Roland Eils

Summary

Affiliation: German Cancer Research Center
Country: Germany

Publications

  1. ncbi Machine learning based analyses on metabolic networks supports high-throughput knockout screens
    Kitiporn Plaimas
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Syst Biol 2:67. 2008
  2. ncbi An ultrasensitive sorting mechanism for EGF receptor endocytosis
    Hannah Schmidt-Glenewinkel
    Division Theoretical Bioinformatics, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
    BMC Syst Biol 2:32. 2008
  3. ncbi Identifying essential genes in bacterial metabolic networks with machine learning methods
    Kitiporn Plaimas
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Syst Biol 4:56. 2010
  4. ncbi Analyzing the regulation of metabolic pathways in human breast cancer
    Gunnar Schramm
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, and Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany
    BMC Med Genomics 3:39. 2010
  5. ncbi Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes
    Patrick Warnat
    Department of Theoretical Bioinformatics B080, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, Heidelberg, Germany
    BMC Cancer 7:89. 2007
  6. ncbi Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy
    Phillip Hundeshagen
    Division of Theoretical Bioinformatics, German Cancer Research Center and Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Heidelberg, Germany
    BMC Biol 9:38. 2011
  7. ncbi Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
    Gunnar Schramm
    Theoretical Bioinformatics, German Cancer Research Center DKFZ, Heidelberg, Germany
    BMC Bioinformatics 8:149. 2007
  8. ncbi GOPET: a tool for automated predictions of Gene Ontology terms
    Arunachalam Vinayagam
    Department of Molecular Biophysics, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69121 Heidelberg, Germany
    BMC Bioinformatics 7:161. 2006
  9. ncbi Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms
    Rainer König
    Department of Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany
    BMC Bioinformatics 7:119. 2006
  10. ncbi Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains
    Alla Bulashevska
    Theoretical Bioinformatics Department, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    BMC Bioinformatics 7:298. 2006

Detail Information

Publications81

  1. ncbi Machine learning based analyses on metabolic networks supports high-throughput knockout screens
    Kitiporn Plaimas
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Syst Biol 2:67. 2008
    ..Computational identification of new drug targets is a major goal of pharmaceutical bioinformatics...
  2. ncbi An ultrasensitive sorting mechanism for EGF receptor endocytosis
    Hannah Schmidt-Glenewinkel
    Division Theoretical Bioinformatics, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
    BMC Syst Biol 2:32. 2008
    ..Several mechanisms to generate this behaviour have been described theoretically, the underlying assumptions of which, however, have not been experimentally demonstrated for the EGF receptor internalization network...
  3. ncbi Identifying essential genes in bacterial metabolic networks with machine learning methods
    Kitiporn Plaimas
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Syst Biol 4:56. 2010
    ..However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective...
  4. ncbi Analyzing the regulation of metabolic pathways in human breast cancer
    Gunnar Schramm
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, and Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany
    BMC Med Genomics 3:39. 2010
    ..However, the metabolic demands of different cancers are very heterogeneous and depend on their origin of tissue, age, gender and other clinical parameters. We investigated tumor specific regulation in the metabolism of breast cancer...
  5. ncbi Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes
    Patrick Warnat
    Department of Theoretical Bioinformatics B080, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, Heidelberg, Germany
    BMC Cancer 7:89. 2007
    ..Additional research effort is needed to describe the patterns of gene expression in this cohort and to identify reliable prognostic markers for this subset of patients...
  6. ncbi Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy
    Phillip Hundeshagen
    Division of Theoretical Bioinformatics, German Cancer Research Center and Institute of Pharmacy and Molecular Biotechnology, BIOQUANT, University of Heidelberg, Heidelberg, Germany
    BMC Biol 9:38. 2011
    ..To date, the identification of clinically-applicable drugs that modulate autophagy has been hampered by the lack of standardized assays capable of precisely reporting autophagic activity...
  7. ncbi Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli
    Gunnar Schramm
    Theoretical Bioinformatics, German Cancer Research Center DKFZ, Heidelberg, Germany
    BMC Bioinformatics 8:149. 2007
    ..Moreover, utilising a network topology based on gene relationships may facilitate interpreting this vast amount of information, and extracting significant patterns within the networks...
