Ola Spjuth

Designing microplate layouts using artificial intelligence

Francisco Rodríguez, María Andreína; Carreras-Puigvert, Jordi; Spjuth, Ola

Ingår i Artificial Intelligence in the Life Sciences, 2023

• DOI för Designing microplate layouts using artificial intelligence
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Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects

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

Ingår i Science of the Total Environment, 2022

• DOI för Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
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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.

Ingår i Communications Biology, 2022

• DOI för Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
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Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

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

Ingår i Nature Communications, 2022

• DOI för Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
• Ladda ner fulltext (pdf) av Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

A phenomics approach for antiviral drug discovery

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

Ingår i BMC Biology, 2021

• DOI för A phenomics approach for antiviral drug discovery
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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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Machine Learning Strategies When Transitioning between Biological Assays

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

Ingår i Journal of Chemical Information and Modeling, s. 3722-3733, 2021

• DOI för Machine Learning Strategies When Transitioning between Biological Assays
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Deep-learning models for lipid nanoparticle-based drug delivery

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

Ingår i Nanomedicine, s. 1097-1110, 2021

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

Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis

Vaivade, Aina; Parakkal Sreenivasan, Akshai; Erngren, Ida; Freyhult, Eva et al.

Ingår i Environment International, 2026

• DOI för Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis
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The time dimension matters: Improving mode of action classification with live-cell imaging

Forsgren, Edvin; Rietdijk, Jonne; Holmberg, David; Juneblad, Julia et al.

Ingår i ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES, 2026

• DOI för The time dimension matters: Improving mode of action classification with live-cell imaging
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Extensive analysis of pollutant interactions: Identification of deleterious synergistic effects at environmentally relevant dose levels using Drosophila and mammalian cells

Lagunas-Rangel, Francisco Alejandro; Åberg, Martin; Liao, Sifang; Espinelli-Amorim, Felippe et al.

Ingår i Science of the Total Environment, 2025

• DOI för Extensive analysis of pollutant interactions: Identification of deleterious synergistic effects at environmentally relevant dose levels using Drosophila and mammalian cells
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Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis

Sreenivasan, Akshai Parakkal; Vaivade, Aina; Noui, Yassine; Emami Khoonsari, Payam et al.

Ingår i npj Digital Medicine, 2025

• DOI för Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
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Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening

Vaivade, Aina; Erngren, Ida; Carlsson, Henrik; Freyhult, Eva et al.

Ingår i Nature Communications, 2025

• DOI för Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
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Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis

Vaivade, Aina; Parakkal Sreenivasan, Akshai; Erngren, Ida; Freyhult, Eva et al.

Ingår i Environment International, 2026

• DOI för Co-exposure to PFAS and hydroxylated PCBs is associated with increased odds of multiple sclerosis
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The time dimension matters: Improving mode of action classification with live-cell imaging

Forsgren, Edvin; Rietdijk, Jonne; Holmberg, David; Juneblad, Julia et al.

Ingår i ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES, 2026

• DOI för The time dimension matters: Improving mode of action classification with live-cell imaging
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Extensive analysis of pollutant interactions: Identification of deleterious synergistic effects at environmentally relevant dose levels using Drosophila and mammalian cells

Lagunas-Rangel, Francisco Alejandro; Åberg, Martin; Liao, Sifang; Espinelli-Amorim, Felippe et al.

Ingår i Science of the Total Environment, 2025

• DOI för Extensive analysis of pollutant interactions: Identification of deleterious synergistic effects at environmentally relevant dose levels using Drosophila and mammalian cells
• Ladda ner fulltext (pdf) av Extensive analysis of pollutant interactions: Identification of deleterious synergistic effects at environmentally relevant dose levels using Drosophila and mammalian cells

Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis

Sreenivasan, Akshai Parakkal; Vaivade, Aina; Noui, Yassine; Emami Khoonsari, Payam et al.

Ingår i npj Digital Medicine, 2025

• DOI för Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
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Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening

Vaivade, Aina; Erngren, Ida; Carlsson, Henrik; Freyhult, Eva et al.

Ingår i Nature Communications, 2025

• DOI för Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
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Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling

Wenson, Leonie; Heldin, Johan; Martin, Marcel; Erbilgin, Yuecel et al.

Ingår i Nature Communications, 2025

• DOI för Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling
• Ladda ner fulltext (pdf) av Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling

PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules

Seal, Srijit; Trapotsi, Maria-Anna; Mahale, Manas; Subramanian, Vigneshwari et al.

Ingår i Journal of Cheminformatics, 2025

• DOI för PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules
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The intracellular free concentration of endocrine disrupting chemicals enables translation between cell-free and cell-based estrogenic activity assays

Munic Kos, Vesna; Arvidsson McShane, Staffan; Islam, Barira; Nikiforova, Violetta et al.

