Rainer Breitling

Summary

Affiliation: University of Glasgow
Country: UK

Publications

  1. pmc What is systems biology?
    Rainer Breitling
    Faculty of Biomedical and Life Sciences, University of Glasgow Scotland, UK
    Front Physiol 1:9. 2010
  2. pmc A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior
    Mi Zhang
    Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Syst Biol 4:81. 2010
  3. pmc Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
    Mohammad T Alam
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Genomics 11:202. 2010
  4. pmc Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
    Rainer Breitling
    Molecular Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    BMC Bioinformatics 6:181. 2005
  5. ncbi request reprint Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
  6. pmc Graph-based iterative Group Analysis enhances microarray interpretation
    Rainer Breitling
    Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
    BMC Bioinformatics 5:100. 2004
  7. ncbi request reprint Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data
    Rainer Breitling
    Bioinformatics Research Centre and Molecular Plant Sciences Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
    J Bioinform Comput Biol 3:1171-89. 2005
  8. pmc Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor
    Rainer Breitling
    Department of Biology, San Diego State University, San Diego, USA
    BMC Pediatr 4:5. 2004
  9. pmc Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
    BMC Bioinformatics 5:34. 2004
  10. pmc Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources
    Evert Jan Blom
    Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
    BMC Genomics 9:495. 2008

Detail Information

Publications79

  1. pmc What is systems biology?
    Rainer Breitling
    Faculty of Biomedical and Life Sciences, University of Glasgow Scotland, UK
    Front Physiol 1:9. 2010
    ..It concludes by attempting to define systems biology as the research endeavor that aims at providing the scientific foundation for successful synthetic biology...
  2. pmc A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior
    Mi Zhang
    Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Syst Biol 4:81. 2010
    ..Here we propose a cellular model for how the temporal pattern of egg-laying might be generated, based on genetic and cell-biological experiments and statistical analyses...
  3. pmc Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
    Mohammad T Alam
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Genomics 11:202. 2010
    ..Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations...
  4. pmc Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
    Rainer Breitling
    Molecular Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    BMC Bioinformatics 6:181. 2005
    ..Usually, results of such experiments are presented in the form of Venn diagrams, which are intuitive and visually appealing, but lack a statistical foundation...
  5. ncbi request reprint Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
    FEBS Lett 573:83-92. 2004
    ..In addition, using RP can lead to a sharp reduction in the number of replicate experiments needed to obtain reproducible results...
  6. pmc Graph-based iterative Group Analysis enhances microarray interpretation
    Rainer Breitling
    Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
    BMC Bioinformatics 5:100. 2004
    ..We applied a graph-based extension of our iterative Group Analysis (iGA) approach to obtain a statistically rigorous identification of the subgraphs of interest in any evidence graph...
  7. ncbi request reprint Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data
    Rainer Breitling
    Bioinformatics Research Centre and Molecular Plant Sciences Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
    J Bioinform Comput Biol 3:1171-89. 2005
    ..The Perl scripts implementing the simulation and evaluation are available upon request. Implementations of the RP method are available for download from the authors website (http://www.brc.dcs.gla.ac.uk/glama)...
  8. pmc Pathogenesis of peroxisomal deficiency disorders (Zellweger syndrome) may be mediated by misregulation of the GABAergic system via the diazepam binding inhibitor
    Rainer Breitling
    Department of Biology, San Diego State University, San Diego, USA
    BMC Pediatr 4:5. 2004
    ..Recent analysis of ZS mouse models has all but invalidated previous hypotheses...
  9. pmc Iterative Group Analysis (iGA): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
    Rainer Breitling
    Plant Science Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
    BMC Bioinformatics 5:34. 2004
    ..The biological interpretation of even a simple microarray experiment can be a challenging and highly complex task. Here we present a new method (Iterative Group Analysis) to facilitate, improve, and accelerate this process...
  10. pmc Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources
    Evert Jan Blom
    Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
    BMC Genomics 9:495. 2008
    ....
  11. pmc Sequence polymorphisms cause many false cis eQTLs
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, Netherlands
    PLoS ONE 2:e622. 2007
    ..Applying this approach to recent mouse and human eQTL data, we demonstrate that indeed many local eQTLs are falsely reported as "cis-acting" or "cis" and can be successfully detected and eliminated with this approach...
  12. ncbi request reprint Feature selection and the class imbalance problem in predicting protein function from sequence
    Ali Al-Shahib
    Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow, UK
    Appl Bioinformatics 4:195-203. 2005
    ..We conclude that this combined approach can generate powerful machine learning classifiers for predicting protein function directly from sequence...
