cell carcinoma of the lung
    Nicole Comtesse
    Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
    Int J Cancer 120:2538-44. 2007
    ..Our results contribute to the understanding of the frequent amplification processes in squamous cell carcinomas of the lung and to the understanding of the translation initiation that appears not to require eIF4E in lung carcinogenesis...
  37. pmc Identification of novel SNPs in glioblastoma using targeted resequencing
    Andreas Keller
    Biomarker Discovery Center Heidelberg, Heidelberg, Germany
    PLoS ONE 6:e18158. 2011
    ..In addition, we identified SNPs in 20 of 21 GBM associated antigens providing further evidence that genetic variations are significantly associated with the immunogenicity of antigens...
  38. doi request reprint MicroRNA signatures in total peripheral blood as novel biomarkers for acute myocardial infarction
    Benjamin Meder
    Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
    Basic Res Cardiol 106:13-23. 2011
    ..The here presented study shows that single miRNAs and especially miRNA signatures derived from peripheral blood, could be valuable novel biomarkers for cardiovascular diseases...
  39. pmc Genome-wide gene amplification during differentiation of neural progenitor cells in vitro
    Ulrike Fischer
    Department of Human Genetics, Saarland University, Homburg Saar, Germany
    PLoS ONE 7:e37422. 2012
    ..Gene amplifications in normal human cells as physiological process has not been reported yet and may bear resemblance to developmental gene amplifications in amphibians and insects...
  40. pmc Autoantibody signature differentiates Wilms tumor patients from neuroblastoma patients
    Jana Schmitt
    Department of Human Genetics, Medical School, Saarland University, Homburg, Germany
    PLoS ONE 6:e28951. 2011
    ..In summary, neuroblastoma appears as a highly immunogenic tumor as demonstrated by the extended number of antigens that separate this tumor from Wilms tumor...
  41. pmc Increased seroreactivity to glioma-expressed antigen 2 in brain tumor patients under radiation
    Sabrina M Heisel
    Department of Human Genetics, Saarland University Medical School, Homburg Saar, Germany
    PLoS ONE 3:e2164. 2008
    ..Most recently, cell culture and animal studies provided the first convincing evidence that radiation not only eliminates tumor cells, but also modulates the immune response and likely improves anti-tumor immunotherapy...
  42. pmc Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets
    Nicole Comtesse
    Department of Human Genetics, Medical School, University of Saarland, Building 60, 66421 Homburg Saar, Germany
    Proc Natl Acad Sci U S A 102:9601-6. 2005
    ..The frequent antibody response against specific antigens offers new diagnostic and therapeutic targets for meningioma. We developed a statistical learning method to differentiate sera of meningioma patients from sera of healthy donors...
  43. doi request reprint Altered microRNA expression profiles of human spermatozoa in patients with different spermatogenic impairments
    Masood Abu-Halima
    Department of Human Genetics, Saarland University, Homburg Saar, Germany
    Fertil Steril 99:1249-1255.e16. 2013
    ..To determine whether microRNAs are differentially expressed in men with normal versus impaired spermatogenesis, and to find a biomarker for accurate diagnosis of male infertility...
  44. doi request reprint New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
    Andreas Keller
    Department of Human Genetics, Saarland University, 66421 Homburg, Saar, Germany
    Nat Commun 3:698. 2012
    ..Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis...
  45. doi request reprint Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies
    Benjamin Meder
    Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
    Circ Cardiovasc Genet 4:110-22. 2011
    ....
  46. ncbi request reprint Evidence for the mode of action of the highly cytotoxic Streptomyces polyketide kendomycin
    Yasser A Elnakady
    Department of Pharmaceutical Biotechnology, Saarland University, P O Box 151150, 66041 Saarbrucken, Germany
    Chembiochem 8:1261-72. 2007
    ..This study therefore provides evidence that kendomycin mediates its cytotoxic effects, at least in part, through proteasome inhibition...
  47. pmc The human miRNA repertoire of different blood compounds
    Petra Leidinger
    Chair for Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
    BMC Genomics 15:474. 2014
    ..In this study we provide insights into the human miRNome of different compounds of the blood including CD3, CD14, CD15, CD19, CD56 positive cells as well as exosomes...
  48. pmc Diagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of microRNA abundance in blood and tissue
    Andrea S Bauer
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    PLoS ONE 7:e34151. 2012
    ..The results could have an immediate diagnostic value for the evaluation of tumor reoccurrence in patients, who have undergone curative surgical resection, and for people with a familial risk of pancreatic cancer...
  49. doi request reprint Proteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography- and mass spectrometry-based approaches
    Katja Melchior
    Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrucken, Germany
    J Proteome Res 8:4604-14. 2009
    ..The results indicate the usefulness of the semi-top-down approach for the investigation of immunogenic antigens in human tumor tissue samples...
  50. pmc Blood born miRNAs signatures that can serve as disease specific biomarkers are not significantly affected by overall fitness and exercise
    Christina Backes
    Department of Human Genetics, Medical School, Saarland University, Homburg Saar, Germany
    PLoS ONE 9:e102183. 2014
    ..These data support the idea of disease associated miRNA patterns useful as biomarkers that are not readily altered by physiological conditions. ..
  51. doi request reprint A set of specific miRNAs is connected with murine and human gastric cancer
    Aftab Ali Shah
    Division of Molecular Genetics, Institute of Human Genetics, University of Tubingen, Germany
    Genes Chromosomes Cancer 52:237-49. 2013
    ..If confirmed in a larger patient pool, these miRNAs could constitute appropriate blood-born biomarkers for GC...
  52. pmc High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing
    Mark Matzas
    Febit group, Heidelberg, Germany
    Nat Biotechnol 28:1291-4. 2010
    ..We use DNA obtained by megacloning to assemble synthetic genes. In principle, millions of DNA fragments can be sequenced, characterized and sorted in a single megacloner run, enabling constructive biology up to the megabase scale...
  53. doi request reprint Comprehensive analysis of microRNA profiles in multiple sclerosis including next-generation sequencing
    Andreas Keller
    Department of Human Genetics, Saarland University, Germany
    Mult Scler 20:295-303. 2014
    ..MicroRNAs (miRNAs) are short, noncoding RNAs with gene regulatory functions whose expression profiles may serve as disease biomarkers...