Rainer Breitling

Rainer Breitling

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Rainer Breitling

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Dynamics of the human skin mediator lipidome in response to dietary ω-3 fatty acid supplementation.

FASEB J 2019 Sep 13:fj201901501R. Epub 2019 Sep 13.

Division of Pharmacy and Optometry, Laboratory for Lipidomics and Lipid Biology, School of Heath Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1096/fj.201901501RDOI Listing
September 2019

SelProm: A Queryable and Predictive Expression Vector Selection Tool for .

ACS Synth Biol 2019 Jul 18;8(7):1478-1483. Epub 2019 Mar 18.

Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry , University of Manchester , Manchester M1 7DN , U.K.

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http://dx.doi.org/10.1021/acssynbio.8b00399DOI Listing
July 2019

Synthetic biology for fibres, adhesives and active camouflage materials in protection and aerospace.

MRS Commun 2019 May 24;9(2):486-504. Epub 2019 Apr 24.

Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYBIOCHEM, School of Chemistry, The University of Manchester, Manchester, UK, M1 7DN.

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http://dx.doi.org/10.1557/mrc.2019.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609449PMC
May 2019

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters.

Commun Biol 2019 28;2:83. Epub 2019 Feb 28.

1Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN United Kingdom.

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http://dx.doi.org/10.1038/s42003-019-0333-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395733PMC
February 2019

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli.

ACS Synth Biol 2019 01 7;8(1):127-136. Epub 2019 Jan 7.

Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry , University of Manchester , Manchester M1 7DN , United Kingdom.

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http://pubs.acs.org/doi/10.1021/acssynbio.8b00398
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http://dx.doi.org/10.1021/acssynbio.8b00398DOI Listing
January 2019

Metabolomics tools for the synthetic biology of natural products.

Curr Opin Biotechnol 2018 12 19;54:114-120. Epub 2018 Mar 19.

Manchester Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester M1 7DN, United Kingdom.

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http://dx.doi.org/10.1016/j.copbio.2018.02.015DOI Listing
December 2018

Defining informative priors for ensemble modeling in systems biology.

Nat Protoc 2018 11;13(11):2643-2663

Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1038/s41596-018-0056-zDOI Listing
November 2018

Mobilising ion mobility mass spectrometry for metabolomics.

Analyst 2018 Sep;143(19):4783-4788

Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1039/c8an00902cDOI Listing
September 2018

Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

J Ind Microbiol Biotechnol 2018 Jul 18;45(7):615-619. Epub 2017 Dec 18.

Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester, M1 7DN, UK.

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http://link.springer.com/10.1007/s10295-017-1993-1
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http://dx.doi.org/10.1007/s10295-017-1993-1DOI Listing
July 2018

Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism.

BMC Genomics 2018 Jul 4;19(1):519. Epub 2018 Jul 4.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/s12864-018-4905-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040156PMC
July 2018

Detection and Quantification of Butyrolactones from Streptomyces.

Methods Mol Biol 2018 ;1673:117-128

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1007/978-1-4939-7309-5_10DOI Listing
June 2018

Selenzyme: enzyme selection tool for pathway design.

Bioinformatics 2018 06;34(12):2153-2154

BBSRC/EPSRC Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology.

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http://dx.doi.org/10.1093/bioinformatics/bty065DOI Listing
June 2018

Orthogonal Regulatory Circuits for Escherichia coli Based on the γ-Butyrolactone System of Streptomyces coelicolor.

ACS Synth Biol 2018 04 19;7(4):1043-1055. Epub 2018 Mar 19.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom.

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http://dx.doi.org/10.1021/acssynbio.7b00425DOI Listing
April 2018

Rational cell culture optimization enhances experimental reproducibility in cancer cells.

Sci Rep 2018 02 14;8(1):3029. Epub 2018 Feb 14.

Manchester Centre for Integrative Systems Biology and Doctoral Training Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1038/s41598-018-21050-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813001PMC
February 2018

Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins.

MBio 2018 01 30;9(1). Epub 2018 Jan 30.

Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom

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http://dx.doi.org/10.1128/mBio.02118-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790912PMC
January 2018

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

Bioinformatics 2017 Sep;33(17):2774-2775

Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, Manchester M1?7DN, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860065PMC
September 2017

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PLoS One 2017 14;12(7):e0179130. Epub 2017 Jul 14.

Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179130PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510799PMC
September 2017

Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.

Trends Biotechnol 2017 06 13;35(6):518-529. Epub 2017 Jan 13.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tibtech.2016.12.008DOI Listing
June 2017

Towards synthesis of monoterpenes and derivatives using synthetic biology.

Curr Opin Chem Biol 2016 10 14;34:37-43. Epub 2016 Jun 14.

SYNBIOCHEM, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1016/j.cbpa.2016.06.002DOI Listing
October 2016

Synthetic Biology of Natural Products.

Cold Spring Harb Perspect Biol 2016 Oct 3;8(10). Epub 2016 Oct 3.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom.

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http://dx.doi.org/10.1101/cshperspect.a023994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5046697PMC
October 2016

Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

Nat Prod Rep 2016 Aug 17;33(8):925-32. Epub 2016 May 17.

Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.

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http://dx.doi.org/10.1039/c6np00018eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063057PMC
August 2016

SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.

Biochem Soc Trans 2016 06;44(3):675-7

BBSRC/EPSRC Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, U.K. SYNBIOCHEM Platform/Theme Lead, School of Chemistry, The University of Manchester, Manchester, U.K. SYNBIOCHEM, The University of Manchester, Manchester, U.K.

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http://dx.doi.org/10.1042/BST20160009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900749PMC
June 2016

Synthetic biology advances for pharmaceutical production.

Curr Opin Biotechnol 2015 Dec 3;35:46-51. Epub 2015 Mar 3.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2015.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617476PMC
December 2015

Butyrolactone signalling circuits for synthetic biology.

Curr Opin Chem Biol 2015 Oct 9;28:91-8. Epub 2015 Jul 9.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.cbpa.2015.06.024DOI Listing
October 2015

Minimum Information about a Biosynthetic Gene cluster.

Authors:
Marnix H Medema Renzo Kottmann Pelin Yilmaz Matthew Cummings John B Biggins Kai Blin Irene de Bruijn Yit Heng Chooi Jan Claesen R Cameron Coates Pablo Cruz-Morales Srikanth Duddela Stephanie Düsterhus Daniel J Edwards David P Fewer Neha Garg Christoph Geiger Juan Pablo Gomez-Escribano Anja Greule Michalis Hadjithomas Anthony S Haines Eric J N Helfrich Matthew L Hillwig Keishi Ishida Adam C Jones Carla S Jones Katrin Jungmann Carsten Kegler Hyun Uk Kim Peter Kötter Daniel Krug Joleen Masschelein Alexey V Melnik Simone M Mantovani Emily A Monroe Marcus Moore Nathan Moss Hans-Wilhelm Nützmann Guohui Pan Amrita Pati Daniel Petras F Jerry Reen Federico Rosconi Zhe Rui Zhenhua Tian Nicholas J Tobias Yuta Tsunematsu Philipp Wiemann Elizabeth Wyckoff Xiaohui Yan Grace Yim Fengan Yu Yunchang Xie Bertrand Aigle Alexander K Apel Carl J Balibar Emily P Balskus Francisco Barona-Gómez Andreas Bechthold Helge B Bode Rainer Borriss Sean F Brady Axel A Brakhage Patrick Caffrey Yi-Qiang Cheng Jon Clardy Russell J Cox René De Mot Stefano Donadio Mohamed S Donia Wilfred A van der Donk Pieter C Dorrestein Sean Doyle Arnold J M Driessen Monika Ehling-Schulz Karl-Dieter Entian Michael A Fischbach Lena Gerwick William H Gerwick Harald Gross Bertolt Gust Christian Hertweck Monica Höfte Susan E Jensen Jianhua Ju Leonard Katz Leonard Kaysser Jonathan L Klassen Nancy P Keller Jan Kormanec Oscar P Kuipers Tomohisa Kuzuyama Nikos C Kyrpides Hyung-Jin Kwon Sylvie Lautru Rob Lavigne Chia Y Lee Bai Linquan Xinyu Liu Wen Liu Andriy Luzhetskyy Taifo Mahmud Yvonne Mast Carmen Méndez Mikko Metsä-Ketelä Jason Micklefield Douglas A Mitchell Bradley S Moore Leonilde M Moreira Rolf Müller Brett A Neilan Markus Nett Jens Nielsen Fergal O'Gara Hideaki Oikawa Anne Osbourn Marcia S Osburne Bohdan Ostash Shelley M Payne Jean-Luc Pernodet Miroslav Petricek Jörn Piel Olivier Ploux Jos M Raaijmakers José A Salas Esther K Schmitt Barry Scott Ryan F Seipke Ben Shen David H Sherman Kaarina Sivonen Michael J Smanski Margherita Sosio Evi Stegmann Roderich D Süssmuth Kapil Tahlan Christopher M Thomas Yi Tang Andrew W Truman Muriel Viaud Jonathan D Walton Christopher T Walsh Tilmann Weber Gilles P van Wezel Barrie Wilkinson Joanne M Willey Wolfgang Wohlleben Gerard D Wright Nadine Ziemert Changsheng Zhang Sergey B Zotchev Rainer Breitling Eriko Takano Frank Oliver Glöckner

