Publications

Due to various collaborations with academic partners, BioControl contributed to a number of scientific publications.

2020–2023

  1. P. Brandt, M. H. Mirhakkak, L. Wagner, D. Driesch, A. Möslinger, P. Fänder, S. Schäuble, G. Panagiotou, S. Vylkova: High-Throughput Profiling of Candida auris Isolates Reveals Clade-Specific Metabolic Differences. In: Microbiology Spectrum, e00498-23, 2023. doi: 10.1128/spectrum.00498-23
  2. A. Pfeil, M. Heinz, T. Hoffmann, T. Weise, D. M. Renz, M. Franz, A. Malich, D. Driesch, P. Oelzner, G. Wolf, J. Böttcher: The relationship between structural analysis of the hand and clinical characteristics in psoriatic arthritis. In: Scientific Reports, 12:18913, 2022. doi: 10.1038/s41598-022-23555-5
  3. E. Garbe, F. Gerwien, D. Driesch, T. Müller, B. Böttcher, M. Gräler, S. Vylkova: Systematic Metabolic Profiling Identifies De Novo Sphingolipid Synthesis as Hypha Associated and Essential for Candida albicans Filamentation. In: mSystems, 7(6):e00539-22, 2022. doi: 10.1128/msystems.00539-22
  4. L. Ringleben, T. Weise, H. T. T. Truong, L. H. Anh, M. Pfaff: Experimental and model-based characterisation of Bacillus spizizenii growth under different temperature, pH and salinity conditions prior to aquacultural wastewater treatment application. In: Biochemical Engineering Journal, 187:108630, 2022. doi: 10.1016/j.bej.2022.108630
  5. B. Böttcher, D. Driesch, T. Krüger, E. Garbe, F. Gerwien, O. Kniemeyer, A. A. Brakhage, S. Vylkova: Impaired amino acid uptake leads to global metabolic imbalance of Candida albicans biofilms In: npj Biofilms and Microbiomes, 8:78, 2022. doi: 10.1038/s41522-022-00341-9
  6. L. Malich, F. Gühne, T. Hoffmann, A. Malich, T. Weise, P. Oelzner, G. Wolf, M. Freesmeyer, A. Pfeil: Distribution patterns of arterial affection and the influence of glucocorticoids on 18F-fluorodeoxyglucose positron emission tomography/CT in patients with giant cell arteritis. In: RMD Open, 8:e002464, 2022. doi: 10.1136/rmdopen-2022-002464
  7. T. E. Klassert, C. Zubiria-Barrera, R. Neubert, M. Stock, A. Schneegans, M. López, D. Driesch, G. Zakonsky, P. Gastmeier, H. Slevogt, R. Leistner: Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment. In: Clinical Microbiology and Infection, 28(8):1105–1112, 2022. doi: 10.1016/j.cmi.2022.02.032
  8. T. E. Klassert, R. Leistner, C. Zubiria-Barrera, M. Stock, M. López, R. Neubert, D. Driesch, P. Gastmeier, H. Slevogt: Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study. In: Microbiome, 9(1):169, 2021, doi: 10.1186/s40168-021-01109-7
  9. F. Padberg, T. Höper, S. Henkel, D. Driesch, A. Luch, S. Zellmer: Novel indirect co-culture of immortalised hepatocytes with monocyte derived macrophages is characterised by pro-inflammatory cytokine networks. In: Toxicology in Vitro, 73:105134, 2021.
    doi: 10.1016/j.tiv.2021.105134
  10. S. Hirschmann, A. Gómez-Mejia, U. Mäder, J. Karsunke, D. Driesch, M. Rohde, S. Häussler, G. Burchhardt, S. Hammerschmidt: The two-component system 09 regulates pneumococcal carbohydrate metabolism and capsule expression. In: Microorganisms, 9(3):468, 2021.
    doi: 10.3390/microorganisms9030468
  11. T. E. Klassert, C. Zubiria-Barrera, S. Kankel, M. Stock, R. Neubert, F. Lorenzo-Diaz, N. Doehring, D. Driesch, D. Fischer, H. Slevogt: Early bacterial colonization and antibiotic resistance gene acquisition in newborns. In: Front. Cell. Infect. Microbiol., 10:332, 2020.
    doi: 10.3389/fcimb.2020.00332
  12. T. Weise, C. Grewe, M. Pfaff: Experimental and model-based analysis to optimize microalgal biomass productivity in a pilot-scale tubular photobioreactor. In: Front. Bioeng. Biotechnol., 8:453, 2020.
    doi: 10.3389/fbioe.2020.00453
  13. B. Böttcher, B. Hoffmann, E. Garbe, T. Weise, Z. Cseresnyés, P.  Brandt, S. Dietrich, D. Driesch, M. T. Figge, S. Vylkova: The transcription factor Stp2 is important for Candida albicans biofilm establishment and sustainability. In: Front. Microbiol., 11:794, 2020.
    doi: 10.3389/fmicb.2020.00794
  14. S. Maenz, O. Brinkmann, I. Hasenbein, C. Braun, E. Kunisch, V. Horbert, F. Gunnella, A. Sachse, S. Bischoff, H. Schubert, K. D. Jandt, J. Bossert, D. Driesch, R. W. Kinne, M. Bungartz: The old sheep: a convenient and suitable model for senile osteopenia. In: Journal of Bone and Mineral Metabolism, 38(5):620–630, 2020.
    doi: 10.1007/s00774-020-01098-x
  15. S. Ruben, E. Garbe, S. Mogavero, D. Albrecht-Eckardt, D. Hellwig, A. Häder, T. Krüger, K. Gerth, I. D. Jacobsen, O. Elshafee, S. Brunke, K. Hünniger, O. Kniemeyer, A. A. Brakhage, J. Morschhäuser, B. Hube, S. Vylkova, O. Kurzai, R. Martin: Ahr1 and Tup1 contribute to the transcriptional control of virulence-associated genes in Candida albicans. In: mBio, 11:2, 2020.
    doi: 10.1128/mBio.00206-20
  1. T. Conrad, O. Kniemeyer, S. G. Henkel, T. Krüger, D. J. Mattern, V. Valiante, R. Guthke, I. D. Jacobsen, A. A. Brakhage, S. Vlaic, J. Linde: Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. In: BMC Systems Biology, 12:88, 2018.
