Works by Breitling, Rainer

Results: 101

Computational tools for the synthetic design of biochemical pathways.

Published in:

Nature Reviews Microbiology, 2012, v. 10, n. 3, p. 191, doi. 10.1038/nrmicro2717

By:

Medema, Marnix H.;
van Raaphorst, Renske;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

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

Published in:

Nature Reviews Microbiology, 2011, v. 9, n. 2, p. 131, doi. 10.1038/nrmicro2478

By:

Medema, Marnix H.;
Breitling, Rainer;
Bovenberg, Roel;
Takano, Eriko

Publication type:

Article

Structure-based Phylogenetic Analysis of Short-chain Alcohol Dehydrogenases and Reclassification of the 17beta-Hydroxysteroid Dehydrogenase Family.

Published in:

Molecular Biology & Evolution, 2001, v. 18, n. 12, p. 2154, doi. 10.1093/oxfordjournals.molbev.a003761

By:

Breitling, Rainer;
Laubner, Daniela;
Adamski, Jerzy

Publication type:

Article

Origin of the paired domain.

Published in:

Development Genes & Evolution, 2000, v. 210, n. 12, p. 644, doi. 10.1007/s004270000106

By:

Breitling, Rainer;
Gerber, J.-K.

Publication type:

Article

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

Published in:

Journal of Industrial Microbiology & Biotechnology, 2018, v. 45, n. 7, p. 615, doi. 10.1007/s10295-017-1993-1

By:

Peña, Alejandro;
Del Carratore, Francesco;
Cummings, Matthew;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol.

Published in:

Synthetic Biology (23977000), 2020, v. 5, n. 1, p. 1, doi. 10.1093/synbio/ysaa012

By:

Dunstan, Mark S;
Robinson, Christopher J;
Jervis, Adrian J;
Yan, Cunyu;
Carbonell, Pablo;
Hollywood, Katherine A;
Currin, Andrew;
Swainston, Neil;
Feuvre, Rosalind Le;
Micklefield, Jason;
Faulon, Jean-Loup;
Breitling, Rainer;
Turner, Nicholas;
Takano, Eriko;
Scrutton, Nigel S

Publication type:

Article

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries.

Published in:

Synthetic Biology (23977000), 2019, v. 4, n. 1, p. N.PAG, doi. 10.1093/synbio/ysz025

By:

Currin, Andrew;
Swainston, Neil;
Dunstan, Mark S;
Jervis, Adrian J;
Mulherin, Paul;
Robinson, Christopher J;
Taylor, Sandra;
Carbonell, Pablo;
Hollywood, Katherine A;
Yan, Cunyu;
Takano, Eriko;
Scrutton, Nigel S;
Breitling, Rainer

Publication type:

Article

Exact Reduction of the Generalized Lotka–Volterra Equations via Integral and Algebraic Substitutions.

Published in:

Computation, 2021, v. 9, n. 5, p. 49, doi. 10.3390/computation9050049

By:

Morrison, Rebecca E.;
Breitling, Rainer;
Schwarz, Karlheinz

Publication type:

Article

New surveyor tools for charting microbial metabolic maps.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 2, p. 156, doi. 10.1038/nrmicro1797

By:

Breitling, Rainer;
Vitkup, Dennis;
Barrett, Michael P.

Publication type:

Article

Increasing the mass accuracy of high-resolution LC-MS data using background ions - a case study on the LTQ-Orbitrap.

Published in:

Proteomics, 2008, v. 8, n. 22, p. 4647, doi. 10.1002/pmic.200800314

By:

Scheltema, Richard A.;
Kamleh, Anas;
Wildridge, David;
Ebikeme, Charles;
Watson, David G.;
Barrett, Michael P.;
Jansen, Ritsert C.;
Breitling, Rainer

Publication type:

Article

Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series.

Published in:

Proteomics, 2007, v. 7, n. 17, p. 3219, doi. 10.1002/pmic.200601047

By:

Roelofsen, Han;
Alvarez-Llamas, Gloria;
Dijkstra, Martijn;
Breitling, Rainer;
Havenga, Klaas;
Bijzet, Johan;
Zandbergen, Wouter;
de Vries, Marcel P.;
Ploeg, Rutger J.;
Vonk, Roel J.

Publication type:

Article

Isopentenyl-Diphosphate Isomerases in Human and Mouse: Evolutionary Analysis of a Mammalian Gene Duplication.