Nat Chem Biol 2015 Sep;11(9):625-31

1] Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany. [2] Jacobs University Bremen gGmbH, Bremen, Germany.

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http://orbit.dtu.dk/files/115504295/Minimum_Information_abou
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http://www.nature.com/doifinder/10.1038/nchembio.1890
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http://dx.doi.org/10.1038/nchembio.1890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714517PMC
September 2015

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

Nucleic Acids Res 2015 Jul 6;43(W1):W237-43. Epub 2015 May 6.

Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany Bioinformatics Group, Wageningen University, Wageningen, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489286PMC
July 2015

LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes.

Metabolomics 2015;11(6):1721-1732. Epub 2015 Jul 9.

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 ; Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G61 1QH UK.

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http://dx.doi.org/10.1007/s11306-015-0827-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605981PMC
July 2015

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.

Bioinformatics 2015 Jun 2;31(12):1999-2006. Epub 2015 Feb 2.

School of Computing Science, University of Glasgow, Glasgow, UK, School of Computing and Mathematical Sciences, Liverpool John Moores University, Merseyside, UK and Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760236PMC
June 2015

Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose.

PLoS Pathog 2015 Mar 16;11(3):e1004689. Epub 2015 Mar 16.

Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, Garscube Campus, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1004689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361558PMC
March 2015

Judging synthetic biology risks.

Science 2015 Jan;347(6218):107

Timothy S. Gardner is Chief Executive Officer of Riffyn, Inc., in Oakland, CA, USA, and an external expert to the European Commission Scientific Committees.

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http://dx.doi.org/10.1126/science.aaa5253DOI Listing
January 2015

A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments.

BMC Bioinformatics 2014 Nov 21;15:367. Epub 2014 Nov 21.

Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/s12859-014-0367-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245829PMC
November 2014

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

Bioinformatics 2014 Oct 9;30(19):2764-71. Epub 2014 Jun 9.

School of Computing Science, University of Glasgow, Glasgow, Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester and Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173012PMC
October 2014

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

PLoS Comput Biol 2014 Sep 4;10(9):e1003822. Epub 2014 Sep 4.

Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands; Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154637PMC
September 2014

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei.

PLoS Comput Biol 2013 5;9(12):e1003371. Epub 2013 Dec 5.

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.

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http://dx.doi.org/10.1371/journal.pcbi.1003371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854711PMC
August 2014

LC-MS metabolomics from study design to data-analysis - using a versatile pathogen as a test case.

Comput Struct Biotechnol J 2013 6;4:e201301002. Epub 2013 Feb 6.

Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium ; Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.

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http://dx.doi.org/10.5936/csbj.201301002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962178PMC
June 2014

Steps towards the synthetic biology of polyketide biosynthesis.

