Jorg D Hoheisel

Summary

Affiliation: German Cancer Research Center
Country: Germany

Publications

  1. ncbi request reprint Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis
    Markus Beier
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D 69120, Heidelberg, Germany
    J Biotechnol 94:15-22. 2002
  2. ncbi request reprint Antibody microarrays: promises and problems
    Wlad Kusnezow
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Biotechniques . 2002
  3. ncbi request reprint The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis
    Diana Stjepandic
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D 69120 Heidelberg, Germany
    Environ Microbiol 4:819-23. 2002
  4. ncbi request reprint Analysis of nutrient-dependent transcript variations in Neurospora crassa
    Verena Aign
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120, Heidelberg, Germany
    Fungal Genet Biol 40:225-33. 2003
  5. ncbi request reprint Microarray technology: beyond transcript profiling and genotype analysis
    Jorg D Hoheisel
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nat Rev Genet 7:200-10. 2006
  6. doi request reprint Affinity-based microarrays for proteomic analysis of cancer tissues
    Jorg D Hoheisel
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, Heidelberg, Germany
    Proteomics Clin Appl 7:8-15. 2013
  7. pmc Systematic interpretation of microarray data using experiment annotations
    Kurt Fellenberg
    Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D 69009 Heidelberg, Germany
    BMC Genomics 7:319. 2006
  8. ncbi request reprint Optimal design of microarray immunoassays to compensate for kinetic limitations: theory and experiment
    Wlad Kusnezow
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Mol Cell Proteomics 5:1681-96. 2006
  9. pmc Manufacturing DNA microarrays from unpurified PCR products
    Frank Diehl
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, 69120 Heidelberg, Germany
    Nucleic Acids Res 30:e79. 2002
  10. doi request reprint ABO blood groups and pancreatic cancer risk and survival: results from the PANcreatic Disease ReseArch (PANDoRA) consortium
    Cosmeri Rizzato
    Genomic Epidemiology Group, German Cancer Research Center DKFZ, Heidelberg, Germany
    Oncol Rep 29:1637-44. 2013

Detail Information

Publications74

  1. ncbi request reprint Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis
    Markus Beier
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D 69120, Heidelberg, Germany
    J Biotechnol 94:15-22. 2002
    ..This rate of 63% nevertheless compares favourably with an extension rate of only 50%, which was achieved under identical conditions, if pre-fabricated oligonucleotides of identical sequence had been spotted to the glass support...
  2. ncbi request reprint Antibody microarrays: promises and problems
    Wlad Kusnezow
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Biotechniques . 2002
    ....
  3. ncbi request reprint The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis
    Diana Stjepandic
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D 69120 Heidelberg, Germany
    Environ Microbiol 4:819-23. 2002
    ..A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions...
  4. ncbi request reprint Analysis of nutrient-dependent transcript variations in Neurospora crassa
    Verena Aign
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120, Heidelberg, Germany
    Fungal Genet Biol 40:225-33. 2003
    ..This is indicative of the occurrence of a high degree of co-regulation of genes in N. crassa. Especially the regulation of the expression of proteins involved in metabolic pathways was found to be strongly regulated at the RNA level...
  5. ncbi request reprint Microarray technology: beyond transcript profiling and genotype analysis
    Jorg D Hoheisel
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nat Rev Genet 7:200-10. 2006
    ....
  6. doi request reprint Affinity-based microarrays for proteomic analysis of cancer tissues
    Jorg D Hoheisel
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, Heidelberg, Germany
    Proteomics Clin Appl 7:8-15. 2013
    ..This review highlights methodological aspects relevant for a biomedically useful analysis of cellular samples and discusses the potential of such studies, in particular, in view of personalised medicine approaches...
  7. pmc Systematic interpretation of microarray data using experiment annotations
    Kurt Fellenberg
    Department of Functional Genome Analysis, German Cancer Research Center, PO 101949, D 69009 Heidelberg, Germany
    BMC Genomics 7:319. 2006
    ..More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format...
  8. ncbi request reprint Optimal design of microarray immunoassays to compensate for kinetic limitations: theory and experiment
    Wlad Kusnezow
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Mol Cell Proteomics 5:1681-96. 2006
    ..In addition, a separate panel of low abundance cytokines in blood plasma was detected with remarkably high signal-to-noise ratios...
