Rainer Breitling
Published papers and preprints

Links to preprints are provided strictly for personal use only.

2010
76. get preprint Bakker BM, Krauth-Siegel RL, Clayton C, Matthews K, Girolami M, Westerhoff HV, Michels PA, Breitling R, Barrett MP (2010): The Silicon Trypanosome. Parasitology in press.

75. get preprint Barrett MP, Bakker BM, Breitling R (2010): Metabolomic systems biology of trypanosomes. Parasitology in press. [PubMed]

74. get preprint Scheltema RA, Decuypere S, 't Kindt R, Dujardin JC, Coombs GH, Breitling R (2010): The potential of metabolomics for Leishmania research in the post-genomics era. Parasitology in press. [PubMed]

73. get preprint Breitling R, Donaldson RA, Gilbert DR, Heiner M (2010): Biomodel Engineering – from Structure to Behavior. Transactions on Computational Systems Biology 12: 1–12.

72. get preprint Kol S, Merlo ME, Scheltema RA, de Vries M, Vonk RJ, Kikkert NA, Dijkhuizen L, Breitling R, Takano E (2010): Metabolomic characterization of the salt stress response in Streptomyces coelicolor. Appl. Environ. Microbiol. in press. [PubMed]

71. get preprint Armengaud P, Breitling R, Amtmann A (2010): Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply. Molecular Plant in press.

70. get preprint Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen ØM, Sletta H, Alam MT, Merlo ME, Moore J, Omara W, Morrissey ER, Juarez-Hermosillo M, Rodríguez-García A, Nentwich M, Thomas L, Legaie R, Gaze WH, Challis GL, Jansen RC, Dijkhuizen L, Rand DA, Wild DL, Bonin M, Reuther J, Wohlleben W, Smith MCM, Burroughs NJ, Martín JF, Hodgson DA, Takano E, Breitling R, Ellingsen TE, Wellington EMH (2010): The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 11: 10. [PubMed]

69. get preprint Michaelis M, Kleinschmidt MC, Barth S, Rothweiler F, Geiler J, Breitling R, Mayer B, Deubzer H, Witt O, Kreuter J, Doerr HW, Cinatl J, Cinatl J jr. (2010): Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines. Biochem Pharmacol. 79:130–136. [PubMed]

68. get preprint Alam MT, Merlo ME, Takano E, Breitling R: Genome-based phylogenetic analysis of Streptomyces and its relatives. Mol. Phylogenet. Evol. 54:763–772. [PubMed]

2009
67. get preprint Scheltema RA, Decuypere S, Dujardin JC, Watson D, Jansen RC, Breitling R (2009): A simple data reduction method for high resolution LC/MS data in metabolomics. Bioanalysis 1: 1569–1578.

66. get preprint van Ham TJ, Breitling R, Swertz M, Nollen EAA (2009): Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms. EMBO Molecular Medicine 1: 360–270. [PubMed]

65. get preprint Gerrits A, Li Y, Tesson BM, Bystrykh LV, Weersing E, Dethmers-Ausema B, Dontje B, Wang X, Breitling R, Jansen RC, de Haan G (2009): Expression Quantitative Trait Loci are highly sensitive to cellular differentiation state. PLoS Genetics e1000692. [PubMed]

64. get preprint Michaelis M, Klassert D, Barth S, Suhan T, Breitling R, Mayer B, Hinsch N, Doerr HW, Cinat J, Cinatl J jr. (2009): Chemoresistance acquisition induces a global shift of expression of angiogenesis-associated genes and increased pro-angiogenic activity in neuroblastoma cells. Molecular Cancer 8: 80. [PubMed]

63. get preprint Li Y, Swertz MA, Vera G, Fu J, Breitling R, Jansen RC (2009): designGG: an R-package and web tool for the optimal design of genetical genomics experiment. BMC Bioinformatics 10: 188. [PubMed]

62. get preprint Rogers S, Scheltema RA, Girolami M, Breitling R (2009): Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics 25: 512–518. [PubMed]

61. get preprint Fu J, Keurentjes JBB, Bouwmeester H, America T, Verstappen FWA, Ward JL, Beale MH, de Vos RCH, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC (2009): System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics 41: 166–167. [PubMed]

