| Year |
Citation |
Score |
| 2020 |
Schaduangrat N, Lampa S, Simeon S, Gleeson MP, Spjuth O, Nantasenamat C. Towards reproducible computational drug discovery. Journal of Cheminformatics. 12: 9. PMID 33430992 DOI: 10.1186/S13321-020-0408-X |
0.375 |
|
| 2020 |
Norinder U, Spjuth O, Svensson F. Using Predicted Bioactivity Profiles to Improve Predictive Modeling Journal of Chemical Information and Modeling. 60: 2830-2837. PMID 32374618 DOI: 10.1021/Acs.Jcim.0C00250 |
0.351 |
|
| 2020 |
Capuccini M, Dahlö M, Toor S, Spjuth O. MaRe: Processing Big Data With Application Containers on Apache Spark Gigascience. 9. PMID 32369166 DOI: 10.1093/Gigascience/Giaa042 |
0.4 |
|
| 2019 |
Capuccini M, Larsson A, Carone M, Novella JA, Sadawi N, Gao J, Toor S, Spjuth O. On-demand virtual research environments using microservices. Peerj. Computer Science. 5: e232. PMID 33816885 DOI: 10.7717/Peerj-Cs.232 |
0.372 |
|
| 2019 |
Lampa S, Dahlö M, Alvarsson J, Spjuth O. SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines. Gigascience. 8. PMID 31029061 DOI: 10.1093/Gigascience/Giz044 |
0.335 |
|
| 2019 |
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, ... ... Spjuth O, et al. Interoperable and scalable data analysis with microservices: Applications in Metabolomics. Bioinformatics (Oxford, England). PMID 30851093 DOI: 10.1093/Bioinformatics/Btz160 |
0.39 |
|
| 2019 |
Novella JA, Khoonsari PE, Herman S, Whitenack D, Capuccini M, Burman J, Kultima K, Spjuth O. Container-based bioinformatics with Pachyderm. Bioinformatics. 35: 839-846. PMID 30101309 DOI: 10.1093/Bioinformatics/Bty699 |
0.415 |
|
| 2018 |
Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, ... ... Spjuth O, et al. PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud. Gigascience. PMID 30535405 DOI: 10.1093/Gigascience/Giy149 |
0.391 |
|
| 2018 |
Lampa S, Alvarsson J, Shane SAM, Berg A, Ahlberg E, Spjuth O. Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction Frontiers in Pharmacology. 9: 1256. PMID 30459617 DOI: 10.3389/Fphar.2018.01256 |
0.323 |
|
| 2018 |
Kensert A, Alvarsson J, Norinder U, Spjuth O. Evaluating parameters for ligand-based modeling with random forest on sparse data sets. Journal of Cheminformatics. 10: 1-10. PMID 30306349 DOI: 10.1186/S13321-018-0304-9 |
0.382 |
|
| 2018 |
Svensson F, Aniceto N, Norinder U, Cortes-Ciriano I, Spjuth O, Carlsson L, Bender A. Conformal Regression for QSAR Modelling - Quantifying Prediction Uncertainty. Journal of Chemical Information and Modeling. PMID 29701973 DOI: 10.1021/Acs.Jcim.8B00054 |
0.341 |
|
| 2018 |
Dahlö M, Scofield DG, Schaal W, Spjuth O. Tracking the NGS revolution: managing life science research on shared high-performance computing clusters. Gigascience. 7. PMID 29659792 DOI: 10.1093/Gigascience/Giy028 |
0.311 |
|
| 2018 |
Lapins M, Arvidsson S, Lampa S, Berg A, Schaal W, Alvarsson J, Spjuth O. A confidence predictor for logD using conformal regression and a support-vector machine Journal of Cheminformatics. 10: 17. PMID 29616425 DOI: 10.1186/S13321-018-0271-1 |
0.381 |
|
| 2018 |
Exner T, Dokler J, Bachler D, Farcal L, Evelo C, Willighagen E, Jennen D, Jabocs M, Doganis P, Sarimveis H, Lynch I, Gkoutos G, Kramer S, Notredame C, Spjuth O, et al. OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment Toxicology Letters. 295: S104. DOI: 10.1016/J.Toxlet.2018.06.617 |
0.348 |
|
| 2017 |
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. The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics. 9: 33. PMID 29086040 DOI: 10.1186/S13321-017-0220-4 |