  9. pmc Manufacturing DNA microarrays from unpurified PCR products
    Frank Diehl
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, 69120 Heidelberg, Germany
    Nucleic Acids Res 30:e79. 2002
    ..In addition, a larger number of arrays can be made from one batch of amplification products...
  10. doi request reprint ABO blood groups and pancreatic cancer risk and survival: results from the PANcreatic Disease ReseArch (PANDoRA) consortium
    Cosmeri Rizzato
    Genomic Epidemiology Group, German Cancer Research Center DKFZ, Heidelberg, Germany
    Oncol Rep 29:1637-44. 2013
    ..In addition, we investigated the possible influence that genetic variability at the ABO locus may have in pancreatic cancer survival, but we observed no effect in our population...
  11. doi request reprint Robust protein profiling with complex antibody microarrays in a dual-colour mode
    Christoph Schröder
    Functional Genome Analysis, German Cancer Research Center DKFZ, Heidelberg, Germany
    Methods Mol Biol 785:203-21. 2011
    ..Here, we present our current protocol, which is used for the simultaneous analysis of the abundance of more than 800 proteins in plasma, urine, and tissue samples...
  12. ncbi request reprint Solid type clear cell carcinoma of the pancreas: differential diagnosis of an unusual case and review of the literature
    Martin Loos
    Department of General Surgery, University of Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg, Germany
    Virchows Arch 450:719-26. 2007
    ..Despite metastatic behavior, the tumor displayed a more favorable course than conventional pancreatic ductal adenocarcinoma. We suggest that this tumor be called solid type clear cell carcinoma of the pancreas...
  13. pmc Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy
    Nicole Marmé
    Institute of Physical Chemistry, University of Heidelberg Im Neuenheimer Feld, 229, 69120 Heidelberg, Germany
    Nucleic Acids Res 34:e90. 2006
    ..The developed technique enables the identification of SNPs in 10(-11) M solutions of PCR amplicons from M.tuberculosis in only 100 s...
  14. doi request reprint Immunoassay-based proteome profiling of 24 pancreatic cancer cell lines
    Mohamed Saiel Saeed Alhamdani
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, Heidelberg, Germany
    J Proteomics 75:3747-59. 2012
    ..Last, 187 proteins were differentially expressed in primary versus metastatic cancer cells, of which the majority is functionally related to cellular movement...
  15. pmc Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies
    Christoph Schröder
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
    Mol Cell Proteomics 9:1271-80. 2010
    ..As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses...
  16. pmc Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines
    Cora Mund
    Division of Epigenetics, Deutsches Krebsforschungszentrum Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nucleic Acids Res 33:e73. 2005
    ..At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines were observed...
  17. doi request reprint Identification of malignancy factors by analyzing cystic tumors of the pancreas
    Andrea Bauer
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Pancreatology 9:34-44. 2009
    ....
  18. ncbi request reprint Kinetics of antigen binding to antibody microspots: strong limitation by mass transport to the surface
    Wlad Kusnezow
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Proteomics 6:794-803. 2006
    ....
  19. pmc Somatic mutations in exocrine pancreatic tumors: association with patient survival
    P Sivaramakrishna Rachakonda
    Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
    PLoS ONE 8:e60870. 2013
    ..02) and a corresponding HR of 3.07 (95%CI 1.33-7.10). Our results are indicative of an association between mutational status and survival in PDAC patients, which if confirmed in subsequent studies can have potential clinical application...
  20. doi request reprint Diagnostic values of GHSR DNA methylation pattern in breast cancer
    Sandeep Kumar Botla
    Division of Functional Genome Analysis, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Breast Cancer Res Treat 135:705-13. 2012
    ..Our data suggest a link between epigenetic down-regulation of GHSR and breast cancer cell invasion...
  21. doi request reprint A universally applicable process for preparing stoichiometrically 1:1 labelled functional proteins
    Achim Friedrich
    Division of Functional Genome Analysis, German Cancer Research Center DKFZ, Heidelberg, Germany
    Proteomics 11:3757-60. 2011
    ..This process allows a gentle purification of a protein fraction that has exactly one label attached to each molecule under conditions that preserve protein structure...
  22. pmc Microarray analysis of nemorosone-induced cytotoxic effects on pancreatic cancer cells reveals activation of the unfolded protein response (UPR)
    Frank Holtrup
    Functional Genome Analysis, German Cancer Research Centre DKFZ, Heidelberg, Germany
    Br J Pharmacol 162:1045-59. 2011
    ..Here, we examine its growth-inhibitory effects on pancreatic cancer cells. Based on transcription profiling, a molecular mode of action is proposed...
