Christina Backes

Summary

Affiliation: Saarland University
Country: Germany

Publications

  1. 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
  2. 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
  3. 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
  4. pmc Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana
    Mara Schuler
    Dept of Biosciences Botany, Campus A2, 4 Saarland University, D 66123 Saarbrucken, Germany
    BMC Plant Biol 11:87. 2011
  5. pmc Immunogenicity of autoantigens
    Christina Backes
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    BMC Genomics 12:340. 2011
  6. doi 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
  7. 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
  8. 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
  9. 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
  10. pmc BNDB - the Biochemical Network Database
    Jan Küntzer
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    BMC Bioinformatics 8:367. 2007

Collaborators

Detail Information

Publications51

  1. 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...
  2. 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...
  3. 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...
  4. pmc Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana
    Mara Schuler
    Dept of Biosciences Botany, Campus A2, 4 Saarland University, D 66123 Saarbrucken, Germany
    BMC Plant Biol 11:87. 2011
    ..Additionally, GeneTrail offers a feature that allows screening of individually defined biological categories that are relevant for the respective research topic...
  5. 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...
  6. doi 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. pmc BNDB - the Biochemical Network Database
    Jan Küntzer
    Center for Bioinformatics, Saarland University, 66041 Saarbrucken, Germany
    BMC Bioinformatics 8:367. 2007
    ..The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources...
  11. 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...
  12. doi request reprint Panel of five microRNAs as potential biomarkers for the diagnosis and assessment of male infertility
    Masood Abu-Halima
    Department of Human Genetics, IVF and Andrology Laboratory, Saarland University, Saar, Germany Department of Obstetrics and Gynecology, IVF and Andrology Laboratory, Saarland University, Saar, Germany Electronic address
    Fertil Steril 102:989-997.e1. 2014
    ..To validate a set of five microRNAs (miRNAs) as specific biomarkers for the assessment of male infertility...
  13. 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...
  14. pmc GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
    Christina Backes
    Department of Human Genetics Building 60 Medical School, University of Saarland, 66421 Homburg Saar, Germany
    Nucleic Acids Res 33:W208-13. 2005
    ..We tested GraBCas on already known substrates and showed its usefulness for protein sequence analysis. GraBCas is available at http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/software/index.html...
  15. 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...
  16. 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...
  17. pmc miFRame: analysis and visualization of miRNA sequencing data in neurological disorders
    Christina Backes
    Chair for Clinical Computational Biology, Saarland University, Saarbrucken, Germany
    J Transl Med 13:224. 2015
    ..Especially for small non-coding RNAs such as microRNAs there is a need for analysis and visualization tools that facilitate interpretation of the results also for clinicians...
  18. pmc High-throughput qRT-PCR validation of blood microRNAs in non-small cell lung cancer
    Petra Leidinger
    Department of Human Genetics, Saarland University, Homburg, Germany
    Oncotarget 7:4611-23. 2016
    ..Although for differentiation between NSCLC patients from COPD patients more markers were required, still high accuracy rates were obtained (5 markers: 78.8%; 10 markers: 83.9%; 50 markers: 87.6%). ..
  19. doi request reprint Bias in High-Throughput Analysis of miRNAs and Implications for Biomarker Studies
    Christina Backes
    Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrucken, Germany
    Anal Chem 88:2088-95. 2016
    ..As a consequence, biomarkers that have been discovered by specific high-throughout technologies have to be carefully considered. Especially for validation of the platform, the selection of reasonable candidates is essential. ..
  20. pmc Posttranscriptional deregulation of signaling pathways in meningioma subtypes by differential expression of miRNAs
    Nicole Ludwig
    Department of Human Genetics Medical School, Saarland University, Homburg Saar, Germany N L, S C M, C B, T v W, V G, E M Institute of Pathology Medical School, Saarland University, Homburg Saar, Germany Y J K, E S, R M B Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrucken, Germany S C M, C B, V G, A K
    Neuro Oncol 17:1250-60. 2015
    ..Meningioma is one of the most frequent primary intracranial tumors. As of yet, there are limited data on the role of miRNAs in meningioma of different histological subtypes and the affected signaling pathways...
  21. pmc Longitudinal study on circulating miRNAs in patients after lung cancer resection
    Petra Leidinger
    Department of Human Genetics, Saarland University, Homburg, Germany
    Oncotarget 6:16674-85. 2015
    ..The relationship between altered plasma levels of specific miRNAs with the development of metastases would partially have gone undetected by an analysis at a single time point only...
  22. doi request reprint Influence of next-generation sequencing and storage conditions on miRNA patterns generated from PAXgene blood
    Christina Backes
    Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrucken, Germany
    Anal Chem 87:8910-6. 2015
    ..Specifically, hsa-miR-1271-5p and hsa-miR-182-5p showed coefficients of variation above 100% indicating a strong influence of the NGS protocol on the abundance of these miRNAs. ..
  23. doi request reprint Circulating serum miRNAs as potential biomarkers for nephroblastoma
    Nicole Ludwig
    Department of Human Genetics, Saarland University, Homburg Saar, Germany
    Pediatr Blood Cancer 62:1360-7. 2015
    ..In Europe, nephroblastoma is treated with preoperative chemotherapy without histological confirmation by biopsy. Therefore, minimal-invasive diagnostic markers confirming nephroblastoma diagnosis are highly warranted...
  24. pmc What makes a blood cell based miRNA expression pattern disease specific?--a miRNome analysis of blood cell subsets in lung cancer patients and healthy controls
