113 entries « 2 of 3 »

2013

Hill, David P; Adams, Nico ; Bada, Mike ; Batchelor, Colin ; Berardini, Tanya Z; Dietze, Heiko ; Drabkin, Harold J; Ennis, Marcus ; Foulger, Rebecca E; Harris, Midori A; Hastings, Janna ; Kale, Namrata S; De Matos, Paula ; Mungall, Christopher J; Owen, Gareth ; Roncaglia, Paola ; Steinbeck, Christoph ; Turner, Steve ; Lomax, Jane

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. Journal Article

BMC Genomics, 14 (1), pp. 513, 2013.

Abstract | Links | BibTeX

Hastings, Janna ; De Matos, Paula ; Dekker, Adriano ; Ennis, Marcus ; Harsha, Bhavana ; Kale, Namrata ; Muthukrishnan, Venkatesh ; Owen, Gareth ; Turner, Steve ; Williams, Mark ; Steinbeck, Christoph

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Journal Article

Nucleic Acids Research, 41 (Database issue), pp. D456–63, 2013.

Abstract | Links | BibTeX

Foster, Joseph M; Moreno, Pablo ; Fabregat, Antonio ; Hermjakob, Henning ; Steinbeck, Christoph ; Apweiler, Rolf ; Wakelam, Michael J O; Vizca{'i}no, Juan Antonio

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. Journal Article

PLoS ONE, 8 (5), pp. e61951, 2013.

Abstract | Links | BibTeX

De Matos, Paula ; Cham, Jennifer A; Cao, Hong ; Alcantara, Rafael ; Rowland, Francis ; Lopez, Rodrigo ; Steinbeck, Christoph

The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics Journal Article

BMC Bioinformatics, 14 (1), pp. 103, 2013.

Abstract | Links | BibTeX

2012

Markley, John L; Akutsu, Hideo ; Asakura, Tetsuo ; Baldus, Marc ; Boelens, Rolf ; Bonvin, Alexandre ; Kaptein, Robert ; Bax, Ad ; Bezsonova, Irina ; Gryk, Michael R; Hoch, Jeffrey C; Korzhnev, Dmitry M; Maciejewski, Mark W; Case, Dave ; Chazin, Walter J; Cross, Timothy A; Dames, Sonja ; Kessler, Horst ; Lange, Oliver ; Madl, Tobias ; Reif, Bernd ; Sattler, Michael ; Eliezer, David ; Fersht, Alan ; Forman-Kay, Julie ; Kay, Lewis E; Fraser, James ; Gross, John ; Kortemme, Tanja ; Sali, Andrej ; Fujiwara, Toshimichi ; Gardner, Kevin ; Luo, Xuelian ; Rizo-Rey, Jose ; Rosen, Michael ; Gil, Roberto R; Ho, Chien ; Rule, Gordon ; Gronenborn, Angela M; Ishima, Rieko ; Klein-Seetharaman, Judith ; Tang, Pei ; van der Wel, Patrick ; Xu, Yan ; Grzesiek, Stephan ; Hiller, Sebastian ; Seelig, Joachim ; Laue, Ernest D; Mott, Helen ; Nietlispach, Daniel ; Barsukov, Igor ; Lian, Lu-Yun ; Middleton, David ; Blumenschein, Tharin ; Moore, Geoffrey ; Campbell, Iain ; Schnell, Jason ; Vakonakis, Ioannis John ; Watts, Anthony ; Conte, Maria R; Mason, James ; Pfuhl, Mark ; Sanderson, Mark R; Craven, Jeremy ; Williamson, Michael ; Dominguez, Cyril ; Roberts, Gordon ; G{ü}nther, Ulrich ; Overduin, Michael ; Werner, Joern ; Williamson, Philip ; Blindauer, Claudia ; Crump, Matthew ; Driscoll, Paul ; Frenkiel, Tom ; Golovanov, Alexander ; Matthews, Steve ; Parkinson, John ; Uhrin, Dusan ; Williams, Mark ; Neuhaus, David ; Oschkinat, Hartmut ; Ramos, Andres ; Shaw, David E; Steinbeck, Christoph ; Vendruscolo, Michele ; Vuister, Geerten W; Walters, Kylie J; Weinstein, Harel ; W{ü}thrich, Kurt ; Yokoyama, Shigeyuki

In support of the BMRB. Journal Article

Nature structural & molecular biology, 19 (9), pp. 854–860, 2012.