0.334 |
|
| 2017 |
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, ... ... Spjuth O, et al. The future of metabolomics in ELIXIR. F1000research. 6. PMID 29043062 DOI: 10.12688/F1000Research.12342.2 |
0.352 |
|
| 2017 |
Lampa S, Willighagen E, Kohonen P, King A, Vrandečić D, Grafström R, Spjuth O. RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. Journal of Biomedical Semantics. 8: 35. PMID 28870259 DOI: 10.1186/S13326-017-0136-Y |
0.397 |
|
| 2017 |
Shoombuatong W, Prathipati P, Prachayasittikul V, Schaduangrat N, Malik AA, Pratiwi R, Wanwimolruk S, S Wikberg JE, Gleeson MP, Spjuth O, Nantasenamat C. Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling. Current Drug Metabolism. PMID 28322159 DOI: 10.2174/1389200218666170320121932 |
0.334 |
|
| 2017 |
Capuccini M, Ahmed L, Schaal W, Laure E, Spjuth O. Large-scale virtual screening on public cloud resources with Apache Spark. Journal of Cheminformatics. 9: 15. PMID 28316653 DOI: 10.1186/S13321-017-0204-4 |
0.327 |
|
| 2016 |
Lampa S, Alvarsson J, Spjuth O. Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. Journal of Cheminformatics. 8: 67. PMID 27942268 DOI: 10.1186/S13321-016-0179-6 |
0.398 |
|
| 2016 |
Spjuth O, Rydberg P, Willighagen EL, Evelo CT, Jeliazkova N. XMetDB: an open access database for xenobiotic metabolism. Journal of Cheminformatics. 8: 47. PMID 27651835 DOI: 10.1186/S13321-016-0161-3 |
0.385 |
|
| 2016 |
Alvarsson J, Lampa S, Schaal W, Andersson C, Wikberg JE, Spjuth O. Large-scale ligand-based predictive modelling using support vector machines. Journal of Cheminformatics. 8: 39. PMID 27516811 DOI: 10.1186/S13321-016-0151-5 |
0.376 |
|
| 2016 |
Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E. Recommendations on e-infrastructures for next-generation sequencing Gigascience. 5: 26-26. PMID 27267963 DOI: 10.1186/S13742-016-0132-7 |
0.385 |
|
| 2015 |
Grafström RC, Nymark P, Hongisto V, Spjuth O, Ceder R, Willighagen E, Hardy B, Kaski S, Kohonen P. Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures. Alternatives to Laboratory Animals : Atla. 43: 325-32. PMID 26551289 DOI: 10.1177/026119291504300506 |
0.392 |
|
| 2015 |
Spjuth O, Krestyaninova M, Hastings J, Shen HY, Heikkinen J, Waldenberger M, Langhammer A, Ladenvall C, Esko T, Persson MÅ, Heggland J, Dietrich J, Ose S, Gieger C, Ried JS, et al. Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. European Journal of Human Genetics : Ejhg. PMID 26306643 DOI: 10.1038/Ejhg.2015.165 |
0.369 |
|
| 2015 |
Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, et al. Experiences with workflows for automating data-intensive bioinformatics. Biology Direct. 10: 43. PMID 26282399 DOI: 10.1186/S13062-015-0071-8 |
0.364 |
|
| 2015 |
Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O. A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data. Gigascience. 4: 26. PMID 26045962 DOI: 10.1186/S13742-015-0058-5 |
0.311 |
|
| 2015 |
Moghadam BT, Alvarsson J, Holm M, Eklund M, Carlsson L, Spjuth O. Scaling predictive modeling in drug development with cloud computing. Journal of Chemical Information and Modeling. 55: 19-25. PMID 25493610 DOI: 10.1021/Ci500580Y |
0.375 |
|
| 2015 |
Dahlö M, Haziza F, Kallio A, Korpelainen E, Bongcam-Rudloff E, Spjuth O. BioImg.org: A catalog of virtual machine images for the life sciences Bioinformatics and Biology Insights. 9: 125-128. DOI: 10.4137/Bbi.S28636 |
0.356 |
|
| 2015 |