FEMS Microbiol Lett 2014 Feb 7;351(2):116-25. Epub 2014 Jan 7.

Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1111/1574-6968.12365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237116PMC
February 2014

Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks.

Bioanalysis 2014 Feb;6(4):511-24

Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary & Life Sciences, University of Glasgow, G61 1QH, UK.

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http://dx.doi.org/10.4155/bio.13.348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048731PMC
February 2014

Phosphoenolpyruvate carboxylase identified as a key enzyme in erythrocytic Plasmodium falciparum carbon metabolism.

PLoS Pathog 2014 Jan 16;10(1):e1003876. Epub 2014 Jan 16.

Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1003876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894211PMC
January 2014

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice.

Curr Opin Biotechnol 2013 Dec 27;24(6):1144-50. Epub 2013 Mar 27.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://www.rug.nl/research/portal/files/2386702/2013CurrOpin
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http://linkinghub.elsevier.com/retrieve/pii/S095816691300063
Publisher Site
http://dx.doi.org/10.1016/j.copbio.2013.03.006DOI Listing
December 2013

Metabolomics for secondary metabolite research.

Metabolites 2013 Nov 11;3(4):1076-83. Epub 2013 Nov 11.

Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

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http://dx.doi.org/10.3390/metabo3041076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937839PMC
November 2013

Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure.

Mol Microbiol 2013 Oct 11;90(2):428-42. Epub 2013 Sep 11.

Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.

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http://dx.doi.org/10.1111/mmi.12374DOI Listing
October 2013

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis.

FEBS J 2013 Sep 19;280(18):4640-51. Epub 2013 Aug 19.

Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.

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http://dx.doi.org/10.1111/febs.12436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768353PMC
September 2013

Modeling challenges in the synthetic biology of secondary metabolism.

ACS Synth Biol 2013 Jul 20;2(7):373-8. Epub 2013 May 20.

Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

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http://dx.doi.org/10.1021/sb4000228DOI Listing
July 2013

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

Nucleic Acids Res 2013 Jul 3;41(Web Server issue):W204-12. Epub 2013 Jun 3.

Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, 72076, Germany.

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http://dx.doi.org/10.1093/nar/gkt449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692088PMC
July 2013

Natural products: tools and more special issue.

ACS Synth Biol 2013 Jul;2(7):352-3

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http://dx.doi.org/10.1021/sb400063nDOI Listing
July 2013

Detecting sequence homology at the gene cluster level with MultiGeneBlast.

Mol Biol Evol 2013 May 14;30(5):1218-23. Epub 2013 Feb 14.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/mst025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670737PMC
May 2013

The exact probability distribution of the rank product statistics for replicated experiments.

FEBS Lett 2013 Mar 8;587(6):677-82. Epub 2013 Feb 8.

Department of Social Science Research Methods, Radboud University Nijmegen, Netherlands.

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http://dx.doi.org/10.1016/j.febslet.2013.01.037DOI Listing
March 2013

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data.

Bioinformatics 2013 Jan 17;29(2):281-3. Epub 2012 Nov 17.

College of Medical Veterinary and Life Sciences, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546800PMC
January 2013

Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation.

Anal Chem 2012 Oct 25;84(20):8442-7. Epub 2012 Sep 25.

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.

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http://dx.doi.org/10.1021/ac3018795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472505PMC
October 2012

Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

J Proteome Res 2012 Aug 20;11(8):4044-51. Epub 2012 Jul 20.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/pr300083xDOI Listing
August 2012

Metabolomics methods for the synthetic biology of secondary metabolism.

FEBS Lett 2012 Jul 15;586(15):2177-83. Epub 2012 Feb 15.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.febslet.2012.02.008DOI Listing
July 2012

msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Mol Cell Proteomics 2012 Jun 7;11(6):M111.015974. Epub 2012 Feb 7.

Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M111.015974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433919PMC
June 2012

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data.

Bioinformatics 2012 Apr 4;28(7):1048-9. Epub 2012 Feb 4.

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.

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http://dx.doi.org/10.1093/bioinformatics/bts069DOI Listing
April 2012

The future of industrial antibiotic production: from random mutagenesis to synthetic biology.

