Biologically valid linear factor models of gene expression. - Mark A. Girolami; Rainer Breitling (Bioinform., 2004)

Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. - Rainer Breitling; Anna Amtmann; Pawel Herzyk (BMC Bioinform., 2004)

Graph-based iterative Group Analysis enhances microarray interpretation. - Rainer Breitling; Anna Amtmann; Pawel Herzyk (BMC Bioinform., 2004)

Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. - Rainer Breitling; Patrick Armengaud; Anna Amtmann (BMC Bioinform., 2005)

GeneRank: Using search engine technology for the analysis of microarray experiments. - Julie L. Morrison; Rainer Breitling; Desmond J. Higham; David R. Gilbert (BMC Bioinform., 2005)

Franksum: new feature selection method for protein function prediction. - Ali Al-Shahib; Rainer Breitling; David R. Gilbert (Int. J. Neural Syst., 2005)

Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data. - Rainer Breitling; Pawel Herzyk (J. Bioinform. Comput. Biol., 2005)

The Latent Process Decomposition of cDNA Microarray Data Sets. - Simon Rogers; Mark A. Girolami; Colin Campbell; Rainer Breitling (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. - Fangxin Hong; Rainer Breitling; Connor W. McEntee; Ben S. Wittner; Jennifer L. Nemhauser; Joanne Chory (Bioinform., 2006)

A lock-and-key model for protein-protein interactions. - Julie L. Morrison; Rainer Breitling; Desmond J. Higham; David R. Gilbert (Bioinform., 2006)

Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. - Ali Al-Shahib; David R. Gilbert; Rainer Breitling (IDEAL, 2007)

Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning. - Michael Biehl; Rainer Breitling; Yang Li 036 (IDEAL, 2007)

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. - 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 (Bioinform., 2007)

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. - Rudi Alberts; Peter Terpstra; Menno Hardonk; Leonid V. Bystrykh; Gerald de Haan; Rainer Breitling; Jan Peter Nap; Ritsert C. Jansen (BMC Bioinform., 2007)

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. - David R. Gilbert; Rainer Breitling; Monika Heiner; Robin Donaldson (Workshop on Membrane Computing, 2008)

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. - Rainer Breitling; David R. Gilbert; Monika Heiner; Richard J. Orton (Briefings Bioinform., 2008)

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. - Fangxin Hong; Rainer Breitling (Bioinform., 2008)

MetaNetter: inference and visualization of high-resolution metabolomic networks. - Fabien Jourdan; Rainer Breitling; Michael P. Barrett; David R. Gilbert (Bioinform., 2008)

09091 Abstracts Collection - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

09091 Executive Summary - Formal Methods in Molecular Biology. - Rainer Breitling; David Roger Gilbert; Monika Heiner; Corrado Priami (Formal Methods in Molecular Biology, 2009)

BioModel Engineering: Its role in Systems Biology and Synthetic Biology. - David Roger Gilbert; Rainer Breitling; Monika Heiner (Formal Methods in Molecular Biology, 2009)

Probabilistic assignment of formulas to mass peaks in metabolomics experiments. - Simon Rogers; Richard A. Scheltema; Mark A. Girolami; Rainer Breitling (Bioinform., 2009)

designGG: an R-package and web tool for the optimal design of genetical genomics experiments. - Yang Li 036; Morris A. Swertz; Gonzalo Vera; Jingyuan Fu; Rainer Breitling; Ritsert C. Jansen (BMC Bioinform., 2009)

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. - Bruno M. Tesson; Rainer Breitling; Ritsert C. Jansen (BMC Bioinform., 2010)

A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. - Mi Zhang; William R. Schafer; Rainer Breitling (BMC Syst. Biol., 2010)

Biomodel Engineering - From Structure to Behavior. - Rainer Breitling; Robin Donaldson; David R. Gilbert; Monika Heiner (Trans. Comp. Sys. Biology, 2010)

Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). - Rainer Breitling; Frank J. Bruggeman; Corrado Priami; Adelinde M. Uhrmacher (Dagstuhl Reports, 2011)

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. - Marnix H. Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A. Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling (Nucleic Acids Res., 2011)

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. - Darren J. Creek; Andris Jankevics; Karl E. V. Burgess; Rainer Breitling; Michael P. Barrett (Bioinform., 2012)

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. - Fiona Achcar; Eduard J. Kerkhoven; Barbara M. Bakker; Michael P. Barrett; Rainer Breitling (PLoS Comput. Biol., 2012)

mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. - Achuthanunni Chokkathukalam; Andris Jankevics; Darren J. Creek; Fiona Achcar; Michael P. Barrett; Rainer Breitling (Bioinform., 2013)

Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering. - Karlheinz Schwarz; Rainer Breitling; Christian Allen (Comput., 2013)

antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. - Kai Blin; Marnix H. Medema; Daniyal Kazempour; Michael A. Fischbach; Rainer Breitling; Eriko Takano; Tilmann Weber (Nucleic Acids Res., 2013)

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. - 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., 2013)

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. - Rónán Daly; Simon Rogers; Joe Wandy; Andris Jankevics; Karl E. V. Burgess; Rainer Breitling (Bioinform., 2014)

A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments. - Tom Heskes; Rob Eisinga; Rainer Breitling (BMC Bioinform., 2014)

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products. - Marnix H. Medema; Yared Paalvast; Don D. Nguyen; Alexey Melnik; Pieter C. Dorrestein; Eriko Takano; Rainer Breitling (PLoS Comput. Biol., 2014)

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. - Joe Wandy; Rónán Daly; Rainer Breitling; Simon Rogers (Bioinform., 2015)

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. - 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; et al. (Nucleic Acids Res., 2015)

antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. - Tilmann Weber; Kai Blin; Srikanth Duddela; Daniel Krug; Hyun Uk Kim; Robert E. Bruccoleri; Sang Yup Lee; Michael A. Fischbach; Rolf Müller 002; Wolfgang Wohlleben; Rainer Breitling; Eriko Takano; et al. (Nucleic Acids Res., 2015)

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. - Francesco Del Carratore; Andris Jankevics; Rob Eisinga; Tom Heskes; Fangxin Hong; Rainer Breitling (Bioinform., 2017)

antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. - Kai Blin; Thomas Wolf 001; 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; et al. (Nucleic Acids Res., 2017)

CodonGenie: optimised ambiguous codon design tools. - Neil Swainston; Andrew Currin; Lucy Green; Rainer Breitling; Philip J. Day; Douglas B. Kell (PeerJ Prepr., 2017)

Selenzyme: enzyme selection tool for pathway design. - Pablo Carbonell; Jerry Wong; Neil Swainston; Eriko Takano; Nicholas J. Turner; Nigel S. Scrutton; Douglas B. Kell; Rainer Breitling; Jean-Loup Faulon (Bioinform., 2018)

Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling. - Areti Tsigkinopoulou; Eriko Takano; Rainer Breitling (PLoS Comput. Biol., 2020)