| 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 |
0.381 |
|
| 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 |
0.396 |
|
| 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 |
0.321 |
|
| 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 |
0.422 |
|
| 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 |
0.344 |
|
| 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 |
0.325 |
|
| 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 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2020 |
Wieslander H, Harrison PJ, Skogberg G, Jackson S, Friden M, Karlsson J, Spjuth O, Wahlby C. Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images. Ieee Journal of Biomedical and Health Informatics. PMID 32750907 DOI: 10.1109/Jbhi.2020.2996300 |
0.3 |
|
| 2018 |
Gupta A, Harrison PJ, Wieslander H, Pielawski N, Kartasalo K, Partel G, Solorzano L, Suveer A, Klemm AH, Spjuth O, Sintorn IM, Wählby C. Deep Learning in Image Cytometry: A Review. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 30565841 DOI: 10.1002/Cyto.A.23701 |
0.297 |
|
| 2019 |
Lampa S, Dahlo M, Alvarsson J, Spjuth O. SciPipe—Turning Scientific Workflows into Computer Programs Computing in Science and Engineering. 21: 109-113. DOI: 10.1109/Mcse.2019.2907814 |
0.296 |
|
| 2016 |
Simeon S, Spjuth O, Lapins M, Nabu S, Anuwongcharoen N, Prachayasittikul V, Wikberg JE, Nantasenamat C. Origin of aromatase inhibitory activity via proteochemometric modeling. Peerj. 4: e1979. PMID 27190705 DOI: 10.7717/Peerj.1979 |
0.296 |
|
| 2017 |
Herman S, Emami Khoonsari P, Aftab O, Krishnan S, Strömbom E, Larsson R, Hammerling U, Spjuth O, Kultima K, Gustafsson M. Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions. Metabolomics : Official Journal of the Metabolomic Society. 13: 79. PMID 28596718 DOI: 10.1007/S11306-017-1213-Z |
0.293 |
|
| 2021 |
Blamey B, Toor S, Dahlö M, Wieslander H, Harrison PJ, Sintorn IM, Sabirsh A, Wählby C, Spjuth O, Hellander A. Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit. Gigascience. 10. PMID 33739401 DOI: 10.1093/gigascience/giab018 |
0.292 |
|
| 2013 |
Claesson A, Spjuth O. On mechanisms of reactive metabolite formation from drugs. Mini Reviews in Medicinal Chemistry. 13: 720-9. PMID 23035789 DOI: 10.2174/1389557511313050009 |
0.287 |
|
| 2018 |
Ahmed L, Georgiev V, Capuccini M, Toor S, Schaal W, Laure E, Spjuth O. Efficient iterative virtual screening with Apache Spark and conformal prediction. Journal of Cheminformatics. 10: 8. PMID 29492726 DOI: 10.1186/S13321-018-0265-Z |
0.286 |
|
| 2023 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. Biorxiv : the Preprint Server For Biology. PMID 37905146 DOI: 10.1101/2023.10.15.562398 |
0.284 |
|
| 2019 |
Exner T, Farcal L, Bachler D, Oki N, Gebele D, Raza A, Kramer S, Floden E, Notredam C, Rambla J, Jennen D, Bayjanov J, Willighagen E, Martens M, Evelo C, ... ... Spjuth O, et al. OpenRiskNet Part I: Development of an open e-infrastructure predictive toxicology and risk assessment F1000research. 8. DOI: 10.7490/F1000Research.1117259.1 |
0.281 |
|
| 2018 |
Herman S, Khoonsari PE, Tolf A, Steinmetz J, Zetterberg H, Åkerfeldt T, Jakobsson PJ, Larsson A, Spjuth O, Burman J, Kultima K. Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis. Theranostics. 8: 4477-4490. PMID 30214633 DOI: 10.7150/Thno.26249 |
0.279 |
|
| 2012 |
Lampa S, Hagberg J, Spjuth O. UPPNEX - A solution for Next Generation Sequencing data management and analysis Embnet.Journal. 17: 44-44. DOI: 10.14806/Ej.17.B.274 |
0.276 |
|
| 2016 |