Bioeng Bugs 2011 Jul-Aug;2(4):230-3. Epub 2011 Jul 1.

Department of Microbial Physiology, University of Groningen, The Netherlands.

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http://dx.doi.org/10.1111/j.1751-7915.2010.00226.xDOI Listing
March 2012

A turning point for natural product discovery--ESF-EMBO research conference: synthetic biology of antibiotic production.

Mol Microbiol 2012 Mar 8;83(5):884-93. Epub 2012 Feb 8.

Department of Microbial Physiology,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborg 7, Groningen, The Netherlands.

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http://dx.doi.org/10.1111/j.1365-2958.2012.07984.xDOI Listing
March 2012

Computational tools for the synthetic design of biochemical pathways.

Nat Rev Microbiol 2012 Jan 23;10(3):191-202. Epub 2012 Jan 23.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://www.nature.com/articles/nrmicro2717
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http://dx.doi.org/10.1038/nrmicro2717DOI Listing
January 2012

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism.

PLoS Comput Biol 2012 Jan 19;8(1):e1002352. Epub 2012 Jan 19.

Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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https://dx.plos.org/10.1371/journal.pcbi.1002352
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http://dx.doi.org/10.1371/journal.pcbi.1002352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269904PMC
January 2012

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2).

Proteomics 2011 Dec 10;11(24):4622-31. Epub 2011 Nov 10.

Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1002/pmic.201100254DOI Listing
December 2011

Toward global metabolomics analysis with hydrophilic interaction liquid chromatography-mass spectrometry: improved metabolite identification by retention time prediction.

Anal Chem 2011 Nov 21;83(22):8703-10. Epub 2011 Oct 21.

Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

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http://dx.doi.org/10.1021/ac2021823DOI Listing
November 2011

Synthetic biology in Streptomyces bacteria.

Methods Enzymol 2011 ;497:485-502

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1016/B978-0-12-385075-1.00021-4DOI Listing
September 2011

Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor.

BMC Res Notes 2011 Sep 7;4:325. Epub 2011 Sep 7.

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.

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http://dx.doi.org/10.1186/1756-0500-4-325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224560PMC
September 2011

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Nucleic Acids Res 2011 Jul 14;39(Web Server issue):W339-46. Epub 2011 Jun 14.

Department of Microbial Physiology, Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125804PMC
July 2011

Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism.

FEBS Lett 2011 Jul 22;585(14):2389-94. Epub 2011 Jun 22.

Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1016/j.febslet.2011.06.014DOI Listing
July 2011

Physiological adaptation of the bacterium Lactococcus lactis in response to the production of human CFTR.

Mol Cell Proteomics 2011 Jul;10(7):M000052MCP200

Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M000052-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134065PMC
July 2011

What is systems biology?

Authors:
Rainer Breitling

Front Physiol 2010 21;1. Epub 2010 May 21.

Faculty of Biomedical and Life Sciences, University of Glasgow Scotland, UK.

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http://dx.doi.org/10.3389/fphys.2010.00009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059953PMC
May 2011

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

Anal Chem 2011 Apr 14;83(7):2786-93. Epub 2011 Mar 14.

Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ac2000994DOI Listing
April 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).

Microb Biotechnol 2011 Mar 8;4(2):239-51. Epub 2010 Dec 8.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, the Netherlands.

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http://dx.doi.org/10.1111/j.1751-7915.2010.00232.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818864PMC
March 2011

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus.

Microb Biotechnol 2011 Mar 2;4(2):300-5. Epub 2010 Nov 2.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.

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http://doi.wiley.com/10.1111/j.1751-7915.2010.00226.x
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http://dx.doi.org/10.1111/j.1751-7915.2010.00226.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818869PMC
March 2011

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms.

Nat Rev Microbiol 2011 02 29;9(2):131-7. Epub 2010 Dec 29.

Department of Microbial Physiology and the Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

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http://dx.doi.org/10.1038/nrmicro2478DOI Listing
February 2011

Computational modelling of kinase signalling cascades.

