Farmaceutisk bioinformatik

Publikationer

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
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
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.. F1000Research, vol. 6 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
Lapins, M., Worachartcheewan, A., Spjuth, O., Georgiev, V., Prachayasittikul, V. et al. (2013). A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms. PLoS ONE, vol. 8, ss. e66566- DOI Mer information
Prusis, P., Junaid, M., Petrovska, R., Yahorava, S., Yahorau, A. et al. (2013). Design and evaluation of substrate-based octapeptide and non substrate-based tetrapeptide inhibitors of dengue virus NS2B-NS3 proteases. Biochemical and Biophysical Research Communications - BBRC, vol. 434, ss. 767-772 DOI Mer information
Rostkowski, M., Spjuth, O., Rydberg, P. (2013). WhichCyp: Prediction of Cytochromes P450 Inhibition. Bioinformatics, vol. 29, ss. 2051-2052 DOI Mer information
Schaal, W., Hammerling, U., Gustafsson, M., Spjuth, O. (2013). Automated QuantMap for rapid quantitative molecular network topology analysis. Bioinformatics, vol. 29, ss. 2369-2370 DOI Mer information
Shutava, I., Lapinsh, M., Wikberg, J. (2013). Melanocortin 4 receptor in silico mutagenesis and docking studies. European Biophysics Journal, vol. 42, ss. S75-S75 Mer information
Spjuth, O., Berg, A., Adams, S., Willighagen, E. (2013). Applications of the InChI in cheminformatics with the CDK and Bioclipse. Journal of Cheminformatics, vol. 5 DOI Mer information
Spjuth, O., Georgiev, V., Carlsson, L., Alvarsson, J., Berg, A. et al. (2013). Bioclipse-R: Integrating management and visualization of life science data with statistical analysis. Bioinformatics, . vol. 29, ss. 286-289 DOI Mer information
Svennebring, A., Wikberg, J. (2013). Net present value approaches for drug discovery. SpringerPlus, vol. 2 DOI Mer information
Willighagen, E., Waagmeester, A., Spjuth, O., Ansell, P., Williams, A. et al. (2013). The ChEMBL database as linked open data. Journal of Cheminformatics, vol. 5, ss. 23- DOI Mer information
Carlsson, L., Spjuth, O., Eklund, M., Boyer, S. (2012). Model building in Bioclipse Decision Support applied to open datasets. Toxicology Letters, vol. 211, ss. S62- DOI Mer information
Eklund, M., Norinder, U., Boyer, S., Carlsson, L. (2012). Benchmarking Variable Selection in QSAR. Molecular Informatics, vol. 31, ss. 173-179 DOI Mer information
Eklund, M., Zwanzig, S. (2012). SimSel: a new simulation method for variable selection. Journal of Statistical Computation and Simulation, vol. 82, ss. 515-527 DOI Mer information
Fossen, T., Rasoanaivo, P., Manjovelo, C., Raharinjato, F., Yahorava, S. et al. (2012). A new protolimonoid from Capuronianthus mahafalensis. Fitoterapia (Milano), vol. 83, ss. 901-906 DOI Mer information
Hardy, B., Apic, G., Carthew, P., Clark, D., Cook, D. et al. (2012). Toxicology Ontology Perspectives. ALTEX. Alternatives zu Tierexperimenten, vol. 29, ss. 139-156 Mer information
Harry, B., Apic, G., Carthew, P., Clark, D., Cook, D. et al. (2012). Food for thought...: A toxicology ontology roadmap. ALTEX. Alternatives zu Tierexperimenten, vol. 29, ss. 129-137 Mer information
Ignatovica, V., Megnis, K., Lapins, M., Schiöth, H., Klovins, J. (2012). Identification and analysis of functionally important amino acids in human purinergic 12 receptor using a Saccharomyces cerevisiae expression system. The FEBS Journal, vol. 279, ss. 180-191 DOI Mer information