Willighagen E, Mélius J, Christian B, Soiland-Reyes S, Bohler A, Kutmon M, Waagmeester A, Pico A, Riutta A, Gray A, Leemans C, Batchelor C, Spjuth O, Nunes N, Evelo C, et al. The BridgeDb framework F1000research. 5. DOI: 10.7490/F1000Research.1113101.1 |
0.274 |
|
| 2024 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. Journal of Chemical Information and Modeling. PMID 38300851 DOI: 10.1021/acs.jcim.3c01834 |
0.273 |
|
| 2008 |
Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JE. Proteochemometric modeling of HIV protease susceptibility. Bmc Bioinformatics. 9: 181. PMID 18402661 DOI: 10.1186/1471-2105-9-181 |
0.262 |
|
| 2019 |
Kramer S, Doganis P, Gebele D, Raza A, Karatzas P, Sarimveis H, Alvarsson J, Spjuth O, Arvidsson S, Exner T, Farcal L, Hardy B, OpenRiskNet. OpenRiskNet Part III: Modelling services in chemical/nano-safety, environmental science and pharmacokinetics F1000research. 8. DOI: 10.7490/F1000Research.1117419.1 |
0.261 |
|
| 2010 |
Junaid M, Lapins M, Eklund M, Spjuth O, Wikberg JE. Proteochemometric modeling of the susceptibility of mutated variants of the HIV-1 virus to reverse transcriptase inhibitors. Plos One. 5: e14353. PMID 21179544 DOI: 10.1371/Journal.Pone.0014353 |
0.26 |
|
| 2021 |
Spjuth O, Capuccini M, Carone M, Larsson A, Schaal W, Novella JA, Stein O, Ekmefjord M, Tommaso PD, Floden E, Notredame C, Moreno P, Hellander A, Khoonsari PE, Herman S, et al. Approaches for containerized scientific workflows in cloud environments with applications in life science F1000research. 10: 513. DOI: 10.12688/F1000RESEARCH.53698.1 |
0.255 |
|
| 2022 |
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O. Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods. Alternatives to Laboratory Animals : Atla. 2611929221148447. PMID 36572567 DOI: 10.1177/02611929221148447 |
0.255 |
|
| 2021 |
Spjuth O, Frid J, Hellander A. The machine learning life cycle and the cloud: implications for drug discovery. Expert Opinion On Drug Discovery. 16: 1071-1079. PMID 34057379 DOI: 10.1080/17460441.2021.1932812 |
0.254 |
|
| 2017 |
Spjuth O, Karlsson A, Clements M, Humphreys K, Ivansson E, Dowling J, Eklund M, Jauhiainen A, Czene K, Grönberg H, Sparén P, Wiklund F, Cheddad A, Pálsdóttir Þ, Rantalainen M, et al. E-Science technologies in a workflow for personalized medicine using cancer screening as a case study. Journal of the American Medical Informatics Association : Jamia. PMID 28444384 DOI: 10.1093/Jamia/Ocx038 |
0.253 |
|
| 2020 |
Ahmed L, Alogheli H, McShane SA, Alvarsson J, Berg A, Larsson A, Schaal W, Laure E, Spjuth O. Predicting target profiles with confidence as a service using docking scores Journal of Cheminformatics. 12. DOI: 10.1186/s13321-020-00464-1 |
0.252 |
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| 2021 |
Arvidsson McShane S, Ahlberg E, Noeske T, Spjuth O. Machine Learning Strategies When Transitioning between Biological Assays. Journal of Chemical Information and Modeling. PMID 34152755 DOI: 10.1021/acs.jcim.1c00293 |
0.249 |
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| 2021 |
Morger A, Svensson F, Arvidsson McShane S, Gauraha N, Norinder U, Spjuth O, Volkamer A. Assessing the calibration in toxicological in vitro models with conformal prediction. Journal of Cheminformatics. 13: 35. PMID 33926567 DOI: 10.1186/s13321-021-00511-5 |
0.249 |
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| 2019 |
Herman S, Åkerfeldt T, Spjuth O, Burman J, Kultima K. Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing–Remitting Multiple Sclerosis Cells. 8: 84. PMID 30678351 DOI: 10.3390/Cells8020084 |
0.243 |
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| 2024 |
Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. Biorxiv : the Preprint Server For Biology. PMID 38766203 DOI: 10.1101/2024.05.04.592531 |
0.243 |
|
| 2024 |
Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. Arxiv. PMID 38745696 |
0.243 |
|
| 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: 125-8. PMID 26401099 DOI: 10.4137/BBI.S28636 |
0.241 |
|
| 2018 |
Spjuth O. Novel Applications of Machine Learning in Cheminformatics Journal of Cheminformatics. 10: 1-2. PMID 30191348 DOI: 10.1186/S13321-018-0301-Z |
0.239 |
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| 2021 |
Ouyang W, Bowman RW, Wang H, Bumke KE, Collins JT, Spjuth O, Carreras-Puigvert J, Diederich B. An Open-Source Modular Framework for Automated Pipetting and Imaging Applications. Advanced Biology. e2101063. PMID 34693668 DOI: 10.1002/adbi.202101063 |
0.234 |
|
| 2021 |
Fagerholm U, Hellberg S, Spjuth O. Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology. Molecules (Basel, Switzerland). 26. PMID 33925103 DOI: 10.3390/molecules26092572 |
0.234 |
|
| 2018 |
Georgieva P, Schaal W, Spjuth O. Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms Toxicology Letters. 295. DOI: 10.1016/J.Toxlet.2018.06.895 |
0.233 |
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| 2021 |
Alvarsson J, Arvidsson McShane S, Norinder U, Spjuth O. Predicting With Confidence: Using Conformal Prediction in Drug Discovery. Journal of Pharmaceutical Sciences. 110: 42-49. PMID 33075380 DOI: 10.1016/j.xphs.2020.09.055 |
0.225 |
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| 2021 |
Norinder U, Spjuth O, Svensson F. Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning. Journal of Cheminformatics. 13: 77. PMID 34600569 DOI: 10.1186/s13321-021-00555-7 |
0.222 |
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| 2022 |
Sheffield NC, Bonazzi VR, Bourne PE, Burdett T, Clark T, Grossman RL, Spjuth O, Yates AD. From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. Scientific Data. 9: 553. PMID 36075919 DOI: 10.1038/s41597-022-01619-5 |
0.22 |
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| 2021 |
Fagerholm U, Hellberg S, Alvarsson J, Arvidsson McShane S, Spjuth O. prediction of volume of distribution of drugs in man using conformal prediction performs on par with animal data-based models. Xenobiotica; the Fate of Foreign Compounds in Biological Systems. 1-6. PMID 34845977 DOI: 10.1080/00498254.2021.2011471 |
0.217 |
|
| 2019 |
Herman S, Niemelä V, Khoonsari PE, Sundblom J, Burman J, Landtblom A, Spjuth O, Nyholm D, Kultima K. Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects. Scientific Reports. 9: 4129. PMID 30858393 DOI: 10.1038/S41598-019-40186-5 |
0.21 |
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| 2023 |
Seal S, Yang H, Trapotsi MA, Singh S, Carreras-Puigvert J, Spjuth O, Bender A. Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. Journal of Cheminformatics. 15: 56. PMID 37268960 DOI: 10.1186/s13321-023-00723-x |
0.21 |
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| 2022 |
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O. predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology. Xenobiotica; the Fate of Foreign Compounds in Biological Systems. 52: 113-118. PMID 35238270 DOI: 10.1080/00498254.2022.2049397 |
0.208 |
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| 2023 |
Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, ... ... Spjuth O, et al. ELIXIR and Toxicology: a community in development. F1000research. 10. PMID 37842337 DOI: 10.12688/f1000research.74502.2 |
0.205 |
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| 2021 |
Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, ... ... Spjuth O, et al. ELIXIR and Toxicology: a community in development F1000research. 10: 1129. DOI: 10.12688/f1000research.74502.1 |
0.205 |
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| 2020 |
Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek R, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, et al. Metabolomics - the stethoscope for the 21st century. Medical Principles and Practice : International Journal of the Kuwait University, Health Science Centre. PMID 33271569 DOI: 10.1159/000513545 |
0.191 |
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| 2022 |
Lukashina N, Kartysheva E, Spjuth O, Virko E, Shpilman A. SimVec: predicting polypharmacy side effects for new drugs. Journal of Cheminformatics. 14: 49. PMID 35883105 DOI: 10.1186/s13321-022-00632-5 |
0.189 |
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| 2024 |
Tal T, Myhre O, Fritsche E, Rüegg J, Craenen K, Aiello-Holden K, Agrillo C, Babin PJ, Escher BI, Dirven H, Hellsten K, Dolva K, Hessel E, Heusinkveld HJ, Hadzhiev Y, ... ... Spjuth O, et al. New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project. Frontiers in Toxicology. 6: 1359507. PMID 38742231 DOI: 10.3389/ftox.2024.1359507 |
0.188 |
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| 2021 |
Lukashina N, Williams MJ, Kartysheva E, Virko E, Kudłak B, Fredriksson R, Spjuth O, Schiöth HB. Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival. International Journal of Molecular Sciences. 22. PMID 34639124 DOI: 10.3390/ijms221910785 |
0.187 |
|
| 2014 |
Siretskiy A, Spjuth O. HTSeq-Hadoop: Extending HTSeq for massively parallel sequencing data analysis using Hadoop Proceedings - 2014 Ieee 10th International Conference On Escience, Escience 2014. 1: 317-323. DOI: 10.1109/eScience.2014.27 |
0.185 |
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| 2021 |
Harrison PJ, Wieslander H, Sabirsh A, Karlsson J, Malmsjö V, Hellander A, Wählby C, Spjuth O. Deep-learning models for lipid nanoparticle-based drug delivery. Nanomedicine (London, England). PMID 33949890 DOI: 10.2217/nnm-2020-0461 |
0.182 |
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| 2022 |
Fagerholm U, Spjuth O, Hellberg S. The impact of reference data selection for the prediction accuracy of intrinsic hepatic metabolic clearance. Journal of Pharmaceutical Sciences. PMID 35793746 DOI: 10.1016/j.xphs.2022.06.024 |
0.178 |
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| 2019 |
Persson B, Borg M, Lantz H, Jareborg N, Hagberg J, Lindvall J, Levander F, Lindberg J, Feilitzen Kv, Oksvold P, Viklund J, Freyhult P, Ahlberg M, Kähäri A, Norling M, ... ... Spjuth O, et al. Elixir-SE – the Swedish node F1000research. 8. DOI: 10.7490/F1000Research.1117046.1 |
0.177 |
|
| 2015 |
Ahlberg E, Spjuth O, Hasselgren C, Carlsson L. Interpretation of conformal prediction classification models Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9047: 323-334. DOI: 10.1007/978-3-319-17091-6_27 |
0.169 |
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| 2024 |
Seal S, Carreras-Puigvert J, Singh S, Carpenter AE, Spjuth O, Bender A. From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability. Molecular Biology of the Cell. mbcE23080298. PMID 38170589 DOI: 10.1091/mbc.E23-08-0298 |
0.168 |
|
| 2020 |
Norinder U, Spjuth O, Svensson F. Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling". Journal of Chemical Information and Modeling. 60: 6722. PMID 33231446 DOI: 10.1021/acs.jcim.0c01327 |
0.166 |
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| 2022 |
