Publications

Publications

2018

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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels T, Foguet C, Glen R, Gonzalez-Beltran A, Guenther U, Handakas E, Hankemeier T, Herman S, Haug K, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khoonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JT, Peluso A, Pireddu L, Piras ME, Reed MA, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek R, Sansone S, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant M, Weber R, Zanetti G, Steinbeck C. Preprint DOI: 10.1101/409151
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In vivo and in vitro identification of Z-BOX C - a new bilirubin oxidation end product.
Ritter M, Neupane S, Seidel RA, Steinbeck C, Pohnert G. Organic & biomolecular chemistry Volume 16 (2018) p.3553-3555 DOI: 10.1039/c8ob00164b

2017

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it.
Spicer RA, Steinbeck C. Metabolomics : Official journal of the Metabolomic Society Volume 14 (2018) p.16 DOI: 10.1007/s11306-017-1309-5
nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton J, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis IA, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin JL, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S. Analytical chemistry Volume 90 (2018) p.649-656 DOI: 10.1021/acs.analchem.7b02795
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Interoperable and scalable data analysis with microservices: Applications in Metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone S, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O. Preprint DOI: 10.1101/213603
A decade after the metabolomics standards initiative it's time for a revision.
Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170138 DOI: 10.1038/sdata.2017.138
Compliance with minimum information guidelines in public metabolomics repositories.
Spicer RA, Salek R, Steinbeck C. Scientific data Volume 4 (2017) p.170137 DOI: 10.1038/sdata.2017.137
The future of metabolomics in ELIXIR.
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. F1000Research Volume 6 (2017) DOI: 10.12688/f1000research.12342.2
Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C. Metabolomics Volume 13 (2017) p.106 DOI: 10.1007/s11306-017-1242-7
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Larralde M, Lawson TN, Weber RJM, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. Bioinformatics (Oxford, England) Volume 33 (2017) p.2598-2600 DOI: 10.1093/bioinformatics/btx169
Automated assembly of species metabolomes through data submission into a public repository.
Salek RM, Conesa P, Cochrane K, Haug K, Williams M, Kale N, Moreno P, Jayaseelan KV, Macias JR, Nainala VC, Hall RD, Reed LK, Viant MR, O'Donovan C, Steinbeck C. GigaScience Volume 6 (2017) p.1-4 DOI: 10.1093/gigascience/gix062
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Nature biotechnology Volume 35 (2017) p.406-409 DOI: 10.1038/nbt.3790
Global open data management in metabolomics.
Haug K, Salek RM, Steinbeck C. Current opinion in chemical biology Volume 36 (2017) p.58-63 DOI: 10.1016/j.cbpa.2016.12.024

2016

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. Metabolomics Volume 13 (2017) p.12 DOI: 10.1007/s11306-016-1147-x
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS. Journal of cheminformatics Volume 8 (2016) p.61 DOI: 10.1186/s13321-016-0174-y
SPLASH, a hashed identifier for mass spectra.
Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. Nature biotechnology Volume 34 (2016) p.1099-1101 DOI: 10.1038/nbt.3689
MetaboLights: An Open-Access Database Repository for Metabolomics Data.
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C. Current protocols in bioinformatics Volume 53 (2016) p.14.13.1-18 DOI: 10.1002/0471250953.bi1413s53
libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. Journal of cheminformatics Volume 8 (2016) p.11 DOI: 10.1186/s13321-016-0123-9
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman SA, Torrance G, Baldacci L, Martínez Cuesta S, Fenninger F, Gopal N, Choudhary S, May JW, Holliday GL, Steinbeck C, Thornton JM. Bioinformatics (Oxford, England) Volume 32 (2016) p.2065-2066 DOI: 10.1093/bioinformatics/btw096
The Time Is Right to Focus on Model Organism Metabolomes.
Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR. Metabolites Volume 6 (2016) DOI: 10.3390/metabo6010008
Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.
Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GA, Raftery D, Steinbeck C, Salek RM, Wishart DS. Journal of proteome research Volume 15 (2016) p.360-373 DOI: 10.1021/acs.jproteome.5b00885

