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

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

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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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

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

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.

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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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, s. 121443-121443, 2024

• DOI för Data management of scientific applications in a reinforcement learning-based hierarchical storage system

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
• Ladda ner fulltext (pdf) av Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

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
• Ladda ner fulltext (pdf) av Federated learning for predicting compound mechanism of action based on image-data from cell painting

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.

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
• Ladda ner fulltext (pdf) av Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening

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, s. 121443-121443, 2024

• DOI för Data management of scientific applications in a reinforcement learning-based hierarchical storage system

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
• Ladda ner fulltext (pdf) av Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank

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
• Ladda ner fulltext (pdf) av Federated learning for predicting compound mechanism of action based on image-data from cell painting

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

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
• Ladda ner fulltext (pdf) av Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data

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
• Ladda ner fulltext (pdf) av CPSign: Conformal Prediction for Cheminformatics Modeling

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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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, s. 100060-100060, 2023

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

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

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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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

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

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

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

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

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
• Ladda ner fulltext (pdf) av From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

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

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

Ingår i Xenobiotica, s. 113-118, 2022

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

Predicting 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

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
• Ladda ner fulltext (pdf) av 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.

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

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

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 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

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
• Ladda ner fulltext (pdf) av 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

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
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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
• Ladda ner fulltext (pdf) av scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data

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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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
• Ladda ner fulltext (pdf) av Metabolomics: The Stethoscope for the Twenty-First Century

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
• Ladda ner fulltext (pdf) av ELIXIR and Toxicology: a community in development

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
• Ladda ner fulltext (pdf) av MaRe: Processing Big Data with application containers on Apache Spark

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
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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
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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
• Ladda ner fulltext (pdf) av Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

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

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

Novel applications of Machine Learning in cheminformatics

Spjuth, Ola

Ingår i Journal of Cheminformatics, 2018

• DOI för Novel applications of Machine Learning in cheminformatics
• Ladda ner fulltext (pdf) av Novel applications of Machine Learning in cheminformatics

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

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

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

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
• Ladda ner fulltext (pdf) av E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

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

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
• Ladda ner fulltext (pdf) av Large-scale ligand-based predictive modelling using support vector machines

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
• Ladda ner fulltext (pdf) av XMetDB: an open access database for xenobiotic metabolism

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
• Ladda ner fulltext (pdf) av Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

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
• Ladda ner fulltext (pdf) av Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research

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

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
• Ladda ner fulltext (pdf) av Automated QuantMap for rapid quantitative molecular network topology analysis

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

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

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

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

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
• Ladda ner fulltext (pdf) av A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms

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

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
• Ladda ner fulltext (pdf) av The ChEMBL database as linked open data

Toxicology Ontology Perspectives

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bioclipse 2: Towards integrated biocheminformatics

Spjuth, Ola; Alvarsson, Jonathan

Ingår i EMBnet.news, s. 25-27, 2009

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

Spjuth, Ola; Alvarsson, Johan; Krachtus, Dieter

Ingår i Eclipse Magazine, 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
• Ladda ner fulltext (pdf) av Bioclipse 2: A scriptable integration platform for the life sciences

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

Wagener, Johannes; Spjuth, Ola; Willighagen, Egon; Wikberg, Jarl

Ingår i BMC Bioinformatics, s. 279, 2009

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

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

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

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
• Ladda ner fulltext (pdf) av Bioclipse: an open source workbench for chemo- and bioinformatics

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

Using Iterative MapReduce for Parallel Virtual Screening

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

Ingår i Journal of medical and bioengineering

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

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

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

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

Robust Knowledge Transfer in Learning Under Privileged Information Framework

Gauraha, Niharika; Söderdahl, Fabian; Spjuth, Ola

• Ladda ner fulltext (pdf) av Robust Knowledge Transfer in Learning Under Privileged Information Framework

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

• Ladda ner fulltext (pdf) av Pharmaceutical Bioinformatics Primer