Seal S, Carreras-Puigvert J, Trapotsi MA, Yang H, Spjuth O, Bender A. Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection. Communications Biology. 5: 858. PMID 35999457 DOI: 10.1038/s42003-022-03763-5 |
0.166 |
|
| 2023 |
Herman S, Arvidsson McShane S, Zjukovskaja C, Khoonsari PE, Svenningsson A, Burman J, Spjuth O, Kultima K. Disease phenotype prediction in multiple sclerosis. Iscience. 26: 106906. PMID 37332601 DOI: 10.1016/j.isci.2023.106906 |
0.163 |
|
| 2013 |
Spjuth O, Georgiev V, Carlsson L, Alvarsson J, Berg A, Willighagen E, Wikberg JE, Eklund M. Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics (Oxford, England). 29: 286-9. PMID 23178637 DOI: 10.1093/Bioinformatics/Bts681 |
0.162 |
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| 2022 |
Sreenivasan AP, Harrison PJ, Schaal W, Matuszewski DJ, Kultima K, Spjuth O. Predicting protein network topology clusters from chemical structure using deep learning. Journal of Cheminformatics. 14: 47. PMID 35841114 DOI: 10.1186/s13321-022-00622-7 |
0.16 |
|
| 2019 |
Kensert A, Harrison PJ, Spjuth O. Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes. Slas Discovery : Advancing Life Sciences R & D. 24: 466-475. PMID 30641024 DOI: 10.1177/2472555218818756 |
0.16 |
|
| 2022 |
Olsson H, Kartasalo K, Mulliqi N, Capuccini M, Ruusuvuori P, Samaratunga H, Delahunt B, Lindskog C, Janssen EAM, Blilie A, Egevad L, Spjuth O, Eklund M. Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction. Nature Communications. 13: 7761. PMID 36522311 DOI: 10.1038/s41467-022-34945-8 |
0.157 |
|
| 2022 |
Fagerholm U, Hellberg S, Alvarsson J, Spjuth O. In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology. Journal of Pharmaceutical Sciences. PMID 35605685 DOI: 10.1016/j.xphs.2022.05.010 |
0.157 |
|
| 2011 |
Guha R, Spjuth O, Willighagen E. Collaborative Cheminformatics Applications Collaborative Computational Technologies For Biomedical Research. 399-422. DOI: 10.1002/9781118026038.ch24 |
0.153 |
|
| 2021 |
Rietdijk J, Tampere M, Pettke A, Georgiev P, Lapins M, Warpman-Berglund U, Spjuth O, Puumalainen MR, Carreras-Puigvert J. A phenomics approach for antiviral drug discovery. Bmc Biology. 19: 156. PMID 34334126 DOI: 10.1186/s12915-021-01086-1 |
0.151 |
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| 2023 |
Braeuning A, Balaguer P, Bourguet W, Carreras-Puigvert J, Feiertag K, Kamstra JH, Knapen D, Lichtenstein D, Marx-Stoelting P, Rietdijk J, Schubert K, Spjuth O, Stinckens E, Thedieck K, van den Boom R, et al. Development of new approach methods for the identification and characterization of endocrine metabolic disruptors-a PARC project. Frontiers in Toxicology. 5: 1212509. PMID 37456981 DOI: 10.3389/ftox.2023.1212509 |
0.15 |
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| 2021 |
Fagerholm U, Spjuth O, Hellberg S. Comparison between lab variability and prediction errors for the unbound fraction of drugs in human plasma. Xenobiotica; the Fate of Foreign Compounds in Biological Systems. 1-6. PMID 34346291 DOI: 10.1080/00498254.2021.1964044 |
0.148 |
|
| 2015 |
Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O. Erratum to: A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data. Gigascience. 4: 61. PMID 26664721 DOI: 10.1186/s13742-015-0100-7 |
0.14 |
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| 2023 |
Harrison PJ, Gupta A, Rietdijk J, Wieslander H, Carreras-Puigvert J, Georgiev P, Wählby C, Spjuth O, Sintorn IM. Evaluating the utility of brightfield image data for mechanism of action prediction. Plos Computational Biology. 19: e1011323. PMID 37490493 DOI: 10.1371/journal.pcbi.1011323 |
