Publications

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, Abrahamsson L, Laure E, Litton J-E, Palmgren J
E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
Journal of the American Medical Informatics Association. 24, 5, 950-957. (2017). DOI: 10.1093/jamia/ocx038
S. Toor, M. Lindberg, I. Fallman, A. Vallin, O. Mohill, P. Freyhult, L. Nilsson, M. Agback, L. Viklund, H. Zazzi, O. Spjuth, M. Capuccini, J. Moller, D. Murtagh and A. Hellander
SNIC Science Cloud (SSC): A National-scale Cloud Infrastructure for Swedish Academia
Accepted to the 13th IEEE e-Science conference 2017. (2017).
Sütterlin S, Dahlö M, Tellgren-Roth C, Schaal W, Melhus Å
High frequency of silver resistance genes in invasive isolates of Enterobacter and Klebsiella species
J Hosp Infect. 96, 3, 256-261. (2017). DOI: 10.1016/j.jhin.2017.04.017
Arvidsson S, Carlsson L, Toccaceli P, and Spjuth O.
Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors
Proceedings of Machine Learning Research. 60, 1-14. (2017).
Willighagen E, Mayfield J, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo C, Guha R, Steinbeck C
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Journal of Cheminformatics. 9, 33 (2017). DOI: 10.1186/s13321-017-0220-4
Herman S, Khoonsari PE, Aftab O, Krishnan S, Strömbom E, Larsson R, Hammerling U, Spjuth O, Kultima M, Gustafsson M
Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions
Metabolomics. 13, 79 (2017). DOI: 10.1007/s11306-017-1213-z
Shoombuatong W, Prathipati P, Prachayasittikul V, Schaduangrat N, Malik AA, Pratiwi R, Wanwimolruk S, Wikberg JES, Gleeson MP, Spjuth O, Nantasenamat C
Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling
Current Drug Metabolism. 18, 6, 540-555. (2017). DOI: 10.2174/1389200218666170320121932
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. (2017). DOI: 10.1186/s13321-017-0204-4
Alogheli H, Olanders G, Schaal W, Brandt P, Karlén A
Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide
J Chem Inf Model. 57, 2, 190-202. (2017). DOI: 10.1021/acs.jcim.6b00443

2016

Spjuth O, Rydberg P, Willighagen EL, Evelo CT, Jeliazkova N
XMetDB: an open access database for xenobiotic metabolism
Journal of Cheminformatics. 8, 47. (2016). DOI: 10.1186/s13321-016-0161-3
Alvarsson J, Lampa S, Schaal W, Andersson C, Wikberg JES, Spjuth O
Large-scale ligand-based predictive modelling using support vector machines
Journal of Cheminformatics. 8, 39. (2016). DOI: 10.1186/s13321-016-0151-5
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, 1 (2016). DOI: 10.1186/s13742-016-0132-7
Simeon S, Spjuth O, Lapins M, Nabu S, Anuwongcharoen N, Prachayasittikul V, Wikberg JES, Nantasenamat C
Origin of aromatase inhibitory activity via proteochemometric modeling
PeerJ. 4, e1979. (2016). DOI: 10.7717/peerj.1979
Spjuth O, Krestyaninova M, Hastings J, Shen H-Y, Heikkinen J, Waldenberger M, Langhammer A, Ladenvall C, Esko T, Persson M-Å, Heggland J, Dietrich J, Ose S, Gieger C, Ried JS, Peters A, Fortier I, de Geus EJC, Klovins J, Zaharenko L, Willemsen G, Hottenga J-J, Litton J-E, Karvanen J, Boomsma DI, Groop L, Rung J, Palmgren J, Pedersen NL, McCarthy MI, van Duijn CM, Hveem K, Metspalu A, Ripatti S, Prokopenko I, Harris JR
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
Eur J Hum Genet. 24, 4, 521--528. (2016). DOI: 10.1038/ejhg.2015.165

2015

Capuccini M, Carlsson L, Norinder U, Spjuth O
Conformal Prediction in Spark: Large-Scale Machine Learning with Confidence
Proceedings - 2015 2nd IEEE/ACM International Symposium on Big Data Computing, BDC 2015. , 61-67. (2015). DOI: 10.1109/BDC.2015.35
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
Altern. Lab. Anim.. 43, 5, 325--332. (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. (2015). DOI: 10.4137/BBI.S28636
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, Schönherr S, Siretskiy A, Vassilev D
Experiences with workflows for automating data-intensive bioinformatics
Biology Direct. 10, 1 (2015). DOI: 10.1186/s13062-015-0071-8
Blom K, Nygren P, Alvarsson J, Larsson R, Andersson CR
Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy
Journal of Laboratory Automation. 21, 1, 178-187. (2015). DOI: 10.1177/2211068215598117
Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O
A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
GigaScience. 4, 1 (2015). DOI: 10.1186/s13742-015-0058-5
Gholami A, Laure E, Somogyi P, Spjuth O, Niazi S, Dowling J
Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers
JOMB. 4, 2, 117--125. (2015). DOI: 10.12720/jomb.4.2.117-125
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. (2015). DOI: 10.1007/978-3-319-17091-6_27
Lindh M, Svensson F, Schaal W, Zhang J, Sköld C, Brandt P, Karlén A
Toward a benchmarking data set able to evaluate ligand- and structure-based virtual screening using public HTS data
J Chem Inf Model. 55, 2, 343-353. (2015). DOI: 10.1021/ci5005465
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, 1, 19-25. (2015). DOI: 10.1021/ci500580y