2015

Data standards can boost metabolomics research, and if there is a will, there is a way.
Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S. Metabolomics Volume 12 (2016) p.14 DOI: 10.1007/s11306-015-0879-3
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. Nucleic acids research Volume 44 (2016) p.D1214-9 DOI: 10.1093/nar/gkv1031
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.
Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C. Metabolomics Volume 11 (2015) p.1587-1597 DOI: 10.1007/s11306-015-0810-y
SpeckTackle: JavaScript charts for spectroscopy.
Beisken S, Conesa P, Haug K, Salek RM, Steinbeck C. Journal of cheminformatics Volume 7 (2015) p.17 DOI: 10.1186/s13321-015-0065-7
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.
Hastings J, Jeliazkova N, Owen G, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E. Journal of biomedical semantics Volume 6 (2015) p.10 DOI: 10.1186/s13326-015-0005-5
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.
Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C. BMC bioinformatics Volume 16 (2015) p.56 DOI: 10.1186/s12859-015-0486-3

2014

Ten recommendations for software engineering in research.
Hastings J, Haug K, Steinbeck C. GigaScience Volume 3 (2014) p.31 DOI: 10.1186/2047-217X-3-31
The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.
Venkata C, Forster MJ, Howe PW, Steinbeck C. PloS one Volume 9 (2014) p.e111576 DOI: 10.1371/journal.pone.0111576
A molecular fragment cheminformatics roadmap for mesoscopic simulation.
Truszkowski A, Daniel M, Kuhn H, Neumann S, Steinbeck C, Zielesny A, Epple M. Journal of cheminformatics Volume 6 (2014) p.45 DOI: 10.1186/s13321-014-0045-3
Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.
Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C. Scientific data Volume 1 (2014) p.140029 DOI: 10.1038/sdata.2014.29
Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking.
Jayaseelan KV, Steinbeck C. BMC bioinformatics Volume 15 (2014) p.234 DOI: 10.1186/1471-2105-15-234
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. Molecular & cellular proteomics : MCP Volume 13 (2014) p.2765-2775 DOI: 10.1074/mcp.o113.036681
MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.
Beisken S, Earll M, Portwood D, Seymour M, Steinbeck C. Molecular informatics Volume 33 (2014) p.307-310 DOI: 10.1002/minf.201400016
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z. PLoS genetics Volume 10 (2014) p.e1004132 DOI: 10.1371/journal.pgen.1004132
Efficient ring perception for the Chemistry Development Kit.
May JW, Steinbeck C. Journal of cheminformatics Volume 6 (2014) p.3 DOI: 10.1186/1758-2946-6-3

2013

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.
Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo LF, Kaleta C, Kost C. The ISME journal Volume 8 (2014) p.953-962 DOI: 10.1038/ismej.2013.211
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The role of reporting standards for metabolite annotation and identification in metabolomic studies.
Salek RM, Steinbeck C, Viant MR, Goodacre R, Dunn WB. GigaScience Volume 2 (2013) p.13 DOI: 10.1186/2047-217x-2-13
OntoQuery: easy-to-use web-based OWL querying.
Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2955-2957 DOI: 10.1093/bioinformatics/btt514
KNIME-CDK: Workflow-driven cheminformatics.
Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C. BMC bioinformatics Volume 14 (2013) p.257 DOI: 10.1186/1471-2105-14-257
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Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. BMC genomics Volume 14 (2013) p.513 DOI: 10.1186/1471-2164-14-513
Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C. Bioinformatics (Oxford, England) Volume 29 (2013) p.2213-2215 DOI: 10.1093/bioinformatics/btt342
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Selection of human tissue-specific elementary flux modes using gene expression data.
Rezola A, Pey J, de Figueiredo LF, Podhorski A, Schuster S, Rubio A, Planes FJ. Bioinformatics Volume 29 (2013) p.2009-2016 DOI: 10.1093/bioinformatics/btt328
Dissemination of metabolomics results: role of MetaboLights and COSMOS.
Salek RM, Haug K, Steinbeck C. GigaScience Volume 2 (2013) p.8 DOI: 10.1186/2047-217X-2-8
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA. PloS one Volume 8 (2013) p.e61951 DOI: 10.1371/journal.pone.0061951
The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat029 DOI: 10.1093/database/bat029
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.
de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R, Steinbeck C. BMC bioinformatics Volume 14 (2013) p.103 DOI: 10.1186/1471-2105-14-103

