Rainer Breitling

(Page should redirect in 5 seconds)
[  Contact Details | Research Interests | Previous Positions | Publications ]
[ Downloads | Conference Contributions | Talks | Miscellaneous | Students  ]


Rainer Breitling

  Research Interests

Since April 2005, I am holding a Personal Research Fellowship from the Caledonian Research Foundation. My current work is mainly concerned with the representation and exploitation of diverse biological evidence in a Systems Biology context. Areas of special interest are the application of differential equation models to the understanding of cell signalling complexity and the development of techniques to deal with incomplete or semi-quantitative parameter data. I am also very interested in the development of new approaches for the analysis of quantitative metabolomics data generated by Fourier Transform Mass Spectrometry.

In another strand of research, together with Pawel Herzyk, I have recently implemented a set of powerful microarray analysis techniques that is now used as the standard tool in the Sir Henry Wellcome Functional Genomics Facility. Have a look at what our users have to say.

I also continue working on the development of new approaches to the analysis of microarray results. This continues a larger project together with Anna Amtmann and Patrick Armengaud of the Molecular Plant Sciences Group, examining the transcriptional response of Arabidopsis plants to a variety of nutrient and environmental stress conditions. Here, I am especially interested in the integration of biological, evolutionary, and biochemical information with the expression data obtained from microarrays. This should facilitate the identification of novel mechanisms that allow plants to cope under adverse conditions. [read original project outline]

I have also prepared a summary of general microarray tips. It is a subjective collection of issues identified during a meta-analysis of data produced in the SHWFGF.



  Previous Positions

4/2005 – 9/2005 University of Glasgow, Glasgow, Scotland. Caledonian Research Foundation Fellow, Department of Biochemistry and Molecular Biology & Bioinformatics Research Centre, Institute of Biomedical and Life Sciences [web]

5/2003 – 3/2005 University of Glasgow, Glasgow, Scotland. Postdoctoral Research Assistant, Department of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences [web]

6/2001 – 4/2003 San Diego State University, San Diego, California. Postdoctoral fellow, Department of Biology [web]

2/2001 – 5/2001 GSF National Research Center, Neuherberg, Germany. Research associate, Institute of Experimental Genetics [web]

12/1998 Palermo University Medical School, Palermo, Italy. Visiting scientist, Institute of Oncology [web]

1/1998 – 12/2000 GSF National Research Center, Neuherberg, Germany. Doctoral student, Institute of Experimental Genetics [web] [thesis]

7/1997 – 12/1997 GSF National Research Center, Neuherberg, Germany. Graduate student, Institute of Mammalian Genetics [web]

10/1996 – 12/1996 University of California, Berkeley, USA. Research assistant, Department of Plant and Microbial Biology [web]

7/1992 – 6/1997 Hannover University and Hannover Medical School, Hannover, Germany. Masters student (biochemistry/ biophysical chemistry) [web]


  Publications

Links to preprints are provided strictly for personal use only.

30. get preprint Morrison J, Breitling R, Higham DJ, Gilbert DR (2005): GeneRank: Using Search Engine Technology for the Analysis of Microarray Experiments. BMC Bioinformatics 6: 233. [BioMedCentral] [PubMed]

29. get preprint Breitling R, Armengaud P, Amtmann A (2005): Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. BMC Bioinformatics 6:181. [BioMedCentral] [PubMed]

28. get preprint Al-Shahib A, Breitling R, Gilbert D (2005): FrankSum: New feature selection method for protein function prediction. International Journal of Neural Systems 15:259–275. [PubMed]

27. get preprint Breitling R, Herzyk P (2005): Rank-based statistics as a non-parametric alternative of the t-statistic for the analysis of biological microarray data. Journal of Bioinformatics and Computational Biology in press.

26. get preprint Breitling R, Herzyk P (2005): Biological master games: Using biologists' reasoning to guide algorithm development for integrated functional genomics. OMICS: A Journal of Integrative Biology 9: 225–232. [PubMed]

25. get preprint Rogers S, Girolami M, Campbell C, Breitling R (2005): The latent process decomposition of cDNA microarray datasets. IEEE/ACM Transact. Comput. Biol. Bioinformatics. 2: 143–156.

24. get preprint Al-Shahib A, Breitling R, Gilbert D (2005): Feature selection and the class imbalance problem in predicting protein function from sequence. Applied Bioinformatics in press.