60. get preprint Breitling R (2009): Robust signaling networks of the adipose secretome. Trends Endocrinol Metabol. 20: 1–7. [PubMed]

59. get preprint Wiederhold E, Gandhi T, Permentier HP, Breitling R, Poolman B, Slotboom DJ (2009): The yeast vacuolar membrane proteome. Mol Cell Proteomics 8: 380–392. [PubMed]

2008
58. get preprint Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, Jansen RC (2008): Genetical Genomics: Spotlight on QTL Hotspots. PLoS Genetics 4:e1000232. [PubMed]

57. get preprint Blom EJ, Breitling R, Hofstede KJ, Roerdink JBTM, van Hijum SAFT, Kuipers OP (2008): Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics 9:495. [PubMed]

56. get preprint Li Y, Breitling R, Jansen RC (2008): Generalizing Genetical Genomics: getting added value from environmental perturbation. Trends Genetics 24:518–524. [PubMed]

55. get preprint Scheltema RA, Kamleh A, Wildridge D, Ebikeme C, Watson DG, Barrett MP, Jansen RC, Breitling R (2008): Increasing the mass accuracy of high-resolution LC-MS data using background ions – a case study on the LTQ-Orbitrap. Proteomics 8:4647–4656. [PubMed]

54. get preprint Breitling R, Gilbert D, Heiner M, Orton R (2008): A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics 9:404–421. [PubMed]

53. get preprint van Ham TJ, Thijssen KL, Breitling R, Hofstra RMW, Plasterk RHA, Nollen EAA (2008): C. elegans model identifies genetic modifiers of α-synuclein inclusion formation during aging. PLoS Genetics 4:e10000027. [PubMed]

52. get preprint Hong F, Breitling R (2008): A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 24:374–382. [PubMed]

51. get preprint Breitling R, Vitkup D, Barrett MP (2008): New surveyor tools for charting microbial metabolic maps. Nature Rev. Microbiol. 6: 156–161. [PubMed]

50. get preprint Jourdan F, Breitling R, Barrett MP, Gilbert D (2008): MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics 24: 143–145. [PubMed]

2007
49. get preprint Al-Shahib A, Gilbert D, Breitling R (2007): Discriminating microbial species using protein sequence properties and machine learning. IDEAL 2007. Lecture Notes in Computer Science 4881: 890–897.

48. get preprint Biehl M, Breitling R, Li Y (2007): Analysis of tiling microarray data by Learning Vector Quantization and Relevance Learning. IDEAL 2007. Lecture Notes in Computer Science 4881: 880–889.

47. get preprint Breitling R (2007): Greased hedgehogs – new links between hedgehog signaling and cholesterol metabolism. BioEssays 29: 1085–1094. [PubMed]

46. get preprint Alberts R, Terpstra P, Li Y, Breitling R, Nap JP, Jansen RC (2007): Sequence polymorphisms cause many false cis eQTLs. PLoS One 2: e622. [PubMed]

45. get preprint Roelofsen H, Alvarez-Llamas G, Dijkstra M, Breitling R, Havenga K, Bijzet J, Zandbergen W, de Vries MP, Ploeg RJ, Vonk RJ (2007): Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series. Proteomics 7:3219–3228. [PubMed]

44. get preprint Alberts R, Terpstra P, Hardonk M, Bystrykh LV, de Haan G, Breitling R, Nap JP, Jansen RC (2007): A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinformatics 8: 132. [PubMed]

43. get preprint Al-Shahib A, Breitling R, Gilbert D (2007): Predicting protein function by machine learning on amino acid sequences – A critical evaluation. BMC Genomics 8: 78. [PubMed]

42. get preprint Kammenga JE, Herman MA, Ouborg NJ, Johnson L, Breitling R (2007): Microarray challenges in ecology. Trends Ecol. Evol. 22: 273–279. [PubMed]

41. get preprint Blom EJ, Bosman DWJ, van Hijum SAFT, Breitling R, Tijsma L, Silvis R, Roerdink JBTM, Kuipers OP (2007): FIVA: Functional Information Viewer and Analyzer, extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics 23: 1161–1163. [PubMed]