2012

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D456-63 DOI: 10.1093/nar/gks1146
The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D773-80 DOI: 10.1093/nar/gks1112
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C. Nucleic acids research Volume 41 (2013) p.D781-6 DOI: 10.1093/nar/gks1004
MetaboLights: towards a new COSMOS of metabolomics data management.
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL. Metabolomics : Official journal of the Metabolomic Society Volume 8 (2012) p.757-760 DOI: 10.1007/s11306-012-0462-0
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In support of the BMRB.
Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. Nature structural & molecular biology Volume 19 (2012) p.854-860 DOI: 10.1038/nsmb.2371
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Detecting and investigating substrate cycles in a genome-scale human metabolic network.
Gebauer J, Schuster S, de Figueiredo LF, Kaleta C. The FEBS journal Volume 279 (2012) p.3192-3202 DOI: 10.1111/j.1742-4658.2012.08700.x
Bioinformatics meets user-centred design: a perspective.
Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G, Steinbeck C. PLoS computational biology Volume 8 (2012) p.e1002554 DOI: 10.1371/journal.pcbi.1002554
Natural product-likeness score revisited: an open-source, open-data implementation.
Jayaseelan KV, Moreno P, Truszkowski A, Ertl P, Steinbeck C. BMC bioinformatics Volume 13 (2012) p.106 DOI: 10.1186/1471-2105-13-106
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Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions.
Kaleta C, de Figueiredo LF, Schuster S. International journal of circumpolar health Volume 71 (2012) p.1-2 DOI: 10.3402/ijch.v71i0.18436
Structured chemical class definitions and automated matching for chemical ontology evolution.
Duan L, Hastings J, de Matos P, Ennis M, Steinbeck C. Journal of cheminformatics Volume 4 (2012) p.P5-P5 DOI: 10.1186/1758-2946-4-S1-P5
Structure-based classification and ontology in chemistry.
Hastings J, Magka D, Batchelor C, Duan L, Stevens R, Ennis M, Steinbeck C. Journal of cheminformatics Volume 4 (2012) p.8 DOI: 10.1186/1758-2946-4-8
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NAD(+) biosynthesis and salvage--a phylogenetic perspective.
Gossmann TI, Ziegler M, Puntervoll P, de Figueiredo LF, Schuster S, Heiland I. The FEBS journal Volume 279 (2012) p.3355-3363 DOI: 10.1111/j.1742-4658.2012.08559.x
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Toward interoperable bioscience data.
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Nature genetics Volume 44 (2012) p.121-126 DOI: 10.1038/ng.1054
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Self-organizing ontology of biochemically relevant small molecules.
Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M. BMC bioinformatics Volume 13 (2012) p.3 DOI: 10.1186/1471-2105-13-3
A database for chemical proteomics: ChEBI.
de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C. Methods in molecular biology (Clifton, N.J.) Volume 803 (2012) p.273-296 DOI: 10.1007/978-1-61779-364-6_19
Accessing and using chemical property databases.
Hastings J, Josephs Z, Steinbeck C. Methods in molecular biology (Clifton, N.J.) Volume 929 (2012) p.193-219 DOI: 10.1007/978-1-62703-050-2_9
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Detecting structural invariants in biological reaction networks.
Behre J, de Figueiredo LF, Schuster S, Kaleta C. Methods in molecular biology (Clifton, N.J.) Volume 804 (2012) p.377-407 DOI: 10.1007/978-1-61779-361-5_20