    doi: 10.1186/s12918-018-0620-8
  2. T. E. Klassert, S. Goyal, M. Stock, D. Driesch, A. Hussain, L. C. Berrocal-Almanza, R. Myakala, G. Sumanlatha, V. Valluri, N. Ahmed, R. R. Schumann, C. Flores, H. Slevogt: AmpliSeq screening of genes encoding the C-type lectin receptors and their signaling components reveals a common variant in MASP1 associated with pulmonary tuberculosis in an Indian population. In: Frontiers in Immunology, 9:242, 2018.
    doi: 10.3389/fimmu.2018.00242
  3. R. Lehmann, M. M. Müller, T. E. Klassert, D. Driesch, M. Stock, A. Heinrich, T. Conrad, C. Moore, U. K. Schier, R. Guthke, H. Slevogt: Differential regulation of the transcriptomic and secretomic landscape of sensor and effector functions of human airway epithelial cells. In: Mucosal Immunology, 11:627–642, 2018.
    doi: 10.1038/mi.2017.100
  4. V. Horbert, M. Lange, T. Reuter, M. Hoffmann, S. Bischoff, J. Borowski, H. Schubert, D. Driesch, J. Mika, C. Hurschler, R. W. Kinne: Comparison of near-infrared spectroscopy with needle indentation and histology for the determination of cartilage thickness in the large animal model sheep. In: Cartilage, 10(2):173–185, 2017.
    doi: 10.1177/1947603517731851
  5. N. Amarsaikhan, D. Albrecht-Eckardt, C. Sasse, G. H. Braus, Z. B. Ogel, O. Kniemeyer: Proteomic profiling of the antifungal drug response of Aspergillus fumigatus to voriconazole. In: International Journal of Medical Microbiology, 307(7):398–408, 2017.
    doi: 10.1016/j.ijmm.2017.07.011
  6. M. M. Müller, R. Lehmann, T. E. Klassert, S. Reifenstein, T. Conrad, C. Moore, A. Kuhn, A. Behnert, R. Guthke, D. Driesch, H. Slevogt: Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression. In: Scientific Reports, 7:838, 2017.
    doi: 10.1038/s41598-017-00828-y
  7. D. Tominski, J. Katchanov, D. Driesch, M. B. Daley, A. Liedtke, A. Schneider, H. Slevogt, K. Arastéh, H. Stocker: The late-presenting HIV-infected patient 30 years after the introduction of HIV testing: spectrum of opportunistic diseases and missed opportunities for early diagnosis. In: HIV Medicine, 18(2):125–132, 2017.
    doi: 10.1111/hiv.12403
  8. L. C. Berrocal-Almanza, S. Goyal, A. Hussain, T. E. Klassert, D. Driesch, Z. Grozdanovic, G. Sumanlatha, N. Ahmed, V. Valluri, M. L. Conrad, N. Dittrich, R. R. Schumann, B. Lala, H. Slevogt: S100A12 is up-regulated in pulmonary tuberculosis and predicts the extent of alveolar infiltration on chest radiography: an observational study. In: Scientific Reports, 6:31798, 2016.
    doi: 10.1038/srep31798
  9. D. Hellwig, J. Voigt, M. Bouzani, J. Löffler, D. Albrecht-Eckardt, M. Weber, S. Brunke, R. Martin, O. Kurzai, K. Hünniger: Candida albicans induces metabolic reprogramming in human NK cells and responds to perforin with a zinc depletion response. In: Frontiers in Microbiology, 7:750, 2016.
    doi: 10.3389/fmicb.2016.00750
  10. M. Böhringer, S. Pohlers, S. Schulze, D. Albrecht-Eckardt, J. Piegsa, M. Weber, R. Martin, K. Hünniger, J. Linde, R. Guthke, O. Kurzai: Candida albicans infection leads to barrier breakdown and a MAPK/NF-κB mediated stress response in the intestinal epithelial cell line C2BBe1. In: Cellular Microbiology, 18(7):889–904, 2016.
    doi: 10.1111/cmi.12566
  11. A. Ghallab, G. Cellière, S. G. Henkel, D. Driesch, S. Hoehme, U. Hofmann, S. Zellmer, P. Godoy, A. Sachinidis, M. Blaszkewicz, R. Reif, R. Marchan, L. Kuepfer, D. Häussinger, D. Drasdo, R. Gebhardt, J. G. Hengstler: Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases. In: Journal of Hepatology, 64(4):860–871, 2016.
    doi: 10.1016/j.jhep.2015.11.018
  12. I. Leonhardt, S. Spielberg, M. Weber, D. Albrecht-Eckardt, M. Bläss, R. Claus, D. Barz, K. Scherlach, C. Hertweck, J. Löffler, K. Hünniger, O. Kurzai: Farnesol - a quorum sensing molecule of Candida albicans modulates innate immunity. In: Mycoses, 58(Suppl. 3):29, Special Issue: Abstracts of the 49. Wissenschaftliche Tagung der Deutschsprachigen Mykologischen Gesellschaft e.V. and 1st International Symposium of the CRC/Transregio FungiNet, 16–19 September 2015, Friedrich-Schiller-Universität Jena, Germany, 2015.
    doi: 10.1111/myc.12361
  13. M. Bartl, M. Pfaff, A. Ghallab, D. Driesch, S. G. Henkel, J. G. Hengstler, S. Schuster, C. Kaleta, R. Gebhardt, S. Zellmer, P. Li: Optimality in the zonation of ammonia detoxification in rodent liver. In: Archives of Toxicology, 89(11):2069–2078, 2015.
    doi: 10.1007/s00204-015-1596-4
  14. Z. Grozdanovic, L. C. Berrocal Almanza, S. Goyal, A. Hussain, T. E. Klassert, D. Driesch, V. Tokaryeva, Y. Y. Löschmann, G. Sumanlatha, N. Ahmed, V. Valluri, R. R. Schumann, B. Lala, H. Slevogt: A novel reading scheme for assessing the extent of radiographic abnormalities and its association with disease severity in sputum smear-positive tuberculosis: an observational study in Hyderabad/India. In: PLOS ONE, 10(9):e0138070, 2015.