Links | BibTeX

Steinbeck, Christoph ; Conesa, Pablo ; Haug, Kenneth ; Mahendraker, Tejasvi ; Williams, Mark ; Maguire, Eamonn ; Rocca-Serra, Philippe ; Sansone, Susanna-Assunta ; Salek, Reza M; Griffin, Julian L

MetaboLights: towards a new COSMOS of metabolomics data management Journal Article

Metabolomics, 8 (5), pp. 757–760, 2012.

Abstract | Links | BibTeX

Pavelin, Katrina ; Cham, Jennifer A; De Matos, Paula ; Brooksbank, Cath ; Cameron, Graham ; Steinbeck, Christoph

Bioinformatics Meets User-Centred Design: A Perspective Journal Article

PLoS Computational Biology, 8 (7), pp. e1002554, 2012.

Abstract | Links | BibTeX

Sansone, Susanna-Assunta ; Rocca-Serra, Philippe ; Field, Dawn ; Maguire, Eamonn ; Taylor, Chris ; Hofmann, Oliver ; Fang, Hong ; Neumann, Steffen ; Tong, Weida ; Amaral-Zettler, Linda ; Begley, Kimberly ; Booth, Tim ; Bougueleret, Lydie ; Burns, Gully ; Chapman, Brad ; Clark, Tim ; Coleman, Lee-Ann ; Copeland, Jay ; Das, Sudeshna ; de Daruvar, Antoine ; De Matos, Paula ; Dix, Ian ; Edmunds, Scott ; Evelo, Chris T; Forster, Mark J; Gaudet, Pascale ; Gilbert, Jack ; Goble, Carole ; Griffin, Julian L; Jacob, Daniel ; Kleinjans, Jos ; Harland, Lee ; Haug, Kenneth ; Hermjakob, Henning ; Sui, Shannan Ho J; Laederach, Alain ; Liang, Shaoguang ; Marshall, Stephen ; McGrath, Annette ; Merrill, Emily ; Reilly, Dorothy ; Roux, Magali ; Shamu, Caroline E; Shang, Catherine A; Steinbeck, Christoph ; Trefethen, Anne ; Williams-Jones, Bryn ; Wolstencroft, Katherine ; Xenarios, Ioannis ; Hide, Winston

Toward interoperable bioscience data Journal Article

Nat Genet, 44 (2), pp. 121–126, 2012.

Abstract | Links | BibTeX

Chepelev, Leonid L; Hastings, Janna ; Ennis, Marcus ; Steinbeck, Christoph ; Dumontier, Michel

Self-organizing ontology of biochemically relevant small molecules. Journal Article

BMC Bioinformatics, 13 (1), pp. 3, 2012.

Abstract | Links | BibTeX

Hastings, Janna ; Magka, Despoina ; Batchelor, Colin ; Duan, Lian ; Stevens, Robert ; Ennis, Marcus ; Steinbeck, Christoph

Structure-based classification and ontology in chemistry. Journal Article

Journal of cheminformatics, 4 (1), pp. 8, 2012.

Abstract | Links | BibTeX

Alcantara, Rafael ; Axelsen, Kristian B; Morgat, Anne ; Belda, Eugeni ; Coudert, Elisabeth ; Bridge, Alan ; Cao, Hong ; De Matos, Paula ; Ennis, Marcus ; Turner, Steve ; Owen, Gareth ; Bougueleret, Lydie ; Xenarios, Ioannis ; Steinbeck, Christoph

Rhea--a manually curated resource of biochemical reactions. Journal Article

Nucleic Acids Research, 40 (Database issue), pp. D754–60, 2012.

Abstract | Links | BibTeX

Jayaseelan, Kalai Vanii ; Moreno, Pablo ; Truszkowski, Andreas ; Ertl, Peter ; Steinbeck, Christoph

Natural product-likeness score revisited: an open-source, open-data implementation. Journal Article

BMC Bioinformatics, 13 (1), pp. 106, 2012.

