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EBIGroupsCheminformatics and Metabolism TeamPublications

Cheminformatics and Metabolism Team - Publications

Papers



[49] Sansone S-A, 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 L-A, 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, Sui SJH, 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.
Toward interoperable bioscience data
Nature Genetics 2012;44:121–126.
abstract full-text PDF

[48] Chepelev LL, Hastings J, Ennis M, Steinbeck S, Dumontier M (2012)
Self-organizing ontology of biochemically relevant small molecules
BMC Bioinformatics 13:3.
abstract full-text PDF

[47] Truszkowski A, Jayaseelan KV, Neumann S, Willighagen EL, Zielesny A and Steinbeck C.
New developments on the cheminformatics open workflow environment CDK-Taverna
Journal of Cheminformatics 2011, 3:54 doi:10.1186/1758-2946-3-54
abstract full-text PDF

[46] Alcantara 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.
Rhea - a manually curated resource of biochemical reactions
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr1126
abstract full-text HTML full-text PDF

[45] de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C. (2012).
A Database for Chemical Proteomics: ChEBI.
Methods in molecular biology (Clifton, N.J.), Vol. 803 (2012), pp. 273-296.
abstract full-text PDF

[44] O'Boyle N, Guha R, Willighagen E, Adams S, Alvarsson J, Bradley JC, Filippov I, Hanson R, Hanwell M, Hutchison G, James C, Jeliazkova N, Lang A, Langner K, Lonie D, Lowe D, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt A, Theisen K, Murray-Rust P. (2011).
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
Journal of Cheminformatics, 3(1), 37. Journal of Cheminformatics, 3(1), 37.
abstract full-text PDF

[43] Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M (2011).
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web.
PLoS ONE, 6(10), e25513.
abstract full-text PDF

[42] Griffin JL, Atherton, HJ, Steinbeck C and Salek RM
A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.
BMC Research Notes 2011, 4:272
abstract full-text PDF

[41] 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
Minimum information about a bioactive entity (MIABE)
(2011) Nature reviews. Drug discovery, 10 (9) 
abstract full-text PDF

[40] Griffin JL., and Steinbeck C. (2010)
So what have data standards ever done for us? The view from metabolomics
Genome Medicine 2010, 2:38 (24 June 2010)
abstract

[39] 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
A large-scale protein-function database
(Nov-2010) Nature chemical biology, 6 (11) :785
abstract full-text PDF

[38] Kuhn T., Steinbeck C., Zielesny A. (2010)
Open Source Workflows
Nachrichten aus der Chemie (2010) 58 (1), 40-42. 2009
abstract full-text PDF

[37] Hastings J., Dumontier M., Hull D., Horridge M., Steinbeck C., Sattler U., Stevens R., Horne T. and Britz K. (2010)
Representing chemicals using OWL, description graphs and rules.
In K. Clark and E. Sirin, editors, OWLED 2010: OWL: Experiences and Directions, Seventh International Workshop, 21-22 June 2010, San Francisco, California, USA. CEUR Workshop Proceedings Volume 614, 2010
full-text PDF

[36] Batchelor C., Hastings J., Steinbeck C. (2010)
Ontological dependence, dispositions and institutional reality in chemistry
Front. Artif. Intell. Appl. Frontiers in Artificial Intelligence and Applications, Vol. 209 (2010), Formal Ontology in Information Systems - Proceedings of the Sixth International Conference (FOIS 2010) Edited by Antony Galton, Riichiro Mizoguchi. pp. 271-284.
abstract

[35] Hastings J., Steinbeck C., Batchelor C., Schulz S. (2010)
What are chemical structures and their relations?
Front. Artif. Intell. Appl. Frontiers in Artificial Intelligence and Applications, Vol. 209 (2010), Formal Ontology in Information Systems - Proceedings of the Sixth International Conference (FOIS 2010) Edited by Antony Galton, Riichiro Mizoguchi. pp. 257-270.
abstract

