Latest publications

  • Wieslander, Håkan; Harrison, Philip J.; Skogberg, Gabriel; Jackson, Sonya et al.

    Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images

    Part of IEEE journal of biomedical and health informatics, p. 371-380, 2021.

    Open access
  • Blamey, Ben; Toor, Salman; Dahlö, Martin; Wieslander, Håkan et al.

    Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit.

    Part of GigaScience, 2021.

    Open access
  • Norinder, Ulf; Spjuth, Ola; Svensson, Fredrik

    Using Predicted Bioactivity Profiles to Improve Predictive Modeling

    Part of Journal of Chemical Information and Modeling, p. 2830-2837, 2020.

  • Ahmed, Laeeq; Alogheli, Hiba; Arvidsson Mc Shane, Staffan; Alvarsson, Jonathan et al.

    Predicting target profiles with confidence as a service using docking scores

    Part of Journal of Cheminformatics, 2020.

    Open access
  • Capuccini, Marco; Dahlö, Martin; Toor, Salman; Spjuth, Ola

    MaRe: Processing Big Data with application containers on Apache Spark

    Part of GigaScience, 2020.

    Open access
  • Kensert, Alexander; Harrison, Philip J; Spjuth, Ola

    Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes

    Part of SLAS discovery : advancing life sciences R & D, p. 466 466-475 475, 2019.

    Open access
  • Lampa, Samuel; Dahlö, Martin; Alvarsson, Jonathan; Spjuth, Ola

    SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

    Part of GigaScience, 2019.

    Open access
  • Herman, Stephanie; Niemelä, Valter; Emami Khoonsari, Payam; Sundblom, Jimmy et al.

    Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects

    Part of Scientific Reports, 2019.

    Open access
  • Emami Khoonsari, Payam; Moreno, Pablo; Bergmann, Sven; Burman, Joachim et al.

    Interoperable and scalable data analysis with microservices: Applications in metabolomics

    Part of Bioinformatics, p. 3752-3760, 2019.

    Open access
  • Novella, Jon Ander; Emami Khoonsari, Payam; Herman, Stephanie; Whitenack, Daniel et al.

    Container-based bioinformatics with Pachyderm

    Part of Bioinformatics, p. 839-846, 2019.

    Open access
  • Lampa, Samuel; Dahlö, Martin; Alvarsson, Jonathan; Spjuth, Ola

    SciPipe - Turning Scientific Workflows into Computer Programs

    Part of Computing in science & engineering (Print), p. 109-113, 2019.

    Open access
  • Peters, Kristian; Bradbury, James; Bergmann, Sven; Capuccini, Marco et al.

    PhenoMeNal: Processing and analysis of metabolomics data in the cloud

    Part of GigaScience, 2019.

    Open access
  • Capuccini, Marco; Larsson, Anders; Carone, Matteo; Novella, Jon Ander et al.

    On-demand virtual research environments using microservices

    Part of PeerJ Computer Science, 2019.

    Open access
  • Herman, Stephanie; Åkerfeldt, Torbjörn; Spjuth, Ola; Burman, Joachim et al.

    Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis

    Part of Cells, 2019.

    Open access
  • Svensson, Fredrik; Aniceto, Natalia; Norinder, Ulf; Cortes-Ciriano, Isidro et al.

    Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty

    Part of Journal of Chemical Information and Modeling, p. 1132-1140, 2018.

  • Lapins, Maris; Arvidsson, Staffan; Lampa, Samuel; Berg, Arvid et al.

    A confidence predictor for logD using conformal regression and a support-vector machine

    Part of Journal of Cheminformatics, 2018.

    Open access
  • Spjuth, Ola

    Novel applications of Machine Learning in cheminformatics

    Part of Journal of Cheminformatics, 2018.

    Open access
  • Kensert, Alexander; Alvarsson, Jonathan; Norinder, Ulf; Spjuth, Ola

    Evaluating parameters for ligand-based modeling with random forest on sparse data sets

    Part of Journal of Cheminformatics, 2018.

    Open access
  • Georgieva, Polina; Schaal, Wesley; Spjuth, Ola

    Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms

    Part of Toxicology Letters, p. S203-S203, 2018.

  • Exner, T. E.; Dokler, J.; Bachler, D.; Farcal, L. R. et al.

    OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment

    Part of Toxicology Letters, p. S104-S104, 2018.

  • Lampa, Samuel; Alvarsson, Jonathan; Arvidsson Mc Shane, Staffan; Berg, Arvid et al.

    Predicting off-target binding profiles with confidence using Conformal Prediction

    Part of Frontiers in Pharmacology, 2018.

    Open access
  • Ahmed, Laeeq; Georgiev, Valentin; Capuccini, Marco; Toor, Salman et al.

    Efficient iterative virtual screening with Apache Spark and conformal prediction

    Part of Journal of Cheminformatics, 2018.

    Open access
  • Dahlö, Martin; Scofield, Douglas; Schaal, Wesley; Spjuth, Ola

    Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

    Part of GigaScience, 2018.

    Open access
  • Oki, Noffisat; Exner, Thomas; Kramer, Stefan; Notredame, Cedric et al.

    OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration, in silico analysis and modelling in risk assessment

    Part of Abstracts of Papers of the American Chemical Society, 2018.

  • Herman, Stephanie; Emami Khoonsari, Payam; Tolf, Andreas; Steinmetz, Julia et al.

    Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.

    Part of Theranostics, p. 4477-4490, 2018.

    Open access
  • Spjuth, Ola; Karlsson, Andreas; Clements, Mark; Humphreys, Keith et al.

    E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

    Part of JAMIA Journal of the American Medical Informatics Association, p. 950-957, 2017.

    Open access
  • Shoombuatong, Watshara; Prathipati, Philip; Prachayasittikul, Veda; Schaduangrat, Nalini et al.

    Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.

    Part of Current drug metabolism, p. 540-555, 2017.

  • Willighagen, Egon L.; Mayfield, John W.; Alvarsson, Jonathan; Berg, Arvid et al.

    The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

    Part of Journal of Cheminformatics, 2017.

    Open access
  • Lampa, Samuel; Willighagen, Egon; Kohonen, Pekka; King, Ali et al.

    RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

    Part of Journal of Biomedical Semantics, 2017.

    Open access
  • van Rijswijk, Merlijn; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta et al.

    The future of metabolomics in ELIXIR.

    Part of F1000 Research, 2017.

    Open access
  • Herman, Stephanie; Emami Khoonsari, Payam; Aftab, Obaid; Krishnan, Shibu et al.

    Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.

    Part of Metabolomics, 2017.

    Open access
  • Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin et al.

    Large-scale virtual screening on public cloud resources with Apache Spark

    Part of Journal of Cheminformatics, 2017.

    Open access
  • Simeon, Saw; Spjuth, Ola; Lapins, Maris; Nabu, Sunanta et al.

    Origin of aromatase inhibitory activity via proteochemometric modeling

    Part of PeerJ, 2016.

    Open access
  • Spjuth, Ola; Rydberg, Patrik; Willighagen, Egon L.; Evelo, Chris T. et al.

    XMetDB: an open access database for xenobiotic metabolism

    Part of Journal of Cheminformatics, 2016.

    Open access
  • Spjuth, Ola; Bongcam-Rudloff, Erik; Dahlberg, Johan; Dahlö, Martin et al.

    Recommendations on e-infrastructures for next-generation sequencing

    Part of GigaScience, 2016.

    Open access
  • Spjuth, Ola; Krestyaninova, Maria; Hastings, Janna; Shen, Huei-Yi et al.

    Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

    Part of European Journal of Human Genetics, p. 521-528, 2016.

    Open access
  • Alvarsson, Jonathan; Lampa, Samuel; Schaal, Wesley; Andersson, Claes et al.

    Large-scale ligand-based predictive modelling using support vector machines

    Part of Journal of Cheminformatics, 2016.

    Open access
  • Lampa, Samuel; Alvarsson, Jonathan; Spjuth, Ola

    Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

    Part of Journal of Cheminformatics, 2016.

    Open access
  • Grafström, Roland C; Nymark, Penny; Hongisto, Vesa; Spjuth, Ola et al.

    Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures

    Part of ATLA (Alternatives to Laboratory Animals), p. 325-332, 2015.

  • Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija et al.

    BioImg.org: A catalog of virtual machine images for the life sciences

    Part of Bioinformatics and Biology Insights, p. 125-128, 2015.

  • Torabi Moghadam, Behrooz; Alvarsson, Jonathan; Holm, Marcus; Eklund, Martin et al.

    Scaling predictive modeling in drug development with cloud computing

    Part of Journal of Chemical Information and Modeling, p. 19-25, 2015.

  • Siretskiy, Alexey; Sundqvist, Tore; Voznesenskiy, Mikhail; Spjuth, Ola

    A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data

    Part of GigaScience, 2015.

    Open access
  • Gholami, Ali; Laure, Erwin; Somogyi, Peter; Spjuth, Ola et al.

    Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers

    Part of Journal of medical and bioengineering, p. 117-125, 2015.

  • Alvarsson, Jonathan; Eklund, Martin; Andersson, Claes; Carlsson, Lars et al.

    Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines

    Part of Journal of Chemical Information and Modeling, p. 3211-3217, 2014.

  • Alvarsson, Jonathan; Eklund, Martin; Engkvist, Ola; Spjuth, Ola et al.

    Ligand-Based Target Prediction with Signature Fingerprints

    Part of Journal of Chemical Information and Modeling, p. 2647-2653, 2014.

  • Spjuth, Ola; Berg, Arvid; Adams, Samuel; Willighagen, Egon

    Applications of the InChI in cheminformatics with the CDK and Bioclipse

    Part of Journal of Cheminformatics, 2013.

    Open access
  • Claesson, Alf; Spjuth, Ola

    On Mechanisms of Reactive Metabolite Formation from Drugs

    Part of Mini-Reviews in medical chemistry, p. 720-729, 2013.

  • Lapins, Maris; Worachartcheewan, Apilak; Spjuth, Ola; Georgiev, Valentin et al.

    A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms

    Part of PLoS ONE, p. e66566-, 2013.

    Open access
  • Willighagen, Egon L; Waagmeester, Andra; Spjuth, Ola; Ansell, Peter et al.

    The ChEMBL database as linked open data

    Part of Journal of Cheminformatics, p. 23-, 2013.

    Open access
  • Rostkowski, Michal; Spjuth, Ola; Rydberg, Patrik

    WhichCyp: Prediction of Cytochromes P450 Inhibition

    Part of Bioinformatics, p. 2051-2052, 2013.