    doi: 10.1371/journal.pone.0138070
  15. I. Leonhardt, S. Spielberg, M. Weber, D. Albrecht-Eckardt, M. Bläss, R. Claus, D. Barz, K. Scherlach, C. Hertweck, J. Löffler, K. Hünniger, O. Kurzai: The fungal quorum-sensing molecule farnesol activates innate immune cells but suppresses cellular adaptive immunity. In: mBio, 6(2):e00143-15, 2015.
    doi: 10.1128/mBio.00143-15
  16. J. Linde, S. Schulze, S. G. Henkel, R. Guthke: Data- and knowledge-based modeling of gene regulatory networks: an update. In: EXCLI Journal, 14:346–378, 2015.
    doi: 10.17179/excli2015-168
  17. S. Schulze, S. G. Henkel, D. Driesch, R. Guthke, J. Linde: Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. In: Front. Microbiol., 6:65, 2015.
    doi: 10.3389/fmicb.2015.00065
  18. S. G. Henkel, A. Ter Beek, S. Steinsiek, S. Stagge, K. Bettenbrock, M. J. Teixeira de Mattos, T. Sauter, O. Sawodny, M. Ederer: Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions. In: PLoS ONE, 9(9):e107640, 2014.
    doi: 10.1371/journal.pone.0107640
  19. D. Woetzel, R. Huber, P. Kupfer, D. Pohlers, M. Pfaff, D. Driesch, T. Häupl, D. Koczan, P. Stiehl, R. Guthke, R. W. Kinne: Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation. In: Arthritis Research & Therapy, 16:R84, 2014.
    doi: 10.1186/ar4526
  20. F. Schliess, S. Hoehme, S. G. Henkel, A. Ghallab, D. Driesch, J. Böttger, R. Guthke, M. Pfaff, J. G. Hengstler, R. Gebhardt, D. Häussinger, D. Drasdo, S. Zellmer: Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration. In: Hepatology, 60(6):2040–2051, 2014.
    doi: 10.1002/hep.27136
  21. M. W. Sieber, M. Guenther, N. Jaenisch, D. Albrecht-Eckardt, M. Kohl, O. W. Witte, C. Frahm: Age-specific transcriptional response to stroke. In: Neurobiology of Aging, 35(7):1744–1754, 2014.
    doi: 10.1016/j.neurobiolaging.2014.01.012
  22. F. F. Stecker, J.-H. Schierz, T. Opfermann, D. Driesch, G. O. Hofmann, T. Winkens, M. Freesmeyer: Frühe dynamische PET/CT-Aufnahmen zur Diagnostik der chronischen Osteomyelitis und Fraktur der unteren Extremität - Pilotstudie. In: Nuklearmedizin, 53(3):117–122, 2014.
    doi: 10.3413/Nukmed-0572-13-03
  23. M. Böhringer, S. Schulze, J. Linde, D. Albrecht-Eckardt, R. Guthke, O. Kurzai: Transcriptional response of C2BBe1 intestinal epithelial cells to Candida albicans infection. In: Mycoses, 56(Suppl. 2):27, Special Issue: Abstracts of the 47th Annual Meeting of the German-Speaking Mycological Society (DMykG), 5–7 September 2013, Tübingen, Germany, 2013.
    doi: 10.1111/myc.12110
  24. R. Martin, A. Haeder, K. Meinhardt, D. Albrecht-Eckardt, S. Brunke, K. Hünniger, B. Hube, J. Morschhäuser, O. Kurzai: Expression dynamics of core filamentation respone genes in the hyperfilamentous Candida albicans tup1Δ mutant. In: Mycoses, 56(Suppl. 2):5, Special Issue: Abstracts of the 47th Annual Meeting of the German-Speaking Mycological Society (DMykG), 5–7 September 2013, Tübingen, Germany, 2013.
    doi: 10.1111/myc.12109
  25. J. Voigt, I. D. Jacobsen, M. Bouzani, J. Loeffler, D. Albrecht-Eckardt, O. Kurzai: Natural killer cells modulate the immune response in Candida-infections. In: International Journal of Medical Microbiology, 303(Suppl. 1), Special Issue: 65th Annual Meeting of the German Society for Hygiene and Microbiology (DGHM), 2013.
  26. A. Darr, T. Opfermann, T. Niksch, D. Driesch, R. J. Marlowe, M. Freesmeyer: Low-Activity 124I-PET/Low-Dose CT Versus 99mTc-Pertechnetate Planar Scintigraphy or 99mTc-Pertechnetate Single-Photon Emission Computed Tomography of the Thyroid: A Pilot Comparison. In: Clinical Nuclear Medicine, 38(10):770–777, 2013.
    doi: 10.1097/RLU.0b013e3182a20d26
  27. R. Martin, D. Albrecht-Eckardt, S. Brunke, B. Hube, K. Hünniger, O. Kurzai: A Core Filamentation Response Network in Candida albicans Is Restricted to Eight Genes. In: PLOS ONE, 8(3):e58613, 2013.
    doi: 10.1371/journal.pone.0058613
  28. M. Weber, S. G. Henkel, S. Vlaic, R. Guthke, E. J. van Zoelen, D. Driesch, Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0. In: BMC Syst Biol, 7:1, 2013.
    doi: 10.1186/1752-0509-7-1
  29. T. Kaulfuss, J. Voigt, R. Martin, D. Driesch, O. Kurzai: Transcriptional dynamics of Candida albicans and human Natural Killer cells during interaction. In: International Journal of Medical Microbiology, 302, Special Issue: 64th Annual Meeting of the German Society for Hygiene and Microbiology (DGHM), 2012.