Ingår i Environmental Toxicology and Pharmacology, 2025

• DOI för The intracellular free concentration of endocrine disrupting chemicals enables translation between cell-free and cell-based estrogenic activity assays
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Federated learning for predicting compound mechanism of action based on image-data from cell painting

Ju, Li; Hellander, Andreas; Spjuth, Ola

Ingår i Artificial Intelligence in the Life Sciences, 2024

• DOI för Federated learning for predicting compound mechanism of action based on image-data from cell painting
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Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data

Seal, Srijit; Williams, Dominic; Hosseini-Gerami, Layla; Mahale, Manas et al.

Ingår i Chemical Research in Toxicology, s. 1290-1305, 2024

• DOI för Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data
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Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

Seal, Srijit; Spjuth, Ola; Hosseini-Gerami, Layla; Garcia-Ortegon, Miguel et al.

Ingår i Journal of Chemical Information and Modeling, s. 1172-1186, 2024

• DOI för Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
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Data management of scientific applications in a reinforcement learning-based hierarchical storage system

Zhang, Tianru; Gupta, Ankit; Francisco Rodríguez, María Andreína; Spjuth, Ola et al.

Ingår i Expert systems with applications, 2024

• DOI för Data management of scientific applications in a reinforcement learning-based hierarchical storage system
• Ladda ner fulltext (pdf) av Data management of scientific applications in a reinforcement learning-based hierarchical storage system

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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Artificial intelligence for high content imaging in drug discovery

Carreras-Puigvert, Jordi; Spjuth, Ola

Ingår i Current opinion in structural biology, 2024

• DOI för Artificial intelligence for high content imaging in drug discovery
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New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project

Tal, Tamara; Myhre, Oddvar; Fritsche, Ellen; Rüegg, Joëlle et al.

Ingår i Frontiers in Toxicology, 2024

• DOI för New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project
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From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability

Seal, Srijit; Carreras-Puigvert, Jordi; Singh, Shantanu; Carpenter, Anne E. et al.

Ingår i Molecular Biology of the Cell, 2024

• DOI för From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
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Designing microplate layouts using artificial intelligence

Francisco Rodríguez, María Andreína; Carreras-Puigvert, Jordi; Spjuth, Ola

Ingår i Artificial Intelligence in the Life Sciences, 2023

• DOI för Designing microplate layouts using artificial intelligence
• Ladda ner fulltext (pdf) av Designing microplate layouts using artificial intelligence

Combining molecular and cell painting image data for mechanism of action prediction

Tian, Guangyan; Harrison, Philip J.; Sreenivasan, Akshai P.; Carreras-Puigvert, Jordi et al.

Ingår i Artificial intelligence in the life sciences, 2023

• DOI för Combining molecular and cell painting image data for mechanism of action prediction
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Combining molecular and cell painting image data for mechanism of action prediction

Tian, Guangyan; Harrison, Philip J.; Sreenivasan, Akshai P.; Carreras-Puigvert, Jordi et al.

Ingår i Artificial Intelligence in the Life Sciences, 2023

• DOI för Combining molecular and cell painting image data for mechanism of action prediction
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Designing microplate layouts using artificial intelligence

Francisco Rodríguez, María Andreína; Carreras-Puigvert, Jordi; Spjuth, Ola

Ingår i Artificial Intelligence in the Life Sciences, s. 100073-100073, 2023

• DOI för Designing microplate layouts using artificial intelligence

Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data

Seal, Srijit; Yang, Hongbin; Trapotsi, Maria-Anna; Singh, Satvik et al.

Ingår i Journal of Cheminformatics, 2023

• DOI för Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
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Evaluating the utility of brightfield image data for mechanism of action prediction

Harrison, Philip John; Gupta, Ankit; Rietdijk, Jonne; Wieslander, Håkan et al.

Ingår i PloS Computational Biology, 2023

• DOI för Evaluating the utility of brightfield image data for mechanism of action prediction
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Development of new approach methods for the identification and characterization of endocrine metabolic disruptors: a PARC project

Braeuning, Albert; Balaguer, Patrick; Bourguet, William; Carreras-Puigvert, Jordi et al.

Ingår i Frontiers in Toxicology, 2023

• DOI för Development of new approach methods for the identification and characterization of endocrine metabolic disruptors: a PARC project
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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

Disease phenotype prediction in multiple sclerosis

Herman, Stephanie; Arvidsson McShane, Staffan; Zhukovsky, Christina; Emami, Payam et al.