Gholami A, Laure E, Somogyi P, Spjuth O, Niazi S, Dowling J. Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers Journal of Medical and Bioengineering. 4: 117-125. DOI: 10.12720/Jomb.4.2.117-125 |
0.334 |
|
| 2014 |
Alvarsson J, Eklund M, Andersson C, Carlsson L, Spjuth O, Wikberg JE. Benchmarking study of parameter variation when using signature fingerprints together with support vector machines. Journal of Chemical Information and Modeling. 54: 3211-7. PMID 25318024 DOI: 10.1021/Ci500344V |
0.322 |
|
| 2014 |
Alvarsson J, Eklund M, Engkvist O, Spjuth O, Carlsson L, Wikberg JE, Noeske T. Ligand-based target prediction with signature fingerprints. Journal of Chemical Information and Modeling. 54: 2647-53. PMID 25230336 DOI: 10.1021/Ci500361U |
0.335 |
|
| 2014 |
Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R. Cancer biology, toxicology and alternative methods development go hand-in-hand. Basic & Clinical Pharmacology & Toxicology. 115: 50-8. PMID 24779563 DOI: 10.1111/Bcpt.12257 |
0.387 |
|
| 2014 |
Spjuth O. NGS data management and analysis for hundreds of projects: Experiences from Sweden Embnet.Journal. 20: 761. DOI: 10.14806/Ej.20.A.761 |
0.374 |
|
| 2013 |
Schaal W, Hammerling U, Gustafsson MG, Spjuth O. Automated QuantMap for rapid quantitative molecular network topology analysis. Bioinformatics (Oxford, England). 29: 2369-70. PMID 23828784 DOI: 10.1093/Bioinformatics/Btt390 |
0.385 |
|
| 2013 |
Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O. Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. Gigascience. 2: 9. PMID 23800020 DOI: 10.1186/2047-217X-2-9 |
0.409 |
|
| 2013 |
Lapins M, Worachartcheewan A, Spjuth O, Georgiev V, Prachayasittikul V, Nantasenamat C, Wikberg JE. A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms. Plos One. 8: e66566. PMID 23799117 DOI: 10.1371/Journal.Pone.0066566 |
0.372 |
|
| 2013 |
Rostkowski M, Spjuth O, Rydberg P. WhichCyp: prediction of cytochromes P450 inhibition. Bioinformatics (Oxford, England). 29: 2051-2. PMID 23740742 DOI: 10.1093/Bioinformatics/Btt325 |
0.36 |
|
| 2013 |
Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ. The ChEMBL database as linked open data. Journal of Cheminformatics. 5: 23. PMID 23657106 DOI: 10.1186/1758-2946-5-23 |
0.401 |
|
| 2013 |
Spjuth O, Berg A, Adams S, Willighagen EL. Applications of the InChI in cheminformatics with the CDK and Bioclipse. Journal of Cheminformatics. 5: 14. PMID 23497723 DOI: 10.1186/1758-2946-5-14 |
0.369 |
|
| 2012 |
Spjuth O, Carlsson L, Alvarsson J, Georgiev V, Willighagen E, Eklund M. Open source drug discovery with bioclipse. Current Topics in Medicinal Chemistry. 12: 1980-6. PMID 23110533 DOI: 10.2174/156802612804910287 |
0.378 |
|
| 2012 |
Williams AJ, Ekins S, Spjuth O, Willighagen EL. Accessing, using, and creating chemical property databases for computational toxicology modeling. Methods in Molecular Biology (Clifton, N.J.). 929: 221-41. PMID 23007432 DOI: 10.1007/978-1-62703-050-2_10 |
0.419 |
|
| 2012 |
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, ... Spjuth O, et al. Toxicology ontology perspectives. Altex. 29: 139-56. PMID 22562487 DOI: 10.14573/Altex.2012.2.139 |
0.433 |
|
| 2012 |
Hardy B, Apic G, Carthew P, Clark D, Cook D, Dix I, Escher S, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, ... Spjuth O, et al. Food for thought ... A toxicology ontology roadmap. Altex. 29: 129-37. PMID 22562486 DOI: 10.14573/Altex.2012.2.129 |
0.421 |
|
| 2012 |
