Bioclipse 2: A scriptable integration platform for the life sciences. - Ola Spjuth; Jonathan Alvarsson; Arvid Berg; Martin Eklund; Stefan Kuhn 001; Carl Mäsak; Gilleain M. Torrance; Johannes Wagener; Egon L. Willighagen; Christoph Steinbeck; Jarl E. S. Wikberg (BMC Bioinform., 2009)

Linking the Resource Description Framework to cheminformatics and proteochemometrics. - Egon L. Willighagen; Jonathan Alvarsson; Annsofie Andersson; Martin Eklund; Samuel Lampa; Maris Lapins; Ola Spjuth; Jarl E. S. Wikberg (J. Biomed. Semant., 2011)

Brunn: An open source laboratory information system for microplates with a graphical plate layout design process. - Jonathan Alvarsson; Claes R. Andersson; Ola Spjuth; Rolf Larsson; Jarl E. S. Wikberg (BMC Bioinform., 2011)

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. - Noel M. O'Boyle; Rajarshi Guha; Egon L. Willighagen; Sam E. Adams; Jonathan Alvarsson; Jean-Claude Bradley; Igor V. Filippov; Robert M. Hanson; Marcus D. Hanwell; Geoffrey R. Hutchison; Craig A. James; Nina Jeliazkova; et al. (J. Cheminformatics, 2011)

Bioclipse-R: integrating management and visualization of life science data with statistical analysis. - Ola Spjuth; Valentin Georgiev; Lars Carlsson; Jonathan Alvarsson; Arvid Berg; Egon L. Willighagen; Jarl E. S. Wikberg; Martin Eklund (Bioinform., 2013)

Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines. - Jonathan Alvarsson; Martin Eklund; Claes R. Andersson; Lars Carlsson; Ola Spjuth; Jarl E. S. Wikberg (J. Chem. Inf. Model., 2014)

Ligand-Based Target Prediction with Signature Fingerprints. - Jonathan Alvarsson; Martin Eklund; Ola Engkvist; Ola Spjuth; Lars Carlsson; Jarl E. S. Wikberg; Tobias Noeske (J. Chem. Inf. Model., 2014)

Scaling Predictive Modeling in Drug Development with Cloud Computing. - Behrooz Torabi Moghadam; Jonathan Alvarsson; Marcus Holm; Martin Eklund; Lars Carlsson; Ola Spjuth (J. Chem. Inf. Model., 2015)

Large-scale ligand-based predictive modelling using support vector machines. - Jonathan Alvarsson; Samuel Lampa; Wesley Schaal; Claes R. Andersson; Jarl E. S. Wikberg; Ola Spjuth (J. Cheminformatics, 2016)

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. - Samuel Lampa; Jonathan Alvarsson; Ola Spjuth (J. Cheminformatics, 2016)

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Evaluating parameters for ligand-based modeling with random forest on sparse data sets. - Alexander Kensert; Jonathan Alvarsson; Ulf Norinder; Ola Spjuth (J. Cheminformatics, 2018)

A confidence predictor for logD using conformal regression and a support-vector machine. - Maris Lapins; Staffan Arvidsson; Samuel Lampa; Arvid Berg; Wesley Schaal; Jonathan Alvarsson; Ola Spjuth (J. Cheminformatics, 2018)

SciPipe - Turning Scientific Workflows into Computer Programs. - Samuel Lampa; Martin Dahlö; Jonathan Alvarsson; Ola Spjuth (Comput. Sci. Eng., 2019)

Predicting target profiles with confidence as a service using docking scores. - Laeeq Ahmed; Hiba Alogheli; Staffan Arvidsson McShane; Jonathan Alvarsson; Arvid Berg; Anders Larsson; Wesley Schaal; Erwin Laure; Ola Spjuth (J. Cheminformatics, 2020)

CPSign: conformal prediction for cheminformatics modeling. - Staffan Arvidsson McShane; Ulf Norinder; Jonathan Alvarsson; Ernst Ahlberg; Lars Carlsson; Ola Spjuth (J. Cheminformatics, 2024)