2006
40. get preprint Li Y, Alvarez OA, Gutteling EW, Tijsterman M, Fu J, Riksen JAG, Hazendonk E, Prins P, Plasterk RHA, Jansen RC, Breitling R, Kammenga JE (2006): Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genetics 2: e222. [PubMed] [Faculty of 1000]

39. get preprint Breitling R, Pitt AR, Barrett MP (2006): Precision mapping of the metabolome. Trends in Biotechnology 24: 543–548. [PubMed]

38. get preprint Hong F, Breitling R, McEntee CW, Wittner BS, Nemhauser JL, Chory J (2006): RankProd: A Bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics 22: 2825–2827. [PubMed]

37. get preprint Breitling R (2006): Biological microarray interpretation: The rules of engagement. Biochim. Biophys. Acta 1759: 319–327. [PubMed]

36. get preprint Breitling R, Ritchie S, Goodenowe D, Stewart ML, Barrett MP (2006): Ab initio prediction of metabolic networks using Fourier Transform Mass Spectrometry data. Metabolomics 2: 155–164.

35. get preprint Benson M, Breitling R (2006): Network theory to understand microarray studies of complex diseases. Curr. Mol. Med. 6: 695–701. [PubMed]

34. get preprint Morrison JL, Breitling R, Higham DJ, Gilbert DR (2006): A lock-and-key model for protein-protein interactions. Bioinformatics 22: 2012–2019. [PubMed]

33. get preprint Hoeller D, Crosetto N, Blagoev B, Raiborg C, Tikkanen R, Wagner S, Kowanetz K, Breitling R, Mann M, Stenmark H, Dikic I (2006): Regulation of ubiquitin-binding proteins by monoubiquitylation. Nature Cell Biol. 8: 163–169. [PubMed] [Faculty of 1000]

32. get preprint Keller B, Ohnesorg T, Mindnich R, Gloeckner CJ, Breitling R, Scharfe M, Moeller G, Blöcker H, Adamski J (2006): Interspecies comparison of gene structure and computational analysis of gene regulation of 17beta-hydroxysteroid dehydrogenase type 1. Mol. Cell. Endocrinol. 248: 168–171. [PubMed]

2005
31. get preprint Breitling R, Hoeller D (2005): Current challenges in quantitative modeling of epidermal growth factor signaling. FEBS Letters 579: 6289–6294. [PubMed]

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 3: 1171–1189. [PubMed]

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. [PubMed]

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 4: 195–203. [PubMed]

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]

2004
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]

2003
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]

2002
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]

2001
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]

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

1999
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]

1998
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.

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

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

Conference contributions

2009
62. Decuypere S, Zheng L, Scheltema RA, Rijal S, Dujardin JC, Breitling R, Watson DG, Coombs GH: Application of metabolomic technologies to unravel the biochemical basis of phenotypic diversity in parasite populations. British Society for Parasitology Spring Meeting 2009. Edinburgh, UK. 5–8 April 2009.

61. Scheltema RA, Decuypere S, Watson D, Jansen RC, Breitling R: Making sense of high resolution LC-MS data on whole-cell extracts. NBIC Conference 2009. Lunteren, The Netherlands. 17–18 March 2009.

60. Decuypere S, Scheltema RA, Zhang L, Brunker K, Rijal S, Chappuis F, Dujardin JC, Breitling R, Watson D, Coombs GH: Metabolomics for global characterisation of phenotypic diversity in Leishmania populations. WorldLeish 4. 4th World Congress on Leishmaniasis 2009. Lucknow, India. 3–7 February 2009. Abstract no. 211

59. Decuypere S, Hertz-Fowler C, Watson D, Rijal S, Coombs GH, Berriman M, Breitling R, Boelaert M, Dujardin JC: GeMInI: a translational research initiative to study global Leishmania genomic and metabolomic diversity and its relationship to clinical phenotypes. WorldLeish 4. 4th World Congress on Leishmaniasis 2009. Lucknow, India. 3–7 February 2009. Abstract no. 213

2008
57. Alam MT, Merlo ME, Gottelt M, Scheltema RA, de Vries MP, Vonk R, Dijkhuizen L, Jansen RC, Takano E, Breitling R: Metabolomics modeling and analysis of the metabolic switch in S. coelicolor. 25th LC/MS Montreux Symposium. Montreux, Switzerland. 12–14 November 2008.

