Publications
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
- 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
J Am Med Inform Assoc.
ocx038 (2017).
DOI: 10.1093/jamia/ocx038
- 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.
[Epub ahead of print] (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
- 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. (2016).
DOI: 10.1186/s13321-016-0179-6
- 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
- Spjuth O
NGS data management and analysis for hundreds of projects: Experiences from Sweden
EMBnet.journal.
20, A, 761. (2014).
DOI: 10.14806/ej.20.a.761
- 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
- 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, 1 (2013).
DOI: 10.1186/2047-217x-2-9
- 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
Proteochemometric modeling of the susceptibility of mutated variants of the HIV-1 virus to reverse transcriptase inhibitors
PLoS One.
5, 12 (2010).
DOI: 10.1371/journal.pone.0014353
- 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 (2010).
DOI: 10.1186/1471-2105-11-362
- 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
2007
2006
