Rainer Breitling

53 papers C 2Journal 43Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Cross-Granularity Representations for Biological Sequences: Insights from ESM and BiGCARP. CoRR Hanlin Xiao, Rainer Breitling, Eriko Takano, Mauricio A. Álvarez
2026	J	`jnl`	Disentangling Similarity and Relatedness in Topic Models. CoRR Hanlin Xiao, Mauricio A. Álvarez, Rainer Breitling
2025	—	`conf`	Cross-Granularity Representations for Biological Sequences: Insights From ESM and BiGCARP. BIBM Hanlin Xiao, Rainer Breitling, Eriko Takano, Mauricio A. Álvarez
2025	—	`conf`	Proscope: Modeling Biosynthetic Diversity Via Probabilistic Structure-Aware Co-Embedding. BIBM Yiting Li, Eriko Takano, Jing Zhang, Ben Draper, Wayne Wei Zhong Yeo, Rainer Breitling
2025	J	`jnl`	Synteny plot quality control with SyntenyQC. Bioinform. Timothy D. J. Kirkwood, Jack A. Connolly, Ee Lui Ang, Huimin Zhao, Eriko Takano, Rainer Breitling
2023	J	`jnl`	ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0 - an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data. Bioinform. Francesco Del Carratore, William Eagles, Juraj Borka, Rainer Breitling
2020	J	`jnl`	Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling. PLoS Comput. Biol. Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling
2018	J	`jnl`	Selenzyme: enzyme selection tool for pathway design. Bioinform. Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J. Turner, Nigel S. Scrutton, Douglas B. Kell, Rainer Breitling, Jean-Loup Faulon
2017	J	`jnl`	CodonGenie: optimised ambiguous codon design tools. PeerJ Comput. Sci. Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell
2017	J	`jnl`	CodonGenie: optimised ambiguous codon design tools. PeerJ Prepr. Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell
2017	J	`jnl`	RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. Bioinform. Francesco Del Carratore, Andris Jankevics, Rob Eisinga, Tom Heskes, Fangxin Hong, Rainer Breitling
2017	J	`jnl`	antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 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
2015	J	`jnl`	Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinform. Joe Wandy, Rónán Daly, Rainer Breitling, Simon Rogers
2015	J	`jnl`	TrypanoCyc: a community-led biochemical pathways database for Nucleic Acids Res. 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
2015	J	`jnl`	antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 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
2014	J	`jnl`	A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments. BMC Bioinform. Tom Heskes, Rob Eisinga, Rainer Breitling
2014	J	`jnl`	MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. Bioinform. Rónán Daly, Simon Rogers, Joe Wandy, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling
2014	J	`jnl`	Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products. PLoS Comput. Biol. Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling
2013	J	`jnl`	Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in PLoS Comput. Biol. 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
2013	J	`jnl`	antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, Tilmann Weber
2013	J	`jnl`	mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. Bioinform. Achuthanunni Chokkathukalam, Andris Jankevics, Darren J. Creek, Fiona Achcar, Michael P. Barrett, Rainer Breitling
2012	J	`jnl`	Dynamic Modelling under Uncertainty: The Case of PLoS Comput. Biol. Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling
2012	J	`jnl`	IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data. Bioinform. Darren J. Creek, Andris Jankevics, Karl E. V. Burgess, Rainer Breitling, Michael P. Barrett
2011	J	`jnl`	Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). Dagstuhl Reports Rainer Breitling, Frank J. Bruggeman, Corrado Priami, Adelinde M. Uhrmacher
2011	J	`jnl`	antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, Rainer Breitling
2010	J	`jnl`	A circuit model of the temporal pattern generator of Caenorhabditis egg-laying behavior. BMC Syst. Biol. Mi Zhang, William R. Schafer, Rainer Breitling
2010	J	`jnl`	Biomodel Engineering - From Structure to Behavior. Trans. Comp. Sys. Biology Rainer Breitling, Robin Donaldson, David R. Gilbert, Monika Heiner
2010	J	`jnl`	DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. BMC Bioinform. Bruno M. Tesson, Rainer Breitling, Ritsert C. Jansen
2010	—	`ed.`	Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies Trans. Computational Systems Biology Corrado Priami, Rainer Breitling, David R. Gilbert, Monika Heiner, Adelinde M. Uhrmacher
2009	—	`conf`	09091 Abstracts Collection - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009	—	`conf`	09091 Executive Summary - Formal Methods in Molecular Biology. Formal Methods in Molecular Biology Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009	—	`conf`	BioModel Engineering: Its role in Systems Biology and Synthetic Biology. Formal Methods in Molecular Biology David Roger Gilbert, Rainer Breitling, Monika Heiner
2009	—	`ed.`	Formal Methods in Molecular Biology, 22.02. - 27.02.2009 Formal Methods in Molecular Biology Rainer Breitling, David Roger Gilbert, Monika Heiner, Corrado Priami
2009	J	`jnl`	Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinform. Simon Rogers, Richard A. Scheltema, Mark A. Girolami, Rainer Breitling
2009	J	`jnl`	designGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinform. Yang Li, Morris A. Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C. Jansen
2008	J	`jnl`	A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinform. Fangxin Hong, Rainer Breitling
2008	J	`jnl`	A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings Bioinform. Rainer Breitling, David R. Gilbert, Monika Heiner, Richard J. Orton
2008	—	`conf`	An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways. Workshop on Membrane Computing David R. Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
2008	J	`jnl`	MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinform. Fabien Jourdan, Rainer Breitling, Michael P. Barrett, David R. Gilbert
2007	J	`jnl`	A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinform. Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V. Bystrykh, Gerald de Haan, Rainer Breitling, Jan Peter Nap, Ritsert C. Jansen
2007	C	`conf`	Analysis of Tiling Microarray Data by Learning Vector Quantization and Relevance Learning. IDEAL Michael Biehl, Rainer Breitling, Yang Li
2007	C	`conf`	Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning. IDEAL Ali Al-Shahib, David R. Gilbert, Rainer Breitling
2007	J	`jnl`	FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinform. 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
2006	J	`jnl`	A lock-and-key model for protein-protein interactions. Bioinform. Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
2006	J	`jnl`	RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinform. Fangxin Hong, Rainer Breitling, Connor W. McEntee, Ben S. Wittner, Jennifer L. Nemhauser, Joanne Chory
2005	J	`jnl`	Franksum: new feature selection method for protein function prediction. Int. J. Neural Syst. Ali Al-Shahib, Rainer Breitling, David R. Gilbert
2005	J	`jnl`	GeneRank: Using search engine technology for the analysis of microarray experiments. BMC Bioinform. Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert
2005	J	`jnl`	Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data. J. Bioinform. Comput. Biol. Rainer Breitling, Pawel Herzyk
2005	J	`jnl`	The Latent Process Decomposition of cDNA Microarray Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. Simon Rogers, Mark A. Girolami, Colin Campbell, Rainer Breitling
2005	J	`jnl`	Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. BMC Bioinform. Rainer Breitling, Patrick Armengaud, Anna Amtmann
2004	J	`jnl`	Biologically valid linear factor models of gene expression. Bioinform. Mark A. Girolami, Rainer Breitling
2004	J	`jnl`	Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinform. Rainer Breitling, Anna Amtmann, Pawel Herzyk
2004	J	`jnl`	Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments. BMC Bioinform. Rainer Breitling, Anna Amtmann, Pawel Herzyk