Ola Spjuth
Professor vid Institutionen för farmaceutisk biovetenskap; Forskning; Farmaceutisk bioinformatik
- Telefon:
- 018-471 46 81
- Mobiltelefon:
- 070-425 06 28
- E-post:
- ola.spjuth@uu.se
- Besöksadress:
- Biomedicinskt centrum BMC, Husargatan 3
- Postadress:
- Box 591
751 24 UPPSALA
- ORCID:
- 0000-0002-8083-2864
Kort presentation
Main research interests are in data-intensive bioinformatics and how automated high-throughput and high-content molecular and cell profiling technologies coupled with AI and predictive modeling on modern e-infrastructures can enable us to study complex phenomena in pharmacology, toxicology and metabolism.
Nyckelord
- bioinformatics
- artificial intelligence
- machine learning
- pharmaceutical bioinformatics
- predictive modeling
- predictive toxicology
- predictive metabolism
- high-content imaging
- cell profiling
- cheminformatics
Biografi
PhD in Bioinformatics from Uppsala University, 2009. Postdoctoral fellowships at Karolinska Institutet, Stockholm and Finnish Institute of Molecular Medicine (FIMM), Helsinki. Was co-director at the UPPMAX high performance computing center at Uppsala University (2010-2017), and headed the Bioinformatics Compute and Storage facility at Science for Life Laboratory in Sweden (2010-2017). Currently employed as Senior Lecturer at Department of Pharmaceutical Biosciences leading the research group in pharmaceutical bioinformatics. Main research interests are in data-intensive bioinformatics and how automated high-throughput and high-content molecular and cell profiling technologies coupled with AI and predictive modeling on modern e-infrastructures can enable us to study complex phenomena in pharmacology, toxicology and metabolism.
Forskning
High-throughput technologies have transformed biomedicine into a data-intensive discipline. This has shifted the focus from traditional data generation and hypothesis testing to more data-driven research, and bioinformatics data analysis has become the bottleneck in many projects. However, the field is characterized by growing data sets and poorly scalable software, threatening to severely constrain many biomedical projects. Our group aims at developing new methods and applications to meet the demands of high-throughput biology and drug discovery, using high-throughput and cloud-based e-infrastructures and Big Data analytics.

Publikationer
Urval av publikationer
Designing microplate layouts using artificial intelligence
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
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
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
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
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
Ingår i Nanomedicine, s. 1097-1110, 2021
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
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
Machine Learning Strategies When Transitioning between Biological Assays
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
Senaste publikationer
Cell Painting: a decade of discovery and innovation in cellular imaging.
Ingår i Nature Methods, s. 254-268, 2025
Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
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
Ingår i Expert systems with applications, s. 121443-121443, 2024
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
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
Alla publikationer
Artiklar i tidskrift
Cell Painting: a decade of discovery and innovation in cellular imaging.
