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Kurt Fellenberg's Home Page

Research Interests:

• Gene expression and cancer biology
• Applied statistics and knowledge representation
• Computational methods for the analysis of microarray data
• Microarray databases and Microarray data warehousing

Short Vita:

• Since 1998: Researcher in the Divisions Functional Genome Analysis and Theoretical Bioinformatics at DKFZ
• 1996-1998: Diploma thesis about cre - steroidreceptor fusion proteins as a tool for inducible gene knockout
• 1996: Lab practical in Klaus Rajewsky's lab (cloning cre vectors)
• 1996: Working at the Center for Parallel Computing
• 1990-1997: Studies in biology at the University of Cologne, Germany
• born 1970

Degrees:

• PhD - 2002
  Thesis: "Storage and analysis of microarray data" [abstract (scroll down page for english version)] [pdf (1.3 MB = 98 pages)]
• Diploma in Biology - 1998
  Thesis: "Optimierung von Cre-Östrogenrezeptor Fusionsproteinen zur lokalen Geninaktivierung in der Haut "

Publications

• Gene expression profiling identifies novel key players involved in the cytotoxic effect of Artesunate on pancreatic cancer cells.
  Youns M, Efferth T, Reichling J, Fellenberg K, Bauer a, Hoheisel JD.
  Biochem Pharmacol. 2000. 78(3):273-83 [abstract] [PDF].

• From experimental setup to data analysis in transcriptomics: copper metabolism in the human pathogen Candida albicans.
  Hauser NC, Dukalska M, Fellenberg k, Rupp S.
  J Biophotonics. 2009. 4:262-268 [abstract] [PDF].

• Genotypic resistance testing in HIV by arrayed primer extension.
  Schanné M, Bodem J, Gerhold-Ay A, Jacob A, Fellenberg K, Kräusslich HG, Hoheisel JD.
  Anal Bioanal Chem. 2008 Jan 18; [Epub ahead of print].

• New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors.
  Giordano FA, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S.
  Methods Inf Med. 2007;46(5):542-7 [abstract].

• Small Trypanosome RNA-Binding Proteins TbUBP1 and TbUBP2 Influence Expression of F-Box Protein mRNAs in Bloodstream Trypanosomes.
  Hartmann C, Benz C, Brems S, Ellis L, Luu VD, Stewart M, D'Orso I, Busold CH, Fellenberg K, Frasch ACC, Carrington M, Hoheisel J, Clayton CE.
  Eukaryotic Cell. 2007. 6:1964-1978 [abstract].

• Systematic interpretation of microarray data using experiment annotations.
  Fellenberg K, Busold CH, Witt O, Bauer A, Beckmann B, Hauser NC, Frohme M, Winter S, Dippon J, Hoheisel JD.
  BMC Genomics. 2006. 7:319 [abstract] [pdf] [supplemental material / data].

• Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data.
  Busold CH, Winter S, Hauser N, Bauer A, Dippon J, Hoheisel J, Fellenberg K.
  Bioinformatics. 2005. 21(10): 2424-2429 [abstract] [pdf].

• Characterization of Antirrhinum petal development and identification of target genes of the class B MADS-box Gene DEFICIENS.
  Bey M, Stüber K, Fellenberg K, Schwarz-Sommer Z, Sommer H, Saedler H, Zachgo S.
  Plant Cell. 2004. 16(12): 3197-3215 [abstract] [pdf] [data].
  

• Bioinformatik (in german).
  Brors B, Fellenberg K.
  in: Molekulare Biotechnologie; Konzepte und Methoden (Wink M, ed.), Wiley-VCH Verlag, Weinheim, 409-440.

• An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
  Hild M, Beckmann B, Haas SA, Koch B, Solovjev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel JD, Paro R.
  Genome Biol. 2003. 5: R3 [abstract] [pdf]

• Use of complex DNA and antibody microarrays as tools in functional analyses.
  Bauer A, Beckmann B, Busold C, Brandt O, Kusnezow W, Pullat J, Aign V, Fellenberg K, Fleischer R, Jacob A, Frohme M, Hoheisel JD.
  Comp Funct Genom. 2003. 4: 520-524.