Abstract | Links | BibTeX

Hastings, Janna ; Josephs, Zara ; Steinbeck, Christoph

Accessing and using chemical property databases. Journal Article

Methods in molecular biology (Clifton, N.J.), 929 (Chapter 9), pp. 193–219, 2012, ISBN: 978-1-62703-049-6.

Abstract | Links | BibTeX

De Matos, Paula ; Adams, Nico ; Hastings, Janna ; Moreno, Pablo ; Steinbeck, Christoph

A database for chemical proteomics: ChEBI. Journal Article

Methods in molecular biology (Clifton, N.J.), 803 (Chapter 19), pp. 273–296, 2012, ISBN: 978-1-61779-363-9.

Abstract | Links | BibTeX

2011

Orchard, Sandra ; Al-Lazikani, Bissan ; Bryant, Steve ; Clark, Dominic ; Calder, Elizabeth ; Dix, Ian ; Engkvist, Ola ; Forster, Mark ; Gaulton, Anna ; Gilson, Michael ; Glen, Robert ; Grigorov, Martin ; Hammond-Kosack, Kim ; Harland, Lee ; Hopkins, Andrew ; Larminie, Christopher ; Lynch, Nick ; Mann, Romeena K; Murray-Rust, Peter ; Lo Piparo, Elena ; Southan, Christopher ; Steinbeck, Christoph ; Wishart, David ; Hermjakob, Henning ; Overington, John ; Thornton, Janet

Minimum information about a bioactive entity (MIABE) Journal Article

Nature Reviews Drug Discovery, 10 (9), pp. 661–669, 2011.

Abstract | Links | BibTeX

Hastings, J; Batchelor, C R; Steinbeck, C; Schulz, S

IOS Press Ebooks - Modularization Requirements in Bio-Ontologies: A Case Study of ChEbi Journal Article

WoMO, 2011.

Abstract | Links | BibTeX

Griffin, Julian L; Atherton, Helen J; Steinbeck, Chris ; Salek, Reza M

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.". Journal Article

BMC Research Notes, 4 (1), pp. 272, 2011.

Abstract | Links | BibTeX

Hastings, Janna ; Batchelor, Colin ; Neuhaus, Fabian ; Steinbeck, Christoph

Whattextquoterights in an textquoteleftis abouttextquoterightlink? Chemical diagrams and the IAO Journal Article

Proceedings of the International Conference on Biomedical Ontology (ICBO2011), Buffalo, USA, 2011.

Links | BibTeX

O'Boyle, Noel M; Guha, Rajarshi ; Willighagen, Egon L; Adams, Samuel E; Alvarsson, Jonathan ; Bradley, Jean-Claude ; Filippov, Igor V; Hanson, Robert M; Hanwell, Marcus D; Hutchison, Geoffrey R; James, Craig A; Jeliazkova, Nina ; Lang, Andrew Sid ; Langner, Karol M; Lonie, David C; Lowe, Daniel M; Pansanel, Jerome ; Pavlov, Dmitry ; Spjuth, Ola ; Steinbeck, Christoph ; Tenderholt, Adam L; Theisen, Kevin J; Murray-Rust, Peter

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal Article

Journal of cheminformatics, 3 (1), pp. 37, 2011.

Abstract | Links | BibTeX

Truszkowski, Andreas ; Jayaseelan, Kalai Vanii ; Neumann, Stefan ; Willighagen, Egon L; Zielesny, Achim ; Steinbeck, Christoph

New developments on the cheminformatics open workflow environment CDK-Taverna. Journal Article

Journal of cheminformatics, 3 (1), pp. 54, 2011.

Abstract | Links | BibTeX

Hastings, Janna ; Chepelev, Leonid ; Willighagen, Egon ; Adams, Nico ; Steinbeck, Christoph ; Dumontier, Michel

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. Journal Article

PLoS ONE, 6 (10), pp. e25513, 2011.

Abstract | Links | BibTeX

2010

Apweiler, Rolf ; Armstrong, Richard ; Bairoch, Amos ; Cornish-Bowden, Athel ; Halling, Peter J; Hofmeyr, Jan-Hendrik S; Kettner, Carsten ; Leyh, Thomas S; Rohwer, Johann ; Schomburg, Dietmar ; Steinbeck, Christoph ; Tipton, Keith

A large-scale protein-function database. Journal Article

Nature Chemical Biology, 6 (11), pp. 785–785, 2010.