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. (2014). DOI: 10.1109/eScience.2014.27
Alvarsson J, Eklund M, Andersson C, Carlsson L, Spjuth O, Wikberg JES
Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines
Journal of Chemical Information and Modeling. 54, 11, 3211--3217. (2014). DOI: 10.1021/ci500344v
Alvarsson J, Eklund M, Engkvist O, Spjuth O, Carlsson L, Wikberg JES, Noeske T
Ligand-based target prediction with signature fingerprints
Journal of Chemical Information and Modeling. 54, 10, 2647–2653. (2014). DOI: 10.1021/ci500361u
Spjuth O, Heikkinen J, Litton J-E, Palmgren J, Krestyaninova M
Data integration between Swedish national clinical health registries and biobanks using an availability system
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8574 LNBI, 32-40. (2014). DOI: 10.1007/978-3-319-08590-6_3
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. 15, 1, 50-58. (2014). DOI: 10.1111/bcpt.12257

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. (2013). DOI: 10.1109/CloudCom.2013.99
Spjuth O, Carlsson L, Alvarsson J, Georgiev V, Willighagen E, Eklund M
Open Source Drug Discovery with Bioclipse
Current Topics in Medicinal Chemistry. 12, 18 (2013). DOI: 10.2174/1568026611212180005
Schaal W, Hammerling U, Gustafsson MG, Spjuth O
Automated QuantMap for rapid quantitative molecular network topology analysis
Bioinformatics. 29, 18, 2369-2370. (2013). DOI: 10.1093/bioinformatics/btt390
Lapins M, Worachartcheewan A, Spjuth O, Georgiev V, Prachayasittikul V, Nantasenamat C, Wikberg JES
A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
PLoS One. 8, 6, e66566. (2013). DOI: 10.1371/journal.pone.0066566
Rostkowski M, Spjuth O, Rydberg P
WhichCyp: prediction of cytochromes P450 inhibition.
Bioinformatics. 29, 16, 2051-2052. (2013). DOI: 10.1093/bioinformatics/btt325
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 (2013). DOI: 10.1186/1758-2946-5-23
Claesson A, Spjuth O
On mechanisms of reactive metabolite formation from drugs.
Mini Rev Med Chem. 13, 5, 720-9. (2013).
Spjuth O, Berg A, Adams S, Willighagen EL
Applications of the InChI in cheminformatics with the CDK and Bioclipse
Journal of Cheminformatics. 5, 3 (2013). DOI: 10.1186/1758-2946-5-14

2012

Spjuth O, Georgiev V, Carlsson L, Alvarsson J, Berg A, Willighagen E, Wikberg JES, Eklund M
Bioclipse-R: integrating management and visualization of life science data with statistical analysis.
Bioinformatics. 29, 2, 286-289. (2012). DOI: 10.1093/bioinformatics/bts681
Spjuth O, Carlsson L, Alvarsson J, Georgiev V, Willighagen E, Eklund M
Open source drug discovery with Bioclipse
Current Topics in Medicinal Chemistry. 12, 18, 1980-1986. (2012). DOI: 10.2174/156802612804910287
Spjuth O
Accessing, using, and creating chemical property databases for computational toxicology modeling
Computational Toxicology, Methods in Molecular Biology. 929, 221-241. (2012). DOI: 10.1007/978-1-62703-050-2_10
Willighagen E, Affentranger R, Grafström R, Hardy B, Jeliazkova N, Spjuth O
Interactive predictive toxicology with Bioclipse and OpenTox
Open Source Software in Life Science Research. , 35--61. (2012). DOI: 10.1533/9781908818249.35
Hardy B, Apic G, Carthew P, Clark D, Cook D, Escher S, Dix I, Hastings J, Heard DJ, Jeliazkova N, Judson P, Matis-Mitchell S, Mitic D, Myatt G, Shah I, Spjuth O, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C
Food for thought ... A toxicology ontology roadmap
ALTEX. 29, 2, 127-138. (2012). DOI: 10.14573/altex.2012.2.129
Carlsson L, Spjuth O, Eklund M, Boyer S
Model building in Bioclipse Decision Support applied to open datasets
Toxicology Letters. 211, S62. (2012). DOI: 10.1016/j.toxlet.2012.03.243
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. (2012). DOI: 10.1016/j.toxlet.2012.03.234
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, Tcheremenskaia O, Toldo L, Watson D, White A, Yang C
Toxicology Ontology Perspectives
ALTEX. 29, 2, 139-156. (2012). DOI: 10.14573/altex.2012.2.139
Lampa S, Hagberg J, Spjuth O
UPPNEX - A solution for Next Generation Sequencing data management and analysis
EMBnet journal. 17, B, 44. (2012). DOI: 10.14806/ej.17.b.274
Krestyaninova M, Spjuth O, Hastings J, Dietrich J, Rebholz-Schuhmann D
Biobank Metaportal to Enhance Collaborative Research: sail.simbioms.org
Journal of Systemics, Cybernetics and Informatics. 10 (2012).