Ingår i iScience, 2023

• DOI för Disease phenotype prediction in multiple sclerosis
• Ladda ner fulltext (pdf) av Disease phenotype prediction in multiple sclerosis

Predicting protein network topology clusters from chemical structure using deep learning

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

Ingår i Journal of Cheminformatics, 2022

• DOI för Predicting protein network topology clusters from chemical structure using deep learning
• Ladda ner fulltext (pdf) av Predicting protein network topology clusters from chemical structure using deep learning

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

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

Ingår i Science of the Total Environment, 2022

• DOI för Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
• Ladda ner fulltext (pdf) av Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects

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

Fagerholm, Urban; Spjuth, Ola; Hellberg, Sven

Ingår i Journal of Pharmaceutical Sciences, s. 2645-2649, 2022

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

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

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

Ingår i Nature Communications, 2022

• DOI för A method for Boolean analysis of protein interactions at a molecular level
• Ladda ner fulltext (pdf) av A method for Boolean analysis of protein interactions at a molecular level

SimVec: predicting polypharmacy side effects for new drugs

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

Ingår i Journal of Cheminformatics, 2022

• DOI för SimVec: predicting polypharmacy side effects for new drugs
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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

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

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

Ingår i Advanced biology, 2022

• DOI för An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
• Ladda ner fulltext (pdf) av An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

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.

Ingår i Communications Biology, 2022

• DOI för Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
• Ladda ner fulltext (pdf) av Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection

Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

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

Ingår i Nature Communications, 2022

• DOI för Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
• Ladda ner fulltext (pdf) av Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

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.

Ingår i Cancer Informatics, s. 1-8, 2022

• DOI för Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening
• Ladda ner fulltext (pdf) av Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening

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.

Ingår i Scientific Data, 2022

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

A phenomics approach for antiviral drug discovery

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

Ingår i BMC Biology, 2021

• DOI för A phenomics approach for antiviral drug discovery
• Ladda ner fulltext (pdf) av A phenomics approach for antiviral drug discovery

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.

Ingår i IEEE journal of biomedical and health informatics, s. 371-380, 2021

• DOI för Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images
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Approaches for containerized scientific workflows in cloud environments with applications in life science

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

Ingår i F1000 Research, s. 513-513, 2021

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

Metabolomics: The Stethoscope for the Twenty-First Century

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

Ingår i Medical principles and practice, s. 301-310, 2021

• DOI för Metabolomics: The Stethoscope for the Twenty-First Century
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Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology

Fagerholm, Urban; Hellberg, Sven; Spjuth, Ola

Ingår i Molecules, 2021

• DOI för Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology
• Ladda ner fulltext (pdf) av Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology

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.

Ingår i International Journal of Molecular Sciences, 2021

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

Fagerholm, Urban; Spjuth, Ola; Hellberg, Sven

Ingår i Xenobiotica, s. 1095-1100, 2021

• DOI för Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma
• Ladda ner fulltext (pdf) av 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.

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

Machine Learning Strategies When Transitioning between Biological Assays

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

Ingår i Journal of Chemical Information and Modeling, s. 3722-3733, 2021

• DOI för Machine Learning Strategies When Transitioning between Biological Assays
• Ladda ner fulltext (pdf) av Machine Learning Strategies When Transitioning between Biological Assays

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.

Ingår i GigaScience, s. 1-14, 2021

• DOI för Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
• Ladda ner fulltext (pdf) av Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit

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.

Ingår i Bioinformatics, s. 3501-3508, 2021

• DOI för scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data
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The machine learning life cycle and the cloud: implications for drug discovery.

Spjuth, Ola; Frid, Jens; Hellander, Andreas

Ingår i Expert Opinion on Drug Discovery, s. 1071-1079, 2021

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

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

Norinder, Ulf; Spjuth, Ola; Svensson, Fredrik

Ingår i Journal of Cheminformatics, 2021

• DOI för Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
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Assessing the calibration in toxicological in vitro models with conformal prediction

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

Ingår i Journal of Cheminformatics, 2021

• DOI för Assessing the calibration in toxicological in vitro models with conformal prediction
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Deep-learning models for lipid nanoparticle-based drug delivery

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

Ingår i Nanomedicine, s. 1097-1110, 2021

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

ELIXIR and Toxicology: a community in development

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

Ingår i F1000 Research, s. 1129-1129, 2021

• DOI för ELIXIR and Toxicology: a community in development
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Synergy Conformal Prediction

Gauraha, Niharika; Spjuth, Ola

Ingår i Proceedings of Machine Learning Research, s. 91-119, 2021

Using Predicted Bioactivity Profiles to Improve Predictive Modeling

Norinder, Ulf; Spjuth, Ola; Svensson, Fredrik

Ingår i Journal of Chemical Information and Modeling, s. 2830-2837, 2020

• DOI för 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

Ingår i GigaScience, 2020

• DOI för MaRe: Processing Big Data with application containers on Apache Spark
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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
• Ladda ner fulltext (pdf) av Predicting target profiles with confidence as a service using docking scores

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

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

Ingår i SLAS Discovery, s. 466-475, 2019

• DOI för Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes
• Ladda ner fulltext (pdf) av 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.

Ingår i Bioinformatics, s. 839-846, 2019

• DOI för Container-based bioinformatics with Pachyderm

PhenoMeNal: Processing and analysis of metabolomics data in the cloud

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

Ingår i GigaScience, 2019

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

On-demand virtual research environments using microservices

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

Ingår i PeerJ Computer Science, 2019

• DOI för On-demand virtual research environments using microservices

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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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.