[34] Kuhn T., Willighagen E.L., Zielesny A. and Steinbeck C. (2010)
CDK-Taverna: an open workflow environment for cheminformatics.
BMC Bioinformatics 11:159.
abstract full-text PDF

[33] de Matos P., Alcántara R., Dekker A., Ennis M., Hastings J., Haug K., Spiteri I., Turner S., Steinbeck C. (2010)
Chemical Entities of Biological Interest: an update.
Nucleic Acids Research 38: D249-D254.
abstract full-text PDF

[32] Spjuth O., Alvarsson J., Berg A., Eklund M., Kuhn S., Masak C., Torrance G., Wagener J., Willighagen E. L., Steinbeck C. and Jarl E.S. (2009)
Bioclipse 2: A scriptable integration platform for the life sciences.
BMC Bioinformatics 10: 397.
abstract full-text PDF

[31] Rijnbeek, M. and Steinbeck, C. (2009)
OrChem - An open source chemistry search engine for Oracle.
Journal of Cheminformatics 1: 17.
abstract full-text PDF

[30] Blinov K.A., Smurnyy Y.D., Elyashberg M.E., Churanova T.S., Kvasha M., Steinbeck C., Lefebvre B.A., Williams A.J. (2008)
Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source.
Journal of Chemical Information and Modeling 48(3): 550–555.
abstract full-text PDF

[29] Kuhn S., Egert B., Neumann S. and Steinbeck C. (2008)
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction.
BMC Bioinformatics. 2008 Sep 25;9(1):400. [Epub ahead of print]
abstract full-text PDF

[28] Willighagen E.L., O´Boyle N.O., Gopalakrishnan H., Jiao D., Guha R., Steinbeck C., Wild D.J. (2007)
Userscripts for the Life Sciences.
BMC Bioinformatics 8(1): 487. [Epub ahead of print].
abstract full-text PDF

[27] Schenk A., Xu Z., Pfeiffer C., Steinbeck C., Hertweck C. (2007)
Geminal bis-Methylation Prevents Polyketide Oxidation and Dimerization in the Benastatin Pathway, Angewandte
Angewandte Chemie International Edition 46(37): 7035-7038.
abstract full-text PDF [Subscription Required]

[26] Kuhn S., Murray-Rust P., Lancashire R.J., Rzepa H., Helmus T. et al. (2007)
Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data.
Journal of Chemical Information and Modeling 47(6): 2015-2034.
abstract full-text PDF

[25] Spjuth O., Helmus T., Willighagen E.L., Kuhn S., Eklund M. et al. (2007)
Bioclipse: An open source workbench for chemo- and bioinformatics.
BMC Bioinformatics 8: 59.
abstract full-text PDF

[24] Steinbeck C., Hoppe C., Kuhn S., Guha R., Willighagen E.L. (2006)
Recent Developments of The Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics.
Current Pharmaceutical Design 12: 2111-2120.
abstract full-text PDF

[23] Hoppe C., Steinbeck C., Wohfahrt G. (2006)
Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials.
Journal of Molecular Graphics & Modelling 24: 328-340.
abstract full-text PDF

[22] Guha R., Howard M.T., Hutchison G.R., Murray-Rust P., Rzepa H. et al. (2005)
The Blue Obelisk - Interoperability in Chemical Informatics.
Journal of Chemical Information and Modelling 46: 991-998.
abstract full-text PDF

[21] Steinbeck C. (2004)
Recent Developments in Automated Structure Elucidation of Natural Products.
Natural Product Reports 21: 512-518.
full-text PDF

[20] Steinbeck C., Kuhn S. (2004)
NMRShiftDB -- compound identification and structure elucidation support through a free community-build web database.
Phytochemistry 65: 2711-2717.
abstract full-text HTML

[19] Han Y.Q., Steinbeck C. (2004)
Evolutionary-algorithm-based strategy for computer-assisted structure elucidation.
Journal of Chemical Information and Computer Sciences 44: 489-498.
abstract full-text PDF

[18] Steinbeck, C. (2003)
Correlations between Chemical Structures and NMR Data.
In: Handbook on Chemoinformatics, Wiley-VCH: Weinheim pp 1368-1377.

