Jonathan Alvarsson

CPSign: Conformal Prediction for Cheminformatics Modeling

Arvidsson McShane, Staffan; Norinder, Ulf; Alvarsson, Jonathan; Ahlberg, Ernst et al.

Ingår i Journal of Cheminformatics, 2024

• DOI för CPSign: Conformal Prediction for Cheminformatics Modeling
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In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i ATLA (Alternatives to Laboratory Animals), s. 39-54, 2023

• DOI för In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods

In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Journal of Pharmaceutical Sciences, s. 2614-2619, 2022

• DOI för In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology

In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Xenobiotica, s. 113-118, 2022

• DOI för In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology

Predicting With Confidence: Using Conformal Prediction in Drug Discovery

Alvarsson, Jonathan; Arvidsson McShane, Staffan; Norinder, Ulf; Spjuth, Ola

Ingår i Journal of Pharmaceutical Sciences, s. 42-49, 2021

• DOI för Predicting With Confidence: Using Conformal Prediction in Drug Discovery
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CPSign: Conformal Prediction for Cheminformatics Modeling

Arvidsson McShane, Staffan; Norinder, Ulf; Alvarsson, Jonathan; Ahlberg, Ernst et al.

Ingår i Journal of Cheminformatics, 2024

• DOI för CPSign: Conformal Prediction for Cheminformatics Modeling
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In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i ATLA (Alternatives to Laboratory Animals), s. 39-54, 2023

• DOI för In Silico Prediction of Human Clinical Pharmacokinetics with ANDROMEDA by Prosilico: Predictions for an Established Benchmarking Data Set, a Modern Small Drug Data Set, and a Comparison with Laboratory Methods

In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Journal of Pharmaceutical Sciences, s. 2614-2619, 2022

• DOI för In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology

In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Xenobiotica, s. 113-118, 2022

• DOI för In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology

In silico prediction of volume of distribution of drugs in man using conformal prediction performs on par with animal data-based models

Fagerholm, Urban; Hellberg, Sven; Alvarsson, Jonathan; Arvidsson McShane, Staffan et al.

Ingår i Xenobiotica, s. 1366-1371, 2021

• DOI för In silico prediction of volume of distribution of drugs in man using conformal prediction performs on par with animal data-based models

Predicting target profiles with confidence as a service using docking scores

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

Ingår i Journal of Cheminformatics, 2020

• DOI för Predicting target profiles with confidence as a service using docking scores
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SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Lampa, Samuel; Dahlö, Martin; Alvarsson, Jonathan; Spjuth, Ola

Ingår i GigaScience, 2019

• DOI för SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
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SciPipe - Turning Scientific Workflows into Computer Programs

Lampa, Samuel; Dahlö, Martin; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Computing in science & engineering (Print), s. 109-113, 2019

• DOI för SciPipe - Turning Scientific Workflows into Computer Programs
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Predicting off-target binding profiles with confidence using Conformal Prediction

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

Ingår i Frontiers in Pharmacology, 2018

• DOI för Predicting off-target binding profiles with confidence using Conformal Prediction
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Evaluating parameters for ligand-based modeling with random forest on sparse data sets

Kensert, Alexander; Alvarsson, Jonathan; Norinder, Ulf; Spjuth, Ola

Ingår i Journal of Cheminformatics, 2018

• DOI för Evaluating parameters for ligand-based modeling with random forest on sparse data sets
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A confidence predictor for logD using conformal regression and a support-vector machine

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

Ingår i Journal of Cheminformatics, 2018

• DOI för A confidence predictor for logD using conformal regression and a support-vector machine
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The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

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

Ingår i Journal of Cheminformatics, 2017

• DOI för The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
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Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

Lampa, Samuel; Alvarsson, Jonathan; Spjuth, Ola

Ingår i Journal of Cheminformatics, 2016

• DOI för Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
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Large-scale ligand-based predictive modelling using support vector machines

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

Ingår i Journal of Cheminformatics, 2016

• DOI för Large-scale ligand-based predictive modelling using support vector machines
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Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy

Blom, Kristin; Nygren, Peter; Alvarsson, Jonathan; Larsson, Rolf et al.

Ingår i JALA, s. 178-187, 2016

• DOI för Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy

Scaling predictive modeling in drug development with cloud computing

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

Ingår i Journal of Chemical Information and Modeling, s. 19-25, 2015

• DOI för Scaling predictive modeling in drug development with cloud computing

Ligand-Based Target Prediction with Signature Fingerprints

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

Ingår i Journal of Chemical Information and Modeling, s. 2647-2653, 2014

• DOI för Ligand-Based Target Prediction with Signature Fingerprints

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

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

Ingår i Journal of Chemical Information and Modeling, s. 3211-3217, 2014

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

Bioclipse-R: Integrating management and visualization of life science data with statistical analysis

Spjuth, Ola; Georgiev, Valentin; Carlsson, Lars; Alvarsson, Jonathan et al.

Ingår i Bioinformatics, s. 286-289, 2013

• DOI för Bioclipse-R: Integrating management and visualization of life science data with statistical analysis

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

O'Boyle, Noel; Guha, Rajarshi; Willighagen, Egon; Adams, Samuel et al.

Ingår i Journal of Cheminformatics, s. 37, 2011

• DOI för Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

Linking the Resource Description Framework to cheminformatics and proteochemometrics

Willighagen, Egon; Alvarsson, Jonathan; Andersson, Annsofie; Eklund, Martin et al.

Ingår i Journal of Biomedical Semantics, s. 6, 2011

• DOI för Linking the Resource Description Framework to cheminformatics and proteochemometrics

Brunn: an open source laboratory information system for microplates with a graphical plate layout design process

Alvarsson, Jonathan; Andersson, Claes; Spjuth, Ola; Larsson, Rolf et al.

Ingår i BMC Bioinformatics, 2011

• DOI för Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
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Bioclipse 2: Towards integrated biocheminformatics

Spjuth, Ola; Alvarsson, Jonathan

Ingår i EMBnet.news, s. 25-27, 2009

Bioclipse 2: A scriptable integration platform for the life sciences

Spjuth, Ola; Alvarsson, Jonathan; Berg, Arvid; Eklund, Martin et al.

Ingår i BMC Bioinformatics, s. 397, 2009

• DOI för Bioclipse 2: A scriptable integration platform for the life sciences
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Predicting With Confidence: Using Conformal Prediction in Drug Discovery

Alvarsson, Jonathan; Arvidsson McShane, Staffan; Norinder, Ulf; Spjuth, Ola

Ingår i Journal of Pharmaceutical Sciences, s. 42-49, 2021

• DOI för Predicting With Confidence: Using Conformal Prediction in Drug Discovery
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Open source drug discovery with Bioclipse

Spjuth, Ola; Carlsson, Lars; Alvarsson, Jonathan; Georgiev, Valentin et al.

Ingår i Current Topics in Medicinal Chemistry, s. 1980-1986, 2012

• DOI för Open source drug discovery with Bioclipse
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Introduction to Pharmaceutical Bioinformatics

Wikberg, Jarl; Eklund, Martin; Willighagen, Egon; Spjuth, Ola et al.

Oakleaf Academic, 2010

Ligand-based Methods for Data Management and Modelling

Alvarsson, Jonathan

2015

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