Carlsson L, Spjuth O, Eklund M, Boyer S. Model building in Bioclipse Decision Support applied to open datasets Toxicology Letters. 211. DOI: 10.1016/J.Toxlet.2012.03.243 |
0.398 |
|
| 2012 |
Spjuth O, Willighagen E, Hammerling U, Dencker L, Grafström R. A novel infrastructure for chemical safety predictions with focus on human health Toxicology Letters. 211: S59. DOI: 10.1016/J.Toxlet.2012.03.234 |
0.422 |
|
| 2011 |
Willighagen EL, Jeliazkova N, Hardy B, Grafström RC, Spjuth O. Computational toxicology using the OpenTox application programming interface and Bioclipse. Bmc Research Notes. 4: 487. PMID 22075173 DOI: 10.1186/1756-0500-4-487 |
0.443 |
|
| 2011 |
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, ... ... Spjuth O, et al. Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of Cheminformatics. 3: 37. PMID 21999342 DOI: 10.1186/1758-2946-3-37 |
0.313 |
|
| 2011 |
Spjuth O, Eklund M, Ahlberg Helgee E, Boyer S, Carlsson L. Integrated decision support for assessing chemical liabilities. Journal of Chemical Information and Modeling. 51: 1840-7. PMID 21774475 DOI: 10.1021/Ci200242C |
0.362 |
|
| 2011 |
Alvarsson J, Andersson C, Spjuth O, Larsson R, Wikberg JE. Brunn: an open source laboratory information system for microplates with a graphical plate layout design process. Bmc Bioinformatics. 12: 179. PMID 21599898 DOI: 10.1186/1471-2105-12-179 |
0.333 |
|
| 2011 |
Spjuth O, Eklund M, Lapins M, Junaid M, Wikberg JE. Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre. Bioinformatics (Oxford, England). 27: 1719-20. PMID 21493651 DOI: 10.1093/Bioinformatics/Btr192 |
0.321 |
|
| 2011 |
Willighagen EL, Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg JE. Linking the Resource Description Framework to cheminformatics and proteochemometrics. Journal of Biomedical Semantics. 2: S6. PMID 21388575 DOI: 10.1186/2041-1480-2-S1-S6 |
0.312 |
|
| 2010 |
Carlsson L, Spjuth O, Adams S, Glen RC, Boyer S. Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. Bmc Bioinformatics. 11: 362. PMID 20594327 DOI: 10.1186/1471-2105-11-362 |
0.323 |
|
| 2010 |
Spjuth O, Willighagen EL, Guha R, Eklund M, Wikberg JE. Towards interoperable and reproducible QSAR analyses: Exchange of datasets. Journal of Cheminformatics. 2: 5. PMID 20591161 DOI: 10.1186/1758-2946-2-5 |
0.391 |
|
| 2010 |
Eklund M, Spjuth O, Wikberg JE. An eScience-Bayes strategy for analyzing omics data. Bmc Bioinformatics. 11: 282. PMID 20504364 DOI: 10.1186/1471-2105-11-282 |
0.368 |
|
| 2009 |
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE. Bioclipse 2: a scriptable integration platform for the life sciences. Bmc Bioinformatics. 10: 397. PMID 19958528 DOI: 10.1186/1471-2105-10-397 |
0.405 |
|
| 2009 |
Wagener J, Spjuth O, Willighagen EL, Wikberg JE. XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. Bmc Bioinformatics. 10: 279. PMID 19732427 DOI: 10.1186/1471-2105-10-279 |
0.345 |
|
| 2008 |
Eklund M, Spjuth O, Wikberg JE. The C1C2: a framework for simultaneous model selection and assessment. Bmc Bioinformatics. 9: 360. PMID 18761753 DOI: 10.1186/1471-2105-9-360 |
0.328 |
|
| 2007 |
Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE. Bioclipse: an open source workbench for chemo- and bioinformatics. Bmc Bioinformatics. 8: 59. PMID 17316423 DOI: 10.1186/1471-2105-8-59 |
0.326 |
|
| 2006 |
Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J. The LCB Data Warehouse. Bioinformatics (Oxford, England). 22: 1024-6. PMID 16455749 DOI: 10.1093/Bioinformatics/Btl036 |
0.38 |
|
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