[17] Steinbeck C. (2003)
Computer-Assisted Structure Elucidation.
In: Handbook on Chemoinformatics, Wiley-VCH: Weinheim, pp 1378-1406.


[16] Steinbeck C., Krause S., Kuhn S. (2003)
NMRShiftDB - Constructing a free chemical information system with open-source components.
Journal of Chemical Information and Computer Sciences 43: 1733-1739.
abstract full-text PDF

[15] Steinbeck C., Han Y.Q., Kuhn S., Horlacher O., Luttmann E. et al. (2003)
The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics.
Journal of Chemical Information and Computer Sciences 43: 493-500.
abstract full-text PDF

[14] Steinbeck C. (2001)
The Automation of Natural Product Structure Elucidation.
Current Opinion in Drug Discovery and Development 4: 338-342.
full-text PDF

[13] Yankep E., Mbafor J.T., Fomum Z.T., Steinbeck C., Messanga B.B. et al. (2001)
Further isoflavonoid metabolites from Millettia griffoniana (Bail).
Phytochemistry 56: 363-368.
abstract full-text HTML

[12] Steinbeck, C. (2001)
SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry.
Journal of Chemical Information & Computer Sciences 41: 1500-1507.
abstract full-text PDF

[11] Krause S., Willighagen E., Steinbeck C. (2000)
JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures.
Molecules 5: 93-98.
full-text PDF

[10] Ho W.C., Steinbeck C., Richert C. (1999)
Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)(2).
Biochemistry 38: 12597-12606.
abstract full-text HTML full-text PDF

[9] Zhang G.L., Rucker G., Breitmaier E., Mayer R., Steinbeck C. (1998)
Alkaloids from Thalictrum przewalskii.
Planta Medica 64: 165-171.
abstract

[8] Steinbeck C., Richert C. (1998)
The role of ionic backbones in rna structure - an unusually stable non-watson-crick duplex of a nonionic analog in an apolar medium.
Journal of the American Chemical Society 120: 11576-11580.
abstract full-text HTML full-text PDF

[7] Steinbeck C., Spitzer V., Starosta M., Vonposer G. (1997)
Identification of two chromenes from Calea serrata by semiautomatic structure elucidation.
Journal of Natural Products 60: 627-628.
abstract

[6] Steinbeck C., Berlin K., Richert C. (1997)
Masp - a Program Predicting Mass Spectra of Combinatorial Libraries.
Journal of Chemical Information & Computer Sciences 37: 49-457.
abstract full-text HTML full-text PDF

[5] Berlin K., Jain R.K., Tetzlaff C., Steinbeck C., Richert C. (1997)
Spectrometrically monitored selection experiments - quantitative laser desorption mass spectrometry of small chemical libraries.
Chemistry & Biology 4: 63-77.
abstract

[4] Steinbeck, C. Lucy (1996)
A Program For Structure Elucidation From NMR Correlation Experiments.
Angewandte Chemie. International Ed. in English 35: 1984-1986.


[3] Berlin K., Steinbeck C., Breitmaier E. (1996)
Synthesis of carba-porphyrinoids from tripyrranes and unsaturated dialdehydes.
Synthesis-Stuttgart 336 ff.


[2] Zhang G.L., Rucker G., Breitmaier E., Nieger M., Mayer R. et al. (1995)
Alkaloids from Dactylicapnos torulosa.
Phytochemistry 40: 299-305.
abstract

[1] Steinbeck C., Schneider C., Rotscheidt K., Breitmaier E. (1995)
A 4-methyl-7-hydroxyphthalide glycoside and other constituents from Quillaja saponaria molina.
Phytochemistry 40: 1313-1315.
abstract

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