Jonathan Alvarsson

CPSign: Conformal Prediction for Cheminformatics Modeling

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

Part of Journal of Cheminformatics, 2024

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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

Part of ATLA (Alternatives to Laboratory Animals), p. 39-54, 2023

• DOI for 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

Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022

• DOI for 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

Part of Xenobiotica, p. 113-118, 2022

• DOI for 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

Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021

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CPSign: Conformal Prediction for Cheminformatics Modeling

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

Part of Journal of Cheminformatics, 2024

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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

Part of ATLA (Alternatives to Laboratory Animals), p. 39-54, 2023

• DOI for 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

Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022

• DOI for 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

Part of Xenobiotica, p. 113-118, 2022

• DOI for 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.

Part of Xenobiotica, p. 1366-1371, 2021

• DOI for 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.

Part of Journal of Cheminformatics, 2020

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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

Part of GigaScience, 2019

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SciPipe - Turning Scientific Workflows into Computer Programs

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

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

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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.

Part of Frontiers in Pharmacology, 2018

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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

Part of Journal of Cheminformatics, 2018

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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.

Part of Journal of Cheminformatics, 2018

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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.

Part of Journal of Cheminformatics, 2017

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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

Part of Journal of Cheminformatics, 2016

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

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

Part of Journal of Cheminformatics, 2016

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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.

Part of JALA, p. 178-187, 2016

• DOI for 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.

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

• DOI for 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.

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

• DOI for 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.

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

• DOI for 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.

Part of Bioinformatics, p. 286-289, 2013

• DOI for 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.

Part of Journal of Cheminformatics, p. 37, 2011

• DOI for 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.

Part of Journal of Biomedical Semantics, p. 6, 2011

• DOI for 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.

Part of BMC Bioinformatics, 2011

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Bioclipse 2: Towards integrated biocheminformatics

Spjuth, Ola; Alvarsson, Jonathan

Part of EMBnet.news, p. 25-27, 2009

Bioclipse 2: A scriptable integration platform for the life sciences

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

Part of BMC Bioinformatics, p. 397, 2009

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Predicting With Confidence: Using Conformal Prediction in Drug Discovery

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

Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021

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Open source drug discovery with Bioclipse

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

Part of Current Topics in Medicinal Chemistry, p. 1980-1986, 2012

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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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