  30. A. Lovas, A. Weidemann, D. Albrecht, L. Wiechert, D. Weih, F. Weih, p100 Deficiency Is Insufficient for Full Activation of the Alternative NF-kB Pathway: TNF Cooperates with p52-RelB in Target Gene Transcription. In:PLoS ONE, Vol. 7(8):e42741, 2012.
    doi: 10.1371/journal.pone.0042741
  31. D. Wartenberg, M. Vödisch, O. Kniemeyer, D. Albrecht-Eckardt, K. Scherlach, R. Winkler, M. Weide, A.A. Brakhage, Proteome analysis of the farnesol-induced stress response in Aspergillus nidulans - The role of a putative dehydrin. In: J Proteomics, Vol. 75(12), 2012, pp. 4038-4049.
    doi: 10.1016/j.jprot.2012.05.023
  32. O. Kniemeyer, J. Teutschbein, D. Albrecht, D. Wartenberg, M. Voedisch, F. Lessing, A. A. Brakhage: Proteomics of Aspergillus. In: Mycoses, 54(Suppl. 2):23, Special Issue: 5th Trends in Medical Mycology, 2011.
    doi: 10.1111/j.1439-0507.2011.02091.x
  33. K. Meinhardt, R. Martin, D. Albrecht-Eckardt, O. Kurzai: Alkaline-induced switch of the filamentous Candida albicans tup1Δ mutant to yeast-like growth. In: Mycoses, 54(5):414, 45th Annual Meeting of the German-Speaking Mycological Society (DMykG), 2011.
    doi: 10.1111/j.1439-0507.2011.02066.x
  34. R. Martin, D. Albrecht-Eckardt, O. Kurzai: The transcriptional program of morphological plasticity in Candida albicans. In: Mycoses, 54(5):410, 45th Annual Meeting of the German-Speaking Mycological Society (DMykG), 2011.
    doi: 10.1111/j.1439-0507.2011.02066.x
  35. D. Albrecht, O. Kniemeyer, F. Mech, M. Gunzer, A.A. Brakhage, R. Guthke, On The Way Toward Systems Biology Of Aspergillus fumigatus Infection. In: Int J Med Microbiol, 301, 2011, pp. 453-459.
    doi: 10.1016/j.ijmm.2011.04.014
  36. S. Priebe, J. Linde, D. Albrecht, R. Guthke, A.A. Brakhage, FungiFun: a web-based application for functional categorization of fungal genes and proteins. In: Fungal Genet Biol, Vol. 48(4), 2011, pp. 353-358.
    doi: 10.1016/j.fgb.2010.11.001
  37. S. Bruns, M. Seidler, D. Albrecht, S. Salvenmoser, N. Remme, A.A. Brakhage, C. Hertweck, O. Kniemeyer, F.M.C. Mueller, Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin. In: Proteomics, 10(17), 2010, pp. 3097-3107.
    doi: 10.1002/pmic.201000129
  38. J. Teutschbein, D. Albrecht, M. Poetsch, R. Winkler, R. Guthke, A.A. Brakhage, O. Kniemeyer, Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic fungus Aspergillus fumigatus. In: J Proteome Res, 9(7), 2010, pp. 3427-3442.
    doi: 10.1021/pr9010684
  39. V. Shelest, D. Albrecht, E. Shelest, DistanceScan: a tool for promoter modeling. In: Bioinformatics, 26(11), 2010, pp. 1460-1462.
    doi: 10.1093/bioinformatics/btq132
  40. D. Albrecht, O. Kniemeyer, A.A. Brakhage, R. Guthke, Missing values in gel-based proteomics. In: Proteomics, 10(6), 2010, pp. 1202-1211.
    doi: 10.1002/pmic.200800576
  41. D. Albrecht, R. Guthke, A.A. Brakhage, O. Kniemeyer, Integrative Analysis of the heat shock response in Aspergillus fumigatus. In: BMC Genomics, 11, 2010, pp. 32.
    doi: 10.1186/1471-2164-11-32
  42. C. Heinze, R. Pilchowski, C. Melle, N. Escher, D. Driesch, H. Wunderlich, K. Junker: Protein profiling of metastatic and non-metastatic renal cell carcinomas. In: Cellular Oncology: the official journal of the International Society for Cellular Oncology, 32, 2010.
  1. M. Hecker, S. Lambeck, S. Toepfer, E. van Someren, R. Guthke, Gene Regulatory Network Inference: Data Integration in Dynamic Models-A Review. In:  BioSystems, Vol. 96, 2009, pp. 86-103.
    doi: 10.1016/j.biosystems.2008.12.004
  2. D. Albrecht, O. Kniemeyer, A. A. Brakhage, R. Guthke: OmniFung: Data Warehouse for integrating -omics data of human-pathogenic fungi. In: Infection, 37(Suppl. 3):10, Special Issue: 4th International Congress "Sepsis and Multiorgan Dysfunction", 2009.
  3. M. Voedisch, D. Albrecht, F. Leßing, A.D. Schmidt, R. Winkler, R. Guthke, A.A. Brakhage, O. Kniemeyer, Two-dimensional proteome reference maps for the human-pathogenic filamentous fungus Aspergillus fumigatus. In: Proteomics, 9(5), 2009, pp. 1407-1415.
    doi: 10.1002/pmic.200800394
  4. A. Lovas, D. Radke, D. Albrecht, Z.B. Yilmaz, U. Moeller, A.J.R. Habenicht, F. Weih, Differential RelA- and RelB-dependent gene transcription in LTβR-stimulated mouse embryonic fibroblasts. In: BMC Genomics, 9, 2008, pp. 606.
    doi: 10.1186/1471-2164-9-606
  5. D. Albrecht, R. Guthke, O. Kniemeyer, A.A. Brakhage, Systems biology of human-pathogenic fungi. In: Daskalaki, A. (Ed.): Handbook of research on systems biology applications in medicine. IGI Global, Vol. 1, 2008, pp. 400-418.
  6. D. Albrecht, O. Kniemeyer, A.A. Brakhage, R. Guthke, Normalisation of 2D DIGE Data - On the Way to a Standard Operating Procedure. In: BIRD08, Schriftenreihe Informatik, 26, 2008, pp. 55-64.
  7. N. Escher, M. Kaatz, C. Melle, C. Hipler, M. Ziemer, D. Driesch, U. Wollina, F. von Eggeling: Posttranslational modifications of transthyretin are serum markers in patients with mycosis fungoides. In: Neoplasia, 9(3):254–259, 2007.
    doi: 10.1593/neo.06805
  8. J. Sanjmyatav, D. Driesch, C. Schwaenen, S. Wessendorf, J. Schubert, K. Junker: Genome-wide copy number profiling and TNM staging of renal cell tumors. In: BJU International, 100, 2007.
