Jonathan Alvarsson
Lecturer at Department of Pharmaceutical Biosciences; Research; Pharmaceutical Bioinformatics
- Telephone:
- +46 18 471 42 81
- Mobile phone:
- +46 70 167 95 56
- E-mail:
- jonathan.alvarsson@uu.se
- Visiting address:
- Biomedicinskt centrum BMC, Husargatan 3
- Postal address:
- Box 591
751 24 UPPSALA
Publications
Recent publications
CPSign: Conformal Prediction for Cheminformatics Modeling
Part of Journal of Cheminformatics, 2024
- DOI for CPSign: Conformal Prediction for Cheminformatics Modeling
- Download full text (pdf) of CPSign: Conformal Prediction for Cheminformatics Modeling
Part of ATLA (Alternatives to Laboratory Animals), p. 39-54, 2023
Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022
Part of Xenobiotica, p. 113-118, 2022
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021
- DOI for Predicting With Confidence: Using Conformal Prediction in Drug Discovery
- Download full text (pdf) of Predicting With Confidence: Using Conformal Prediction in Drug Discovery
All publications
Articles in journal
CPSign: Conformal Prediction for Cheminformatics Modeling
Part of Journal of Cheminformatics, 2024
- DOI for CPSign: Conformal Prediction for Cheminformatics Modeling
- Download full text (pdf) of CPSign: Conformal Prediction for Cheminformatics Modeling
Part of ATLA (Alternatives to Laboratory Animals), p. 39-54, 2023
Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022
Part of Xenobiotica, p. 113-118, 2022
Part of Xenobiotica, p. 1366-1371, 2021
Predicting target profiles with confidence as a service using docking scores
Part of Journal of Cheminformatics, 2020
- DOI for Predicting target profiles with confidence as a service using docking scores
- Download full text (pdf) of Predicting target profiles with confidence as a service using docking scores
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Part of GigaScience, 2019
- DOI for SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
- Download full text (pdf) of SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
SciPipe - Turning Scientific Workflows into Computer Programs
Part of Computing in science & engineering (Print), p. 109-113, 2019
- DOI for SciPipe - Turning Scientific Workflows into Computer Programs
- Download full text (pdf) of SciPipe - Turning Scientific Workflows into Computer Programs
Predicting off-target binding profiles with confidence using Conformal Prediction
Part of Frontiers in Pharmacology, 2018
- DOI for Predicting off-target binding profiles with confidence using Conformal Prediction
- Download full text (pdf) of Predicting off-target binding profiles with confidence using Conformal Prediction
Evaluating parameters for ligand-based modeling with random forest on sparse data sets
Part of Journal of Cheminformatics, 2018
- DOI for Evaluating parameters for ligand-based modeling with random forest on sparse data sets
- Download full text (pdf) of Evaluating parameters for ligand-based modeling with random forest on sparse data sets
A confidence predictor for logD using conformal regression and a support-vector machine
Part of Journal of Cheminformatics, 2018
- DOI for A confidence predictor for logD using conformal regression and a support-vector machine
- Download full text (pdf) of A confidence predictor for logD using conformal regression and a support-vector machine
Part of Journal of Cheminformatics, 2017
- DOI for The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
- Download full text (pdf) of The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Part of Journal of Cheminformatics, 2016
- DOI for Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
- Download full text (pdf) of Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
Large-scale ligand-based predictive modelling using support vector machines
Part of Journal of Cheminformatics, 2016
- DOI for Large-scale ligand-based predictive modelling using support vector machines
- Download full text (pdf) of Large-scale ligand-based predictive modelling using support vector machines
Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy
Part of JALA, p. 178-187, 2016
Scaling predictive modeling in drug development with cloud computing
Part of Journal of Chemical Information and Modeling, p. 19-25, 2015
Ligand-Based Target Prediction with Signature Fingerprints
Part of Journal of Chemical Information and Modeling, p. 2647-2653, 2014
Part of Journal of Chemical Information and Modeling, p. 3211-3217, 2014
Bioclipse-R: Integrating management and visualization of life science data with statistical analysis
Part of Bioinformatics, p. 286-289, 2013
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Part of Journal of Cheminformatics, p. 37, 2011
Linking the Resource Description Framework to cheminformatics and proteochemometrics
Part of Journal of Biomedical Semantics, p. 6, 2011
Part of BMC Bioinformatics, 2011
- DOI for Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
- Download full text (pdf) of Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
Bioclipse 2: Towards integrated biocheminformatics
Part of EMBnet.news, p. 25-27, 2009
Bioclipse 2: A scriptable integration platform for the life sciences
Part of BMC Bioinformatics, p. 397, 2009
- DOI for Bioclipse 2: A scriptable integration platform for the life sciences
- Download full text (pdf) of Bioclipse 2: A scriptable integration platform for the life sciences
Articles, review/survey
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021
- DOI for Predicting With Confidence: Using Conformal Prediction in Drug Discovery
- Download full text (pdf) of Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Open source drug discovery with Bioclipse
Part of Current Topics in Medicinal Chemistry, p. 1980-1986, 2012
- DOI for Open source drug discovery with Bioclipse
- Download full text (pdf) of Open source drug discovery with Bioclipse
Books
Introduction to Pharmaceutical Bioinformatics
Oakleaf Academic, 2010