56. Breitling R, Gilbert D, Heiner M: BioModel Engineering – from Structure to Behaviour. 6th Conference on Computational Methods in Systems Biology. Rostock, Germany. 12–15 October 2008.

55. Gandhi T, Permentier H, Poolman B, Breitling R: Machine learning based membrane protein identification from tandem mass spectra. European Conference on Computational Biology. Cagliari, Italy. 22–26 September 2008.

54. Breitling R, Scheltema RA, Barrett MP: Bioinformatics for high-accuracy metabolome mass spectrometry. German Conference on Bioinformatics 2008. Dresden, Germany. 9–12 September 2008. (selected highlight presentation)

53. Scheltema RA, Wildridge D, Barrett MP, Jansen RC, Breitling R: Unprecedented mass accuracy using Orbitrap Mass Spectrometry. 7th Annual World Congress HUPO 2008. Amsterdam, The Netherlands. 16–20 August 2008.

52. Fu J, Keurentjes J, America T, Scheltema RA, Dijkstra M, Vreugdenhil D, Breitling R, Koornneef M, Jansen RC: Genetic basis of proteome variation in Arabidopsis. 7th Annual World Congress HUPO 2008. Amsterdam, The Netherlands. 16–20 August 2008.

51. Gandhi T, Permentier H, Poolman B, Breitling R: Machine learning-based membrane protein identification. 7th Annual World Congress HUPO 2008. Amsterdam, The Netherlands. 16–20 August 2008.

50. Wiederhold E, Gandhi T, Permentier H, Breitling R, Slotboom DJ, Poolman B: Membrane proteome of S. cerevisiae vacuoles. 7th Annual World Congress HUPO 2008. Amsterdam, The Netherlands. 16–20 August 2008.

49. Gilbert DR, Heiner M, Donaldson R, Breitling R: A unifying framework for modelling and analysing biochemical pathways using Petri nets. 1st FORSYS Symposium. Berlin, Germany. 19–20 June 2008.

48. Tesson B, Gerrits A, Li Y, Bystrykh L, Weersing E, Dethmers-Ausema B, Dontje B, Breitling R, Jansen RC, de Haan G: A multi-cell type genetical genomics approach to study cell fate decisions during hematopoietic development. 7th Annual Meeting of the Complex Trait Consortium. Montréal, Canada. 31 May–3 June 2008. (oral presentation)

47. Li Y, Breitling R, Jansen RC: Generalized Genetical Genomics: the added value from environmental perturbation. 7th Annual Meeting of the Complex Trait Consortium. Montréal, Canada. 31 May–3 June 2008. (oral presentation)

46. Breitling R, Scheltema RA: Computational metabolomics – turning numbers into networks. Second Bertinoro Systems Biology Workshop. Bertinoro (Forlì-Cesena), Italy. 13–18 April 2008. (oral presentation)

45. Gilbert D, Heiner M, Donaldson R, Breitling R: A unifying framework for modelling and analysing biochemical pathways using Petri nets. European Science Foundation–University of Barcelona Conference in Biomedicine – Systems Biology. Sant Feliu de Guixols, Spain. 12–17 April 2008.

44. Wildridge D, Scheltema R, Jourdan F, Kamleh A, Ebikeme C, Vincent I, Breitling R, Watson D, Bringaud F, Burchmore R, Barrett M, Using Fourier Transform Mass Spectrometry to elucidate metabolic changes in trypanosomatids. British Society for Parasitology Spring Meeting. Newcastle, UK. 30 March–2 April 2008.

43. Vincent I, Wildridge D, Ebikeme C, Scheltema R, Jourdan F, Kamleh A, Breitling R, Watson D, Burchmore R, Barrett M: The metabolome of the African trypanosome. Genomes to Systems Conference 2008. Manchester, UK. 17–19 March, 2008.