2011

Wikberg JES, Spjuth O, Eklund M, Lapins M
Chemoinformatics Taking Biology into Account: Proteochemometrics
Computational Approaches in Cheminformatics and Bioinformatics. , 57-92. (2011). DOI: 10.1002/9781118131411.ch3
Willighagen EL, Jeliazkova N, Hardy B, Grafström RC, Spjuth O
Computational toxicology using the OpenTox application programming interface and Bioclipse
BMC Research Notes. 4 (2011). DOI: 10.1186/1756-0500-4-487
O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley, J-C, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang ASID, Langner KM, Lonie DC, Lowe DM, Pansanel, Jérôme, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, Murray-Rust P
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
Journal of Cheminformatics. 3, 37 (2011). DOI: 10.1186/1758-2946-3-37
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, 8, 1840-1847. (2011). DOI: 10.1021/ci200242c
Alvarsson J, Andersson C, Spjuth O, Larsson R, Wikberg JES
Brunn: An open source laboratory information system for microplates with a graphical plate layout design process
BMC Bioinformatics. 12 (2011). DOI: 10.1186/1471-2105-12-179
Guha R, Spjuth O, Willighagen E
Collaborative Cheminformatics Applications
Collaborative Computational Technologies for Biomedical Research. , 399-422. (2011). DOI: 10.1002/9781118026038.ch24
Spjuth O, Eklund M, Lapins M, Junaid M, Wikberg JES
Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre
Bioinformatics. 27, 12, 1719-1720. (2011). DOI: 10.1093/bioinformatics/btr192
Willighagen EL, Alvarsson J, Andersson A, Eklund M, Lampa S, Lapins M, Spjuth O, Wikberg JES
Linking the Resource Description Framework to cheminformatics and proteochemometrics
Journal of Biomedical Semantics. 2, 1 (2011). DOI: 10.1186/2041-1480-2-S1-S6

2010

Spjuth O, Willighagen EL, Guha R, Eklund M, Wikberg JES
Towards interoperable and reproducible QSAR analyses: Exchange of datasets
Journal of Cheminformatics. 2, 1 (2010). DOI: 10.1186/1758-2946-2-5
Eklund M, Spjuth O, Wikberg JES
An eScience-Bayes strategy for analyzing omics data
BMC Bioinformatics. 11 (2010). DOI: 10.1186/1471-2105-11-282

2009

Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JES
Bioclipse 2: A scriptable integration platform for the life sciences
BMC Bioinformatics. 10 (2009). DOI: 10.1186/1471-2105-10-397
Wagener J, Spjuth O, Willighagen EL, Wikberg JES
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
BMC Bioinformatics. 10, 279. (2009). DOI: 10.1186/1471-2105-10-279

2008

Eklund M, Spjuth O, Wikberg JES
The C1C2: A framework for simultaneous model selection and assessment
BMC Bioinformatics. 9 (2008). DOI: 10.1186/1471-2105-9-360
Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JES
Proteochemometric modeling of HIV protease susceptibility
BMC Bioinformatics. 9 (2008). DOI: 10.1186/1471-2105-9-181

2007

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES
Bioclipse: An open source workbench for chemo- and bioinformatics
BMC Bioinformatics. 8 (2007). DOI: 10.1186/1471-2105-8-59

2006

Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J.
The LCB Data Warehouse
Bioinformatics. 22, 8, 1024-6. (2006). DOI: 10.1093/bioinformatics/btl036

Posters

The BridgeDb framework
15th European Conference on Computational Biology (ECCB), The Hague. Sep 2016
Conformal prediction in Spark: Large-Scale Machine Learning with Confidence
2015 IEEE/ACM 2nd Int Symp on Big Data Comp (BDC), Limassol, Cyprus. Dec 2015
Machine Learning in Drug Discovery
Swedish e-Science Academy 2015, Lund. Oct 2015
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Presentations

Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors
Conformal Prediction and Probabilistic Predictions with Applicationsi (COPA) 2017, Stockholm. Jun 2017
The case for cloud computing in Life Sciences
CloudBeer Stockholm 2017, Stockholm. Mar 2017
Analyzing Big Data in Medicine with Virtual Research Environments and Microservices
Big Data in Medicine symposium series at Uppsala University., Uppsala. Nov 2016
Interoperability and scalability with microservices in science
OpenTox Euro 2016, Rheinfelden, Germany. Oct 2016
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