Published in:

Journal of Molecular Evolution, 2003, v. 57, n. 3, p. 282, doi. 10.1007/s00239-003-2476-8

By:

Breitling, Rainer;
Laubner, Daniela;
Clizbe, Daun;
Adamski, Jerzy;
Krisans, Skaidrite K.

Publication type:

Article

ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0—an improved Bayesian-based method for the annotation of LC–MS/MS untargeted metabolomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 7, p. 1, doi. 10.1093/bioinformatics/btad455

By:

Carratore, Francesco Del;
Eagles, William;
Borka, Juraj;
Breitling, Rainer

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2013, v. 41, p. W204, doi. 10.1093/nar/gkt449

By:

Blin, Kai;
Medema, Marnix H.;
Kazempour, Daniyal;
Fischbach, Michael A.;
Breitling, Rainer;
Takano, Eriko;
Weber, Tilmann

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W339, doi. 10.1093/nar/gkr466

By:

Medema, Marnix H.;
Blin, Kai;
Cimermancic, Peter;
de Jager, Victor;
Zakrzewski, Piotr;
Fischbach, Michael A.;
Weber, Tilmann;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

Steatoda nobilis, a false widow on the rise: a synthesis of past and current distribution trends.

Published in:

NeoBiota, 2019, n. 42, p. 19, doi. 10.3897/neobiota.42.31582

By:

Bauer, Tobias;
Feldmeier, Stephan;
Krehenwinkel, Henrik;
Wieczorrek, Carsten;
Reiser, Nils;
Breitling, Rainer

Publication type:

Article

Exploring novel bacterial terpene synthases.

Published in:

PLoS ONE, 2020, v. 15, n. 4, p. 1, doi. 10.1371/journal.pone.0232220

By:

Reddy, Gajendar Komati;
Leferink, Nicole G. H.;
Umemura, Maiko;
Ahmed, Syed T.;
Breitling, Rainer;
Scrutton, Nigel S.;
Takano, Eriko

Publication type:

Article

System-wide molecular evidence for phenotypic buffering in Arabidopsis.

Published in:

Nature Genetics, 2009, v. 41, n. 2, p. 166, doi. 10.1038/ng.308

By:

Jingyuan Fu;
Keurentjes, Joost J. B.;
Bouwmeester, Harro;
America, Twan;
Verstappen, Francel W. A.;
Ward, Jane L.;
Beale, Michael H.;
de Vos, Ric C. H.;
Dijkstra, Martijn;
Scheltema, Richard A.;
Johannes, Frank;
Koornneef, Maarten;
Vreugdenhil, Dick;
Breitling, Rainer;
Jansen, Ritsert C.

Publication type:

Article

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

Published in:

FEBS Journal, 2013, v. 280, n. 18, p. 4640, doi. 10.1111/febs.12436

By:

Achcar, Fiona;
Barrett, Michael P.;
Breitling, Rainer

Publication type:

Article

Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State.

Published in:

PLoS Genetics, 2009, v. 5, n. 10, p. 1, doi. 10.1371/journal.pgen.1000692

By:

Gerrits, Alice;
Yang Li;
Tesson, Bruno M.;
Bystrykh, Leonid V.;
Weersing, Ellen;
Ausema, Albertina;
Dontje, Bert;
Xusheng Wang;
Breitling, Rainer;
Jansen, Ritsert C.;
de Haan, Gerald

Publication type:

Article

Genetical Genomics: Spotlight on QTL Hotspots.

Published in:

2008

By:

Breitling, Rainer;
Yang Li;
Tesson, Bruno M.;
Jingyuan Fu;
Chunlei Wu;
Wiltshire, Tim;
Gerrits, Alice;
Bystrykh, Leonid V.;
de Haan, Gerald;
Su, Andrew I.;
Ritsert C. Jansen

Publication type:

Opinion

C. elegans Model Identifies Genetic Modifiers of α-Synuclein Inclusion Formation During Aging.

Published in:

PLoS Genetics, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pgen.1000027

By:

van Ham, Tjakko J.;
Thijssen, Karen L.;
Breitling, Rainer;
Hofstra, Robert M. W.;
Plasterk, Ronald H. A.;
Nollen, Ellen A. A.

Publication type:

Article

Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans.

Published in:

PLoS Genetics, 2006, v. 3, n. 6, p. 2155, doi. 10.1371/journal.pgen.0020222

By:

Yang Li;
Álvarez, Olga Alda;
Gutteling, Evert W.;
Tijsterman, Marcel;
Jingyuan Fu;
Riksen, Joost A. G.;
Hazendonk, Esther;
Prins, Pjotr;
Plasterk, Ronald H. A.;
Jansen, Ritsert C.;
Breitling, Rainer;
Kammenga, Jan E.