  8. ncbi GOPET: a tool for automated predictions of Gene Ontology terms
    Arunachalam Vinayagam
    Department of Molecular Biophysics, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69121 Heidelberg, Germany
    BMC Bioinformatics 7:161. 2006
    ..These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions...
  9. ncbi Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms
    Rainer König
    Department of Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany
    BMC Bioinformatics 7:119. 2006
    ..On a proteomic level, biochemical research has elucidated an increasingly complete image of the metabolic architecture, especially for less complex organisms like the well studied bacterium Escherichia coli...
  10. ncbi Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains
    Alla Bulashevska
    Theoretical Bioinformatics Department, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    BMC Bioinformatics 7:298. 2006
    ..Although many efforts have been made to predict subcellular location from sequence information only, there is the need for further research to improve the accuracy of prediction...
  11. ncbi Bayesian statistical modelling of human protein interaction network incorporating protein disorder information
    Svetlana Bulashevska
    Theoretical Bioinformatics Department, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    BMC Bioinformatics 11:46. 2010
    ....
  12. ncbi Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
    Patrick Warnat
    Department of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    BMC Bioinformatics 6:265. 2005
    ..Although similar questions for the same type of cancer are addressed in these different studies, a comparative analysis of their results is hampered by the use of heterogeneous microarray platforms and analysis methods...
  13. ncbi Computational imaging in cell biology
    Roland Eils
    Intelligent Bioinformatics Systems Division, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
    J Cell Biol 161:477-81. 2003
    ..These applications illustrate the potential of computational imaging to enhance our knowledge of the dynamics of cellular structures and processes...
  14. ncbi Model-based dissection of CD95 signaling dynamics reveals both a pro- and antiapoptotic role of c-FLIPL
    Nicolai Fricker
    Division of Immunogenetics, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
    J Cell Biol 190:377-89. 2010
    ....
  15. ncbi Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation
    Astrid Riehl
    Signal Transduction and Growth Control, German Cancer Research Center DKFZ, DKFZ ZMBH Alliance, Heidelberg, Germany
    BMC Genomics 11:537. 2010
    ....
  16. ncbi Prediction of small molecule binding property of protein domains with Bayesian classifiers based on Markov chains
    Alla Bulashevska
    Theoretical Bioinformatics Department, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Comput Biol Chem 33:457-60. 2009
    ..The software is available from the author upon request...
  17. ncbi Automated analysis of the mitotic phases of human cells in 3D fluorescence microscopy image sequences
    Nathalie Harder
    University of Heidelberg, IPMB, and DKFZ Heidelberg, Dept Bioinformatics and Functional Genomics, Im Neuenheimer Feld 364, D 69120 Heidelberg, Germany
    Med Image Comput Comput Assist Interv 9:840-8. 2006
    ..Our scheme proves a high accuracy, suggesting a promising future for automating the evaluation of high-throughput experiments...
  18. ncbi Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered
    Alla Bulashevska
    Department of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    J Theor Biol 254:799-803. 2008
    ..2005. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21 (16), 3435-3438]. Further strength of our approach is the ease of implementation...
  19. ncbi Normalizing for individual cell population context in the analysis of high-content cellular screens
    Bettina Knapp
    Heidelberg University, Viroquant Research Group Modeling, Bioquant BQ26, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Bioinformatics 12:485. 2011
    ..However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology...
  20. ncbi High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer
    Daniel E Stange
    Division of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Clin Cancer Res 12:345-52. 2006
    ..CONCLUSIONS: Molecular profiling using bacterial artificial chromosome arrays identified DNA copy number imbalances on 1q and 16p as significant classifiers of histologic and molecular subgroups...
  21. ncbi Understanding apoptosis by systems biology approaches
    Inna N Lavrik
    Division of Immunogenetics, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
    Mol Biosyst 5:1105-11. 2009
    ....
  22. ncbi Tropical--parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images
    Markus Ulrich
    Department of Theoretical Bioinformatics, German Cancer Research Center Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Bioinformatics 22:2709-10. 2006
    ..AVAILABILITY: Tropical is available free of charge for academic use at http://www.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp after signing a material transfer agreement...
