Rainer Breitling

Publication Activity (10 Years)

Years Active: 2004-2020
Publications (10 Years): 9

Top Topics

Computational Chemistry

Mass Spectrometry

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling. PLoS Comput. Biol. 16 (7) (2020)
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) (2018)
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) (2017)
Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell
CodonGenie: optimised ambiguous codon design tools. PeerJ Prepr. 5 (2017)
Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell
CodonGenie: optimised ambiguous codon design tools. PeerJ Comput. Sci. 3 (2017)
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) (2017)
Joe Wandy, Rónán Daly, Rainer Breitling, Simon Rogers
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinform. 31 (12) (2015)
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
. Nucleic Acids Res. 43 (Database-Issue) (2015)
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) (2015)
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)
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 (2014)
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) (2014)
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
. PLoS Comput. Biol. 9 (12) (2013)
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) (2013)
Karlheinz Schwarz, Rainer Breitling, Christian Allen
: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering. Comput. 1 (2) (2013)
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) (2013)
Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling
Energy Metabolism. PLoS Comput. Biol. 8 (1) (2012)
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) (2012)
Rainer Breitling, Frank J. Bruggeman, Corrado Priami, Adelinde M. Uhrmacher
Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). Dagstuhl Reports 1 (4) (2011)
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) (2011)
Mi Zhang, William R. Schafer, Rainer Breitling
A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. BMC Syst. Biol. 4 (2010)
Bruno M. Tesson, Rainer Breitling, Ritsert C. Jansen
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinform. 11 (2010)
Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology 12 (2010)
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
09091 Executive Summary - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology (2009)
Simon Rogers, Richard A. Scheltema, Mark A. Girolami, Rainer Breitling
Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinform. 25 (4) (2009)
David Roger Gilbert, Rainer Breitling, Monika Heiner
BioModel Engineering: Its role in Systems Biology and Synthetic Biology. Formal Methods in Molecular Biology (2009)
Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
09091 Abstracts Collection - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology (2009)
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)
David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing (2008)
Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert
MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinform. 24 (1) (2008)
Fangxin Hong, Rainer Breitling
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinform. 24 (3) (2008)
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) (2008)
Ali Al-Shahib, David R. Gilbert, Rainer Breitling
Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL (2007)
Michael Biehl, Rainer Breitling, Yang Li
Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning. IDEAL (2007)
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)
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) (2007)
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) (2006)
Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
A lock-and-key model for protein-protein interactions. Bioinform. 22 (16) (2006)
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) (2005)
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 (2005)
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) (2005)
Ali Al-Shahib, Rainer Breitling, David R. Gilbert
Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. 15 (4) (2005)
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 (2005)
Rainer Breitling, Anna Amtmann, Pawel Herzyk
Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinform. 5 (2004)
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 (2004)
Mark A. Girolami, Rainer Breitling
Biologically valid linear factor models of gene expression. Bioinform. 20 (17) (2004)