2013

Chokkathukalam, A., Jankevics, A., Creek, D.J., Achcar, F., Barrett, M.P., and Breitling, R. (2013) mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinformatics, 29 (2). pp. 281-283. ISSN 1367-4803 (doi:10.1093/bioinformatics/bts674)

2012

Creek, D.J., Chokkathukalam, A., Jankevics, A., Burgess, K.E.V., Breitling, R., and Barrett, M.P. (2012) Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Analytical Chemistry, 84 (20). pp. 8442-8447. ISSN 0003-2700 (doi:10.1021/ac3018795)

Nguyen, Q., Merlo, M.E., Medema, M.H., Jankevics, A., Breitling, R., and Takano, E. (2012) Metabolomics methods for the synthetic biology of secondary metabolism. Febs Letters, 586 (15). pp. 2177-2183. ISSN 0014-5793 (doi:10.1016/j.febslet.2012.02.008)

Hoekman, B., Breitling, R., Suits, F., Bischoff, R., and Horvatovich, P. (2012) msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies. Molecular and Cellular Proteomics, 11 (6). M111.015974. ISSN 1535-9476 (doi:10.1074/mcp.M111.015974)

Rogers, S., Daly, R., and Breitling, R. (2012) Mixture model clustering for peak filtering in metabolomics. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, 4-6 Jun 2012, Ulm, Germany.

Achcar, F., Kerkhoven, E.J., SilicoTryp Consortium, , Bakker, B.M., Barrett, M.P., and Breitling, R. (2012) Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PLoS Computational Biology, 8 (1). e1002352. ISSN 1553-734X (doi:10.1371/journal.pcbi.1002352)

Achcar, F., Kerkhoven, E.J., Bakker, B.M., Barrett, M.P., and Breitling, R. (2012) Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism. PLoS Computational Biology, 8 (1). e1002352. ISSN 1553-734X (doi:10.1371/journal.pcbi.1002352)

Creek, D.J., Jankevics, A., Burgess, K.E.V., Breitling, R., and Barrett, M.P. (2012) IDEOM: an excel interface for analysis of LC-MS based metabolomics data. Bioinformatics, 28 (7). pp. 1048-1049. ISSN 1367-4803 (doi:10.1093/bioinformatics/bts069)

Jankevics, A., Merlo, M.E., Vries, M., Vonk, R.J., Takano, E., and Breitling, R. (2012) Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets. Metabolomics, 8 (S1). pp. 29-36. ISSN 1573-3882 (doi:10.1007/s11306-011-0341-0)

Medema, M.H., van Raaphorst, R., Takano, E., and Breitling, R. (2012) Computational tools for the synthetic design of biochemical pathways. Nature Reviews Microbiology, 10 (3). pp. 191-202. ISSN 1740-1526 (doi:10.1038/nrmicro2717)

Takano, E., Bovenberg, R.A.L., and Breitling, R. (2012) A turning point for natural product discovery - ESF-EMBO research conference: synthetic biology of antibiotic production. Molecular Microbiology, 83 (5). pp. 884-893. ISSN 0950-382X (doi:10.1111/j.1365-2958.2012.07984.x)

Zakrzewski, P., Medema, M.H., Gevorgyan, A., Kierzek, A.M., Breitling, R., and Takano, E. (2012) MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models. PLoS ONE, 7 (12). e51511. ISSN 1932-6203 (doi:10.1371/journal.pone.0051511)

2011

Medema, M. H., Blin, K., Cimermancic, P., de Jager, V., Zakrzewski, P., Fischbach, M. A., Weber, T., Takano, E., and Breitling, R. (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 39 (2). W339-W346. ISSN 0305-1048 (doi:10.1093/nar/gkr466)

Steen, A., Wiederhold, E., Gandhi, T., Breitling, R., and Slotboom, D.J. (2011) Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR. Molecular & Cellular Proteomics, 10 (7). ISSN 1535-9476 (doi:10.1074/mcp.M000052-MCP201)

D'Alia, D., Eggle, D., Nieselt, K., Hu, W.-S., Breitling, R., and Takano, E. (2011) Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2). Microbial Biotechnology, 4 (2). pp. 239-251. ISSN 1751-7915 (doi:10.1111/j.1751-7915.2010.00232.x)

Medema, M.H., Alam, M.T., Heijne, W.H.M., van den Berg, M.A., Müller, U., Trefzer, A., Bovenberg, R.A.L., Breitling, R., and Takano, E. (2011) Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus. Microbial Biotechnology, 4 (2). pp. 300-305. ISSN 1751-7915 (doi:10.1111/j.1751-7915.2010.00226.x)

Alam, M., Takano, E., and Breitling, R. (2011) Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor. BMC Research Notes, 4 (1). p. 325. ISSN 1756-0500 (doi:10.1186/1756-0500-4-325)

Alam, M.t., Medema, Marnix H., Takano, Eriko, and Breitling, R. (2011) Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism. Febs Letters, 585 (14). pp. 2389-2394. ISSN 0014-5793 (doi:10.1016/j.febslet.2011.06.014)