  23. doi request reprint Epigenetically deregulated microRNA-375 is involved in a positive feedback loop with estrogen receptor alpha in breast cancer cells
    Pedro de Souza Rocha Simonini
    Division of Functional Genome Analysis, Helmholtz University Young Investigator Group Molecular RNA Biology and Cancer, German Cancer Research Center DKFZ and Institute of Pathology, University of Heidelberg, Heidelberg, Germany
    Cancer Res 70:9175-84. 2010
    ..Additionally, we found that RASD1 negatively regulates ERα expression. Our findings define a forward feedback pathway in control of ERα expression, highlighting new strategies to treat ERα-positive invasive breast tumors...
  24. ncbi request reprint Fluorescent sample labeling for DNA microarray analyses
    Verena Beier
    Functional Genoe Analysis, Deutsches Krebsforschungzentrum, Heidelberg, Germany
    Methods Mol Biol 283:127-35. 2004
    ....
  25. ncbi request reprint Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray
    Susanne Diehl
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, 69120 Heidelberg, Germany
    Mol Biochem Parasitol 123:115-23. 2002
    ..A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays...
  26. doi request reprint Lack of replication of seven pancreatic cancer susceptibility loci identified in two Asian populations
    Daniele Campa
    German Cancer Research Center DKFZ, Heidelberg, Germany
    Cancer Epidemiol Biomarkers Prev 22:320-3. 2013
    ..Two recent genome-wide association studies (GWAS) of pancreatic ductal adenocarcinoma (PDAC), conducted, respectively, in a Japanese and in a Chinese population, identified eight novel loci affecting PDAC risk...
  27. doi request reprint Berberine inhibits cell growth and mediates caspase-independent cell death in human pancreatic cancer cells
    Lina Pinto-Garcia
    Department of Functional Genome Analysis, German Cancer Research Center DKFZ, Heidelberg, Germany
    Planta Med 76:1155-61. 2010
    ..The activation of these signalling pathways might be explained by the fact that berberine intercalates DNA and induces DNA strand break through inhibition of topoisomerases and induction of DNA lesions...
  28. ncbi request reprint Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data
    Christian H Busold
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Bioinformatics 21:2424-9. 2005
    ..Up to now functional categories that are relevant for one or more experimental context(s) have been commonly extracted from a set of regulated genes and presented in long lists...
  29. pmc Pancreatic cancer susceptibility loci and their role in survival
    Cosmeri Rizzato
    German Cancer Research Center DKFZ, Heidelberg, Germany
    PLoS ONE 6:e27921. 2011
    ..In conclusion, we found that rs8028529 could be, if these results are replicated, a promising marker for both risk and prognosis for this lethal disease...
  30. doi request reprint Single-step procedure for the isolation of proteins at near-native conditions from mammalian tissue for proteomic analysis on antibody microarrays
    Mohamed Saiel Saeed Alhamdani
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    J Proteome Res 9:963-71. 2010
    ..In Western blot and antibody microarray assays, they outperformed the other buffer systems, indicating that they should also be useful for other types of proteomic studies...
  31. ncbi request reprint Peptide nucleic acids on microarrays and other biosensors
    Ole Brandt
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Trends Biotechnol 22:617-22. 2004
    ..In our opinion, all of these factors contribute significantly toward the establishment of faster and more reliable analytical processes and opens new fields of application...
  32. pmc Proteome variations in pancreatic stellate cells upon stimulation with proinflammatory factors
    Aseel J Marzoq
    From the Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany and
    J Biol Chem 288:32517-27. 2013
    ..The identified direct effects of individual cytokines on human pancreatic stellate cells provide new insights about their contribution to pancreatic cancer promotion. ..
  33. ncbi request reprint Peptide nucleic acid microarrays
    Anette Jacob
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Methods Mol Biol 283:283-93. 2004
    ..In this chapter, protocols are presented for the whole production process as well as sample hybridization...
  34. pmc Concurrent epigenetic silencing of wnt/β-catenin pathway inhibitor genes in B cell chronic lymphocytic leukaemia
    Evgeny A Moskalev
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    BMC Cancer 12:213. 2012
    ....