  9. K. Junker, J. Mueller, R. Pilchowski, C. Melle, F. von Eggeling, D. Driesch, J. Schubert: Identification of serum amyloid alpha and transthyretin as biomarkers for clear cell renal cell carcinomas. In: European Urology Supplements, 6(2):134, 2007.
    doi: 10.1016/S1569-9056(07)60446-1
  10. D. Albrecht, O. Kniemeyer, A.A. Brakhage, R. Guthke, Integration of transcriptome and proteome data from human-pathogenic fungi by using a data warehouse. In: J Integrative Bioinf, 4, 2007, pp. 52.
    doi: 10.2390/biecoll-jib-2007-52
  11. R. Guthke, O. Kniemeyer, D. Albrecht, A.A. Brakhage, U. Moeller, Discovery of gene regulatory networks in Aspergillus fumigatus. In: Lect Notes Bioinf 4366, 2007, pp. 22-41.
    doi: 10.1007/978-3-540-71037-0_3
  12. S. Toepfer, R. Guthke, D. Driesch, D. Woetzel, M. Pfaff, The NetGenerator Algorithm: Reconstruction of Gene Regulatory Networks. In: Lect Notes Bioinformatics 4366, 2007, pp. 119-130.
    doi: 10.1007/978-3-540-71037-0_8
  13. O. Reichelt, J. Müller, F. von Eggeling, D. Driesch, H. Wunderlich, J. Schubert, H.-J. Gröne, G. Stein, U. Ott, K. Junker: Prediction of renal allograft rejection by urinary protein analysis using ProteinChip Arrays (surface-enhanced laser desorption/ionization time-of-flight mass spectrometry). In: Urology, 67(3):472–475, 2006.
    doi: 10.1016/j.urology.2005.09.038
  14. N. Escher, B. Spies-Weisshart, M. Kaatz, C. Melle, A. Bleul, D. Driesch, Uwe Wollina, F. von Eggeling: Identification of HNP3 as a tumour marker in CD4+ and CD4- lymphocytes of patients with cutaneous T-cell lymphoma. In: European Journal of Cancer, 42(2):249–255, 2006.
    doi: 10.1016/j.ejca.2005.07.033
  15. R. Guthke, W. Schmidt-Heck, G. Pless, R. Gebhardt, M. Pfaff, J.C. Gerlach, K. Zeilinger, Dynamic Model of Amino Acid and Carbohydrate Metabolism in Primary Human Liver Cells. In: Lect Notes Bioinformatics, 4345, 2006, pp. 137-149.
    doi: 10.1007/11946465_13
  16. R. Guthke, K. Zeilinger, S. Sickinger, W. Schmidt-Heck, H. Buentemeyer, K. Iding, J. Lehmann, M. Pfaff, G. Pless, J.C. Gerlach, Dynamics of Amino Acid Metabolism of Primary Human Liver Cells in 3D Bioreactors. In: Bioprocess Biosyst Eng, Vol. 28, 2006, pp. 331-340.
    doi: 10.1007/s00449-005-0040-1
  17. K. Junker, J. Mueller, D. Driesch, F. von Eggeling, J. Schubert: Detection and differentiation of bladder cancer in urine by proteinchip-technology. In: European Urology Supplements, 4(3):19, 2005.
    doi: 10.1016/S1569-9056(05)80075-2
  18. A. Busch, S. Michel, C. Hoppe, D. Driesch, U. Claussen and F. von Eggeling, Proteome Analysis of Maternal Serum Samples for Trisomy 21 Pregnancies using ProteinChip Arrays and Bioinformatics. In: Journal of Histochemistry & Cytochemistry, Vol. 53(3), 2005, ISSN 0022-1554, pp. 341-343.
    doi: 10.1369/jhc.4B6377.2005
  19. R. Guthke, U. Moeller, M. Hoffmann, F. Thies and S. Toepfer, Dynamic Network Reconstruction from Gene Expression Data Applied to Immune Response during Bacterial Infection. In: Bioinformatics, Vol. 21, No. 8, 2005, ISSN 1367-4803, pp. 1626-1634.
    doi: 10.1093/bioinformatics/bti226
  20. R. Guthke, W. Schmidt-Heck, M. Pfaff, S. Toepfer, D. Driesch, K. Iding, H. Buentemeyer, J. Lehmann, K. Zeilinger, G. Pless, P. Neuhaus and J. Gerlach, Network Based Analysis of the System Dynamics of a Bioartificial 3D Human Liver Cell Bioreactor for Extracorporeal Liver Support. In: 2nd World Congress on Regenerative Medicine, May 18-20, 2005, Leipzig, Germany. Abstract and Poster P44. The International Journal of Artificial Organs, Vol. 28, No. 4, 2005, ISSN 0391-3988, pp. 379-378.
  21. R. Guthke, W. Schmidt-Heck, M. Pfaff, S. Toepfer, D. Driesch, K. Zeilinger, G. Pless, K. Iding, H. Buentemeyer, J. Lehmann, P. Neuhaus and J.C. Gerlach, Kinetic Characterization of Amino Acid Metabolism in a 3D Liver Cell Bioreactor. (in German), GASL 2005, 21st Annual Meeting of the German Association for the Study of the Liver, Session on Metabolism/Transport/Tumours, January 28-29, 2005, Ulm, Germany. Abstract and Poster 2.22. Zeitschrift fuer Gastroenterologie/German Journal of Gastroenterology, Vol. 43, 2005, ISSN 0044-2771, p. 76.
  22. K. Junker, J. Gneist, C. Melle, D. Driesch, J. Schubert, U. Claussen and F. von Eggeling, Identification of Protein Pattern in Kidney Cancer using ProteinChip® Arrays and Bioinformatics. In: International Journal of Molecular Medicine, Vol. 15, 2005, ISSN 1107-3756, pp. 285-290.
    PMID: 15647845
  23. J. Mueller, F. von Eggeling, D. Driesch, J. Schubert, C. Melle and K. Junker, ProteinChip Technology Reveals Distinctive Protein Expression Profiles in the Urine of Bladder Cancer Patients. In: European Urology, Vol. 47, 2005, ISSN 0302-2838, pp. 885-894.
    doi: 10.1016/j.eururo.2005.02.016
  24. M. Pfaff, S. Toepfer, K. Zeilinger, S. Roth, D. Driesch, D. Woetzel, W. Schmidt-Heck, R. Guthke, T. Witaschek, J.C. Gerlach, Systems Analysis of the Dynamic Input/Output Behaviour of a Multi-compartment Capillary Membrane Bioreactor for High-density Liver Cell Culture. In: Biomed Tech, Vol. 50(1), 2005, pp. 1617-1618.