• Correspondence analysis with microarray data.
  Fellenberg K, Vingron M, Hauser NC, Hoheisel JD.
  in: Perspectives in Gene Expression (Appasani K, ed.), Eaton Publishing, Westborough, 307-343.

• How to discover pathogenic mechanisms - new evaluation tools towards drug discovery.
  Hauser NC, Fellenberg K, Rupp S.
  Screening. 2002. 3:28-31.

• Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis.
  Fellenberg K, Hauser NC, Brors B, Hoheisel JD, Vingron M.
  Bioinformatics. 2002. 18: 423-433 [abstract] [pdf] [supplemental material / data]

• Patent (pending): Microarray data warehouse.
  Fellenberg K, Hauser NC.
  EU (EP1300778), US, Canada. Oct 4th, 2001 (prio.)

• Monitoring the switch from housekeeping to pathogen defence metabolism in Arabidopsis thaliana using cDNA arrays.
  Scheideler M, Schlaich NL, Fellenberg K, Beißbarth T, Hauser NC, Vingron M, Slusarenko AJ, Hoheisel JD.
  J Biol Chem. 2002. 277(12): 10555-10561 [abstract] [pdf] [data].

• Microarray data representation, annotation and storage.
  Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel JD, Fellenberg K.
  in: Advances in Biochemical Engineering/Biotechnology. 2002. Vol. 77 ("Chip Technology"): 113-139 [abstract] [pdf]

• Transkriptionelle Untersuchungen auf DNS-Microarrays; Aspekte der Daten-Evaluation und Interpretation (in german).
  Hoheisel JD, Fellenberg K, Brors B, Diehl F, Hauser NC, Vingron M.
  BIOforum. 2001. 12/01: 908-910

• Correspondence anaylsis applied to microarray data.
  Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M.
  Proc Natl Acad Sci USA. 2001. 98(19): 10781-10786 [abstract] [pdf] [data].

• Whole genome analysis of a wine yeast strain.
  Hauser NC, Fellenberg K, Gil R, Bastuck S, Hoheisel JD, Perez-Ortin JE.
  Comp Funct Genom. 2001. 2(4): 69-79 [abstract] [pdf].

• Processing and quality control of DNA array hybridization data.
  Beißbarth T, Fellenberg K, Brors B, Arribas-Prat R, Boer JM, Hauser NC, Scheideler M,
  Hoheisel JD, Schuetz G, Poustka A, Vingron M.
  Bioinformatics. 2000. 16(11): 1014-1022 [abstract] [pdf].

• DNA microchips; transcriptional profiling and beyond.
  Beier M, Matysiak S, Hauser N, Scheideler M, Würtz S, Fellenberg K, Vingron M, Hoheisel JD.
  Chimia. 2000. 54: 29-30.
  

Conference Contributions

• Correspondence analysis applied to microarray data.
  Fellenberg K.
  Invited talk, 25th Annual Conference of the German Classification Society. Munich, Germany, March 14-16, 2001 [abstract].

• The use of bioinformatics in the interpretation of multiple comparisons.
  Fellenberg K.
  Invited talk, EuroBiochips Conference. Hamburg, Germany, June 5-7, 2000.

Teaching

• Analysis and Interpretation of Complex Transcript Data.
  Fellenberg K, Busold C, Hauser NC, Hoheisel JD.
  Hands-on practical course on self-written software at the DKFZ, Germany, June 27-30, 2005.
  lecture notes and practical

• Correspondence Analysis and Data Warehousing with Microarray Data.
  Fellenberg K.
  Postgrad. bioinformatics lecture at the "Akademie f. Weiterbildung". Mannheim, Germany, since 2002.
  [lecture notes as pdf (1.4 MB = 63 pages)] [practical]

Miscellaneous

• Technical report: M-CHIPS storage concept.
  Fellenberg K [pdf].

• Poster: Transcription Profiling using DNA Array Data.
  Hauser N, Fellenberg K, Beißbarth, T [PDF].

• Genestart biotech award (1500 Euro)
  www.spektrum-verlag.de/biospektrum/pdf/1031.pdf on p.244 (in German).

Address

Kurt Fellenberg - Last Change: 2005-5-16