  13. pmc Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans
    Yang Li
    Groningen Bioinformatics Centre, University of Groningen, 9751 NN, Haren, The Netherlands
    Genetics 186:405-10. 2010
    ..Our findings suggest that the regulatory mechanism of alternative splicing in C. elegans is robust toward genetic variation at the genome-wide scale, which is in striking contrast to earlier observations in humans...
  14. pmc designGG: an R-package and web tool for the optimal design of genetical genomics experiments
    Yang Li
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    BMC Bioinformatics 10:188. 2009
    ..The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial...
  15. doi request reprint Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis
    Fiona Achcar
    Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
    FEBS J 280:4640-51. 2013
    ....
  16. pmc mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
    Achuthanunni Chokkathukalam
    College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
    Bioinformatics 29:281-3. 2013
    ..Here, we describe mzMatch-ISO, a new extension to the metabolomics analysis pipeline mzMatch.R...
  17. doi request reprint Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples
    Tejas Gandhi
    Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Proteome Res 9:5922-8. 2010
    ..Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides...
  18. doi request reprint Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus
    Marnix H Medema
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Microb Biotechnol 4:300-5. 2011
    ....
  19. doi request reprint Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap
    Richard A Scheltema
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Proteomics 8:4647-56. 2008
    ..The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general...
  20. pmc Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply
    Patrick Armengaud
    Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
    Mol Plant 3:390-405. 2010
    ..A putative role of JA for enhancing the defense potential of K-deficient plants was further supported by the observation that plants grown on low K were less damaged by thrips than plants grown with sufficient K...
  21. pmc The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling
    Patrick Armengaud
    Plant Sciences Group, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
    Plant Physiol 136:2556-76. 2004
    ..g. calmodulins). On the basis of our results, we propose candidate genes involved in K(+) perception and signaling as well as a network of molecular processes underlying plant adaptation to K(+) deficiency...
  22. ncbi request reprint The latent process decomposition of cDNA microarray data sets
    Simon Rogers
    Bioinformatics Research Centre, Department of Computing Science, A416, Fourth Floor, Davidson Building, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
    IEEE/ACM Trans Comput Biol Bioinform 2:143-56. 2005
    ..To illustrate its wider applicability, we also illustrate its performance on a microarray data set for yeast...
  23. ncbi request reprint IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data
    Darren J Creek
    Institute of Infection, Immunity and Inflammation, Wellcome Trust Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
    Bioinformatics 28:1048-9. 2012
    ....
  24. pmc antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
    Marnix H Medema
    Department of Microbial Physiology, Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
    Nucleic Acids Res 39:W339-46. 2011
    ..antiSMASH is available at http://antismash.secondarymetabolites.org...
  25. doi request reprint PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis
    Richard A Scheltema
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
    Anal Chem 83:2786-93. 2011
    ..The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum...
  26. doi request reprint System-wide molecular evidence for phenotypic buffering in Arabidopsis
    Jingyuan Fu
    Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands
    Nat Genet 41:166-7. 2009
    ..We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs...
  27. pmc Expression quantitative trait loci are highly sensitive to cellular differentiation state
    Alice Gerrits
    Department of Cell Biology, Section Stem Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    PLoS Genet 5:e1000692. 2009
    ..Therefore, future genetical genomics studies should aim at studying multiple well-defined and highly purified cell types in order to construct as comprehensive a picture of the changing functional regulatory relationships as possible...
  28. doi request reprint Generalizing genetical genomics: getting added value from environmental perturbation
    Yang Li
    Groningen Bioinformatics Centre, University of Groningen, 9751 NN Haren, The Netherlands
    Trends Genet 24:518-24. 2008
    ..Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach...
  29. pmc The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways
    Marnix H Medema
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Genome Biol Evol 2:212-24. 2010
    ..Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria...
  30. pmc Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation
    Darren J Creek
    Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
    Anal Chem 84:8442-7. 2012
    ..This untargeted approach to stable isotope tracing facilitates the biochemical analysis of known pathways and yields rapid identification of previously unexplored areas of metabolism...
  31. doi request reprint Computational tools for the synthetic design of biochemical pathways
    Marnix H Medema
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
    Nat Rev Microbiol 10:191-202. 2012
    ..Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology...
  32. doi request reprint The potential of metabolomics for Leishmania research in the post-genomics era
    Richard A Scheltema
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Parasitology 137:1291-302. 2010
    ..To illustrate the concepts and the expected results of metabolomics analyses, we also present an overview of comparative metabolic profiles of drug-sensitive and drug-resistant Leishmania donovani clinical isolates...