  25. W. Schmidt-Heck, K. Zeilinger, G. Pless, J.C. Gerlach, M. Pfaff, R. Guthke Prediction of the Performance of Human Liver Cell Bioreactors by Donor Organ Data. In: Lect Notes Bioinformatics 3745, 2005, pp. 109-119.
    doi: 10.1007/11573067_12
  26. K. Zeilinger, M. Pfaff, R. Guthke, W. Schmidt-Heck, S. Toepfer, D. Woetzel, D. Driesch, G. Pless, P. Neuhaus and J.C. Gerlach, Prediction of Metabolic Functions of Primary Human Liver Cells Maintained in Perfused 3D Multi-Compartment Bioreactors for Extracorporeal Liver Support. In: GASL 2005, 21st Annual Meeting of the German Association for the Study of the Liver, Session on Transplantation / Liver Surgery, January 28-29, 2005, Ulm, Germany. Abstract and Poster 3.41. Zeitschrift fuer Gastroenterologie/German Journal of Gastroenterology, Vol. 43, 2005, ISSN 0044-2771, p. 99.
  27. O. Reichelt, K. Junker, J. Müller, D. Driesch, G. Stein, J. Schubert: Prediction of renal allograft rejection by urinary protein analysis using seldi mass spectroscopy. In: European Urology Supplements, 3(2):4, 2004.
    doi: 10.1016/S1569-9056(04)90009-7
  28. C. Melle, R. Kaufmann, M. Hommann, A. Bleul, D. Driesch, G. Ernst and F. von Eggeling, Proteomic Profiling in Microdissected Hepatocellular Carcinoma Tissue using ProteinChip® Technology. In: International Journal of Oncology 24, 2004, ISSN 1019-6439, pp. 885-891.
    PMID: 15010826
  29. M. Pfaff, K. Weller, D. Woetzel, R. Guthke, K. Schroeder, G. Stein, R. Pohlmeier and J. Vienken, Prediction of Cardiovaskular Risk in Hemodialysis Patients by Data Mining. In: Special Topic: 4th BioSignal Interpretation (BSI) Workshop 2002 (Eds.: S. Cerutti, D. Hudson, C. Zywietz), Methods of Information in Medicine 43, 2004, ISSN 0026-1270, pp. 106-113.
    PMID: 15026849
  30. M. Pfaff, D. Woetzel, K. Weller, R. Guthke, J. Vienken and G. Stein, Predictive Data Mining in Hemodialysis by Cluster and Rule Based Methods. In: BMT 2004 Biomedizinische Technik, 38th Annual Meeting of the German Society for Biomedical Engineering, Session on Computer Aided Diagnosis, September 22-24, 2004, TU Ilmenau, Germany. Abstract, Paper and Talk. Talk: Schedule: Programme p. 72; Abstract and Paper in: U. Boenick, A. Bolz (Eds.): Biomedizinische Technik/Biomedical Engineering, Vol. 49, Suppl. Vol. 2, Part 1, 2004, ISSN 0939-4990, pp. 478-479.
  31. W. Schmidt-Heck, K. Zeilinger, M. Pfaff, S. Toepfer, D. Driesch, G. Pless, P. Neuhaus, J.C. Gerlach and R. Guthke, Network Analysis of the Kinetics of Amino Acid Metabolism in a Liver Cell Bioreactor. In: ISBMDA 2004, 5th International Symposium on Biological and Medical Data Analysis, Session on Bioinformatics, November 18-19, 2004, Barcelona, Spain. Abstract, Paper and Talk. Proceedings (Eds.: J.M. Barreiro, F. Martin-Sanchez, V. Maojo, F. Sanz) in Lecture Notes in Computer Science 3337, 2004, ISBN 3-540-23946-2, pp. 427-438.
    doi: 10.1007/978-3-540-30547-7_43
  32. K. Junker, D. Driesch, J. Schubert, F. von Eggeling: Proteome analysis in kidney cancer using a new combination of protein chip and maldi-tof technology. In: European Urology Supplements, 2(1):180, 2003.
    doi: 10.1016/S1569-9056(03)80713-3
  33. V. Monossov, M. Pfaff and R. Guthke, Extraction and Validation of Rule Based Knowledge from Gene Expression Data. In: GCB03 German Conference on Bioinformatics, October 12-14, 2003, Munich, Germany. Abstract and Poster. Proceedings - Volume II: Posters (Eds.: H.-W. Mewes, V. Heun, D. Frishman, S. Kramer) pp. 137-139.
  34. S. Toepfer, D. Driesch, D. Woetzel, M. Pfaff and R. Guthke, Reconstruction of Gene Regulatory Networks: A Novel Structure Optimization Method for Dynamic Models. In: GCB03 German Conference on Bioinformatics, October 12-14, 2003, Munich, Germany. Abstract and Poster P144. Proceedings - Volume II: Posters (Eds.: H.-W. Mewes, V. Heun, D. Frish-man, S. Kramer) p. 222.
  35. D. Driesch, D. Woetzel, R. Guthke, M. Pfaff, Fuzzy Cluster and Fuzzy Rule Cancer Status Prediction Based on Gene Expression Data. In: BSI 2002 4th International Workshop on Biosignal Interpretation, June 24-26, 2002, Como, Italy. Abstract, Paper and Talk. Session S1 on Data Processing in Genomics and Proteomics. Proceedings (Eds.: S. Cerutti, M. Akay, L.T. Mainardi, S. Sato and C. Zywietz), Published by the Department of Biomedical Engineering, Polytechnic University of Milan, Italy. Talk: Schedule: p. iii; Abstract and Paper: pp. 7-10.