Ingår i Nature Methods, s. 254-268, 2025
Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
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
Ingår i Expert systems with applications, s. 121443-121443, 2024
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
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
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
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
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
Ingår i Current opinion in structural biology, 2024
- DOI för Artificial intelligence for high content imaging in drug discovery
- Ladda ner fulltext (pdf) av Artificial intelligence for high content imaging in drug discovery
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
- Ladda ner fulltext (pdf) av New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project
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
- Ladda ner fulltext (pdf) av From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
Combining molecular and cell painting image data for mechanism of action prediction
Ingår i Artificial Intelligence in the Life Sciences, s. 100060-100060, 2023
Designing microplate layouts using artificial intelligence
Ingår i Artificial Intelligence in the Life Sciences, s. 100073-100073, 2023
Ingår i Journal of Cheminformatics, 2023
- DOI för Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
- Ladda ner fulltext (pdf) av Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
Evaluating the utility of brightfield image data for mechanism of action prediction
Ingår i PloS Computational Biology, 2023
- DOI för Evaluating the utility of brightfield image data for mechanism of action prediction
- Ladda ner fulltext (pdf) av Evaluating the utility of brightfield image data for mechanism of action prediction
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
- Ladda ner fulltext (pdf) av Development of new approach methods for the identification and characterization of endocrine metabolic disruptors: a PARC project
Ingår i ATLA (Alternatives to Laboratory Animals), s. 39-54, 2023
Designing microplate layouts using artificial intelligence
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
Ingår i ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES, 2023
- DOI för Combining molecular and cell painting image data for mechanism of action prediction
- Ladda ner fulltext (pdf) av Combining molecular and cell painting image data for mechanism of action prediction
Disease phenotype prediction in multiple sclerosis
Ingår i iScience, 2023
- DOI för Disease phenotype prediction in multiple sclerosis
- Ladda ner fulltext (pdf) av Disease phenotype prediction in multiple sclerosis
Ingår i Journal of Pharmaceutical Sciences, s. 2645-2649, 2022
A method for Boolean analysis of protein interactions at a molecular level
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
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
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
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
Ingår i Journal of Cheminformatics, 2022
- DOI för SimVec: predicting polypharmacy side effects for new drugs
- Ladda ner fulltext (pdf) av SimVec: predicting polypharmacy side effects for new drugs
Ingår i Journal of Pharmaceutical Sciences, s. 2614-2619, 2022
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
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
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
Ingår i Xenobiotica, s. 113-118, 2022
Predicting protein network topology clusters from chemical structure using deep learning
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
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
Ingår i F1000 Research, s. 513-513, 2021
A phenomics approach for antiviral drug discovery
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
Ingår i Nanomedicine, s. 1097-1110, 2021
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
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
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
Ingår i Xenobiotica, s. 1366-1371, 2021
Machine Learning Strategies When Transitioning between Biological Assays
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
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
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.
Ingår i Expert Opinion on Drug Discovery, s. 1071-1079, 2021
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
Ingår i Journal of Cheminformatics, 2021
- DOI för Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
- Ladda ner fulltext (pdf) av Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
Assessing the calibration in toxicological in vitro models with conformal prediction
Ingår i Journal of Cheminformatics, 2021
- DOI för Assessing the calibration in toxicological in vitro models with conformal prediction
- Ladda ner fulltext (pdf) av Assessing the calibration in toxicological in vitro models with conformal prediction
Metabolomics: The Stethoscope for the Twenty-First Century
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
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
Ingår i Proceedings of Machine Learning Research, s. 91-119, 2021
Using Predicted Bioactivity Profiles to Improve Predictive Modeling
Ingår i Journal of Chemical Information and Modeling, s. 2830-2837, 2020
MaRe: Processing Big Data with application containers on Apache Spark
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
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
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
Ingår i Bioinformatics, s. 839-846, 2019
PhenoMeNal: Processing and analysis of metabolomics data in the cloud
Ingår i GigaScience, 2019
On-demand virtual research environments using microservices
Ingår i PeerJ Computer Science, 2019
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Ingår i GigaScience, 2019
- DOI för SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
- Ladda ner fulltext (pdf) av SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
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
Ingår i Bioinformatics, s. 3752-3760, 2019
- DOI för Interoperable and scalable data analysis with microservices: Applications in metabolomics
- Ladda ner fulltext (pdf) av Interoperable and scalable data analysis with microservices: Applications in metabolomics
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
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
Ingår i Journal of Chemical Information and Modeling, s. 1132-1140, 2018
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
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
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
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
Ingår i Journal of Cheminformatics, 2018
A confidence predictor for logD using conformal regression and a support-vector machine
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
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
Ingår i Abstracts of Papers of the American Chemical Society, 2018
Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms
Ingår i Toxicology Letters, 2018
Ingår i Toxicology Letters, 2018
Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.
Ingår i Current drug metabolism, s. 540-555, 2017
The future of metabolomics in ELIXIR.
Ingår i F1000 Research, 2017
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
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
Ingår i Journal of Cheminformatics, 2017
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
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.
