Publikationer

Herman, S., Niemelä, V., Emami Khoonsari, P., Sundblom, J., Burman, J. et al. (2019). Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects. Scientific Reports, . vol. 9 DOI Mer information
Herman, S., Åkerfeldt, T., Spjuth, O., Burman, J., Kultima, K. (2019). Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis. Cells, vol. 8 8 DOI Mer information
Kensert, A., Harrison, P., Spjuth, O. (2019). Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes. SLAS discovery : advancing life sciences R & D, vol. 24 24, ss. 466 466-475 475 DOI Mer information
Lampa, S., Dahlö, M., Alvarsson, J., Spjuth, O. (2019). SciPipe-Turning Scientific Workflows into Computer Programs. Computing in science & engineering (Print), . vol. 21, ss. 109-113 DOI Mer information
Novella, J., Emami Khoonsari, P., Herman, S., Whitenack, D., Capuccini, M. et al. (2019). Container-based bioinformatics with Pachyderm. Bioinformatics, vol. 35, ss. 839-846 DOI Mer information
Peters, K., Bradbury, J., Bergmann, S., Capuccini, M., Cascante, M. et al. (2019). PhenoMeNal: Processing and analysis of metabolomics data in the cloud. GigaScience, vol. 8 DOI Mer information
Ahmed, L., Georgiev, V., Capuccini, M., Toor, S., Schaal, W. et al. (2018). Efficient iterative virtual screening with Apache Spark and conformal prediction. Journal of Cheminformatics, vol. 10 DOI Mer information
Dahlö, M., Scofield, D., Schaal, W., Spjuth, O. (2018). Tracking the NGS revolution: managing life science research on shared high-performance computing clusters. GigaScience, vol. 7 DOI Mer information
Exner, T., Dokler, J., Bachler, D., Farcal, L., Evelo, C. et al. (2018). OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment. Toxicology Letters, vol. 295, ss. S104-S104 DOI Mer information
Georgieva, P., Schaal, W., Spjuth, O. (2018). Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms. Toxicology Letters, vol. 295, ss. S203-S203 DOI Mer information
Herman, S., Emami Khoonsari, P., Tolf, A., Steinmetz, J., Zetterberg, H. et al. (2018). Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.. Theranostics, vol. 8, ss. 4477-4490 DOI Mer information
Kensert, A., Alvarsson, J., Norinder, U., Spjuth, O. (2018). Evaluating parameters for ligand-based modeling with random forest on sparse data sets. Journal of Cheminformatics, . vol. 10 DOI Mer information
Lampa, S., Alvarsson, J., Arvidsson Mc Shane, S., Berg, A., Ahlberg, E. et al. (2018). Predicting off-target binding profiles with confidence using Conformal Prediction. Frontiers in Pharmacology, vol. 9 DOI Mer information
Lampa, S., Dahlö, M., Alvarsson, J., Spjuth, O. (2018). SciPipe - A workflow library for agile development of complex and dynamic bioinformatics pipelines. DOI Mer information
Lapins, M., Arvidsson, S., Lampa, S., Berg, A., Schaal, W. et al. (2018). A confidence predictor for logD using conformal regression and a support-vector machine. Journal of Cheminformatics, vol. 10 DOI Mer information
Oki, N., Exner, T., Kramer, S., Notredame, C., Jennen, D. et al. (2018). OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration, in silico analysis and modelling in risk assessment. Abstract of Papers of the American Chemical Society, vol. 255 Mer information
Spjuth, O. (2018). Novel applications of Machine Learning in cheminformatics. Journal of Cheminformatics, . vol. 10 DOI Mer information
Svensson, F., Aniceto, N., Norinder, U., Cortes-Ciriano, I., Spjuth, O. et al. (2018). Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty. Journal of Chemical Information and Modeling, vol. 58, ss. 1132-1140 DOI Mer information
Andersen, M., Nagaev, I., Meyer, M., Nagaeva, O., Wikberg, J. et al. (2017). Melanocortin 2, 3 and 4 Receptor Gene Expressions are Downregulated in CD8(+) T Cytotoxic Lymphocytes and CD19(+) B Lymphocytes in Rheumatoid Arthritis Responding to TNF-alfa Inhibition. Scandinavian Journal of Immunology, . vol. 86, ss. 31-39 DOI Mer information
Capuccini, M., Ahmed, L., Schaal, W., Laure, E., Spjuth, O. (2017). Large-scale virtual screening on public cloud resources with Apache Spark. Journal of Cheminformatics, vol. 9 DOI Mer information
Herman, S., Emami Khoonsari, P., Aftab, O., Krishnan, S., Strömbom, E. et al. (2017). Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.. Metabolomics, vol. 13 DOI Mer information