23. get preprint Deluca D, Krazeisen A, Breitling R, Prehn C, Möller G, Adamski J (2005): Inhibition of 17beta-hydroxysteroid dehydrogenases by phytoestrogens: comparison with other steroid metabolizing enzymes. J. Steroid Biochem. Mol. Biol. 93: 285–292. [PubMed]

22. get preprint Armengaud P, Breitling R, Amtmann A (2004): The potassium-dependent transcriptome of Arabidopsis thaliana reveals a prominent role of jasmonic acid in nutrient signaling. Plant Physiol. 136: 2556–2576. [PubMed] [Supplementary Webpage]

21. get preprint Breitling R, Amtmann A, Herzyk P (2004): Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics 5: 100. [PubMed] [Updated GiGA software]

20. get preprint Breitling R, Armengaud P, Amtmann A, Herzyk P (2004): Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Letters 573: 83–92. [PubMed] [Supplement] [Erratum] [Perl Implementation] [Windows executable] [BioConductor package] [Faculty of 1000]

19. get preprint Girolami M, Breitling R (2004): Biologically valid linear factor models of gene expression. Bioinformatics 20: 3021–3033. [PubMed] [Supplement]

18. get preprint Breitling R, Amtmann A, Herzyk P (2004): Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinformatics 5: 34. [PubMed] [Addendum]

17. get preprint Breitling R (2004): Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor. BMC Pediatrics 4: 5. [PubMed]

16. get preprint Marijanovic Z, Laubner D, Möller G, Gege C, Husen B, Adamski J, Breitling R (2003): Closing the gap: Identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis. Mol. Endocrinol. 17: 1715–1725. [PubMed]

15. get preprint Breitling R, Laubner D, Clizbe D, Adamski J, Krisans SK (2003): Isopentenyl-diphosphate isomerases in human and mouse – evolutionary analysis of a mammalian gene duplication. J. Mol. Evol. 57: 282–291. [PubMed]

14. get preprint Laubner D, Breitling R, Adamski J (2003): Embryonic expression of cholesterogenic genes is restricted to distinct domains and colocalizes with apoptotic regions in mice. Mol. Brain Res. 115: 87–92. [PubMed]

13. get preprint Breitling R, Sharif O, Hartman ML, Krisans SK (2002): Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells. Eukaryot. Cell 1: 978–986. [PubMed]

12. get preprint Breitling R & Krisans SK (2002): A second gene for peroxisomal HMG-CoA reductase? A genomic reassessment. J. Lipid Res. 43: 2031–2036. [PubMed]

11. Krazeisen A, Breitling R, Möller G, Adamski J (2002): Human 17beta-hydroxysteroid dehydrogenase type 5 is inhibited by dietary flavonoids. Adv. Exp. Med. Biol. 505: 151–161. [PubMed]

10. get preprint Breitling R, Laubner D, Adamski J (2001): Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family. Mol. Biol. Evol. 18: 2154–2164. [PubMed] [Faculty of 1000]

9. get preprint Breitling R, Krazeisen A, Möller G, Adamski J (2001): 17beta-hydroxysteroid dehydrogenase type 7 — an ancient 3-ketosteroid reductase of cholesterogenesis. Mol. Cell. Endocrinol. 171: 199–204. [PubMed]

8. get preprint Breitling R, Marijanovic Z, Perovic D, Adamski J (2001): Evolution of 17beta-HSD type 4, a multifunctional protein of beta-oxidation. Mol. Cell. Endocrinol. 171: 205–210. [PubMed]

7. get preprint Krazeisen A, Breitling R, Möller G, Adamski J (2001): Phytoestrogens inhibit human 17beta-hydroxysteroid dehydrogenase type 5. Mol. Cell. Endocrinol. 171: 151–162. [PubMed]

6. get preprint Fritz S, Wessler I, Breitling R, Rossmanith W, Ojeda SR, Dissen GA, Amsterdam A, Mayerhofer A (2001): Expression of muscarinic receptor types in the primate ovary and evidence for non-neuronal acetylcholine synthesis. J. Clin. Endocrinol. Metabol. 86: 349–354. [PubMed]

5. get preprint Breitling R & Gerber JK (2000): Origin of the paired domain. Dev. Genes Evol. 210: 644–650. [PubMed]

4. get preprint Krazeisen A, Breitling R, Imai K, Fritz S, Möller G, Adamski J (1999): Determination of cDNA, gene structure and chromosomal localization of the novel human 17beta-hydroxysteroid dehydrogenase type 7. FEBS Lett. 460: 373–379. [PubMed]

3. Comolli LR, Zhou J, Linden T, Breitling R, Flores J, Hung T, Jamshidi A, Huang LS, Fernández-Velasco JG (1998): In vivo and in vitro studies on the interaction between cytochrome f and plastocyanin in Chlamydomonas reinhardtii. In: Garab G (ed.): Photosynthesis: Mechanisms and Effects, vol. III, pp. 1589–1592, Kluwer, Netherlands.