Links | BibTeX

Hastings, Janna ; Batchelor, Colin ; Steinbeck, Christoph ; Schulz, Stefan

What are chemical structures and their relations? Journal Article

pp. 257–270, 2010, ISBN: 978-1-60750-534-1.

Abstract | Links | BibTeX

Griffin, Julian L; Steinbeck, Christoph

So what have data standards ever done for us? The view from metabolomics. Journal Article

Genome medicine, 2 (6), pp. 38, 2010.

Abstract | Links | BibTeX

Hastings, Janna ; Dumontier, Michel ; Hull, Duncan ; Horridge, Matthew ; Steinbeck, Christoph ; Sattler, Ulrike ; Stevens, Robert ; H{ö}rne, Tertia ; Britz, Katarina

Representing chemicals using OWL, description graphs and rules Journal Article

CEUR Workshop Proceedings, 614 , 2010.

Links | BibTeX

Kuhn, Thomas ; Willighagen, Egon L; Zielesny, Achim ; Steinbeck, Christoph

CDK-Taverna: an open workflow environment for cheminformatics. Journal Article

BMC Bioinformatics, 11 (1), pp. 159, 2010.

Abstract | Links | BibTeX

De Matos, Paula ; Alcantara, Rafael ; Dekker, Adriano ; Ennis, Marcus ; Hastings, Janna ; Haug, Kenneth ; Spiteri, Inmaculada ; Turner, Steve ; Steinbeck, Christoph

Chemical Entities of Biological Interest: an update. Journal Article

Nucleic Acids Research, 38 (Database issue), pp. D249–54, 2010.

Abstract | Links | BibTeX

Hastings, Janna ; Steinbeck, Christoph ; Jansen, Ludger ; Schulz, Stefan

Substance concentrations as conditions for the realization of dispositions Journal Article

Semantic Applications in Life Sciences: Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, KR-MED, pp. 9–10, 2010.

Links | BibTeX

Batchelor, Colin ; Hastings, Janna ; Steinbeck, Christoph

Ontological dependence, dispositions and institutional reality in chemistry Journal Article

Proceeding of the 2010 conference on Formal Ontology in Information Systems, pp. 271–284, 2010.

Links | BibTeX

2009

Rijnbeek, Mark ; Steinbeck, Christoph

OrChem - An open source chemistry search engine for Oracle(R). Journal Article

Journal of cheminformatics, 1 (1), pp. 17, 2009.

Abstract | Links | BibTeX

Spjuth, Ola ; Alvarsson, Jonathan ; Berg, Arvid ; Eklund, Martin ; Kuhn, Stefan ; Masak, Carl ; Torrance, Gilleain ; Wagener, Johannes ; Willighagen, Egon L; Steinbeck, Christoph ; Wikberg, Jarl E S

Bioclipse 2: a scriptable integration platform for the life sciences. Journal Article

BMC Bioinformatics, 10 (1), pp. 397, 2009.

Abstract | Links | BibTeX

2008

Blinov, K A; Smurnyy, Y D; Elyashberg, M E; Churanova, T S; Kvasha, M; Steinbeck, C; Lefebvre, B A; Williams, A J

Performance validation of neural network based (13)c NMR prediction using a publicly available data source. Journal Article

Journal of Chemical Information and Modeling, 48 (3), pp. 550–555, 2008.

Abstract | Links | BibTeX

Kuhn, Stefan ; Egert, Bj{ö}rn ; Neumann, Steffen ; Steinbeck, Christoph

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction. Journal Article

BMC Bioinformatics, 9 (1), pp. 400, 2008.

Abstract | Links | BibTeX

Blinov, K A; Smurnyy, Y D; Elyashberg, M E; Churanova, T S; Kvasha, M; Steinbeck, C; Lefebvre, B A; Williams, A J

Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source Journal Article

Journal of Chemical Information and Modeling, 48 (3), pp. 550–555, 2008.

Links | BibTeX

2007

Kuhn, Stefan ; Helmus, Tobias ; Lancashire, Robert J; Murray-Rust, Peter ; Rzepa, Henry S; Steinbeck, Christoph ; Willighagen, Egon L

Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data. Journal Article

Journal of Chemical Information and Modeling, 47 (6), pp. 2015–2034, 2007.