0.133 |
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| 2021 |
Jakobsson JET, Spjuth O, Lagerström MC. scConnect: a method for exploratory analysis of cell-cell communication based on single cell RNA sequencing data. Bioinformatics (Oxford, England). PMID 33974001 DOI: 10.1093/bioinformatics/btab245 |
0.133 |
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| 2022 |
Rietdijk J, Aggarwal T, Georgieva P, Lapins M, Carreras-Puigvert J, Spjuth O. Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects. The Science of the Total Environment. 832: 155058. PMID 35390365 DOI: 10.1016/j.scitotenv.2022.155058 |
0.131 |
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| 2024 |
Carreras-Puigvert J, Spjuth O. Artificial intelligence for high content imaging in drug discovery. Current Opinion in Structural Biology. 87: 102842. PMID 38797109 DOI: 10.1016/j.sbi.2024.102842 |
0.12 |
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| 2024 |
Braeuning A, Balaguer P, Bourguet W, Carreras-Puigvert J, Feiertag K, Kamstra JH, Knapen D, Lichtenstein D, Marx-Stoelting P, Rietdijk J, Schubert K, Spjuth O, Stinckens E, Thedieck K, van den Boom R, et al. Corrigendum: Development of new approach methods for the identification and characterization of endocrine metabolic disruptors-a PARC project. Frontiers in Toxicology. 6: 1394396. PMID 38590784 DOI: 10.3389/ftox.2024.1394396 |
0.116 |
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| 2021 |
Seal S, Trapotsi M, Puigvert J, Yang H, Spjuth O, Bender A. Cell morphology descriptors and gene ontology profiles improve prediction for mitochondrial toxicity Toxicology Letters. 350: S81-S82. DOI: 10.1016/s0378-4274(21)00437-9 |
0.108 |
|
| 2022 |
Raykova D, Kermpatsou D, Malmqvist T, Harrison PJ, Sander MR, Stiller C, Heldin J, Leino M, Ricardo S, Klemm A, David L, Spjuth O, Vemuri K, Dimberg A, Sundqvist A, et al. A method for Boolean analysis of protein interactions at a molecular level. Nature Communications. 13: 4755. PMID 35963857 DOI: 10.1038/s41467-022-32395-w |
0.1 |
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| 2013 |
Ahmed L, Edlund A, Laure E, Spjuth O. Using iterative MapReduce for parallel virtual screening Proceedings of the International Conference On Cloud Computing Technology and Science, Cloudcom. 2: 27-32. DOI: 10.1109/CloudCom.2013.99 |
0.083 |
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| 2023 |
Raykova D, Kermpatsou D, Malmqvist T, Harrison PJ, Sander MR, Stiller C, Heldin J, Leino M, Ricardo S, Klemm A, David L, Spjuth O, Vemuri K, Dimberg A, Sundqvist A, et al. Author Correction: A method for Boolean analysis of protein interactions at a molecular level. Nature Communications. 14: 5450. PMID 37673885 DOI: 10.1038/s41467-023-41325-3 |
0.077 |
|
| 2011 |
Wikberg JES, Spjuth O, Eklund M, Lapins M. Chemoinformatics Taking Biology into Account: Proteochemometrics Computational Approaches in Cheminformatics and Bioinformatics. 57-92. DOI: 10.1002/9781118131411.ch3 |
0.076 |
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| 2022 |
Schaal W, Ameur A, Olsson-Strömberg U, Hermanson M, Cavelier L, Spjuth O. Migrating to Long-Read Sequencing for Clinical Routine TKI Resistance Mutation Screening. Cancer Informatics. 21: 11769351221110872. PMID 35860345 DOI: 10.1177/11769351221110872 |
0.073 |
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| 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. Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics. 9: 53. PMID 29086079 DOI: 10.1186/s13321-017-0231-1 |
0.066 |
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