Ingår i Scientific Reports, 2019

• DOI för Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects
• Ladda ner fulltext (pdf) av Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects

Interoperable and scalable data analysis with microservices: Applications in metabolomics

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

Ingår i Bioinformatics, s. 3752-3760, 2019

• DOI för Interoperable and scalable data analysis with microservices: Applications in metabolomics
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Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis

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

Ingår i Cells, 2019

• DOI för Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis
• Ladda ner fulltext (pdf) av Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis

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
• Ladda ner fulltext (pdf) av SciPipe - Turning Scientific Workflows into Computer Programs

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

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

Ingår i Journal of Chemical Information and Modeling, s. 1132-1140, 2018

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

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.

Ingår i Theranostics, s. 4477-4490, 2018

• DOI för Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.
• Ladda ner fulltext (pdf) av 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.

Ingår i Frontiers in Pharmacology, 2018

• DOI för Predicting off-target binding profiles with confidence using Conformal Prediction
• Ladda ner fulltext (pdf) av Predicting off-target binding profiles with confidence using Conformal Prediction

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

Dahlö, Martin; Scofield, Douglas; Schaal, Wesley; Spjuth, Ola

Ingår i GigaScience, 2018

• DOI för Tracking the NGS revolution: managing life science research on shared high-performance computing clusters
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Novel applications of Machine Learning in cheminformatics

Spjuth, Ola

Ingår i Journal of Cheminformatics, 2018

• DOI för Novel applications of Machine Learning in cheminformatics
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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
• Ladda ner fulltext (pdf) av A confidence predictor for logD using conformal regression and a support-vector machine

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
• Ladda ner fulltext (pdf) av Evaluating parameters for ligand-based modeling with random forest on sparse data sets

Efficient iterative virtual screening with Apache Spark and conformal prediction

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

Ingår i Journal of Cheminformatics, 2018

• DOI för Efficient iterative virtual screening with Apache Spark and conformal prediction

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.

Ingår i Abstracts of Papers of the American Chemical Society, 2018

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.

Ingår i Toxicology Letters, 2018

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

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

Georgieva, Polina; Schaal, Wesley; Spjuth, Ola

Ingår i Toxicology Letters, 2018

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

Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.

Shoombuatong, Watshara; Prathipati, Philip; Prachayasittikul, Veda; Schaduangrat, Nalini et al.

Ingår i Current drug metabolism, s. 540-555, 2017

• DOI för Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.

The future of metabolomics in ELIXIR.

van Rijswijk, Merlijn; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta et al.

Ingår i F1000 Research, 2017

• DOI för The future of metabolomics in ELIXIR.

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

Lampa, Samuel; Willighagen, Egon; Kohonen, Pekka; King, Ali et al.

Ingår i Journal of Biomedical Semantics, 2017

• DOI för RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
• Ladda ner fulltext (pdf) av RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

Large-scale virtual screening on public cloud resources with Apache Spark

Capuccini, Marco; Ahmed, Laeeq; Schaal, Wesley; Laure, Erwin et al.

Ingår i Journal of Cheminformatics, 2017

• DOI för Large-scale virtual screening on public cloud resources with Apache Spark

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
• Ladda ner fulltext (pdf) av The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.

Herman, Stephanie; Emami Khoonsari, Payam; Aftab, Obaid; Krishnan, Shibu et al.

Ingår i Metabolomics, 2017

• DOI för Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.
• Ladda ner fulltext (pdf) av Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.

E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

Spjuth, Ola; Karlsson, Andreas; Clements, Mark; Humphreys, Keith et al.

Ingår i JAMIA Journal of the American Medical Informatics Association, s. 950-957, 2017

• DOI för E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
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Origin of aromatase inhibitory activity via proteochemometric modeling

Simeon, Saw; Spjuth, Ola; Lapins, Maris; Nabu, Sunanta et al.

Ingår i PeerJ, 2016

• DOI för Origin of aromatase inhibitory activity via proteochemometric modeling
• Ladda ner fulltext (pdf) av Origin of aromatase inhibitory activity via proteochemometric modeling

Recommendations on e-infrastructures for next-generation sequencing

Spjuth, Ola; Bongcam-Rudloff, Erik; Dahlberg, Johan; Dahlö, Martin et al.

Ingår i GigaScience, 2016

• DOI för Recommendations on e-infrastructures for next-generation sequencing

XMetDB: an open access database for xenobiotic metabolism

Spjuth, Ola; Rydberg, Patrik; Willighagen, Egon L.; Evelo, Chris T. et al.

Ingår i Journal of Cheminformatics, 2016

• DOI för XMetDB: an open access database for xenobiotic metabolism
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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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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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Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

Spjuth, Ola; Krestyaninova, Maria; Hastings, Janna; Shen, Huei-Yi et al.