  23. ncbi PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways
    Gunnar Schramm
    Department of Bioinformatics and Functional Genomics, University of Heidelberg, Heidelberg, Germany
    Bioinformatics 26:1225-31. 2010
    ..Availability and Implementation: PathWave is implemented in a package for R (www.r-project.org) version 2.6.0 or higher. It is freely available from http://www.ichip.de/software/pathwave.html...
  24. ncbi Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining
    Il Han Kim
    University of Heidelberg, BIOQUANT, IPMB, and German Cancer Research Center DKFZ, Dept Bioinformatics and FunctionalGenomics, Biomedical Computer Vision Group, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    BMC Biotechnol 7:92. 2007
    ..Direct comparisons of these detection methods are scarce, however...
  25. ncbi Systems biological analysis of epidermal growth factor receptor internalization dynamics for altered receptor levels
    Hannah Schmidt-Glenewinkel
    Division of Theoretical Bioinformatics, German Cancer Research Center, University of Heidelberg, 69120 Heidelberg, Germany
    J Biol Chem 284:17243-52. 2009
    ..Finally, determining the ratio of internalized versus surface-located ligand.receptor complexes for this cell line confirmed that it follows a convex curve, supporting our model predictions...
  26. ncbi RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens
    Nora Rieber
    Viroquant Research Group Modeling, University of Heidelberg, Bioquant BQ26, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Bioinformatics 25:678-9. 2009
    ..The results of the analysis are presented as a set of HTML pages. Additionally, all values and plots are available as either text files or pdf and png files. AVAILABILITY: http://bioconductor.org/..
  27. ncbi Non-rigid registration of 3D multi-channel microscopy images of cell nuclei
    Siwei Yang
    Biomedical Computer Vision Group, Dept Theoretical Bioinformatics, DKFZ Heidelberg, Germany
    Med Image Comput Comput Assist Interv 9:907-14. 2006
    ..We also describe an extension of our approach which is applied for the registration of 3D+t (4D) image series of moving cell nuclei...
  28. ncbi Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection
    Petr Matula
    University of Heidelberg, Department of Bioinformatics and Functional Genomics, BIOQUANT, IPMB, Heidelberg, Germany
    Cytometry A 75:309-18. 2009
    ..Our image analysis approach allows for the automatic and accurate determination of changes in viral infection based on high-throughput single-cell-based siRNA cell array imaging experiments...
  29. ncbi Automatic identification of subcellular phenotypes on human cell arrays
    Christian Conrad
    Intelligent Bioinformatics Systems, German Cancer Research Center (DKFZ, 69120 Heidelberg, Germany
    Genome Res 14:1130-6. 2004
    ..Our classification method can be adapted to virtually any microscopic assay based on cell morphology, opening a wide range of applications including large-scale RNAi screening in human cells...
  30. ncbi Gene expression analysis on biochemical networks using the Potts spin model
    Rainer König
    Division Intelligent Bioinformatics Systems, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Bioinformatics 20:1500-5. 2004
    ..coli treated with tryptophan excess, starvation and trpyptophan repressor mutants. We observed fragmentation of the tryptophan biosynthesis pathway, which corresponds well to the commonly known regulatory response of the cells...
  31. ncbi Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design
    Rainer König
    Division of Theoretical Bioinformatics, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nucleic Acids Res 32:e29. 2004
    ..Finally, we compared microarray-based gene expression profiles with the corresponding expression patterns obtained by whole-mount in situ hybridizations, resulting in a 90% correspondence...
  32. ncbi Applying Support Vector Machines for Gene Ontology based gene function prediction
    Arunachalam Vinayagam
    Department of Molecular Biophysics, Deutsches Krebsforschungszentrum DKFZ, TP3, Im Neuenheimer Feld 580, Heidelberg, D 69120, Germany
    BMC Bioinformatics 5:116. 2004
    ..However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions...