Creek, D.J., Jankevics, A., Breitling, R., Watson, D.G., Barrett, M.P., and Burgess, K.E.V. (2011) Toward global metabolomics snalysis with Hydrophilic Interaction Liquid Chromatography–Mass Spectrometry: improved metabolite identification by retention time prediction. Analytical Chemistry, 83 (22). pp. 8703-8710. ISSN 0003-2700 (doi:10.1021/ac2021823)

Jankevics, A., Merlo, M.E., de Vries, M., Vonk, R.J., Takano, E., and Breitling, R. (2011) Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2). Proteomics, 11 (24). pp. 4622-4631. ISSN 1615-9853 (doi:10.1002/pmic.201100254)

Medema, M.H., Breitling, R., Bovenberg, R., and Takano, E. (2011) Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nature Reviews Microbiology, 9 (2). pp. 131-137. ISSN 1740-1526 (doi:10.1038/nrmicro2478)

Medema, M.H., Breitling, R., and Takano, E. (2011) Synthetic Biology in Streptomyces Bacteria. In: Methods in Enzymology. Academic Press, pp. 485-502. ISBN 978-0-12-386471-0

Merlo, M.E., Jankevicks, A., Takano, E., and Breitling, R. (2011) Exploring the metabolic state of microorganisms using metabolomics. Bioanalysis, 3 (21). pp. 2443-2458. ISSN 1757-6180 (doi:10.4155/bio.11.248)

Michaelis, M. et al. (2011) Adaptation of cancer cells from different entities to the MDM2 inhibitor nutlin-3 results in the emergence of p53-mutated multi-drug-resistant cancer cells. Cell Death and Disease, 2 (12). e243. ISSN 2041-4889 (doi:10.1038/cddis.2011.129)

Scheltema, R.A., Jankevics, A., Jansen, R.C., Swertz, M.A., and Breitling, R. (2011) PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. Analytical Chemistry, 83 (7). pp. 2786-2793. ISSN 0003-2700 (doi:10.1021/ac2000994)

t’Kindt, R., Jankevics, A., Scheltema, R.A., Zheng, L., Watson, D.G., Dujardin, J.-C., Breitling, R., and Coombs, G.H. (2011) Erratum to: Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis. Analytical and Bioanalytical Chemistry, 400 (2). p. 635. ISSN 1618-2642 (doi:10.1007/s00216-011-4796-7)

2010

Bakker, B., Krauth-Siegel, R.L., Clayton, C., Matthews, K., Girolami, M., Westerhoff, H.V., Michels, P.A.M., Breitling, R., and Barrett, M.P. (2010) The silicon trypanosome. Parasitology, 137 (9). pp. 1333-1341. ISSN 0031-1820 (doi:10.1017/S0031182010000466)

Barrett, M.P., Bakker, B.M., and Breitling, R. (2010) Metabolomic systems biology of trypanosomes. Parasitology, 137 (9). pp. 1285-1290. ISSN 0031-1820 (doi:10.1017/S003118201000017X)

Alam, M.T., Merlo, M.E., Takano, E., and Breitling, R. (2010) Genome-based phylogenetic analysis of Streptomyces and its relatives. Molecular Phylogenetics and Evolution, 54 (3). pp. 763-772. ISSN 1055-7903 (doi:10.1016/j.ympev.2009.11.019)

Armengaud, P., Breitling, R., and Amtmann, A. (2010) Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply. Molecular Plant, 3 (2). pp. 390-405. ISSN 1674-2052 (doi:10.1093/mp/ssq012)

Michaelis, M. et al. (2010) Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines. Biochemical Pharmacology, 79 (2). pp. 130-136. ISSN 0006-2952 (doi:10.1016/j.bcp.2009.08.013)

Alam, M.T., Merlo, M.E., Hodgson, D.A., Wellington, E.M.H., Takano, E., and Breitling, R. (2010) Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11 (202). pp. 1-9. ISSN 1471-2164 (doi:10.1186/1471-2164-11-202)

Nieselt, K. et al. (2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11 (10). (doi:10.1186/1471-2164-11-10)

Tesson, B.M., Breitling, R., and Jansen, R.C. (2010) DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinformatics, 11 (1). p. 497. ISSN 1471-2105 (doi:10.1186/1471-2105-11-497)

Zhang, Mi, Schafer, William R, and Breitling, R. (2010) A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. BMC Systems Biology, 4 (81). pp. 1-9. ISSN 1752-0509 (doi:10.1186/1752-0509-4-81)

t'Kindt, R. et al. (2010) Metabolomics to unveil and understand phenotypic diversity between pathogen populations. PLoS Neglected Tropical Diseases, 4 (11). e904. ISSN 1935-2727 (doi:10.1371/journal.pntd.0000904)

t’Kindt, R., Jankevics, A., Scheltema, R.A., Zheng, L., Watson, D.G., Dujardin, J.C., Breitling, R., Coombs, G.H., and Decuypere, S. (2010) Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis. Analytical and Bioanalytical Chemistry, 398 (5). pp. 2059-2069. ISSN 1618-2642 (doi:10.1007/s00216-010-4139-0)