  33. doi request reprint Genome-based phylogenetic analysis of Streptomyces and its relatives
    Mohammad Tauqeer Alam
    Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Mol Phylogenet Evol 54:763-72. 2010
    ..g., Salinispora tropica). The most important application area of such a phylogenetic analysis will be in the comparative re-annotation of genome sequences and the reconstruction of Streptomyces metabolic networks for biotechnology...
  34. pmc Metabolomic characterization of the salt stress response in Streptomyces coelicolor
    Stefan Kol
    Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, Netherlands
    Appl Environ Microbiol 76:2574-81. 2010
    ....
  35. doi request reprint Synthetic biology in Streptomyces bacteria
    Marnix H Medema
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
    Methods Enzymol 497:485-502. 2011
    ..In this chapter, we first provide an overview of the synthetic biology challenges in Streptomyces and then present the existing toolbox of molecular methods that can be employed in this organism...
  36. pmc DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
    Bruno M Tesson
    Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Bioinformatics 11:497. 2010
    ..Here, sensitive and untargeted means that the method should be able to construct de novo modules by grouping genes based on shared, but subtle, differential correlation patterns...
  37. pmc Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR
    Anton Steen
    Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Mol Cell Proteomics 10:M000052MCP200. 2011
    ..The different stress responses elicited in E. coli and L. lactis upon membrane protein production indicate that different strategies are needed to overcome low expression yields and toxicity...
  38. doi request reprint The silicon trypanosome
    Barbara M Bakker
    Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
    Parasitology 137:1333-41. 2010
    ..We expect that, in the long run, the quantitative modelling enabled by the Silicon Trypanosome will play a key role in selecting the most suitable targets for developing new anti-parasite drugs...
  39. ncbi request reprint Biologically valid linear factor models of gene expression
    Mark Girolami
    Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, UK
    Bioinformatics 20:3021-33. 2004
    ..A microarray data representation which enables clear biological interpretation is a desirable analysis tool...
  40. ncbi request reprint The silicon trypanosome: a test case of iterative model extension in systems biology
    Fiona Achcar
    Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    Adv Microb Physiol 64:115-43. 2014
    ..During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology...
  41. pmc Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei
    Eduard J Kerkhoven
    Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 9:e1003371. 2013
    ..We illustrate this strategy by exploring the mechanism underlying the essential function of one of the PPP enzymes, and validate it by confirming the model predictions experimentally. ..
  42. pmc Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism
    Fiona Achcar
    Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    PLoS Comput Biol 8:e1002352. 2012
    ..This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies...
  43. ncbi request reprint New surveyor tools for charting microbial metabolic maps
    Rainer Breitling
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    Nat Rev Microbiol 6:156-61. 2008
    ..Data integration will play a particularly important part in exploiting the new experimental opportunities...
  44. doi request reprint The yeast vacuolar membrane proteome
    Elena Wiederhold
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    Mol Cell Proteomics 8:380-92. 2009
    ..Our work provides a wealth of information on vacuolar biology and a solid basis for further characterization of vacuolar functions...
  45. ncbi request reprint FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
    Evert Jan Blom
    Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, Groningen, The Netherlands
    Bioinformatics 23:1161-3. 2007
    ..Our software assists in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. AVAILABILITY: http://bioinformatics.biol.rug.nl/standalone/fiva/..
  46. pmc A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    BMC Bioinformatics 8:132. 2007
    ..To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases...
  47. ncbi request reprint Biological master games: using biologists' reasoning to guide algorithm development for integrated functional genomics
    Rainer Breitling
    Plant Science Group, Bioinformatics Research Centre, University of Glasgow, Glasgow, United Kingdom
    OMICS 9:225-32. 2005
    ..The results can be used either as helpful tools to guide data visualization and exploration, or as the input for downstream computational applications in a systems biology framework...
  48. ncbi request reprint A lock-and-key model for protein-protein interactions
    Julie L Morrison
    Bioinformatics Research Centre, Department of Computing Science, University of Glasgow G12 8QQ, UK
    Bioinformatics 22:2012-9. 2006
    ....
  49. ncbi request reprint Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks
    Achuthanunni Chokkathukalam
    Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
    Bioanalysis 6:511-24. 2014
    ....
  50. doi request reprint Probabilistic assignment of formulas to mass peaks in metabolomics experiments
    Simon Rogers
    Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, UK
    Bioinformatics 25:512-8. 2009
    ..One of the major challenges is the correct identification of the observed mass peaks, including the assignment of their empirical formula, based on the measured mass...