  35. ncbi request reprint Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies
    Wlad Kusnezow
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Heidelberg, Germany
    Proteomics 7:1786-99. 2007
    ..Microarray data were in accord with quantitative cytokine levels measured by ELISA and Luminex, demonstrating comparable reliability and femtomolar range sensitivity of the established microarray approach...
  36. pmc Genes and proteins differentially expressed during in vitro malignant transformation of bovine pancreatic duct cells
    R Jesnowski
    Clinical Cooperation Unit Molecular Gastroenterology E180, German Cancer Research Center Heidelberg and Department of Medicine II, Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany
    Neoplasia 9:136-46. 2007
    ..Thus, we were able to establish an in vitro model of pancreatic carcinogenesis, which enabled us to identify genes and proteins differentially expressed during the early steps of malignant transformation...
  37. pmc Assessment and optimisation of normalisation methods for dual-colour antibody microarrays
    Martin Sill
    Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
    BMC Bioinformatics 11:556. 2010
    ..Therefore, it might be beneficial to select invariant features among the features already represented on available arrays for normalisation by a dedicated selection algorithm...
  38. doi request reprint Analysis conditions for proteomic profiling of mammalian tissue and cell extracts with antibody microarrays
    Mohamed Saiel Saeed Alhamdani
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Heidelberg, Germany
    Proteomics 10:3203-7. 2010
    ....
  39. pmc High-definition DNA methylation profiles from breast and ovarian carcinoma cell lines with differing doxorubicin resistance
    Michael Boettcher
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    PLoS ONE 5:e11002. 2010
    ..Our results provide detailed DNA methylation information from two separate model systems for acquired doxorubicin resistance and suggest the occurrence of similar methylation changes in both systems upon exposure to the drug...
  40. doi request reprint Gene expression profiling identifies novel key players involved in the cytotoxic effect of Artesunate on pancreatic cancer cells
    Mahmoud Youns
    Department of Functional Genome Analysis, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Biochem Pharmacol 78:273-83. 2009
    ..The present analysis is a starting point for the generation of hypotheses on candidate genes and for a more detailed dissection of the functional role of individual genes for the activity of Artesunate in tumor cells...
  41. ncbi request reprint Antibody microarrays: an evaluation of production parameters
    Wlad Kusnezow
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Proteomics 3:254-64. 2003
    ..Altogether, data from more than 700 individual array experiments were taken into account. In addition to home-made slides, commercially available systems were also included in the analysis...
  42. 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...
  43. ncbi request reprint Generation of high density protein microarrays by cell-free in situ expression of unpurified PCR products
    Philipp Angenendt
    Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Mol Cell Proteomics 5:1658-66. 2006
    ..Finally we adapted the system to the high throughput expression of libraries by designing a single primer pair for the introduction of the required T7 promoter and demonstrated the in situ expression using 384 randomly chosen clones...
  44. ncbi request reprint Creation of a minimal tiling path of genomic clones for Drosophila: provision of a common resource
    Volker Hollich
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Biotechniques 37:282-4. 2004
    ..2% of chromosomal arm 2R, 79.0% of 2L, 89.6% of 3R, and 80.5% of chromosome 4. In total, the 25,135 clones represent 76.7 Mb--equivalent to about 67% of the genome--and would be suitable for producing a microarray on a single slide...
  45. ncbi request reprint Monitoring methylation changes in cancer
    Verena Beier
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Adv Biochem Eng Biotechnol 104:1-11. 2007
    ..Secondly, a microarray-based approach for detecting methylation-specific sequence polymorphisms via an on-chip enzymatic primer extension is described...
  46. pmc Genotypic resistance testing in HIV by arrayed primer extension
    Michaela Schanne
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
    Anal Bioanal Chem 391:1661-9. 2008
    ..The validation included HIV subtype B, prevalent in industrialised countries, as well as non-subtype B samples that are more common elsewhere...
  47. doi request reprint DNA microarray preparation by light-controlled in situ synthesis
    Markus Beier
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Curr Protoc Nucleic Acid Chem . 2005
    ..Spatial resolution is achieved by carefully controlling the illumination of defined spots on the glass substrate, on which the oligonucleotide probes are synthesized using straightforward phosphoramidite chemistry...