Publication type:

Article

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.

Published in:

Bioinformatics, 2008, v. 24, n. 3, p. 374, doi. 10.1093/bioinformatics/btm620

By:

Fangxin Hong;
Rainer Breitling

Publication type:

Article

MetaNetter: inference and visualization of high-resolution metabolomic networks.

Published in:

Bioinformatics, 2008, v. 24, n. 1, p. 143, doi. 10.1093/bioinformatics/btm536

By:

Fabien Jourdan;
Rainer Breitling;
Michael P. Barrett;
David Gilbert

Publication type:

Article

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.

Published in:

Bioinformatics, 2007, v. 23, n. 9, p. 1161, doi. 10.1093/bioinformatics/btl658

By:

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

Publication type:

Article

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.

Published in:

Bioinformatics, 2006, v. 22, n. 22, p. 2825, doi. 10.1093/bioinformatics/btl476

By:

Hong, Fangxin;
Breitling, Rainer;
McEntee, Connor W.;
Wittner, Ben S.;
Nemhauser, Jennifer L.;
Chory, Joanne

Publication type:

Article

Biologically valid linear factor models of gene expression.

Published in:

Bioinformatics, 2004, v. 20, n. 17, p. 3021, doi. 10.1093/bioinformatics/bth354

By:

Mark Girolami;
Rainer Breitling

Publication type:

Article

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

Published in:

Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0333-6

By:

Del Carratore, Francesco;
Zych, Konrad;
Cummings, Matthew;
Takano, Eriko;
Medema, Marnix H.;
Breitling, Rainer

Publication type:

Article

South European spiders from the Duffey collection in the Manchester Museum (Arachnida: Araneae).

Published in:

Arachnology, 2020, v. 18, n. 4, p. 333, doi. 10.13156/arac.2020.18.4.333

By:

Breitling, Rainer

Publication type:

Article

reGenotyper: Detecting mislabeled samples in genetic data.

Published in:

PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0171324

By:

Zych, Konrad;
Snoek, Basten L.;
Elvin, Mark;
Rodriguez, Miriam;
Van der Velde, K. Joeri;
Arends, Danny;
Westra, Harm-Jan;
Swertz, Morris A.;
Poulin, Gino;
Kammenga, Jan E.;
Breitling, Rainer;
Jansen, Ritsert C.;
Li, Yang

Publication type:

Article

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

Published in:

Microbial Biotechnology, 2011, v. 4, n. 2, p. 300, doi. 10.1111/j.1751-7915.2010.00226.x

By:

Medema, Marnix H.;
Alam, Mohammad T.;
Heijne, Wilbert H. M.;
van den Berg, Marco A.;
Müller, Ulrike;
Trefzer, Axel;
Bovenberg, Roel A. L.;
Breitling, Rainer;
Takano, Eriko

Publication type:

Article

Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2).

Published in:

Microbial Biotechnology, 2011, v. 4, n. 2, p. 239, doi. 10.1111/j.1751-7915.2010.00232.x

By:

D'Alia, Davide;
Eggle, Daniela;
Nieselt, Kay;
Hu, Wei-Shou;
Breitling, Rainer;
Takano, Eriko

Publication type:

Article

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

Published in:

Proteomics, 2011, v. 11, n. 24, p. 4622, doi. 10.1002/pmic.201100254

By:

Jankevics, Andris;
Merlo, M. Elena;
de Vries, Marcel;
Vonk, Roel J.;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.

Published in:

Briefings in Bioinformatics, 2008, v. 9, n. 5, p. 404, doi. 10.1093/bib/bbn026

By:

Breitling, Rainer;
Gilbert, David;
Heiner, Monika;
Orton, Richard

Publication type:

Article

Defining informative priors for ensemble modeling in systems biology.