Methods Mol Biol 2010 ;661:369-84

School of Information Science, Computing and Mathematics, Brunel University, Uxbridge, Middlesex, UK.

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http://dx.doi.org/10.1007/978-1-60761-795-2_22DOI Listing
December 2010

Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis.

Anal Bioanal Chem 2010 Nov 8;398(5):2059-69. Epub 2010 Sep 8.

Department of Parasitology, Unit of Molecular Parasitology, Institute of Tropical Medicine, 2000 Antwerp, Belgium.

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http://dx.doi.org/10.1007/s00216-010-4139-0DOI Listing
November 2010

Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples.

J Proteome Res 2010 Nov 30;9(11):5922-8. Epub 2010 Sep 30.

Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/pr1006944DOI Listing
November 2010

Metabolomics to unveil and understand phenotypic diversity between pathogen populations.

PLoS Negl Trop Dis 2010 Nov 30;4(11):e904. Epub 2010 Nov 30.

Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium.

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http://dx.doi.org/10.1371/journal.pntd.0000904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994915PMC
November 2010

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules.

BMC Bioinformatics 2010 Oct 6;11:497. Epub 2010 Oct 6.

Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976757PMC
October 2010

Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans.

Genetics 2010 Sep 6;186(1):405-10. Epub 2010 Jul 6.

Groningen Bioinformatics Centre, University of Groningen, 9751 NN, Haren, The Netherlands.

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http://dx.doi.org/10.1534/genetics.110.119677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940304PMC
September 2010

The potential of metabolomics for Leishmania research in the post-genomics era.

Parasitology 2010 Aug 29;137(9):1291-302. Epub 2010 Jan 29.

Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1017/S0031182009992022DOI Listing
August 2010

Metabolomic systems biology of trypanosomes.

Parasitology 2010 Aug 17;137(9):1285-90. Epub 2010 Feb 17.

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.

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http://dx.doi.org/10.1017/S003118201000017XDOI Listing
August 2010

The silicon trypanosome.

Parasitology 2010 Aug 6;137(9):1333-41. Epub 2010 May 6.

Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.

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http://dx.doi.org/10.1017/S0031182010000466DOI Listing
August 2010

The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways.

Genome Biol Evol 2010 Jul 12;2:212-24. Epub 2010 Jul 12.

Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.

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http://dx.doi.org/10.1093/gbe/evq013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997539PMC
July 2010

A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior.

BMC Syst Biol 2010 Jun 7;4:81. Epub 2010 Jun 7.

Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/1752-0509-4-81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887794PMC
June 2010

Metabolomic characterization of the salt stress response in Streptomyces coelicolor.

Appl Environ Microbiol 2010 Apr 26;76(8):2574-81. Epub 2010 Feb 26.

Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, Netherlands.

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http://dx.doi.org/10.1128/AEM.01992-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849216PMC
April 2010

Genome-based phylogenetic analysis of Streptomyces and its relatives.

Mol Phylogenet Evol 2010 Mar 3;54(3):763-72. Epub 2009 Dec 3.

Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1016/j.ympev.2009.11.019DOI Listing
March 2010

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor.

BMC Genomics 2010 Mar 26;11:202. Epub 2010 Mar 26.

Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853524PMC
March 2010

Coronatine-insensitive 1 (COI1) mediates transcriptional responses of Arabidopsis thaliana to external potassium supply.

Mol Plant 2010 Mar;3(2):390-405

Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK.

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http://dx.doi.org/10.1093/mp/ssq012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845782PMC
March 2010

Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms.

EMBO Mol Med 2009 Nov;1(8-9):360-70

Department of Genetics, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1002/emmm.200900051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378155PMC
November 2009

Expression quantitative trait loci are highly sensitive to cellular differentiation state.

PLoS Genet 2009 Oct 16;5(10):e1000692. Epub 2009 Oct 16.

Department of Cell Biology, Section Stem Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1000692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757904PMC
October 2009

designGG: an R-package and web tool for the optimal design of genetical genomics experiments.

BMC Bioinformatics 2009 Jun 18;10:188. Epub 2009 Jun 18.

Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706229PMC
June 2009