    Petra Leidinger
    Institute of Human Genetics, Medical School, Saarland University, Building 60, 66421 Homburg Saar, Germany
    Oncotarget 5:9484-97. 2014
    ..The data indicate that additional blood components, like erythrocytes, platelets, or exosomes might contribute to the disease specificity of a miRNA signature. ..
  25. 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...
  26. pmc 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...
  27. 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...
  28. pmc From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS
    Sabine C Mueller
    From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrucken, Germany, Department of Human Genetics, Saarland University, 66421 Homburg, Germany
    J Biol Chem 291:1582-90. 2016
    ..Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer. ..
  29. doi request reprint Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy
    Christina Backes
    Chair for Clinical Bioinformatics, Saarland University, Building E2 1, 66123, Saarbrucken, Germany
    Hum Genet 135:31-40. 2016
    ..The applied approach is cutoff free and considers a ranked list of genetic variants as input. ..
  30. 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...
  31. 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...
  32. pmc Towards Clinical Applications of Blood-Borne miRNA Signatures: The Influence of the Anticoagulant EDTA on miRNA Abundance
    Petra Leidinger
    Department of Human Genetics, Medical School, Saarland University, Building 60, 66421, Homburg Saar, Germany
    PLoS ONE 10:e0143321. 2015
    ..For all six blood donors at the four conditions (24 samples) we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays...
  33. pmc Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis
    Andreas Keller
    Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
    J Neuroinflammation 12:196. 2015
    ..Here, we analyzed miRNA profiles in serum and whole blood of patients with NMOSD and clinically isolated syndrome (CIS)/relapsing-remitting MS (RRMS) as well as healthy controls by next-generation sequencing (NGS)...
  34. pmc miRNAs can be generally associated with human pathologies as exemplified for miR-144
    Andreas Keller
    Chair for Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
    BMC Med 12:224. 2014
    ..Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists...
  35. pmc The blood-borne miRNA signature of lung cancer patients is independent of histology but influenced by metastases
    Petra Leidinger
    Department of Human Genetics, Medical School, Saarland University, Building 60, Homburg Saar 66421, Germany
    Mol Cancer 13:202. 2014
    ..4% [94.9%-95.9%]. Here, we now separately analyzed the miRNA expression in blood of non-small cell lung cancer (NSCLC), including squamous cell lung cancer and adenocarcinoma, and small cell lung cancer (SCLC) patients...
  36. 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...
  37. ncbi request reprint Integrative analysis of cancer-related data using CAP
    Pierre Dönnes
    Center for Bioinformatics, Saarland University, Saarbrucken, Germany
    FASEB J 18:1465-7. 2004
    ..CAP is freely available at the following web site: http://www.bioinf.uni-sb.de/CAP/...
  38. 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...
  39. pmc EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon-Mann-Whitney Test
    Alexander Marx
    Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, Saarbrucken 66123, Germany
    Genomics Proteomics Bioinformatics 14:55-61. 2016
    ..To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/. ..
  40. pmc Regulatory microRNA networks: complex patterns of target pathways for disease-related and housekeeping microRNAs
    Sachli Zafari
    Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrucken 66123, Germany
    Genomics Proteomics Bioinformatics 13:159-68. 2015
    ..Our approach provides important insights into miRNAs and their role in regulatory networks. The methodology can be applied to systematically investigate the differences in target genes and pathways of arbitrary miRNA sets. ..
  41. doi request reprint Circulating Biomarker Panels in Alzheimer's Disease
    Sachli Zafari
    Clinical Bioinformatics, Saarland University, Saarbrx00FC cken, Germany
    Gerontology 61:497-503. 2015
    ..In this review, we provide an overview of different circulating AD biomarkers, starting with a brief summary of CSF markers and focusing on novel biomarker signatures such as small noncoding RNA profiles. ..
  42. pmc Gene amplification during differentiation of mammalian neural stem cells in vitro and in vivo
    Ulrike Fischer
    Department of Human Genetics, Saarland University, 66421 Homburg Saar, Germany
    Oncotarget 6:7023-39. 2015
    ..5. Gene amplification is not only a cancer-related mechanism but is also conserved in evolution, occurring during differentiation of mammalian neural stem cells. ..
  43. 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. ..
  44. 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...
  45. 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...
  46. 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...
  47. doi request reprint Cardiac remodeling in Gαq and Gα11 knockout mice
    Kathrina Wiesen
    Institute of Veterinary Physiology, Vetsuisse Faculty and the Zürich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland Institute for Molecular Cell Biology and Research Centre for Molecular Imaging and Screening, Saarland University, 66421 Homburg Saar, Germany
    Int J Cardiol 202:836-45. 2016
    ..Although both Gαq- and Gα11-protein signaling are believed to be involved in the regulation of cardiac hypertrophy, their detailed contribution to myocardial function remains elusive...
  48. doi request reprint Secretion and immunogenicity of the meningioma-associated antigen TXNDC16
    Christian Harz
    Department of Human Genetics, Medical School, Saarland University, 66421 Homburg Saar, Germany
    J Immunol 193:3146-54. 2014
    ..2% using a set of only five immunogenic TXNDC16 epitopes. ..
  49. pmc Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis
    Christina Backes
    Chair for Clinical Bioinformatics, Saarland University, Saarbrucken, Germany
    BMC Genomics 15:622. 2014
    ..To determine significance thresholds for associated pathways, correction for multiple testing and over-representation permutation testing is applied...
  50. 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...
  51. 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...