  51. ncbi request reprint Isopentenyl-diphosphate isomerases in human and mouse: evolutionary analysis of a mammalian gene duplication
    Rainer Breitling
    Department of Biology, San Diego State University, San Diego, CA 92182, USA
    J Mol Evol 57:282-91. 2003
    ..The significant positive fitness effect of IDI2, revealed by the pattern of sequence conservation, as well as its specific expression pattern underscores the importance of the IDI gene duplication in mammals...
  52. pmc GeneRank: using search engine technology for the analysis of microarray experiments
    Julie L Morrison
    Bioinformatics Research Centre, University of Glasgow, Glasgow, UK
    BMC Bioinformatics 6:233. 2005
    ..Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information...
  53. doi request reprint The future of industrial antibiotic production: from random mutagenesis to synthetic biology
    Marnix H Medema
    Department of Microbial Physiology, University of Groningen, The Netherlands
    Bioeng Bugs 2:230-3. 2011
    ....
  54. ncbi request reprint Biological microarray interpretation: the rules of engagement
    Rainer Breitling
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Biochim Biophys Acta 1759:319-27. 2006
    ..These new approaches make it much easier to extract biologically relevant and reliable hypotheses in an objective and reasonably unbiased fashion...
  55. ncbi request reprint Network theory to understand microarray studies of complex diseases
    Mikael Benson
    Department of Pediatrics, Queen Silvia Children s Hospital, SE 41685 Gothenburg, Sweden, and Groningen Bioinformatics Centre, University of Groningen, The Netherlands
    Curr Mol Med 6:695-701. 2006
    ..This review aims to give an introduction to network theory and how it can be applied to microarray studies of complex diseases...
  56. doi request reprint Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2)
    Davide D'Alia
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Microb Biotechnol 4:239-51. 2011
    ..In conclusion, our time series analysis demonstrates new details of the regulatory effects of the γ-butyrolactone system in Streptomyces...
  57. doi request reprint Phosphoenolpyruvate carboxylase identified as a key enzyme in erythrocytic Plasmodium falciparum carbon metabolism
    Janet Storm
    Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    PLoS Pathog 10:e1003876. 2014
    ..Moreover, these findings imply that PEPC may be an exploitable target for future drug discovery...
  58. doi request reprint Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)
    Andris Jankevics
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
    Proteomics 11:4622-31. 2011
    ..The identified global rearrangement of metabolism suggests the usefulness of RNA interference as an efficient strategy to manipulate the physiology of bacteria with wider biotechnological applicability in microorganisms...
  59. doi request reprint Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism
    Mohammad Tauqeer Alam
    Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
    FEBS Lett 585:2389-94. 2011
    ..As has been reported for low-degree metabolites in several organisms, low-degree enzymes (in linear pathways) turn out to be generally more essential than high-degree enzymes (in metabolic hubs)...
  60. doi request reprint A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production
    Eriko Takano
    Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborg 7, Groningen, The Netherlands
    Mol Microbiol 83:884-93. 2012
    ....
  61. doi request reprint Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms
    Marnix H Medema
    Department of Microbial Physiology and the Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
    Nat Rev Microbiol 9:131-7. 2011
    ..Re-engineered versions of secondary metabolite biosynthetic pathways identified from any genomic sequence can then be inserted into these systems in a plug-and-play fashion...
  62. ncbi request reprint Precision mapping of the metabolome
    Rainer Breitling
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    Trends Biotechnol 24:543-8. 2006
    ..Data from perturbation studies and isotope-tracking experiments can complement this information to create metabolic maps de novo and chart unexplored areas of metabolism...
  63. ncbi request reprint Current challenges in quantitative modeling of epidermal growth factor signaling
    Rainer Breitling
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    FEBS Lett 579:6289-94. 2005
    ..We discuss recent developments in the field that address these emerging aspects in a new generation of more realistic - and potential more useful - models of EGF signaling...
  64. ncbi request reprint FrankSum: new feature selection method for protein function prediction
    Ali Al-Shahib
    Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom
    Int J Neural Syst 15:259-75. 2005
    ..We conclude that feature selection is vital for successful protein function prediction and FrankSum is one of the feature selection methods that can be applied successfully to such a domain...
  65. pmc Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor
    Mohammad Tauqeer Alam
    Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences, Joseph Black Building B3, 10, University of Glasgow, G12 8QQ, Glasgow, UK
    BMC Res Notes 4:325. 2011
    ..abstract:..