Lampa, S., Willighagen, E., Kohonen, P., King, A., Vrandečić, D. et al. (2017). RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. Journal of Biomedical Semantics, vol. 8 DOI Mer information
Pratiwi, R., Malik, A., Schaduangrat, N., Prachayasittikul, V., Wikberg, J. et al. (2017). CryoProtect: A Web Server for Classifying Antifreeze Proteins from Nonantifreeze Proteins. Journal of Chemistry . DOI Mer information
Shoombuatong, W., Prathipati, P., Prachayasittikul, V., Schaduangrat, N., Malik, A. et al. (2017). Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.. Current drug metabolism, vol. 18, ss. 540-555 DOI Mer information
Simeon, S., Li, H., Win, T., Malik, A., Kandhro, A. et al. (2017). PepBio: predicting the bioactivity of host defense peptides. RSC Advances, vol. 7, ss. 35119-35134 DOI Mer information
Spjuth, O., Karlsson, A., Clements, M., Humphreys, K., Ivansson, E. et al. (2017). E-Science technologies in a workflow for personalized medicine using cancer screening as a case study. JAMIA Journal of the American Medical Informatics Association, . vol. 24, ss. 950-957 DOI Mer information
van Rijswijk, M., Beirnaert, C., Caron, C., Cascante, M., Dominguez, V. et al. (2017). The future of metabolomics in ELIXIR.. F1000 Research, vol. 6 DOI Mer information
Willighagen, E., Mayfield, J., Alvarsson, J., Berg, A., Carlsson, L. et al. (2017). The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics, vol. 9 DOI Mer information
Win, T., Malik, A., Prachayasittikul, V., Wikberg, J., Nantasenamat, C. et al. (2017). HemoPred: a web server for predicting the hemolytic activity of peptides. Future Medicinal Chemistry, . vol. 9, ss. 275-291 DOI Mer information
Alvarsson, J., Lampa, S., Schaal, W., Andersson, C., Wikberg, J. et al. (2016). Large-scale ligand-based predictive modelling using support vector machines. Journal of Cheminformatics, vol. 8 DOI Mer information
Andersen, M., Meyer, M., Nagaev, I., Nagaeva, O., Wikberg, J. et al. (2016). Resistin Gene Transcription Is Regulated in Adaptive and Innate Immunity in Rheumatoid Arthritis. Annals of the Rheumatic Diseases, . vol. 75, ss. 904-904 DOI Mer information
Andersen, M., Meyer, M., Nagaev, I., Nagaeva, O., Wikberg, J. et al. (2016). The Melanocortin System Is Responsive in Disease Driving Immune Cells in Rheumatoid Arthritis and May Offer A Pathway To Curative Treatment. Annals of the Rheumatic Diseases, . vol. 75, ss. 903-904 DOI Mer information
Fossen, T., Yahorau, A., Yahorava, S., Raharinjato, F., Razafimahefa, S. et al. (2016). New Polyfunctional Phragmalin Limonoids from Neobeguea mahafalensis. Planta Medica, vol. 82, ss. 1087-1095 DOI Mer information
Lampa, S., Alvarsson, J., Spjuth, O. (2016). Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. Journal of Cheminformatics, vol. 8 DOI Mer information
Nagaev, I., Andersen, M., Olesen, M., Nagaeva, O., Wikberg, J. et al. (2016). Resistin Gene Expression is Downregulated in CD4(+) T Helper Lymphocytes and CD14(+) Monocytes in Rheumatoid Arthritis Responding to TNF-alpha Inhibition. Scandinavian Journal of Immunology, vol. 84, ss. 229-236 DOI Mer information
Shoombuatong, W., Nabu, S., Simeon, S., Prachayasittikul, V., Lapins, M. et al. (2016). Extending proteochemometric modeling for unraveling the sorption behavior of compound-soil interaction. Chemometrics and Intelligent Laboratory Systems, vol. 151, ss. 219-227 DOI Mer information
Simeon, S., Anuwongcharoen, N., Shoombuatong, W., Malik, A., Prachayasittikul, V. et al. (2016). Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking. PeerJ, vol. 4 DOI Mer information
Simeon, S., Shoombuatong, W., Anuwongcharoen, N., Preeyanon, L., Prachayasittikul, V. et al. (2016). osFP: a web server for predicting the oligomeric states of fluorescent proteins. Journal of Cheminformatics, vol. 8 DOI Mer information
Simeon, S., Spjuth, O., Lapins, M., Nabu, S., Anuwongcharoen, N. et al. (2016). Origin of aromatase inhibitory activity via proteochemometric modeling. PeerJ, vol. 4 DOI Mer information
Spjuth, O., Bongcam-Rudloff, E., Dahlberg, J., Dahlö, M., Kallio, A. et al. (2016). Recommendations on e-infrastructures for next-generation sequencing. GigaScience, vol. 5 DOI Mer information
Spjuth, O., Krestyaninova, M., Hastings, J., Shen, H., Heikkinen, J. et al. (2016). Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. European Journal of Human Genetics, vol. 24, ss. 521-528 DOI Mer information
