Latest publications

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

Ouyang, Wei; Bowman, Richard W; Wang, Haoran; Bumke, Kaspar E et al.

Part of Advanced biology, 2022.

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Predicting protein network topology clusters from chemical structure using deep learning

Sreenivasan, Akshai P.; Harrison, Philip J; Schaal, Wesley; Matuszewski, Damian J. et al.

Part of Journal of Cheminformatics, 2022.

DOI for Predicting protein network topology clusters from chemical structure using deep learning Download full text (pdf) of Predicting protein network topology clusters from chemical structure using deep learning

SimVec: predicting polypharmacy side effects for new drugs

Lukashina, Nina; Kartysheva, Elena; Spjuth, Ola; Virko, Elizaveta et al.

Part of Journal of Cheminformatics, 2022.

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Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection

Seal, Srijit; Carreras-Puigvert, Jordi; Trapotsi, Maria-Anna; Yang, Hongbin et al.

Part of Communications Biology, 2022.

DOI for Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection Download full text (pdf) of Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection

The Impact of Reference Data Selection for the Prediction Accuracy of Intrinsic Hepatic Metabolic Clearance

Fagerholm, Urban; Spjuth, Ola; Hellberg, Sven

Part of Journal of Pharmaceutical Sciences, p. 2645-2649, 2022.

DOI for The Impact of Reference Data Selection for the Prediction Accuracy of Intrinsic Hepatic Metabolic Clearance

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

Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects

Rietdijk, Jonne; Aggarwal, Tanya; Georgiev, Polina; Lapins, Maris et al.

Part of Science of the Total Environment, 2022.

DOI for Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects Download full text (pdf) of Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects

From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

Sheffield, Nathan C.; Bonazzi, Vivien R.; Bourne, Philip E.; Burdett, Tony et al.

Part of Scientific Data, 2022.

DOI for From biomedical cloud platforms to microservices: next steps in FAIR data and analysis Download full text (pdf) of From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

A method for Boolean analysis of protein interactions at a molecular level

Raykova, Doroteya; Kermpatsou, Despoina; Malmqvist, Tony; Harrison, Philip J et al.

Part of Nature Communications, 2022.

DOI for A method for Boolean analysis of protein interactions at a molecular level Download full text (pdf) of A method for Boolean analysis of protein interactions at a molecular level

Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening

Schaal, Wesley; Ameur, Adam; Olsson-Strömberg, Ulla; Hermansson, Monica et al.

Part of Cancer Informatics, p. 1-8, 2022.

DOI for Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening Download full text (pdf) of Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening

Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

Olsson, Henrik; Kartasalo, Kimmo; Mulliqi, Nita; Capuccini, Marco et al.

Part of Nature Communications, 2022.

DOI for Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction Download full text (pdf) of Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology

Fagerholm, Urban; Hellberg, Sven; Spjuth, Ola

Part of Molecules, 2021.

DOI for Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology Download full text (pdf) of Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology

Machine Learning Strategies When Transitioning between Biological Assays

Arvidsson McShane, Staffan; Ahlberg, Ernst; Noeske, Tobias; Spjuth, Ola

Part of Journal of Chemical Information and Modeling, p. 3722-3733, 2021.

DOI for Machine Learning Strategies When Transitioning between Biological Assays Download full text (pdf) of Machine Learning Strategies When Transitioning between Biological Assays

Deep-learning models for lipid nanoparticle-based drug delivery

Harrison, Philip J.; Wieslander, Håkan; Sabirsh, Alan; Karlsson, Johan et al.

Part of Nanomedicine, p. 1097-1110, 2021.

DOI for Deep-learning models for lipid nanoparticle-based drug delivery

scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data

Jakobsson, Jon E. T.; Spjuth, Ola; Lagerström, Malin C.

Part of Bioinformatics, p. 3501-3508, 2021.

DOI for scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data Download full text (pdf) of scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data

Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma

Fagerholm, Urban; Spjuth, Ola; Hellberg, Sven

Part of Xenobiotica, p. 1095-1100, 2021.

DOI for Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma Download full text (pdf) of Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma

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

A phenomics approach for antiviral drug discovery

Rietdijk, Jonne; Tampere, Marianna; Pettke, Aleksandra; Georgiev, Polina et al.

Part of BMC Biology, 2021.

DOI for A phenomics approach for antiviral drug discovery Download full text (pdf) of A phenomics approach for antiviral drug discovery

The machine learning life cycle and the cloud: implications for drug discovery.

Spjuth, Ola; Frid, Jens; Hellander, Andreas

Part of Expert Opinion on Drug Discovery, p. 1071-1079, 2021.