  48. pmc Establishment and characterization of a highly tumourigenic and cancer stem cell enriched pancreatic cancer cell line as a well defined model system
    Johannes Fredebohm
    Functional Genome Analysis, German Cancer Research Center, Heidelberg, Germany
    PLoS ONE 7:e48503. 2012
    ..All of these attributes make this cell line an extremely valuable model to study the biology of and pharmaceutical effects on pancreatic cancer...
  49. 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...
  50. doi request reprint Transcript profiling identifies novel key players mediating the growth inhibitory effect of NS-398 on human pancreatic cancer cells
    Mahmoud Youns
    Functional Genome Analysis, German Cancer Research Centre DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Eur J Pharmacol 650:170-7. 2011
    ..Moreover, we reported, for the first time, that the growth inhibitory effect of NS-398 is mediated by down-regulation of RRM2, CTGF, MCM2 and PCNA and up-regulation of NAG-1 in all cell lines...
  51. doi request reprint Analysis of DNA-protein interactions: from nitrocellulose filter binding assays to microarray studies
    Reham Helwa
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Anal Bioanal Chem 398:2551-61. 2010
    ..This article gives an overview of early and recent methodologies applied to such ends...
  52. doi request reprint The transcriptome of the colonial marine hydroid Hydractinia echinata
    Jorge Soza-Ried
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    FEBS J 277:197-209. 2010
    ..Finally, a database was created to store all the acquired information (http://www.mchips.org/hydractinia_echinata.html)...
  53. doi request reprint Plasma protein analysis of patients with different B-cell lymphomas using high-content antibody microarrays
    Christoph Schröder
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Proteomics Clin Appl 7:802-12. 2013
    ..In this study, plasma samples from a multicentric case-control study on lymphoma were analyzed for the identification of proteins useful for diagnosis...
  54. doi request reprint Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays
    Stephan Bau
    febit biomed gmbh, Im Neuenheimer Feld 519, 69120, Heidelberg, Germany
    Anal Bioanal Chem 393:171-5. 2009
    ..6 and 107.5-fold for the individual target regions. This method represents a flexible and cost-effective approach for large-scale resequencing of complex genomes...
  55. pmc Replication and virus-induced transcriptome of HAdV-5 in normal host cells versus cancer cells--differences of relevance for adenoviral oncolysis
    Dominik E Dorer
    Helmholtz University Group Oncolytic Adenoviruses, German Cancer Research Center Deutsches Krebsforschungszentrum DKFZ, Department of Dermatology, Heidelberg University Hospital, Heidelberg, Germany
    PLoS ONE 6:e27934. 2011
    ..Our results provide a rationale for improving oncolytic adenoviruses either by adaptation of viral infection to target tumor cells or by modulating tumor cell functions to better support viral replication...
  56. ncbi request reprint Solid supports for microarray immunoassays
    Wlad Kusnezow
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    J Mol Recognit 16:165-76. 2003
    ..The sensitivity of microspot immunoassays predicted by the current analyte theory is not yet a reality, indicating the extent of both the technology's potential and the size of the task still ahead...
  57. ncbi request reprint Antibody microarrays: the crucial impact of mass transport on assay kinetics and sensitivity
    Wlad Kusnezow
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Expert Rev Mol Diagn 6:111-24. 2006
    ..Finally, the review addresses the question of whether ambient analyte immunoassay is truly a separate category of microspot assay, with the conclusion that this may be a flawed concept...
  58. pmc Decoding pooled RNAi screens by means of barcode tiling arrays
    Michael Boettcher
    Department for Functional Genome Analysis, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
    BMC Genomics 11:7. 2010
    ..Here we describe a novel method to decode pooled RNAi screens, namely barcode tiling array analysis, and demonstrate how this approach can be used to precisely quantify the abundance of individual shRNAs from a pool...
  59. doi request reprint Secretome profiling with antibody microarrays
    Shakhawan Abdulrahman Mustafa
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Mol Biosyst 7:1795-801. 2011
    ..This review looks at recent applications of this novel platform technology in secretome analysis and reflects on the future...
  60. doi request reprint Single-molecule detection on a protein-array assay platform for the exposure of a tuberculosis antigen
    Ronny Schmidt
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    J Proteome Res 10:1316-22. 2011
    ..Samples containing about 600 antigen molecules per microliter produced a distinct signal. The methodology developed can be employed for any set of target molecules for which appropriate antibodies exist...