  33. ncbi Group testing for pathway analysis improves comparability of different microarray datasets
    Theodora Manoli
    Theoretical Bioinformatics, German Cancer Reseach Center, 69120 Heidelberg, Germany
    Bioinformatics 22:2500-6. 2006
    ..Moreover, pathways recurrently identified in these analyses are more likely to be reliable than those from a single analysis on a single dataset...
  34. ncbi Dynamics within the CD95 death-inducing signaling complex decide life and death of cells
    Leo Neumann
    Division of Theoretical Bioinformatics, German Cancer Research Center DKFZ, Heidelberg, Germany
    Mol Syst Biol 6:352. 2010
    ..We present an integrated model describing the complex dynamics of CD95-mediated apoptosis and NF-kappaB signaling...
  35. ncbi Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
    Nathalie Harder
    University of Heidelberg, IPMB, BIOQUANT, and DKFZ Heidelberg, Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, D 69120 Heidelberg, Germany
    Genome Res 19:2113-24. 2009
    ..Our approach can be readily applied to comparable assays aiming at uncovering the dynamic cause of cell division phenotypes...
  36. ncbi Quantitative motion analysis and visualization of cellular structures
    Daniel Gerlich
    Intelligent Bioinformatics Systems, DKFZ, Im Neuenheimer Feld 280, D 69120, Heidelberg, Germany
    Methods 29:3-13. 2003
    ..In this review, we discuss concepts for automated analysis of multidimensional image data from live cell microscopy and their application to the dynamics of cell nuclear subcompartments...
  37. ncbi Gene expression signature predicting pathologic complete response with gemcitabine, epirubicin, and docetaxel in primary breast cancer
    Olaf Thuerigen
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    J Clin Oncol 24:1839-45. 2006
    ..CONCLUSION: In conclusion, our gene expression signature allows prediction of pCR to PST containing G, E, and Doc with unprecedented high overall accuracy and robustness...
  38. ncbi CGH-Profiler: data mining based on genomic aberration profiles
    Falk Schubert
    Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    BMC Bioinformatics 6:188. 2005
    ..This semantic description of chromosomal imbalances hinders a large-scale statistical analysis across different experiments, e.g. for finding aberration patterns associated with a particular disease type or state...
  39. ncbi Integration of activating and inhibitory receptor signaling by regulated phosphorylation of Vav1 in immune cells
    Sven Mesecke
    Division of Theoretical Bioinformatics, German Cancer Research Center, 69120 Heidelberg, Germany
    Sci Signal 4:ra36. 2011
    ..Our data support a central role for Vav1 in determining the cytotoxic activity of NK cells and provide insight into the molecular mechanism of the integration of positive and negative signals during lymphocyte activation...
  40. ncbi Inferring genetic regulatory logic from expression data
    Svetlana Bulashevska
    Division Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Bioinformatics 21:2706-13. 2005
    ..We tested our method with previously published data of the Saccharomyces cerevisiae cell cycle and found relations between genes consistent with biological knowledge...
  41. ncbi Enhancers regulate progression of development in mammalian cells
    Anna Lena Kranz
    Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, and Bioquant, University of Heidelberg, INF 267, 69120 Heidelberg, Germany
    Nucleic Acids Res 39:8689-702. 2011
    ..Altogether, we characterized three classes of TFs: with binding sites being enriched at the TSS (like SP1), depleted at the TSS (like FOX), and rather uniformly distributed...
  42. ncbi Gene network dynamics controlling keratinocyte migration
    Hauke Busch
    B080 Division of Theoretical Bioinformatics, German Cancer Research Center DKFZ, Heidelberg, Germany
    Mol Syst Biol 4:199. 2008
    ..Context information for enhancing, delaying or stopping migration is provided by the activity of the protein kinase A signaling pathway. Our study reveals the complex orchestration of multiple pathways controlling cell migration...
  43. ncbi RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors
    Tobias Bauer
    Department of Theoretical Bioinformatics, German Cancer Research Center DKFZ, INF 280, 69120 Heidelberg, Germany
    Bioinformatics 27:2239-47. 2011
    ..Identifying genome-wide targets of transcription factors (TFs) provides the basis to discover the involvement of TFs and TF cooperativeness in cellular systems and pathogenesis...
