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ORCIDRainer Breitling
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- affiliation: University of Groningen, Netherlands
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2020 – today
- 2020
[j38]Areti Tsigkinopoulou, Eriko Takano
, Rainer Breitling:
Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling. PLoS Comput. Biol. 16(7) (2020)
2010 – 2019
- 2018
- [j37]Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J. Turner, Nigel S. Scrutton, Douglas B. Kell, Rainer Breitling, Jean-Loup Faulon:
Selenzyme: enzyme selection tool for pathway design. Bioinform. 34(12): 2153-2154 (2018) - 2017
- [j36]Francesco Del Carratore, Andris Jankevics, Rob Eisinga, Tom Heskes, Fangxin Hong, Rainer Breitling:
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. Bioinform. 33(17): 2774-2775 (2017) - [j35]Kai Blin, Thomas Wolf, Marc G. Chevrette, Xiaowen Lu, Christopher J. Schwalen, Satria A. Kautsar, Hernando G. Suarez Duran, Emmanuel L. C. de los Santos, Hyun Uk Kim, Mariana Nave, Jeroen S. Dickschat, Douglas A. Mitchell, Ekaterina Shelest, Rainer Breitling, Eriko Takano, Sang Yup Lee, Tilmann Weber, Marnix H. Medema:
antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45(Webserver-Issue): W36-W41 (2017) - [j34]Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell:
CodonGenie: optimised ambiguous codon design tools. PeerJ Comput. Sci. 3: e120 (2017) - [i5]Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell:
CodonGenie: optimised ambiguous codon design tools. PeerJ Prepr. 5: e2797 (2017) - 2015
- [j33]Joe Wandy, Rónán Daly, Rainer Breitling, Simon Rogers:
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinform. 31(12): 1999-2006 (2015) - [j32]Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling, Frédéric Bringaud, Peter Bütikofer, Amy M. Cattanach, Bridget Bannerman-Chukualim, Darren J. Creek, Kathryn Crouch, Harry P. de Koning, Hubert Denise, Charles Ebikeme, Alan H. Fairlamb, Michael A. J. Ferguson, Michael L. Ginger, Christiane Hertz-Fowler, Eduard J. Kerkhoven, Pascal Mäser, Paul A. M. Michels, Archana Nayak, David W. Nes, Derek P. Nolan, Christian Olsen, Fatima Silva-Franco, Terry K. Smith, Martin C. Taylor, Aloysius G. M. Tielens, Michael D. Urbaniak, Jaap J. van Hellemond, Isabel M. Vincent, Shane R. Wilkinson, Susan Wyllie, Fred R. Opperdoes, Michael P. Barrett, Fabien Jourdan:
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res. 43(Database-Issue): 637-644 (2015) - [j31]Tilmann Weber, Kai Blin, Srikanth Duddela, Daniel Krug, Hyun Uk Kim, Robert E. Bruccoleri, Sang Yup Lee, Michael A. Fischbach, Rolf Müller, Wolfgang Wohlleben, Rainer Breitling, Eriko Takano, Marnix H. Medema:
antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43(Webserver-Issue): W237-W243 (2015) - 2014
- [j30]Rónán Daly, Simon Rogers, Joe Wandy, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling:
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. Bioinform. 30(19): 2764-2771 (2014) - [j29]Tom Heskes, Rob Eisinga, Rainer Breitling:
A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments. BMC Bioinform. 15: 367 (2014) - [j28]Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling:
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products. PLoS Comput. Biol. 10(9) (2014) - 2013
- [j27]Achuthanunni Chokkathukalam, Andris Jankevics, Darren J. Creek, Fiona Achcar, Michael P. Barrett, Rainer Breitling:
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinform. 29(2): 281-283 (2013) - [j26]Karlheinz Schwarz, Rainer Breitling, Christian Allen:
Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering. Comput. 1(2): 27-30 (2013) - [j25]Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, Tilmann Weber:
antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 41(Webserver-Issue): 204-212 (2013) - [j24]Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybilo, Nicole N. Driessen, David R. Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett:
Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Comput. Biol. 9(12) (2013) - 2012
- [j23]Darren J. Creek, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling, Michael P. Barrett:
IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. Bioinform. 28(7): 1048-1049 (2012) - [j22]Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling:
Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLoS Comput. Biol. 8(1) (2012) - 2011
- [j21]Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, Rainer Breitling:
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39(Web-Server-Issue): 339-346 (2011) - [i4]Rainer Breitling, Frank J. Bruggeman, Corrado Priami, Adelinde M. Uhrmacher:
Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). Dagstuhl Reports 1(4): 41-64 (2011) - 2010
- [j20]Bruno M. Tesson, Rainer Breitling, Ritsert C. Jansen:
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinform. 11: 497 (2010) - [j19]Mi Zhang, William R. Schafer, Rainer Breitling:
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. BMC Syst. Biol. 4: 81 (2010) - [j18]Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner:
Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology 12: 1-12 (2010) - [e2]Corrado Priami, Rainer Breitling, David R. Gilbert, Monika Heiner, Adelinde M. Uhrmacher:
Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies. Lecture Notes in Computer Science 5945, Springer 2010, ISBN 978-3-642-11711-4 [contents]
2000 – 2009
- 2009
- [j17]Simon Rogers, Richard A. Scheltema, Mark A. Girolami, Rainer Breitling:
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinform. 25(4): 512-518 (2009) - [j16]Yang Li, Morris A. Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C. Jansen:
designGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinform. 10 (2009) - [e1]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
Formal Methods in Molecular Biology, 22.02. - 27.02.2009. Dagstuhl Seminar Proceedings 09091, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Germany 2009 [contents] - [i3]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
09091 Abstracts Collection - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology 2009 - [i2]Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami:
09091 Executive Summary - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology 2009 - [i1]David Roger Gilbert, Rainer Breitling, Monika Heiner:
BioModel Engineering: Its role in Systems Biology and Synthetic Biology. Formal Methods in Molecular Biology 2009 - 2008
- [j15]Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton:
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings Bioinform. 9(5): 404-421 (2008) - [j14]Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert:
MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinform. 24(1): 143-145 (2008) - [j13]Fangxin Hong, Rainer Breitling:
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinform. 24(3): 374-382 (2008) - [c3]David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson:
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing 2008: 13-28 - 2007
- [j12]Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B. T. M. Roerdink, Oscar P. Kuipers:
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinform. 23(9): 1161-1163 (2007) - [j11]Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V. Bystrykh, Gerald de Haan, Rainer Breitling, Jan Peter Nap, Ritsert C. Jansen:
A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinform. 8 (2007) - [c2]Michael Biehl, Rainer Breitling, Yang Li:
Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning. IDEAL 2007: 880-889 - [c1]Ali Al-Shahib, David R. Gilbert, Rainer Breitling:
Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL 2007: 890-897 - 2006
- [j10]Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert:
A lock-and-key model for protein-protein interactions. Bioinform. 22(16): 2012-2019 (2006) - [j9]Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, Joanne Chory:
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinform. 22(22): 2825-2827 (2006) - 2005
- [j8]Rainer Breitling, Patrick Armengaud, Anna Amtmann:
Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. BMC Bioinform. 6: 181 (2005) - [j7]Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert:
GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinform. 6: 233 (2005) - [j6]Ali Al-Shahib, Rainer Breitling, David R. Gilbert:
Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. 15(4): 259-275 (2005) - [j5]Rainer Breitling, Pawel Herzyk:
Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data. J. Bioinform. Comput. Biol. 3(5): 1171-1190 (2005) - [j4]Simon Rogers, Mark A. Girolami, Colin Campbell, Rainer Breitling:
The Latent Process Decomposition of cDNA Microarray Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 2(2): 143-156 (2005) - 2004
- [j3]Mark A. Girolami, Rainer Breitling:
Biologically valid linear factor models of gene expression. Bioinform. 20(17): 3021-3033 (2004) - [j2]Rainer Breitling, Anna Amtmann, Pawel Herzyk:
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinform. 5: 34 (2004) - [j1]Rainer Breitling, Anna Amtmann, Pawel Herzyk:
Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinform. 5: 100 (2004)
Coauthor Index
aka: David Roger Gilbert
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