  36. R. Guthke, W. Schmidt-Heck, D. Hahn and M. Pfaff, Gene Expression Data Mining for Functional Genomics using Fuzzy Technology. Book Contribution. In: H.-J. Zimmermann, G. Tselentis, M. van Someren, G. Dounias (Eds.): International Series in Intelligent Technologies: Advances in Computational Intelligence and Learning: Methods and Applications. Kluwer Academic Publishers, 2002, ISBN 0-7923-7645-5, pp. 475-487.
    doi: 10.1007/978-94-010-0324-7_33
  37. M. Pfaff, R. Guthke, D. Woetzel and D. Driesch, Gene Expression Based Cancer Status Prediction for Individual Patients by an Optimized Cluster and Rule Based System. In: G.D. Dounias, A.V. Roudsari (Eds.): Intelligent E-Health Applications in Medicine and Other Medical Applications of Adaptive / Hybrid Intelligent Systems. Special Session Proceedings of the EUNITE 2002 Symposium, September 19-21, 2002, Albufeira, Portugal, Organized by IBA D: Human, Medical & Health Care, Published by the University of the Aegean, Greece, in Collaboration with EUNITE, The European Network on Intelligent Technologies for Smart Adaptive Systems, 2002, pp. 104-122.
  38. M. Pfaff, K. Weller, D. Woetzel, R. Guthke, K. Schroeder, G. Stein, R. Pohlmeier and J. Vienken, Prediction of Cardiovascular Risk in Hemodialysis Patients by Data Mining. In: BSI 2002 4th International Workshop on Biosignal Interpretation, June 24-26, 2002, Como, Italy. Abstract, Paper and Poster. Poster Session P2. Proceedings (Eds.: S. Cerutti, M. Akay, L.T. Mainardi, S. Sato and C. Zywietz), Published by the Department of Biomedical Engineering, Polytechnic University of Milan, Italy. Poster: Schedule: p. x; Abstract and Paper: pp. 445-450.
  39. R. Berkholz and R. Guthke, Model based sequential experimental design for bioprocess optimisation - an overview. In: Focus in Biotechnology, Vol. IV (M. Hofmann and P. Thonart, eds.), pp. 129-141, Kluwer Academic Publishers, 2002.
    doi: 10.1007/0-306-46889-1_8
  40. R. Berkholz, M. Pfaff, R. Guthke: Experimental Design for Bioprocess Optimization using Deterministic and Hybrid Models. Biotech Journal International, Globetech Publications, Wilton, USA, 2001.
  41. B. Fahnert, D. Hahn, R. Guthke: Knowledge-Based Assessment of Gene Expression Data from Chemiluminescence Detection. J. Biotechnology, 2002.
    doi: 10.1016/S0168-1656(01)00417-5
  42. R. Guthke, W. Schmidt-Heck, R. Berkholz: Data mining based hybrid modelling and experimental design for bioprocess optimisation. In: Proc. 2nd Conf. of the European Society for Fuzzy Logic and Technology - EUSFLAT 2001, Leicester, England, September 5 - 7, 2001, pp. 301-304, 2001.
  43. R. Guthke, W. Schmidt-Heck, D. Hahn, M. Pfaff: Gene expression Data Mining for Functional Genomics. In: Proc. 8th Internatioal Conf. on Computer Appl. in Biotechnol., CAB8, Quebec City, Canada, 24 - 27 June 2001 (D. Dochain and M. Perrier, eds.), pp. 73-78, IFAC and EFB, 2001.
  44. R. Guthke, W. Schmidt-Heck, R. Berkholz: Gene Expression Based Adaptive Fuzzy Control of Bioprocesses - State of the Art and Prospects. In: Proc. Europ. Symp. on Intelligent Technologies, Hybrid Systems and their implementation on Smart Adaptive Systems. 13 - 15 December 2001, Tenerife, Spain, 2001.
  45. D. Hahn, B. Fahnert, R. Guthke: Datenverarbeitung von "panorama e.coli gene arrays": Hintergrunderfassung, Normalisierung, Visualisierung der Ergebnisdaten. Poster, Statusseminar Chiptechnologien: Vom Genom zum Proteom, Frankfurt am Main, January 22 - 23, 2001.
  46. T. Kroll, D. Hahn, R. Guthke, S. Woelfl: Comparison of methods for background correction and standardisation. Poster, 3rd Int. Meeting on Microarray Data Standards, Annotations, Ontologies and Databases, Stanford University, Palo Alto, USA, March 28 - 31, 2001.
  47. M. Pfaff, D. Woetzel, K. Weller, K. Schroeder, R. Pohlmeier, J. Vienken, G. Stein, R. Guthke: Cluster and Rule Based Prediction in Hemodialysis: Adaptivity vs Robustness. In: Proc. Europ. Symp. on Intelligent Technologies, Hybrid Systems and their implementation on Smart Adaptive Systems. 13 - 15 December 2001, Tenerife, Spain, 2001.
  48. D. Woetzel, M. Pfaff, K. Weller, K. Schroeder, R. Pohlmeier, J. Vienken, G. Stein, R. Guthke: Data Mining & Prediction Tools to Support Patient Care in Hemodialysis. In: Intelligent Systems in Patient Care (K. Adlassnig, ed.), (Wien), pp. 163-165, Oesterreichische Computer Gesellschaft, 2001.
  49. R. Berkholz, D. Roehlig, R. Guthke: Data and knowledge based experimental design for fermentation process optimization. Enzyme and Microbial Technology, vol. 27, pp. 784-788, 2000.
    doi: 10.1016/S0141-0229(00)00301-X
  50. R. Berkholz, R. Guthke, W. Schmidt-Heck, D. Roehlig: Experimental Design for Bioprocess Optimization: Numerical and Experimental Results. In: 11th International Biotechnology Symposium, 3 - 8 September 2000 Berlin, Germany.
  51. R. Guthke, W. Schmidt-Heck, M. Pfaff: Gene Expression Data Analysis Methods for Functional Genomics. In: ESIT 2000 - European Symposium on Intelligent Techniques, 14 - 15 September 2000 Aachen, Germany.
  52. R. Guthke, D. Hahn, B. Fahnert, T. Kroll, S. Woelfl: Gene Expression Data Mining by Fuzzy-C-Means Clustering and Fuzzy Rule Generation. Lecture 11th Int. Biotechnology Symp. Berlin September 3 - 8, 2000.
  53. R. Guthke, B. Fahnert, D. Hahn, R. Berkholz: E.coli Gene Expression Data Mining using Fuzzy Technologies for Functional Genomics. German Conference in Bioinformatics - GCB00, Heidelberg, October 5 - 7, 2000.