2011

New developments on the cheminformatics open workflow environment CDK-Taverna.
Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A, Steinbeck C. Journal of cheminformatics Volume 3 (2011) p.54 DOI: 10.1186/1758-2946-3-54
Rhea--a manually curated resource of biochemical reactions.
Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C. Nucleic acids research Volume 40 (2012) p.D754-60 DOI: 10.1093/nar/gkr1126
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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P. Journal of cheminformatics Volume 3 (2011) p.37 DOI: 10.1186/1758-2946-3-37
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.
Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M. PloS one Volume 6 (2011) p.e25513 DOI: 10.1371/journal.pone.0025513
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Pathway analysis of NAD+ metabolism.
de Figueiredo LF, Gossmann TI, Ziegler M, Schuster S. The Biochemical journal Volume 439 (2011) p.341-348 DOI: 10.1042/bj20110320
Minimum information about a bioactive entity (MIABE).
Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Nature reviews. Drug discovery Volume 10 (2011) p.661-669 DOI: 10.1038/nrd3503
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A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.".
Griffin JL, Atherton HJ, Steinbeck C, Salek RM. BMC research notes Volume 4 (2011) p.272 DOI: 10.1186/1756-0500-4-272
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In silico evidence for gluconeogenesis from fatty acids in humans.
Kaleta C, de Figueiredo LF, Werner S, Guthke R, Ristow M, Schuster S. PLoS computational biology Volume 7 (2011) p.e1002116 DOI: 10.1371/journal.pcbi.1002116
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Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach.
Schuster S, de Figueiredo LF, Schroeter A, Kaleta C. Bio Systems Volume 105 (2011) p.147-153 DOI: 10.1016/j.biosystems.2011.05.007
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Special issue: integration of OMICs datasets into metabolic pathway analysis.
Kaleta C, de Figueiredo LF, Heiland I, Klamt S, Schuster S. Bio Systems Volume 105 (2011) p.107-108 DOI: 10.1016/j.biosystems.2011.05.008
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Modularization requirements in bio-ontologies: A case study of ChEbi
Hastings J, Batchelor C, Steinbeck C, Schulz S. Advances in molecular bioinformatics Volume 230 (2011) p.63-70 DOI: 10.3233/978-1-60750-799-4-63

2010

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A large-scale protein-function database.
Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K. Nature chemical biology Volume 6 (2010) p.785 DOI: 10.1038/nchembio.460
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So what have data standards ever done for us? The view from metabolomics.
Griffin JL, Steinbeck C. Genome medicine Volume 2 (2010) p.38 DOI: 10.1186/gm159
OrChem: an open source chemistry search engine for Oracle.
Rijnbeek ML, Steinbeck C. Journal of cheminformatics Volume 2 (2010) p.P28-P28 DOI: 10.1186/1758-2946-2-S1-P28
CDK-Taverna: an open workflow environment for cheminformatics.
Kuhn T, Willighagen EL, Zielesny A, Steinbeck C. BMC bioinformatics Volume 11 (2010) p.159 DOI: 10.1186/1471-2105-11-159

2009

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Bioclipse 2: a scriptable integration platform for the life sciences.
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE. BMC bioinformatics Volume 10 (2009) p.397 DOI: 10.1186/1471-2105-10-397
Chemical Entities of Biological Interest: an update.
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C. Nucleic acids research Volume 38 (2010) p.D249-54 DOI: 10.1093/nar/gkp886
OrChem - An open source chemistry search engine for Oracle(R).
Rijnbeek M, Steinbeck C. Journal of cheminformatics Volume 1 (2009) p.17 DOI: 10.1186/1758-2946-1-17
New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J. Chemistry Central journal Volume 3 (2009) p.O3 DOI: 10.1186/1752-153x-3-s1-o3

2008

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Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.
Kuhn S, Egert B, Neumann S, Steinbeck C. BMC bioinformatics Volume 9 (2008) p.400 DOI: 10.1186/1471-2105-9-400
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Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project.
Kuhn T, Zielesny A, Steinbeck C. Chemistry Central journal Volume 2 (2008) p.P27-P27 DOI: 10.1186/1752-153x-2-s1-p27
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Performance validation of neural network based (13)c NMR prediction using a publicly available data source.
Blinov KA, Smurnyy YD, Elyashberg ME, Churanova TS, Kvasha M, Steinbeck C, Lefebvre BA, Williams AJ. Journal of chemical information and modeling Volume 48 (2008) p.550-555 DOI: 10.1021/ci700363r