Ingår i European Journal of Human Genetics, s. 521-528, 2016

• DOI för Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
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BioImg.org: A catalog of virtual machine images for the life sciences

Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi; Korpelainen, Eija et al.

Ingår i Bioinformatics and Biology Insights, s. 125-128, 2015

• DOI för BioImg.org: A catalog of virtual machine images for the life sciences

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data

Siretskiy, Alexey; Sundqvist, Tore; Voznesenskiy, Mikhail; Spjuth, Ola

Ingår i GigaScience, 2015

• DOI för A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
• Ladda ner fulltext (pdf) av A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data

Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers

Gholami, Ali; Laure, Erwin; Somogyi, Peter; Spjuth, Ola et al.

Ingår i Journal of medical and bioengineering, s. 117-125, 2015

• DOI för Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers

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

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures

Grafström, Roland C; Nymark, Penny; Hongisto, Vesa; Spjuth, Ola et al.

Ingår i ATLA (Alternatives to Laboratory Animals), s. 325-332, 2015

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

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data

Lampa, Samuel; Dahlö, Martin; Olason, Pall I; Hagberg, Jonas et al.

Ingår i GigaScience, s. 1-10, 2013

• DOI för Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
• Ladda ner fulltext (pdf) av Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data

Applications of the InChI in cheminformatics with the CDK and Bioclipse

Spjuth, Ola; Berg, Arvid; Adams, Samuel; Willighagen, Egon

Ingår i Journal of Cheminformatics, 2013

• DOI för Applications of the InChI in cheminformatics with the CDK and Bioclipse
• Ladda ner fulltext (pdf) av Applications of the InChI in cheminformatics with the CDK and Bioclipse

Automated QuantMap for rapid quantitative molecular network topology analysis

Schaal, Wesley; Hammerling, Ulf; Gustafsson, Mats G; Spjuth, Ola

Ingår i Bioinformatics, s. 2369-2370, 2013

• DOI för Automated QuantMap for rapid quantitative molecular network topology analysis
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On Mechanisms of Reactive Metabolite Formation from Drugs

Claesson, Alf; Spjuth, Ola

Ingår i Mini-Reviews in medical chemistry, s. 720-729, 2013

• DOI för On Mechanisms of Reactive Metabolite Formation from Drugs

A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms

Lapins, Maris; Worachartcheewan, Apilak; Spjuth, Ola; Georgiev, Valentin et al.

Ingår i PLOS ONE, 2013

• DOI för A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
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WhichCyp: Prediction of Cytochromes P450 Inhibition

Rostkowski, Michal; Spjuth, Ola; Rydberg, Patrik

Ingår i Bioinformatics, s. 2051-2052, 2013

• DOI för WhichCyp: Prediction of Cytochromes P450 Inhibition

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

The ChEMBL database as linked open data

Willighagen, Egon L; Waagmeester, Andra; Spjuth, Ola; Ansell, Peter et al.

Ingår i Journal of Cheminformatics, s. 23, 2013

• DOI för The ChEMBL database as linked open data
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A novel infrastructure for chemical safety predictions with focus on human health

Spjuth, Ola; Willighagen, Egon; Hammerling, Ulf; Dencker, Lennart et al.

Ingår i Toxicology Letters, 2012

• DOI för A novel infrastructure for chemical safety predictions with focus on human health

Model building in Bioclipse Decision Support applied to open datasets

Carlsson, Lars; Spjuth, Ola; Eklund, Martin; Boyer, Scott

Ingår i Toxicology Letters, 2012

• DOI för Model building in Bioclipse Decision Support applied to open datasets

Food for thought...: A toxicology ontology roadmap

Harry, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic et al.

Ingår i ALTEX. Alternatives zu Tierexperimenten, s. 129-137, 2012

Accessing, using, and creating chemical property databases for computational toxicology modeling

Williams, Antony J; Ekins, Sean; Spjuth, Ola; Willighagen, Egon L

Ingår i Methods in molecular biology (Clifton, N.J.), s. 221-241, 2012

• DOI för Accessing, using, and creating chemical property databases for computational toxicology modeling

Toxicology Ontology Perspectives

Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic et al.

Ingår i ALTEX. Alternatives zu Tierexperimenten, s. 139-156, 2012

UPPNEX: A solution for next generation sequencing data management and analysis

Lampa, Samuel; Hagberg, Jonas; Spjuth, Ola

Ingår i EMBnet.journal, s. 44-44, 2012

• DOI för UPPNEX: A solution for next generation sequencing data management and analysis

Computational toxicology using OpenTox & Bioclipse

Willighagen, Egon; Spjuth, Ola; Grafström, Roland

Ingår i Toxicology Letters, 2012

• DOI för Computational toxicology using OpenTox & Bioclipse

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

Computational toxicology using the OpenTox application programming interface and Bioclipse

Willighagen, Egon; Jeliazkova, Nina; Hardy, Barry; Grafström, Roland et al.