Spjuth, O., Rydberg, P., Willighagen, E., Evelo, C., Jeliazkova, N. (2016). XMetDB: an open access database for xenobiotic metabolism. Journal of Cheminformatics, vol. 8 DOI Mer information
Dahlö, M., Haziza, F., Kallio, A., Korpelainen, E., Bongcam-Rudloff, E. et al. (2015). BioImg.org: A catalog of virtual machine images for the life sciences. Bioinformatics and Biology Insights, vol. 9, ss. 125-128 DOI Mer information
Eklund, M., Norinder, U., Boyer, S., Carlsson, L. (2015). The application of conformal prediction to the drug discovery process. Annals of Mathematics and Artificial Intelligence, vol. 74, ss. 117-132 DOI Mer information
Gholami, A., Laure, E., Somogyi, P., Spjuth, O., Niazi, S. et al. (2015). Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers. Journal of medical and bioengineering, vol. 4, ss. 117-125 DOI Mer information
Grafström, R., Nymark, P., Hongisto, V., Spjuth, O., Ceder, R. et al. (2015). Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures. ATLA (Alternatives to Laboratory Animals), vol. 43, ss. 325-332 Mer information
Nabu, S., Nantasenamat, C., Owasirikul, W., Lawung, R., Isarankura-Na-Ayudhya, C. et al. (2015). Proteochemometric model for predicting the inhibition of penicillin-binding proteins. Journal of Computer-Aided Molecular Design, vol. 29, ss. 127-141 DOI Mer information
Siretskiy, A., Sundqvist, T., Voznesenskiy, M., Spjuth, O. (2015). A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data. GigaScience, vol. 4 DOI Mer information
Torabi Moghadam, B., Alvarsson, J., Holm, M., Eklund, M., Carlsson, L. et al. (2015). Scaling predictive modeling in drug development with cloud computing. Journal of Chemical Information and Modeling, vol. 55, ss. 19-25 DOI Mer information
Alvarsson, J., Eklund, M., Andersson, C., Carlsson, L., Spjuth, O. et al. (2014). Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines. Journal of Chemical Information and Modeling, vol. 54, ss. 3211-3217 DOI Mer information
Alvarsson, J., Eklund, M., Engkvist, O., Spjuth, O., Carlsson, L. et al. (2014). Ligand-Based Target Prediction with Signature Fingerprints. Journal of Chemical Information and Modeling, vol. 54, ss. 2647-2653 DOI Mer information
Andersen, M., Olesen, M., Nagaev, I., Nagaeva, O., Wikberg, J. et al. (2014). Adalimumab (Humira (R)) normalizes melanocortin receptor subtype 2, 3, and 4 expression in CD8+, CD14+, and CD19+leucocyte subsets in rheumatoid arthritis. Scandinavian Journal of Rheumatology, vol. 43, ss. 25-26 Mer information
Eklund, M., Norinder, U., Boyer, S., Carlsson, L. (2014). Choosing Feature Selection and Learning Algorithms in QSAR. J CHEM INF MODEL, vol. 54, ss. 837-843 DOI Mer information
Grigorjeva, L., Liepinsh, E., Razafimahefa, S., Yahorau, A., Yahorava, S. et al. (2014). Semisynthesis of Libiguin A and Its Analogues by Trans-Lactonization of Phragmalin. Journal of Organic Chemistry, vol. 79, ss. 4148-4153 DOI Mer information
Nantasenamat, C., Simeon, S., Owasirikul, W., Songtawee, N., Lapins, M. et al. (2014). Illuminating the Origins of Spectral Properties of Green Fluorescent Proteins via Proteochemometric and Molecular Modeling. Journal of Computational Chemistry, vol. 35, ss. 1951-1966 DOI Mer information
Razafimahefa, S., Mutulis, F., Mutule, I., Liepinsh, E., Dambrova, M. et al. (2014). Libiguins A and B: Novel Phragmalin Limonoids Isolated from Neobeguea mahafalensis Causing Profound Enhancement of Sexual Activity. Planta Medica, vol. 80, ss. 306-314 DOI Mer information
Claesson, A., Spjuth, O. (2013). On Mechanisms of Reactive Metabolite Formation from Drugs. Mini-Reviews in medical chemistry, vol. 13, ss. 720-729 DOI Mer information
Junaid, M., Angsuthanasombat, C., Wikberg, J., Ali, N., Katzenmeier, G. (2013). A straightforward experimental approach to expression, purification, refolding, and enzymatic analysis of recombinant dengue virus NS2B(H)-NS3pro protease. Biochemistry (Moscow), vol. 78, ss. 920-924 DOI Mer information
Junaid, M., Angsuthanasombat, C., Wikberg, J., Ali, N., Katzenmeier, G. (2013). Modulation of enzymatic activity of dengue virus nonstructural protein NS3 nucleoside triphosphatase/helicase by poly(U). Biochemistry (Moscow), vol. 78, ss. 925-932 DOI Mer information
Lampa, S., Dahlö, M., Olason, P., Hagberg, J., Spjuth, O. (2013). Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. GigaScience, vol. 2, ss. 1-10 DOI Mer information