2. Breitling R (1996): A peculiar sleeping position in Evarcha falcata (Clerck, 1757). Newsl. Br. Arachnol. Soc. 77: 12.

1. Breitling R (1993): Zur Entdeckerpriorität der Oberkieferkinese bei Xenodon [On the first description of jaw kinesis in Xenodon]. Salamandra 29: 155-156.

  Conference Contributions

27. Armengaud P, Breitling R, Amtmann A: Transcriptional profiling to unravel (JA-mediated) potassium signalling and adaptation responses. 2nd Conference of Polish Society of Experimental Plant Biology. Poznan, Poland. September 26-29, 2005.

26. Breitling R, Amtmann A, Herzyk P: Automated interpretation tools for microarray analysis. 4th Annual Meeting of the Complex Trait Consortium. Groningen, NL. June 26-29, 2005. P64.

25. Prins P, Breitling R, Alda O, Bakker J, Kammenga J, Jansen R: Assessing quality of microarrays in relation to genetical genomics experiments. 4th Annual Meeting of the Complex Trait Consortium. Groningen, NL. June 26-29, 2005. P56.

24. Armengaud P, Breitling R, Amtmann A: Jasmonate signalling in plant mineral nutrition. Plant Signalling from Genes to Biochemistry/2nd Glasgow Phoenix Meeting. Glasgow, UK. November 11-12, 2004. P019.

23. Barrett MP, Stewart ML, Breitling R, Hall JE, Tidwell RR, Goodenowe D, Richie S: Drug induced changes to the Trypanosoma brucei metabolome. TriTryp Genomes Meeting. Seattle, Washington. September 13-16, 2004. 8.4.

22. get preprint Breitling R, Amtmann A, Herzyk P: Microarray experiments: New statistical tools facilitate biological interpretation. 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology (ECCB). Glasgow, UK. July 31-August 4, 2004. F-40.

21. get preprint Morrison J, Breitling R, Higham DJ, Gilbert DR: Search engine technology for microarray expression data. 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology (ECCB). Glasgow, UK. July 31-August 4, 2004. F-92. ("Best poster" award winner!)

20. Armengaud P, Breitling R, Amtmann A: Transcriptional profiling of K starved plants reveals a central role of jasmonic acid signalling in nutrient management. 13th International Workshop on Plant Membrane Biology. Montpellier, France. July 6-10, 2004. P8-9.

19. Breitling R, Amtmann A, Herzyk P: New methods for analyzing microarray data. 9th Annual Structural Biology Symposium. Galveston, Texas. April 30-May 1, 2004.

18. Breitling R, Amtmann A, Herzyk P: New methods for analysing microarray data. Society for Experimental Biology Annual Main Meeting 2004. Edinburgh, UK. March 29-April 2, 2004. P4.19.

17. Armengaud P, Breitling R, Amtmann A: Perception of plant K status at the transcriptional level. Society for Experimental Biology Annual Main Meeting 2004. Edinburgh, UK. March 29-April 2, 2004. P4.5.

16. Williams H, Herzyk P, Breitling R, O’Dowd A, Georgiades E, Pitsiladis YP, MacFarlane N, Behan WMH: Identification of altered gene expression in polymyositis using Affymetrix high density oligonucleotide arrays. 105th Meeting of the British Neuropathological Society. London, UK. January 7-9, 2004. [Neuropathol. Appl. Neurobiol., 30: 205]

15. Armengaud P, Breitling R, Amtmann A: Analysis of potassium-dependent gene expression in growing Arabidopsis seedlings. Society for Experimental Biology Plant Transport Group Meeting. Cambridge, UK. September 10-11, 2003.

14. Breitling R, Sharif O, Hartman M, Krisans SK: Lysine biosynthesis is a basal function of baker’s yeast peroxisomes. 42nd American Society for Cell Biology Annual Meeting. San Francisco, California. December 14-18, 2002. 743. [Mol. Biol. Cell 13(Suppl.): 132a]

13. Breitling R, Deluca D, Enseleit A, Gerber JK, Graedler F, Gloeckner CJ, Krazeisen A, Laubner D, Ohnesorg T, Keller B, Marijanovic Z, Mindnich R, Möller G, Perovic D, Schertel C, Schieweg M, Schüren S, Völkl A, Zieglmeier G, Adamski J: 17beta-hydroxysteroid dehydrogenases – tackling them from all directions. 15th International Symposium of Journal of Steroid Biochemistry and Molecular Biology. Munich, Germany. May 17-20, 2002. 142 P.