Ingår i BMC Research Notes, s. 487, 2011

• DOI för Computational toxicology using the OpenTox application programming interface and Bioclipse

Integrated Decision Support for Assessing Chemical Liabilities

Spjuth, Ola; Eklund, Martin; Helgee, Ernst Ahlberg; Boyer, Scott et al.

Ingår i Journal of chemical information and modeling, s. 1840-1847, 2011

• DOI för Integrated Decision Support for Assessing Chemical Liabilities

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
• Ladda ner fulltext (pdf) av Brunn: an open source laboratory information system for microplates with a graphical plate layout design process

Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV Drug Research Centre

Spjuth, Ola; Eklund, Martin; Lapins, Maris; Junaid, Muhammad et al.

Ingår i Bioinformatics, s. 1719-1720, 2011

• DOI för Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV Drug Research Centre

Proteochemometric Modeling of the Susceptibility of Mutated Variants of the HIV-1 Virus to Reverse Transcriptase Inhibitors

Junaid, Muhammad; Lapins, Maris; Eklund, Martin; Spjuth, Ola et al.

Ingår i PLoS ONE, 2010

• DOI för Proteochemometric Modeling of the Susceptibility of Mutated Variants of the HIV-1 Virus to Reverse Transcriptase Inhibitors

Towards interoperable and reproducible QSAR analyses: Exchange of data sets

Spjuth, Ola; Willighagen, Egon; Guha, Rajarshi; Eklund, Martin et al.

Ingår i Journal of Cheminformatics, 2010

• DOI för Towards interoperable and reproducible QSAR analyses: Exchange of data sets
• Ladda ner fulltext (pdf) av Towards interoperable and reproducible QSAR analyses: Exchange of data sets

Use of Historic Metabolic Biotransformation Data as a Means of Anticipating Metabolic Sites Using MetaPrint2D and Bioclipse

Carlsson, Lars; Spjuth, Ola; Adams, Samuel; Glen, Robert et al.

Ingår i BMC Bioinformatics, s. 362, 2010

• DOI för Use of Historic Metabolic Biotransformation Data as a Means of Anticipating Metabolic Sites Using MetaPrint2D and Bioclipse

An eScience-Bayes strategy for analyzing omics data

Eklund, Martin; Spjuth, Ola; Wikberg, Jarl

Ingår i BMC Bioinformatics, s. 282, 2010

• DOI för An eScience-Bayes strategy for analyzing omics data

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Wagener, Johannes; Spjuth, Ola; Willighagen, Egon L; Wikberg, Jarl E. S.

Ingår i BMC Bioinformatics, s. 279, 2009

• DOI för XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
• Ladda ner fulltext (pdf) av XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Bioclipse 2.0: Life Science setzt auf die Staerken von Eclipse.

Spjuth, Ola; Alvarsson, Johan; Krachtus, Dieter

Ingår i Eclipse Magazine, 2009

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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Proteochemometric modeling of HIV protease susceptibility

Lapins, Maris; Eklund, Martin; Spjuth, Ola; Prusis, Peteris et al.

Ingår i BMC Bioinformatics, s. 181, 2008

• DOI för Proteochemometric modeling of HIV protease susceptibility

The C¹C²: a framework for simultaneous model selection and assessment

Eklund, Martin; Spjuth, Ola; Wikberg, Jarl E S

Ingår i BMC Bioinformatics, s. 360, 2008

• DOI för The C¹C²: a framework for simultaneous model selection and assessment

Bioclipse: an open source workbench for chemo- and bioinformatics

Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan et al.

Ingår i BMC Bioinformatics, s. 59, 2007

• DOI för Bioclipse: an open source workbench for chemo- and bioinformatics
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Eine visuelle Open-Source-Platform für Chemo- und Bioinformatik

Spjuth, Ola

Ingår i JAVAmagazin, 2006

The LCB Data Warehouse

Ameur, Adam; Yankovski, Vladimir; Enroth, Stefan; Spjuth, Ola et al.

Ingår i Bioinformatics, s. 1024-1026, 2006

• DOI för The LCB Data Warehouse

Using Bioclipse to integrate bioinformatics functionality

Spjuth, Ola

Ingår i EMBnet.news, s. 5-11, 2005

An Information System for Proteochemometrics

Spjuth, Ola; Eklund, Martin; Wikberg, Jarl

Ingår i CDK News, s. 54-56, 2005

• Ladda ner fulltext (pdf) av An Information System for Proteochemometrics

Computational drug repurposing: approaches, evaluation of in silico resources and case studies

Tanoli, Ziaurrehman; Fernández-Torras, Adrià; Özcan, Umut Onur; Kushnir, Aleksandr et al.

Ingår i Nature reviews. Drug discovery, s. 521-542, 2025

• DOI för Computational drug repurposing: approaches, evaluation of in silico resources and case studies

Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

Seal, Srijit; Mahale, Manas; García-Ortegón, Miguel; Joshi, Chaitanya K. et al.