Published in:

Nature Protocols, 2018, v. 13, n. 11, p. 2643, doi. 10.1038/s41596-018-0056-z

By:

Tsigkinopoulou, Areti;
Hawari, Aliah;
Uttley, Megan;
Breitling, Rainer

Publication type:

Article

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0179130

By:

Swainston, Neil;
Batista-Navarro, Riza;
Carbonell, Pablo;
Dobson, Paul D.;
Dunstan, Mark;
Jervis, Adrian J.;
Vinaixa, Maria;
Williams, Alan R.;
Ananiadou, Sophia;
Faulon, Jean-Loup;
Mendes, Pedro;
Kell, Douglas B.;
Scrutton, Nigel S.;
Breitling, Rainer

Publication type:

Article

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

Published in:

Metabolomics, 2015, v. 11, n. 6, p. 1721, doi. 10.1007/s11306-015-0827-2

By:

Kim, Dong-Hyun;
Achcar, Fiona;
Breitling, Rainer;
Burgess, Karl;
Barrett, Michael

Publication type:

Article

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics.

Published in:

Metabolomics, 2013, v. 9, p. 44, doi. 10.1007/s11306-012-0434-4

By:

Dunn, Warwick;
Erban, Alexander;
Weber, Ralf;
Creek, Darren;
Brown, Marie;
Breitling, Rainer;
Hankemeier, Thomas;
Goodacre, Royston;
Neumann, Steffen;
Kopka, Joachim;
Viant, Mark

Publication type:

Article

Separating the wheat from the chaff: a prioritisation pipeline for the analysis of metabolomics datasets.

Published in:

Metabolomics, 2012, v. 8, p. 29, doi. 10.1007/s11306-011-0341-0

By:

Jankevics, Andris;
Merlo, Maria;
Vries, Marcel;
Vonk, Roel;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast.

Published in:

Molecular Biology & Evolution, 2013, v. 30, n. 5, p. 1218, doi. 10.1093/molbev/mst025

By:

Medema, Marnix H.;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

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

Published in:

2011

By:

t'Kindt, Ruben;
Jankevics, Andris;
Scheltema, Richard;
Zheng, Liang;
Watson, David;
Dujardin, Jean-Claude;
Breitling, Rainer;
Coombs, Graham;
Decuypere, Saskia

Publication type:

Correction Notice

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

Published in:

Analytical & Bioanalytical Chemistry, 2010, v. 398, n. 5, p. 2059, doi. 10.1007/s00216-010-4139-0

By:

t'Kindt, Ruben;
Jankevics, Andris;
Scheltema, Richard A.;
Liang Zheng;
Watson, David G.;
Dujardin, Jean-Claude;
Breitling, Rainer;
Coombs, Graham H.;
Decuypere, Saskia

Publication type:

Article

Selenzyme: enzyme selection tool for pathway design.

Published in:

Bioinformatics, 2018, v. 34, n. 12, p. 2153, doi. 10.1093/bioinformatics/bty065

By:

Carbonell, Pablo;
Wong, Jerry;
Swainston, Neil;
Takano, Eriko;
Turner, Nicholas J;
Scrutton, Nigel S;
Kell, Douglas B;
Breitling, Rainer;
Faulon, Jean-Loup

Publication type:

Article

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

Published in:

Bioinformatics, 2017, v. 33, n. 17, p. 2774, doi. 10.1093/bioinformatics/btx292

By:

Del Carratore, Francesco;
Breitling, Rainer;
Jankevics, Andris;
Eisinga, Rob;
Heskes, Tom;
Fangxin Hong

Publication type:

Article

Incorporating peak grouping information for alignment of multiple liquid chromatographymass spectrometry datasets.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 1999, doi. 10.1093/bioinformatics/btv072

By:

Wandy, Joe;
Daly, Rónán;
Breitling, Rainer;
Rogers, Simon

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2764, doi. 10.1093/bioinformatics/btu370

By:

Daly, Rónán;
Rogers, Simon;
Wandy, Joe;
Jankevics, Andris;
Burgess, Karl E. V.;
Breitling, Rainer

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 2, p. 281, doi. 10.1093/bioinformatics/bts674

By:

Chokkathukalam, Achuthanunni;
Jankevics, Andris;
Creek, Darren J.;
Achcar, Fiona;
Barrett, Michael P.;
Breitling, Rainer

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 7, p. 1048, doi. 10.1093/bioinformatics/bts069

By:

Creek, Darren J.;
Jankevics, Andris;
Burgess, Karl E. V.;
Breitling, Rainer;
Barrett, Michael P.

Publication type:

Article

Probabilistic assignment of formulas to mass peaks in metabolomics experiments.

Published in:

Bioinformatics, 2009, v. 25, n. 4, p. 512, doi. 10.1093/bioinformatics/btn642

By:

Simon Rogers;
Richard A. Scheltema;
Mark Girolami;
Rainer Breitling

Publication type:

Article