2007
42. van Ham T, Thijssen K, Breitling R, Hofstra R, Plasterk R, Nollen E: Identification of modifiers of alpha-synuclein inclusion in a C. elegans model by genome-wide RNAi. XVII WFN World Congress on Parkinson's Disease and Related Disorders. Amsterdam, Netherlands. 9–13 December, 2007. [Parkinsonism Relat. Disord. 13 (Suppl. 2): S90]

41. Breitling R: Exploring metabolic space using bioinformatics. 3rd Benelux Bioinformatics Conference. Leuven, Belgium. 12–13 November, 2007. (oral presentation)

40. Scheltema RA, Stellaard F, Jansen RC, Barrett MP, Breitling R: MetabolomeExplorer: Inferring metabolic networks from high resolution mass spectrometry data. 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB). Vienna, Austria. 21–25 July, 2007. C086.

39. Li Y, Alvarez OA, Gutteling EW, Fu J, Riksen JAG, Prins P, Jansen RC, Breitling R, Kammenga JE: Genetical genomics reveals gene expression plasticity induced by environmental changes in C. elegans. 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB). Vienna, Austria. 21–25 July, 2007. B21.

38. Scheltema RA, Kamleh M, Watson D, Barrett MP, Jansen RC, Breitling R. Novel analytical concepts for high-resolution metabolomics using the Orbitrap. Metabolomics Society 3rd Annual Conference. Manchester, UK. 11–14 June, 2007.

37. Breitling R, Barrett MP: New algorithms for high-resolution metabolomics – A case study on trypanosome parasites. 4th International Symposium on Networks in Bioinformatics ISNB 2007. Amsterdam, Netherlands. 18–19 April, 2007. (oral presentation)

36. Scheltema RA, Stellaard F, Jansen RC, Barrett MP, Breitling R: MetabolomeExplorer – Inferring Metabolic Networks From High Resolution Mass Spectrometry Data. 2nd Netherlands Bioinformatics Conference. Amsterdam, Netherlands. 16–17 April, 2007. (oral presentation)

35. Breitling R, Barrett MP: New algorithms for high-resolution metabolomics – A case study on trypanosome parasites. Dagstuhl Seminar on Similarity-based Clustering. International Conference and Research Centre for Computer Science, Schloss Dagstuhl, Germany. 25–30 March, 2007. (oral presentation)

34. Li Y, Breitling R: Analyzing genome tiling microarrays for the detection of novel expressed genes. Dagstuhl Seminar on Similarity-based Clustering. International Conference and Research Centre for Computer Science, Schloss Dagstuhl, Germany. 25–30 March, 2007. (oral presentation)

2006
33. Li Y, Breitling R, Jansen RC: Detecting transcriptionally active regions using genomic tiling data of C. elegans. 2nd Benelux Bioinformatics Conference. Wageningen, Netherlands. 17–18 October, 2006.

32. Li Y, Alvarez OA, Gutteling EW, Fu J, Riksen JAG, Prins P, Breitling R, Jansen RC, Kammenga JE: Mapping the determinants of gene expression plasticity by genetical genomics in C. elegans. 2nd Benelux Bioinformatics Conference. Wageningen, Netherlands. 17–18 October, 2006.

31. Barrett MP, Breitling R: High resolution mass spectrometry approaches to investigate the Trypanosoma brucei metabolome and action of trypanocidal drugs. ICOPA XI. 11th International Congress of Parasitology. Glasgow, UK. August 6–11, 2006.

30. Dijkstra M, Charbon B, Breitling R, Roelofsen H, Vonk RJ, Jansen RC: Interpreting SELDI-TOF mass spectra: a view on sources of variation. Biomarker discovery by mass spectrometry. Amsterdam, NL. May 18–19, 2006.

29. Li Y, Alvarez OA, Gutteling EW, Breitling R, Fu J, Riksen JAG, Prins P, Kammenga JE, Jansen RC: Environmental changes induce differential linkages of gene expression in C. elegans. Netherlands Bioinformatics Conference. Ede, NL. April 24, 2006.

2005
28. get preprint Morrison J, Breitling R, Higham DJ, Gilbert DR: Identifying bipartite subgraphs within protein-protein interaction networks. 4th European Conference on Computational Biology (ECCB). Madrid, Spain. September 28–October 1, 2005.

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.

2004
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]

2003
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.

2002
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.

2001
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]

2000
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. (oral presentation)

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