  44. ncbi Artesunate activates mitochondrial apoptosis in breast cancer cells via iron-catalyzed lysosomal reactive oxygen species production
    Anne Hamacher-Brady
    Division of Theoretical Bioinformatics, Applied Systems Biology Group, German Cancer Research Center, 69120 Heidelberg, Germany
    J Biol Chem 286:6587-601. 2011
    ....
  45. ncbi Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images
    Apichat Suratanee
    Department of Bioinformatics and Functional Genomics, University of Heidelberg, Heidelberg, Germany
    Bioinformatics 26:i653-8. 2010
    ..The method is generic and has the potential to be used for a large variety of different viruses and treatments being screened by imaging techniques...
  46. ncbi Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis
    Dirk A Ridder
    Department of Pharmacology, University of Heidelberg, Germany
    Brain Res 1272:3-13. 2009
    ..Thus, our in silico analysis may provide additional information on transcriptional regulation in stroke and suggests several novel transcriptional programs for further exploration...
  47. ncbi Autoantibodies against the exocrine pancreas in autoimmune pancreatitis: gene and protein expression profiling and immunoassays identify pancreatic enzymes as a major target of the inflammatory process
    J Matthias Lohr
    Molecular Gastroenterology, German Cancer Research Center, Heidelberg, Germany
    Am J Gastroenterol 105:2060-71. 2010
    ..The objective was to identify novel markers of disease and to unravel the pathogenesis of AIP...
  48. ncbi 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin - poor tracks
    Christian P Bacher
    Division of Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    BMC Cell Biol 5:45. 2004
    ..Typically, such studies generate a wealth of data that require novel methods in image analysis and computational tools to quantitatively track particle movement on the background of moving cells and shape changing nuclei...
  49. ncbi Global gene expression profiling and cluster analysis in Xenopus laevis
    Danila Baldessari
    Division of Molecular Embryology, German Cancer Research Center (DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Mech Dev 122:441-75. 2005
    ..The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes...
  50. ncbi Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
    Simon Reiss
    The Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
    Cell Host Microbe 9:32-45. 2011
    ..Our analysis suggests that the direct activation of a lipid kinase by HCV NS5A contributes critically to the integrity of the membranous viral replication complex...
  51. ncbi Probing compressibility of the nuclear interior in wild-type and lamin deficient cells using microscopic imaging and computational modeling
    Paula González Avalos
    University of Heidelberg, Bioquant and IPMB, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    J Biomech 44:2642-8. 2011
    ..Combined with knockdown and overexpression screens, it paves the way towards a high-throughput measurement of intracellular mechanical properties in functional phenotyping screens...
  52. ncbi Genome-wide expression screens indicate a global role for protein kinase CK2 in chromatin remodeling
    Thomas Barz
    Biochemische Zellphysiologie (B0200) and Intelligente Bioinformatiksysteme (H0900, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
    J Cell Sci 116:1563-77. 2003
    ..Our data are compatible with the idea that CK2 acts at different levels of cellular organization and that CK2 has a global role in transcription-related chromatin remodeling...
  53. ncbi Global chromosome positions are transmitted through mitosis in mammalian cells
    Daniel Gerlich
    Intelligent Bioinformatics Systems, German Cancer Research Center (DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Cell 112:751-64. 2003
    ....
  54. ncbi Inferring a system model of subcellular topoisomerase II beta localization dynamics
    Chaitanya A Athale
    Intelligent Bioinformatics Systems, German Cancer Research Centre DKFZ, Heidelberg, Germany
    OMICS 8:167-75. 2004
    ..This model is then validated by comparing it with alternative scenarios and shown to have predictive power...
  55. ncbi Etiology-dependent molecular mechanisms in human hepatocarcinogenesis
    Christof Schlaeger
    Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
    Hepatology 47:511-20. 2008
    ..CONCLUSION: Our findings suggest that MDM4 and EEF1A2 act as etiology-independent oncogenes in a significant percentage of HCCs...
  56. ncbi Pathways of urothelial cancer progression suggested by Bayesian network analysis of allelotyping data
    Svetlana Bulashevska
    Division Intelligent Bioinformatics Systems, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
    Int J Cancer 110:850-6. 2004
    ..Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html...