Ingår i Chemical Research in Toxicology, s. 759-807, 2025

• DOI för Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World
• Ladda ner fulltext (pdf) av Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World

Cell Painting: a decade of discovery and innovation in cellular imaging

Seal, Srijit; Trapotsi, Maria-Anna; Spjuth, Ola; Singh, Shantanu et al.

Ingår i Nature Methods, s. 254-268, 2025

• DOI för Cell Painting: a decade of discovery and innovation in cellular imaging

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
• Ladda ner fulltext (pdf) av Predicting With Confidence: Using Conformal Prediction in Drug Discovery

Towards reproducible computational drug discovery

Schaduangrat, Nalini; Lampa, Samuel; Simeon, Saw; Gleeson, Matthew Paul et al.

Ingår i Journal of Cheminformatics, 2020

• DOI för Towards reproducible computational drug discovery
• Ladda ner fulltext (pdf) av Towards reproducible computational drug discovery

Deep Learning in Image Cytometry: A Review

Gupta, Anindya; Harrison, Philip J.; Wieslander, Håkan; Pielawski, Nicolas et al.

Ingår i Cytometry Part A, s. 366-380, 2019

• DOI för Deep Learning in Image Cytometry: A Review
• Ladda ner fulltext (pdf) av Deep Learning in Image Cytometry: A Review

Experiences with workflows for automating data-intensive bioinformatics

Spjuth, Ola; Bongcam-Rudloff, Erik; Carrasco Hernández, Guillermo; Forer, Lukas et al.

Ingår i Biology Direct, 2015

• DOI för Experiences with workflows for automating data-intensive bioinformatics

Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand

Kohonen, Pekka; Ceder, Rebecca; Smit, Ines; Vesa, Hongisto et al.

Ingår i Basic & Clinical Pharmacology & Toxicology, s. 50-58, 2014

• DOI för Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand

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
• Ladda ner fulltext (pdf) av Open source drug discovery with Bioclipse

Introduction to Pharmaceutical Bioinformatics

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

Oakleaf Academic, 2010

Bioclipse: Integration of Data and Software in the Life Sciences

Spjuth, Ola

2009

• Ladda ner fulltext (pdf) av Bioclipse: Integration of Data and Software in the Life Sciences

Data Integration between Swedish National Clinical Health Registries and Biobanks Using an Availability System

Spjuth, Ola; Heikkinen, Jani; Litton, Jan-Eric; Palmgren, Juni et al.

Ingår i Data Integration in the Life Sciences, s. 32-40, Springer International Publishing, 2014

• DOI för Data Integration between Swedish National Clinical Health Registries and Biobanks Using an Availability System

Chemoinformatics taking Biology into Account: Proteochemometrics

Wikberg, Jarl; Spjuth, Ola; Eklund, Martin; Lapins, Maris

Ingår i Computational Approaches in Cheminformatics and Bioinformatics, John Wiley & Sons, 2012

• DOI för Chemoinformatics taking Biology into Account: Proteochemometrics

Collaborative Cheminformatics Applications

Guha, Rajarshi; Spjuth, Ola; Willighagen, Egon

Ingår i Collaborative Computational Technologies for Biomedical Research, John Wiley & Sons, 2011

• DOI för Collaborative Cheminformatics Applications

Minimising Source-Plate Swaps for Robotised Compound Dispensing in Microplates

Gindullin, Ramiz; Francisco Rodríguez, María Andreína; Seashore-Ludlow, Brinton; Spjuth, Ola

Ingår i Integration of Constraint Programming, Artificial Intelligence, and Operations Research, s. 256-273, 2025

• DOI för Minimising Source-Plate Swaps for Robotised Compound Dispensing in Microplates

Is brightfield all you need for MoA prediction?

Gupta, Ankit; Harrison, Philip J; Wieslander, Håkan; Rietdijk, Jonne et al.

2022

Scalable federated machine learning with FEDn

Ekmefjord, Morgan; Ait-Mlouk, Addi; Alawadi, Sadi; Akesson, Mattias et al.

Ingår i 2022 22nd IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2022), s. 555-564, 2022

• DOI för Scalable federated machine learning with FEDn

Synergy Conformal Prediction

Gauraha, Niharika; Spjuth, Ola

Ingår i Proceedings of the Tenth Symposium on Conformal and Probabilistic Prediction and Applications, s. 91-110, 2021

• Ladda ner fulltext 1 (pdf) av Synergy Conformal Prediction
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Synergy Conformal Prediction for Regression

Gauraha, Niharika; Spjuth, Ola

Ingår i Proceedings of the 10th international conference on pattern recognition applications and methods (icpram), s. 212-221, 2021

• DOI för Synergy Conformal Prediction for Regression

A Constraint Programming Approach to Microplate Layout Design

Francisco Rodríguez, María Andreína; Spjuth, Ola

s. 1-3, 2020

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy

Stein, Oliver; Blamey, Ben; Karlsson, Johan; Sabirsh, Alan et al.