12. Laubner D, Breitling R, Adamski J: Expression of cholesterogenic enzymes during embryogenesis is not ubiquitous but reveals a distinct spatial pattern. 15th International Symposium of Journal of Steroid Biochemistry and Molecular Biology. Munich, Germany. May 17-20, 2002. 146 P.

11. Breitling R, Sharif O, Hartman M, Krisans SK: Lysine biosynthesis is a basal function of baker’s yeast peroxisomes. 8th San Diego Cell Biology Meeting. La Jolla, California. April 19, 2002.

10. Breitling R, Masuda K, Keller B, Lusis AJ, Möller G, Krisans SK, Adamski J: Duplicated human genes of isopentenyl diphosphate-dimethylallyl diphosphate isomerase are differentially regulated. Kern Aspen Lipid Conference. Aspen, Colorado. August 18-21, 2001. I-2.

9. Laubner D, Breitling R, Adamski J: Surprising expression pattern of cholesterogenic enzymes during embryonic mouse development. Society for Developmental Biology 60th Annual Meeting. Seattle, Washington. July 18-22, 2001. 109 B87. [Dev. Biol. 235(1): 195]

8. Laubner D, Adamski J, Breitling R: Steroids, a crucial factor for the evolution of vertebrates. XIth International Congress on Genes, Gene Families and Isozymes. Stockholm, Sweden. June 30-July 4, 2001. P47.

7. Breitling R, Masuda K, Keller B, Lusis AJ, Möller G, Krisans SK, Adamski J: Gene duplication of human isopentenyl diphosphate:dimethylallyl diphosphate isomerase: structural, functional and evolutionary aspects. ENDO 2001, The Endocrine Society’s 83rd Annual Meeting. Denver, Colorado. June 20-23, 2001. P1-29.

6. Breitling R & Adamski J: Structure-based placement of 17beta-hydroxysteroid dehydrogenases within a phylogenetic tree of the short-chain alcohol dehydrogenases. ENDO 2001, The Endocrine Society’s 83rd Annual Meeting. Denver, Colorado. June 20-23, 2001. P2-6.

5. Breitling R & Adamski J: Protein structures as indicators of phylogeny – Analysis of the short-chain alcohol dehydrogenase superfamily. 10th International Congress of Human Genetics. Vienna, Austria. May 15-19, 2001. [Eur. J. Hum. Genet. 9(Suppl. 1): P1127]

4. Laubner D, Breitling R, Adamski J: Cholesterogenic enzymes are expressed in neural crest derivatives and limb buds; implications for the pathogenesis of CHILD-syndrome and Conradi-Hünermann-Happle syndrome. 10th International Congress of Human Genetics. Vienna, Austria. May 15-19, 2001. [Eur. J. Hum. Genet. 9(Suppl. 1): P1651]

3. Breitling R, Krazeisen A, Möller G, Adamski J: Human 17beta-hydroxysteroid dehydrogenase type 7 – an enzyme in search of a function. 44th Annual Meeting of the German Society for Endocrinology. Munich, Germany. May 31-June 3, 2000.

2. Krazeisen A, Breitling R, Möller G, Adamski J: Human 17beta-hydroxysteroid dehydrogenase type IV is inhibited by phytoestrogens. “Recent progress in research on 17ß-hydroxysteroid dehydrogenases: impact on medicine”. Elmau Castle, Germany. April 4-8, 2000.

1. Breitling R, Krazeisen A, Möller G, Adamski J: Characterization of human 17beta-hydroxysteroid dehydrogenase type 7. “Recent progress in research on 17ß-hydroxysteroid dehydrogenases: impact on medicine”. Elmau Castle, Germany. April 4-8, 2000.



  Invited Talks

Advanced MSc IT Bioinformatics Lecture, University of Glasgow.
8 March, 2005. Analysis of gene expression data [PPT] [PDF]
22 February, 2005. Modelling biological systems with differential equations [PPT] [PDF]

28 October, 2004. Department of Mathematics, University of Strathclyde, Scotland.

27 May, 2004. Scottish Bioinformatics Forum Visionary Meeting, University of Glasgow.

17 May, 2004. Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin.

13 May, 2004. Genostem Workshop on Microarray Analysis, MPI for Molecular Genetics (Dept. of Human Molecular Genetics) and Charite University Hospital (Dept. of Rheumatology), Berlin. [PPT]

26 March, 2004. Functional Genomics Colloquium, University of Glasgow.

13 February, 2004. MSc IT Bioinformatics Lecture, University of Glasgow.

28 January, 2004. Computational Biology Discussion Group, University of Glasgow.

  Miscellaneous Material

get preprint Breitling R (2004): Building the "Popper Machine": A necessary research goal for systems biology. unpublished.



Nedstat Basic last updated: 16/October/2005. [home]