Publications

Publications

2018

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

2017

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

Navigating freely-available software tools for metabolomics analysis.
Spicer R, Salek RM, Moreno P, Cañueto D, Steinbeck C.
Metabolomics : Official journal of the Metabolomic Society Volume 13 (2017) p.106
DOI: 10.1007/s11306-017-1242-7

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) p.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.
Journal of cheminformatics Volume 9 (2017) p.33
DOI: 10.1186/s13321-017-0220-4

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

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

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

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 : Official journal of the Metabolomic Society Volume 13 (2017) p.12
DOI: 10.1007/s11306-016-1147-x

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.
Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C.
Journal of cheminformatics Volume 9 (2017) p.53
DOI: 10.1186/s13321-017-0231-1

2016

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

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

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

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

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 : Official journal of the Metabolomic Society Volume 12 (2016) p.14
DOI: 10.1007/s11306-015-0879-3

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

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

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

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) p.
DOI: 10.3390/metabo6010008

2015

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

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

Updates in Rhea--a manually curated resource of biochemical reactions.
Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.
Nucleic acids research Volume 43 (2015) p.D459-64
DOI: 10.1093/nar/gku961

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

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 : Official journal of the Metabolomic Society Volume 11 (2015) p.1587-1597
DOI: 10.1007/s11306-015-0810-y

2014

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

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

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

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

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

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

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

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

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

2013

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 Volume 29 (2013) p.2955-2957
DOI: 10.1093/bioinformatics/btt514

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

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

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 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

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

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

Metingear: a development environment for annotating genome-scale metabolic models.
May JW, James AG, Steinbeck C.
Bioinformatics Volume 29 (2013) p.2213-2215
DOI: 10.1093/bioinformatics/btt342

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

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

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

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

2012

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

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

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

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

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

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

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

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 Volume 8 (2012) p.757-760
DOI: 10.1007/s11306-012-0462-0

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

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

2011

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

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

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

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

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

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

2010

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

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

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

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

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

2008

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

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

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