DOI for The machine learning life cycle and the cloud: implications for drug discovery.

Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival

Lukashina, Nina; Williams, Michael J.; Kartysheva, Elena; Virko, Elizaveta et al.

Part of International Journal of Molecular Sciences, 2021.

DOI for Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival Download full text (pdf) of Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival

Assessing the calibration in toxicological in vitro models with conformal prediction

Morger, Andrea; Svensson, Fredrik; Arvidsson McShane, Staffan; Gauraha, Niharika et al.

Part of Journal of Cheminformatics, 2021.

DOI for Assessing the calibration in toxicological in vitro models with conformal prediction Download full text (pdf) of Assessing the calibration in toxicological in vitro models with conformal prediction

Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning

Norinder, Ulf; Spjuth, Ola; Svensson, Fredrik

Part of Journal of Cheminformatics, 2021.

DOI for Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning Download full text (pdf) of Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning

Metabolomics: The Stethoscope for the Twenty-First Century

Ashrafian, Hutan; Sounderajah, Viknesh; Glen, Robert; Ebbels, Timothy et al.

Part of Medical principles and practice, p. 301-310, 2021.

DOI for Metabolomics: The Stethoscope for the Twenty-First Century Download full text (pdf) of Metabolomics: The Stethoscope for the Twenty-First Century

Synergy Conformal Prediction

Gauraha, Niharika; Spjuth, Ola

Part of Proceedings of Machine Learning Research, p. 91-119, 2021.

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

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

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

DOI for Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images Download full text (pdf) of Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images

Approaches for containerized scientific workflows in cloud environments with applications in life science

Spjuth, Ola; Capuccini, Marco; Carone, Matteo; Larsson, Anders et al.

Part of F1000 Research, p. 513-513, 2021.

DOI for Approaches for containerized scientific workflows in cloud environments with applications in life science

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

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

Part of GigaScience, p. 1-14, 2021.

DOI for Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit Download full text (pdf) of Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit

ELIXIR and Toxicology: a community in development

Martens, Marvin; Stierum, Rob; Schymanski, Emma L.; Evelo, Chris T. et al.

Part of F1000 Research, p. 1129-1129, 2021.

DOI for ELIXIR and Toxicology: a community in development Download full text (pdf) of ELIXIR and Toxicology: a community in development

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.

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

Using Predicted Bioactivity Profiles to Improve Predictive Modeling

Norinder, Ulf; Spjuth, Ola; Svensson, Fredrik

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

DOI for Using Predicted Bioactivity Profiles to Improve Predictive Modeling

MaRe: Processing Big Data with application containers on Apache Spark

Capuccini, Marco; Dahlö, Martin; Toor, Salman; Spjuth, Ola

Part of GigaScience, 2020.

DOI for MaRe: Processing Big Data with application containers on Apache Spark Download full text (pdf) of MaRe: Processing Big Data with application containers on Apache Spark

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

Kensert, Alexander; Harrison, Philip J; Spjuth, Ola

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

DOI for Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes Download full text (pdf) of Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes

Container-based bioinformatics with Pachyderm

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

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

DOI for Container-based bioinformatics with Pachyderm

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.

DOI for SciPipe - Turning Scientific Workflows into Computer Programs Download full text (pdf) of SciPipe - Turning Scientific Workflows into Computer Programs

On-demand virtual research environments using microservices

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

Part of PeerJ Computer Science, 2019.

DOI for On-demand virtual research environments using microservices

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

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

Part of Cells, 2019.

DOI for Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis Download full text (pdf) of Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis

Interoperable and scalable data analysis with microservices: Applications in metabolomics

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

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

DOI for Interoperable and scalable data analysis with microservices: Applications in metabolomics Download full text (pdf) of Interoperable and scalable data analysis with microservices: Applications in metabolomics

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

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

Part of Scientific Reports, 2019.

DOI for Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects Download full text (pdf) of Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects

PhenoMeNal: Processing and analysis of metabolomics data in the cloud

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

Part of GigaScience, 2019.

DOI for PhenoMeNal: Processing and analysis of metabolomics data in the cloud

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.

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

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

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

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

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

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

Georgieva, Polina; Schaal, Wesley; Spjuth, Ola

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

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

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

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

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

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

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

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

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

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

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

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

DOI for Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis. Download full text (pdf) of Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.

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.

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

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

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

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

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

Efficient iterative virtual screening with Apache Spark and conformal prediction

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

Part of Journal of Cheminformatics, 2018.

DOI for Efficient iterative virtual screening with Apache Spark and conformal prediction