Abstract | Links | BibTeX

Spjuth, Ola ; Helmus, Tobias ; Willighagen, Egon L; Kuhn, Stefan ; Eklund, Martin ; Wagener, Johannes ; Murray-Rust, Peter ; Steinbeck, Christoph ; Wikberg, Jarl E S

Bioclipse: an open source workbench for chemo- and bioinformatics. Journal Article

BMC Bioinformatics, 8 (1), pp. 59, 2007.

Abstract | Links | BibTeX

Willighagen, E L; O'Boyle, N M; Gopalakrishnan, H; Jiao, D; Guha, R; Steinbeck, C; Wild, D J

Userscripts for the life sciences Journal Article

BMC Bioinformatics, 8 (1), pp. 487, 2007.

Links | BibTeX

Schenk, Ang{'e}la ; Xu, Zhongli ; Pfeiffer, Corina ; Steinbeck, Christoph ; Hertweck, Christian

Geminal bismethylation prevents polyketide oxidation and dimerization in the benastatin pathway. Journal Article

Angewandte Chemie. International Ed. in English, 46 (37), pp. 7035–7038, 2007.

Links | BibTeX

2006

Steinbeck, Christoph ; Hoppe, Christian ; Kuhn, Stefan ; Guha, Rajarshi ; Willighagen, Egon L

Recent Developments of The Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics Journal Article

Current pharmaceutical design, 12 (17), pp. 2111–2120, 2006.

Links | BibTeX

Hoppe, C; Steinbeck, C; Wohlfahrt, G

Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials Journal Article

Journal of Molecular Graphics & Modelling, 24 (5), pp. 328–340, 2006.

Abstract | Links | BibTeX

Guha, Rajarshi ; Howard, Michael T; Hutchison, Geoffrey R; Murray-Rust, Peter ; Rzepa, Henry ; Steinbeck, Christoph ; Wegner, Joerg ; Willighagen, Egon L

The Blue Obelisk - Interoperability in Chemical Informatics Journal Article

Journal of Chemical Information and Modeling, 46 (3), pp. 991–998, 2006.

Abstract | Links | BibTeX

2005

Steinbeck, C; Kuhn, Stefan

Eine offene NMR-Datenbank Journal Article

Nachrichten Aus Der Chemie, 53 , pp. 1039–1040, 2005.

BibTeX

2004

Steinbeck, Christoph ; Kuhn, Stefan

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. Journal Article

Phytochemistry, 65 (19), pp. 2711–2717, 2004.

Abstract | Links | BibTeX

Steinbeck, C

Recent developments in automated structure elucidation of natural products Journal Article

Natural Product Reports, 21 (4), pp. 512–518, 2004.

Links | BibTeX

Han, Y Q; Steinbeck, C

Evolutionary-algorithm-based strategy for computer-assisted structure elucidation Journal Article

Journal of Chemical Information & Computer Sciences, 44 (2), pp. 489–498, 2004.

Abstract | Links | BibTeX

2003

Steinbeck, C

Correlations between Chemical Structures and NMR Data Incollection

Gasteiger, Johann ; Engel, Thomas (Ed.): pp. 1368–1377, John Wiley & Sons, Weinheim, 2003, ISBN: 3527618279.

Links | BibTeX

Steinbeck, C; Krause, S; Kuhn, S

NMRShiftDB - Constructing a free chemical information system with open-source components Journal Article

Journal of Chemical Information & Computer Sciences, 43 (6), pp. 1733–1739, 2003.

Abstract | Links | BibTeX

Steinbeck, C; Han, Y Q; Kuhn, S; Horlacher, O; Luttmann, E; Willighagen, E

The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics Journal Article

Journal of Chemical Information & Computer Sciences, 43 (2), pp. 493–500, 2003.

Abstract | Links | BibTeX

Steinbeck, C

Correlations between Chemical Structures and NMR Data Incollection

pp. 1368–1377, John Wiley & Sons, Weinheim, 2003, ISBN: 3527618279.

Links | BibTeX

2001

Steinbeck, C

The automation of natural product structure elucidation. Journal Article

Current Opinion in Drug Discovery and Development, 4 (3), pp. 338–342, 2001.

Abstract | Links | BibTeX

113 entries « 2 of 3 »