Ingår i 2020 IEEE International Conference on Big Data (Big Data), s. 2207-2216, 2020

• DOI för Smart Resource Management for Data Streaming using an Online Bin-packing Strategy

Split knowledge transfer in learning under privileged information framework

Gauraha, Niharika; Söderdahl, Fabian; Spjuth, Ola

Ingår i Proceedings of the Eighth Symposium on Conformal and Probabilistic Prediction and Applications, s. 43-52, 2019

Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets

Spjuth, Ola; Brännström, Robin Carrión; Carlsson, Lars; Gauraha, Niharika

Ingår i Proceedings of the Eighth Symposium on Conformal and Probabilistic Prediction and Applications, s. 53-65, 2019

Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors

Arvidsson, Staffan; Carlsson, Lars; Paulo, Toccaceli; Spjuth, Ola

Ingår i Conformal and Probabilistic Prediction with Applications (COPA) 2017, s. 118-131, 2017

SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia

Toor, Salman; Lindberg, Mathias; Fällman, Ingemar; Vallin, Andreas et al.

Ingår i Proc. 13th International Conference on e-Science, s. 219-227, 2017

• DOI för SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia

Conformal prediction in Spark: Large-scale machine learning with confidence

Capuccini, Marco; Carlsson, Lars; Norinder, Ulf; Spjuth, Ola

Ingår i Proc. 2nd International Symposium on Big Data Computing, s. 61-67, 2015

• DOI för Conformal prediction in Spark: Large-scale machine learning with confidence

Interpretation of Conformal Prediction Classification Models

Ahlberg, Ernst; Spjuth, Ola; Hasselgren, Catrin; Carlsson, Lars

Ingår i STATISTICAL LEARNING AND DATA SCIENCES, s. 323-334, 2015

• DOI för Interpretation of Conformal Prediction Classification Models

HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis using Hadoop

Siretskiy, Alexey; Spjuth, Ola

Ingår i Proc. 10th International Conference on e-Science, s. 317-323, 2014

• DOI för HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis using Hadoop

Using Iterative MapReduce for Parallel Virtual Screening

Laeeq, Ahmed; Edlund, Åke; Laure, Erwin; Spjuth, Ola

Ingår i 2013 IEEE 5th International Conference on Cloud Computing Technology and Science, s. 27-32, 2013

• DOI för Using Iterative MapReduce for Parallel Virtual Screening

NGS data management and analysis for hundreds of projects: Experiences from Sweden

Spjuth, Ola

Ingår i NGS Data after the Gold Rush, 2013

• DOI för NGS data management and analysis for hundreds of projects: Experiences from Sweden

Synergy Conformal Prediction for Regression

Gauraha, Niharika; Spjuth, Ola

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Robust Knowledge Transfer in Learning Under Privileged Information Framework

Gauraha, Niharika; Söderdahl, Fabian; Spjuth, Ola

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A biochemical signature of progressive multiple sclerosis

Herman, Stephanie; Emami Khoonsari, Payam; Bergman, Joakim; Svenningsson, Anders et al.

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Moreno, Pablo; Pireddu, Luca; Roger, Pierrick; Goonasekera, Nuwan et al.

• DOI för Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Exploring the evolution of cellular morphological changes after drug administration based on brightfield image data

Harrison, Philip J.; Rietdijk, Jonne; Holmberg, David; Carreras-Puigvert, Jordi et al.

AROS: Open Source Lab Automation Enables Fully Automated CellPainting

Dahlö, Martin; Larsson, Anders; Rosén, Dan; Francisco Rodríguez, María Andreína et al.

Pharmaceutical Bioinformatics Primer

Spjuth, Ola

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Assessment of Environmental Chemicals Using Morphological Profiling of Cells

Rietdijk, Jonne; Hernandez Valenzuela, Sofia; Georgieva, Polina; Carreras-Puigvert, Jordi et al.

A Systematic Host-Centric Approach to Identifying Repurposed Drugs for Viral Infections

Asp, Elin; Rietdijk, Jonne; Tampere, Marianna; Axelsson, Hanna et al.

PFAS and OH-PCB Exposure is Associated with an Altered Bile Acid Homeostasis in Multiple Sclerosis

Vaivade, Aina; Erngren, Ida; Freyhult, Eva; Emami Khoonsari, Payam et al.

Identifying transition to secondary progressive multiple sclerosis across international registries using uncertainty-aware machine learning

Parakkal Sreenivasan, Akshai; Noui, Yassine; Erngren, Ida; Spjuth, Ola et al.

Prospective validation of a machine learning model for early identification of secondary progressive multiple sclerosis

Parakkal Sreenivasan, Akshai; Noui, Yassine; Erngren, Ida; Spjuth, Ola et al.