  54. M. Pfaff, K. Schroeder, D. Woetzel, K. Weller, R. Guthke, R. Pohlmeier, J. Vienken, G. Stein: Dialysis Data Mining to Examine Relations between Therapy and Outcome. Conf. of The American Society of Nephrology, 2000.
  1. R. Berkholz, R. Guthke, W. Schmidt-Heck: Sequentielle Versuchsplanung zur Optimierung von Bioprozessen mit Produktbildung im Uebergangszustand. In: DECHEMA/GVC-Tagung 'Wechselwirkung zwischen Biologie und Prozessfuehrung', Erfurt, 10.-11.Mai 1999.
  2. D. Driesch, M. Pfaff, R. Guthke: Data Mining to Investigate Relations Between Seed and Main Culture Performance. In: 7th European Congress on Intelligent Techniques & Soft Computing Aachen, Germany, September 13 - 16, 1999 - Abstracts of the Papers & Proceedings on CD-ROM (H.-J. Zimmermann, ed.), (Aachen), p. 234, Verlag Mainz, 1999.
  3. R. Guthke, W. Schmidt-Heck, P. Mueller, H. Rodig, R. Berkholz: Data and Knowledge Based Experimental Design for Bioprocess Optimization. In: Proceedings of the German Conference on Bioinformatics - GCB'99, October 4 - 6, 1999, Hannover, Germany, pp. 199-200, 1999.
  4. R. Guthke, V. Schroeckh, R. Berkholz, M. Pfaff: Data Mining and Model based Experimental Design of Fed Batch Fermentations for Bioprocess Optimization and Functional Genomics. Invited Lecture, Conference on Datamining in Bioinformatics, EMBL-European Bioinformatics Institute, Hinxton, Cambridge, UK, November 10 - 12, 1999.
  5. R. Guthke, V. Schroeckh, R. Berkholz, M. Pfaff: Data Mining and Model based Experimental Design of Fed Batch Fermentations for Bioprocess Optimization and Functional Genomics. Poster, Workshop "Funktionelle Genomforschung an Mikroorganismen", Dechema-Haus, Frankfurt/Main, November 4 - 5, 1999.
  6. R. Guthke, W. Schmidt-Heck, P. Mueller, H. Rodig, R. Berkholz: Data and Knowledge Based Experimental Design for Bioprocess Optimization. 9th Europ. Congress on Biotechnol., Brussels, Belgium, July 11 - 15, 1999.
  7. R. Guthke, P. Mueller, H. Rodig, S. Lau, D. Driesch: Data Mining for Bioprocess Optimization: Applications of Wavelet Analysis and Decision Trees. In: 3rd International Data Analysis Symposium, September 13 - 17, 1999, Aachen, Germany, 1999.
  8. R. Guthke, W. Schmidt-Heck. P. Mueller, H. Rodig, R. Berkholz: Data and Knowledge Based Experimental Design for Bioprocess Optimization. In: 9th European Congress on Biotechnology, 11 - 15 July 1999 Brussels, Belgium, 1999.
  9. M. Pfaff, R. Guthke, R. Pohlmeier, K. Schroeder, G. Stein, J. Vienken: Using Data Mining Methods to Assess Factors Associated with Dialysis Outcome. Journal of the American Society of Nephrology, vol. 10, p. 253A, 1999. A1281.
  10. R. Guthke, W. Schmidt-Heck, M. Pfaff: Knowledge Acquisition and Knowledge Based Bioprocess Control. Journal of Biotechnology, vol. 65, pp. 37-46, 1998.
    doi: 10.1016/S0168-1656(98)00120-5
  11. R. Guthke, M. Pfaff, F. Meyer: Optimized Fuzzy Rule Generation for Fermentation Control. In: 7th International Conference on Computer Applications in Biotechnology CAB7, May 31 - June 4, 1998, Osaka, Japan (T. Yoshida and S. Shioya, eds.), pp. 303-308, 1998.
  12. P. Angelov, R. Guthke, R. Berkholz: Optimal control of a fermentation process using neural networks and genetic algorithms. In: 6th European Congress on Intelligent Techniques & Soft Computing Aachen, Germany, September 7 - 10, 1998 - Proceedings (H.-J. Zimmermann, ed.), (Aachen), pp. 1591-1595, Verlag Mainz, 1998.
  13. M. Pfaff and D. Driesch, Bioactivity Pattern Recognition. In: 6th European Congress on Intelligent Techniques & Soft Computing Aachen, Germany, September 7 - 10, 1998 - Proceedings (H.-J. Zimmermann, ed.), vol. 3, (Aachen), pp. 1574-1579, Verlag Mainz, 1998.
  14. F. Meyer, Computerintegrierte Bioverfahrensentwicklung am Beispiel der dynamischen Mikrofiltration. In: Dissertation, Gesamthochschule Essen, 1997.
  15. F. Meyer, R. Guthke, W. Knorre: Modellierung waehrend der Bioverfahrensentwicklung - ein kritischer Vergleich unterschiedlicher Modellierungstechniken. Poster, GVC/VDI-Tagung "Verfahrenstechnische Grundlagen und Modellierung von Bioprozessen" Goslar, May 5 - 6, 1997.
  16. M. Pfaff and R. Guthke, Intelligent methods for bioprocess analysis and control. Poster, 13th Meeting der Society for General Microbiology, Univ. of Reading/ England, 7-9 Jan. 1997.
  17. M. Pfaff, W. Schmidt-Heck, F. Meyer, R. Guthke: Bioprocess data analysis applied to wastewater treatment. Poster, 13th Meeting der Society for General Microbiology, Univ. of Reading / England, January 7 - 9, 1997.
  18. R. Guthke, W. Schmidt-Heck, F. Meyer: Data Analysis and Knowledge Acquisition in Biotechnology. 1st Int. Data Analysis Symposium, Aachen, September 12, 1997 Invited Paper.
  19. R. Guthke, W. Schmidt-Heck, M. Pfaff: Knowledge acquisition and knowledge based control of fermentations. Invited paper to the 8th Europ. Congress on Biotechnology, Budapest / Hungary, August 17 - 21, 1997.