  57. ncbi Structural analysis of interphase X-chromatin based on statistical shape theory
    Siwei Yang
    Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BIOQUANT, IPMB, Heidelberg, Germany
    Biochim Biophys Acta 1783:2089-99. 2008
    ..We found that geometric normalization with respect to the nucleus shape based on non-rigid image registration has a significant influence on the location of the genomic regions...
  58. ncbi Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles
    Claudia Schoch
    Laboratory for Leukemia Diagnostics, Department of Internal Medicine III, University Hospital Grosshadern, Ludwig Maximilians University, 81366 Munich, Germany
    Proc Natl Acad Sci U S A 99:10008-13. 2002
    ..By using two different strategies for microarray data analyses, this study revealed a unique correlation between AML-specific cytogenetic aberrations and gene expression profiles...
  59. ncbi From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression
    Oleg Schmidt-Kittler
    , , , Germany
    Proc Natl Acad Sci U S A 100:7737-42. 2003
    ..Thus, our data challenge the widely held view that the precursors of metastasis are derived from the most advanced clone within the primary tumor...
  60. ncbi Topology of genes and nontranscribed sequences in human interphase nuclei
    Markus O Scheuermann
    Division of Molecular Genetics, Deutsches Krebsforschungszentrum, D-69120 Heidelberg, Germany
    Exp Cell Res 301:266-79. 2004
    ..However, the nontranscribed sequences were found predominantly at the nuclear periphery or at the nucleoli, whereas genes tended to localize on chromosome surfaces exposed to the nuclear interior...
  61. ncbi Distinct molecular phenotype of malignant CD34(+) hematopoietic stem and progenitor cells in chronic myelogenous leukemia
    Ralf Kronenwett
    Department of Hematology, Oncology and Clinical Immunology, Heinrich Heine University Duesseldorf, Moorenstr 5, 40225 Duesseldorf, Germany
    Oncogene 24:5313-24. 2005
    ..05), suggesting that the adenosine A1 receptor is of functional relevance in CML hematopoietic progenitor cells...
  62. ncbi Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling
    Alexander Schramm
    Department of Pediatric Oncology and Hematology, University Hospital of Essen, Hufelandstr 55, Essen 45122, Germany
    Oncogene 24:7902-12. 2005
    ..Our data suggest that microarray-derived data in addition to traditional clinical factors will be useful for risk assessment and defining biological properties of neuroblastoma...
  63. ncbi Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
    Ziv Bar-Joseph
    Department of Computer Science, School of Computer Science and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    Proc Natl Acad Sci U S A 105:955-60. 2008
    ..This conclusion was supported by both bioinformatic analysis and experiments performed on other cell types. We suggest that this approach will help pinpoint genetic elements contributing to normal cell growth and cellular transformation...
  64. ncbi Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification
    Andre Oberthuer
    Children s Hospital, Department of Pediatric Oncology and Hematology, University of Cologne, Kerpener Strasse 62, D 50924 Cologne, Germany
    J Clin Oncol 24:5070-8. 2006
    ..To develop a gene expression-based classifier for neuroblastoma patients that reliably predicts courses of the disease...
  65. ncbi Local gene density predicts the spatial position of genetic loci in the interphase nucleus
    Andrea E Murmann
    Department of Medicine, Section Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
    Exp Cell Res 311:14-26. 2005
    ..Thus, alterations in gene density directly at translocation junctions could explain the change in the position of affected genes in leukemia cells...
  66. ncbi A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials
    Svenja Debey
    Molecular Tumor Biology and Tumor Immunology, Clinic I for Internal Medicine, University of Cologne, Kerpenerstrasse 62, 50937 Cologne, Germany
    Genomics 87:653-64. 2006
    ....
  67. ncbi Systems biology and artificial life: towards predictive modeling of biological systems
    Jan T Kim
    School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
    Artif Life 14:1-2. 2008
  68. ncbi Visualizing telomere dynamics in living mammalian cells using PNA probes
    Chris Molenaar
    Department of Molecular Cell Biology, Leiden University Medical Center, 2333 AL Leiden, The Netherlands
    EMBO J 22:6631-41. 2003
    ..Furthermore, telomeres were shown to associate with promyelocytic leukemia (PML) bodies in a dynamic manner...