2009

Scheltema, R.A., Decuypere, S., Dujardin, J.C., Watson, D.G., Jansen, R.C., and Breitling, R. (2009) Simple data-reduction method for high-resolution LCMS data in metabolomics. Bioanalysis, 1 (9). pp. 1551-1557. ISSN 1757-6180 (doi:10.4155/bio.09.146)

Breitling, R. (2009) Robust signaling networks of the adipose secretome. Trends in Endocrinology and Metabolism, 20 (1). pp. 1-7. ISSN 1043-2760 (doi:10.1016/j.tem.2008.08.006)

Fu, J. et al. (2009) System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics, 41 (2). pp. 166-167. ISSN 1061-4036 (doi:10.1038/ng.308)

Gerrits, A., Li, Y., Tesson, B.M., Bystrykh, L.V., Dontje, B., Wang, X., Breitling, R., Jansen, R.C., and de Haan, G. (2009) Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genetics, 5 (10). e1000692. ISSN 1553-7390 (doi:10.1371/journal.pgen.1000692)

Li, Y., Swertz, M., Vera, G., Fu, J.Y., Breitling, R., and Jansen, R. (2009) DesignGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics, 10 (188). (doi:10.1186/1471-2105-10-188)

Michaelis, M., Klassert, D., Barth, S., Suhan, T., Breitling, R., Mayer, B., Hinsch, N., Doerr, H., and Cinatl, J. (2009) Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells. Molecular Cancer, 8 (80). (doi:10.1186/1476-4598-8-80)

Wiederhold, E., Gandhi, T., Permentier, H.P., Breitling, R., Poolman, B., and Slotboom, D.J. (2009) The yeast vacuolar membrane proteome. Molecular and Cellular Proteomics, 8 (2). pp. 380-392. ISSN 1535-9476 (doi:10.1074/mcp.M800372-MCP200)

van Ham, T.J., Breitling, R., Swertz, M., and Nollen, E.A.A. (2009) Neurodegenerative diseases: lessons from genome-wide screens in small model organisms. EMBO Molecular Medicine, 1 (8-9). pp. 360-370. ISSN 1757-4676 (doi:10.1002/emmm.200900051)

2008

Scheltema, R.A., Kamleh, A., Wildridge, D., Ebikeme, C., Watson, D.G., Barrett, M., Jansen, R.C., and 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 (22). pp. 4647-4656. ISSN 1615-9853 (doi:10.1002/pmic.200800314)

Breitling, R. et al. (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genetics, 4 (10). e1000232 . ISSN 1553-7390 (doi:10.1371/journal.pgen.1000232)

Li, Y., Breitling, R., and Jansen, R.C. (2008) Generalizing genetical genomics: getting added value from environmental perturbation. Trends in Genetics, 24 (10). pp. 518-524. ISSN 0168-9525 (doi:10.1016/j.tig.2008.08.001)

Hong, F., and Breitling, R. (2008) A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics, 24 (3). pp. 374-382. ISSN 1367-4803 (doi:10.1093/bioinformatics/btm620)

Breitling, R., Vitkup, D., and Barrett, M.P. (2008) New surveyor tools for charting microbial metabolic maps. Nature Reviews Microbiology, 6 . pp. 156-161. ISSN 1740-1526 (doi:10.1038/nrmicro1797)

Blom, E.J., Breitling, R., Hofstede, K.J., Roerdink, J.B.T.M., van Hijum, S.A.F.T., and Kuipers, O.P. (2008) Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics, 9 . p. 945. (doi:10.1186/1471-2164-9-495)

van Ham, T.J., Thijssen, K.L., Breitling, R., Hofstra, R.M.W., Plasterk, R.H.A., and Nollen, E.A.A. (2008) C-elegans model identifies genetic modifiers of alpha-synuclein inclusion formation during aging. PLoS Genetics, 4 (3). e1000027. ISSN 1553-7390 (doi:10.1371/journal.pgen.1000027)

2006

Morrison, J.L., Breitling, R., Higham, D.J., and Gilbert, D.R. (2006) A lock-and-key model for protein-protein interactions. Bioinformatics, 22 . pp. 2012-2019. (doi:10.1093/bioinformatics/btl338)

2005

Rogers, S., Girolami, M., Campbell, C., and Breitling, R. (2005) The latent process decomposition of cDNA microarray data sets. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2 (2). pp. 143-156. ISSN 1545-5963 (doi:10.1109/TCBB.2005.29)

Morrison, J.L., Breitling, R., Higham, D.J., and Gilbert, D.R. (2005) GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinformatics, 6:233 . ISSN 1471-2105 (doi:10.1186/1471-2105-6-233)