  61. ncbi request reprint DNA-probes for the highly sensitive identification of single nucleotide polymorphism using single-molecule spectroscopy
    Achim Friedrich
    Department of Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    FEBS Lett 581:1644-8. 2007
    ..This method leads to a subnanomolar sensitivity for this single nucleotide specific DNA assay technique...
  62. ncbi request reprint Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis
    Kurt Fellenberg
    Department of Theoretical Bioinformatics, German Cancer Research Center, PO Box 101949, D 69009 Heidelberg, Germany
    Bioinformatics 18:423-33. 2002
    ..However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis...
  63. pmc In vivo activity and pharmacokinetics of nemorosone on pancreatic cancer xenografts
    Robert J Wolf
    Division of Functional Genome Analysis, German Cancer Research Center DKFZ, Heidelberg, Germany Department of General Surgery, University of Heidelberg, Heidelberg, Germany
    PLoS ONE 8:e74555. 2013
    ..It is concluded that nemorosone is a potential anti-cancer lead compound with good bioavailability, little side-effects and promising growth-inhibitory effects, thus representing a valuable compound for a combination therapy approach. ..
  64. pmc Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples
    Janne Pullat
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    BMC Genomics 8:282. 2007
    ....
  65. pmc Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons
    Rafael Queiroz
    Zentrum fur Molekulare Biologie der Universitat Heidelberg, ZMBH DKFZ Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
    BMC Genomics 10:495. 2009
    ..We describe here the transitions in gene expression that occur during differentiation of in-vitro cultured bloodstream forms to procyclic forms...
  66. doi request reprint Synthesis of 5'-O-phosphoramidites with a photolabile 3'-O-protecting group
    Markus Beier
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Curr Protoc Nucleic Acid Chem . 2004
    ....
  67. doi request reprint Depletion of RAD17 sensitizes pancreatic cancer cells to gemcitabine
    Johannes Fredebohm
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    J Cell Sci 126:3380-9. 2013
    ..In contrast to CHK1, RAD17 knockdown by itself does not lead to abnormal DNA segregation, suggesting a more specific action. ..
  68. doi request reprint RNA-directed epigenomic reprogramming: an emerging principle of a more targeted cancer therapy?
    Evgeny A Moskalev
    Functional Genome Analysis, Deutsches Krebsforschungszentrum DKFZ, Heidelberg, Germany
    Genes Chromosomes Cancer 51:105-10. 2012
    ..In consideration of the early onset of epigenetic aberrations, such an approach could even be useful for cancer prevention...
  69. ncbi request reprint Another side of genomics: synthetic biology as a means for the exploitation of whole-genome sequence information
    Peer Stähler
    Febit Biotech GmbH, Heidelberg, Germany
    J Biotechnol 124:206-12. 2006
    ..Synthetic genes will then be the tools of choice to obtain any sequence at any time in any laboratory...
  70. pmc PNA microarrays for hybridisation of unlabelled DNA samples
    Ole Brandt
    Functional Genome Analysis and Protein Analysis Facility, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nucleic Acids Res 31:e119. 2003
    ..Overall best results in terms of selectivity and sensitivity were obtained with thiol-modified PNAs on maleimide surfaces...
  71. pmc Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression
    Evgeny A Moskalev
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
    Nucleic Acids Res 39:e77. 2011
    ..The process can be applied irrespective of the locus interrogated and the number of sites analysed, avoiding an optimization of the amplification conditions for each individual locus...
  72. ncbi request reprint Microcystic tubulopapillary carcinoma of the pancreas: a new tumor entity?
    Irene Esposito
    Department of Pathology, University of Heidelberg, Im Neuenheimer Feld 220, 69120, Heidelberg, Germany
    Virchows Arch 444:447-53. 2004
    ..These data suggest that the neoplasm most likely represents a new pancreatic tumor entity, which we would like to refer to as microcystic tubulopapillary tumor...
  73. pmc Oncoproteomic profiling with antibody microarrays
    Mohamed Ss Alhamdani
    Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany
    Genome Med 1:68. 2009
    ..Here, we review the technical aspects and challenges in the development and use of antibody microarray assays and examine recently reported applications in oncoproteomics...
  74. ncbi request reprint Late ischemic preconditioning of the myocardium alters the expression of genes involved in inflammatory response
    Dmitrij Zubakov
    Functional Genome Analysis, German Cancer Research Center DKFZ Heidelberg, Im Neuenheimer Feld 580, D 69120, Heidelberg, Germany
    FEBS Lett 547:51-5. 2003
    ....