  69. ncbi Systemic spread is an early step in breast cancer
    Yves Hüsemann
    Department of Pathology, Division of Oncogenomics, University of Regensburg, Regensburg 93053, Germany
    Cancer Cell 13:58-68. 2008
    ..Therefore, release from dormancy of early-disseminated cancer cells may frequently account for metachronous metastasis...
  70. ncbi Microarray analysis reveals differential gene expression patterns and regulation of single target genes contributing to the opposing phenotype of TrkA- and TrkB-expressing neuroblastomas
    Johannes H Schulte
    University Children s Hospital of Essen, Germany
    Oncogene 24:165-77. 2005
    ..Fine-tuning of the malignant phenotype may be achieved by additional ligand stimulation with subsequent activation of a few specific genes...
  71. ncbi Distinct gene expression patterns associated with FLT3- and NRAS-activating mutations in acute myeloid leukemia with normal karyotype
    Kai Neben
    Division of Molecular Genetics B060, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Oncogene 24:1580-8. 2005
    ..In conclusion, we showed that unique gene expression patterns can be correlated with FLT3-ITD and FLT3-TKD. This might lead to the identification of further pathogenetic relevant candidate genes particularly in AML with normal karyotype...
  72. ncbi Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus
    Masafumi Muratani
    Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Cell Biol 4:106-10. 2002
    ..One class of PML bodies is particularly noteworthy in that it moves by a metabolic-energy-dependent mechanism. This represents the first example of metabolic-energy-dependent transport of a nuclear body within the mammalian cell nucleus...
  73. ncbi Argonaute--a database for gene regulation by mammalian microRNAs
    Priyanka Shahi
    Medical Research Center, University Hospital, Mannheim D-68167 Mannheim, Germany
    Nucleic Acids Res 34:D115-8. 2006
    ..The web interface allows the user to get information for a single or multiple miRNAs, either selected or uploaded through a text file. Argonaute currently has information on 839 miRNAs from human, mouse and rat...
  74. ncbi Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes
    Andreas Bolzer
    Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
    PLoS Biol 3:e157. 2005
    ..Chromatin domains, which are gene-poor, form a layer beneath the nuclear envelope, while gene-dense chromatin is enriched in the nuclear interior. We discuss the possible functional implications of this finding...
  75. ncbi Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome
    Alexander Schramm
    Division of Hematology and Oncology, University Children s Hospital Essen, Essen, Germany
    Clin Cancer Res 13:1459-65. 2007
    ..To assess the feasibility of predicting neuroblastoma outcome using highly parallel quantitative real-time PCR data...
  76. ncbi Classification of neuroblastoma patients by published gene-expression markers reveals a low sensitivity for unfavorable courses of MYCN non-amplified disease
    Andre Oberthuer
    Children s Hospital, Department of Pediatric Oncology and Hematology and Center for Molecular Medicine Cologne CMMC, University of Cologne, Kerpener Strasse 62, D 50924 Cologne, Germany
    Cancer Lett 250:250-67. 2007
    ..5%. However, patients with unfavorable outcome of MYCN non-amplified disease were largely misclassified (accuracy: 35%), suggesting that these courses are not identified by current marker genes...
  77. ncbi Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer
    Julian A Schardt
    , , Germany
    Cancer Cell 8:227-39. 2005
    ..Because early changes have the highest probability of being shared by genetically unstable tumor cells, the genetic characterization of disseminated tumor cells provides a novel rationale for selecting patients for targeted therapies...
  78. ncbi Breast cancer: a candidate gene approach across the estrogen metabolic pathway
    Christina Justenhoven
    Molecular Mechanisms of Origin and Treatment of Breast Cancer, Dr Margarete Fischer Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, Germany
    Breast Cancer Res Treat 108:137-49. 2008
    ..The tested polymorphisms of the estrogen metabolic pathway may not play a direct role in breast cancer risk. Therefore, future association studies should be extended to other polymorphisms and other regulatory pathways...