  66. doi request reprint Metabolomic systems biology of trypanosomes
    Michael P Barrett
    Faculty of Biomedical and Life Sciences and Wellcome Trust Centre of Molecular Parasitology, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow G12 8TA, United Kingdom
    Parasitology 137:1285-90. 2010
    ..Here we discuss recent developments in metabolomic analysis, from the perspective of trypanosome research, highlighting remaining challenges and the most promising areas for future research...
  67. doi request reprint Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: improved metabolite identification by retention time prediction
    Darren J Creek
    Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
    Anal Chem 83:8703-10. 2011
    ....
  68. doi request reprint Robust signaling networks of the adipose secretome
    Rainer Breitling
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Trends Endocrinol Metab 20:1-7. 2009
    ..Recent advances in whole-genome association studies, global molecular profiling and quantitative modeling are currently fueling the emergence of this novel research strategy...
  69. pmc Mapping determinants of gene expression plasticity by genetical genomics in C. elegans
    Yang Li
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    PLoS Genet 2:e222. 2006
    ..Our results suggest widespread genetic variation of differential expression responses to environmental impacts and demonstrate the potential of genetical genomics for mapping the molecular determinants of phenotypic plasticity...
  70. pmc Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells
    Rainer Breitling
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Eukaryot Cell 1:978-86. 2002
    ..This is the first well-documented example of pathway misregulation in response to peroxisome deficiency and will be useful in understanding the phenotypic details of human peroxisome-deficient patients (Zellweger syndrome)...
  71. doi request reprint A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
    Fangxin Hong
    Department of Biostatistics, Division of Information Sciences, City of Hope National Medical Center, Beckman Research Institute, 1500 Duarte Rd, Duarte, CA 91010, USA
    Bioinformatics 24:374-82. 2008
    ..While these methods address the question from different angles, it is not clear how they compare with each other...
  72. ncbi request reprint MetaNetter: inference and visualization of high-resolution metabolomic networks
    Fabien Jourdan
    UMR1089 Xénobiotiques INRA ENVT, 180 chemin de Tournefeuille, St Martin du Touch, BP3 31931 Toulouse, France
    Bioinformatics 24:143-5. 2008
    ..This open source, multi-platform software has been successfully used to interpret metabolomic experiments and will enable others using filtered, high mass accuracy mass spectrometric data sets to build and analyse networks...
  73. doi request reprint A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
    Rainer Breitling
    Groningen Bioinformatics Centre at University of Groningen, The Netherlands
    Brief Bioinform 9:404-21. 2008
    ..The ultimate aim is to introduce a general approach that provides the foundations for a structured formal engineering of large-scale models of biochemical networks...
  74. ncbi request reprint Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series
    Han Roelofsen
    Centre for Medical Biomics, University Medical Centre Groningen, Groningen, The Netherlands
    Proteomics 7:3219-28. 2007
    ..We present an approach to analyze temporal variation in the proteome. This approach may be useful to evaluate surgical, nutritional, and pharmacological interventions...
  75. ncbi request reprint RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
    Fangxin Hong
    Plant Biology Laboratory La Jolla, CA, USA
    Bioinformatics 22:2825-7. 2006
    ..A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements...
  76. pmc Predicting protein function by machine learning on amino acid sequences--a critical evaluation
    Ali Al-Shahib
    Biomedical Informatics Signals and Systems Research Laboratory, Department of Electronic, Electrical and Computer Engineering, The University of Birmingham, Birmingham, UK
    BMC Genomics 8:78. 2007
    ..Until now, however, it has been unclear if this ability would be transferable to proteins of unknown function, which may show distinct biases compared to experimentally more tractable proteins...
  77. pmc C. elegans model identifies genetic modifiers of alpha-synuclein inclusion formation during aging
    Tjakko J van Ham
    Department of Genetics, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands
    PLoS Genet 4:e1000027. 2008
    ..The processes and genes identified here present a framework for further study of the disease mechanism and provide candidate susceptibility genes and drug targets for Parkinson's disease and other alpha-synuclein related disorders...
  78. ncbi request reprint Closing the gap: identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis
    Zrinka Marijanovic
    GSF National Research Center for Environment and Health, Institute of Experimental Genetics, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Mol Endocrinol 17:1715-25. 2003
    ..In its function as the 3-ketosteroid reductase of cholesterol biosynthesis, HSD17B7 is a novel candidate for inborn errors of cholesterol metabolism...
  79. ncbi request reprint Microarray challenges in ecology
    Jan E Kammenga
    Laboratory of Nematology, Wageningen University, Binnenhaven 5, 6709 PD, Wageningen, The Netherlands
    Trends Ecol Evol 22:273-9. 2007
    ....