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
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
Ingår i GigaScience, 2016
Large-scale ligand-based predictive modelling using support vector machines
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
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
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
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
Ingår i Bioinformatics and Biology Insights, s. 125-128, 2015
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
Ingår i Journal of medical and bioengineering, s. 117-125, 2015
Scaling predictive modeling in drug development with cloud computing
Ingår i Journal of Chemical Information and Modeling, s. 19-25, 2015
Ingår i ATLA (Alternatives to Laboratory Animals), s. 325-332, 2015
Ligand-Based Target Prediction with Signature Fingerprints
Ingår i Journal of Chemical Information and Modeling, s. 2647-2653, 2014
Ingår i Journal of Chemical Information and Modeling, s. 3211-3217, 2014
Automated QuantMap for rapid quantitative molecular network topology analysis
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
Ingår i Mini-Reviews in medical chemistry, s. 720-729, 2013
Applications of the InChI in cheminformatics with the CDK and Bioclipse
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
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
Ingår i Bioinformatics, s. 286-289, 2013
A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
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
Ingår i Bioinformatics, s. 2051-2052, 2013
The ChEMBL database as linked open data
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
Ingår i ALTEX. Alternatives zu Tierexperimenten, s. 139-156, 2012
Food for thought...: A toxicology ontology roadmap
Ingår i ALTEX. Alternatives zu Tierexperimenten, s. 129-137, 2012
Accessing, using, and creating chemical property databases for computational toxicology modeling
Ingår i Methods in molecular biology (Clifton, N.J.), s. 221-241, 2012
Model building in Bioclipse Decision Support applied to open datasets
Ingår i Toxicology Letters, 2012
A novel infrastructure for chemical safety predictions with focus on human health
Ingår i Toxicology Letters, 2012
UPPNEX: A solution for next generation sequencing data management and analysis
Ingår i EMBnet.journal, s. 44-44, 2012
Computational toxicology using OpenTox & Bioclipse
Ingår i Toxicology Letters, 2012
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Ingår i Journal of Cheminformatics, s. 37, 2011
Linking the Resource Description Framework to cheminformatics and proteochemometrics
Ingår i Journal of Biomedical Semantics, s. 6, 2011
Integrated Decision Support for Assessing Chemical Liabilities
Ingår i Journal of chemical information and modeling, s. 1840-1847, 2011
Computational toxicology using the OpenTox application programming interface and Bioclipse
Ingår i BMC Research Notes, s. 487, 2011
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
Ingår i Bioinformatics, s. 1719-1720, 2011
Ingår i BMC Bioinformatics, s. 362, 2010
Towards interoperable and reproducible QSAR analyses: Exchange of data sets
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
Ingår i BMC Bioinformatics, s. 282, 2010
Ingår i PLoS ONE, 2010
Bioclipse 2: Towards integrated biocheminformatics
Ingår i EMBnet.news, s. 25-27, 2009
Bioclipse 2.0: Life Science setzt auf die Staerken von Eclipse.
Ingår i Eclipse Magazine, 2009
Bioclipse 2: A scriptable integration platform for the life sciences
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
Ingår i BMC Bioinformatics, s. 279, 2009
The C1C2: a framework for simultaneous model selection and assessment
Ingår i BMC Bioinformatics, s. 360, 2008
Proteochemometric modeling of HIV protease susceptibility
Ingår i BMC Bioinformatics, s. 181, 2008
Bioclipse: an open source workbench for chemo- and bioinformatics
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
Ingår i JAVAmagazin, 2006
Ingår i Bioinformatics, s. 1024-1026, 2006
Using Bioclipse to integrate bioinformatics functionality
Ingår i EMBnet.news, s. 5-11, 2005
An Information System for Proteochemometrics
Ingår i CDK News, s. 54-56, 2005
Using Iterative MapReduce for Parallel Virtual Screening
Ingår i Journal of medical and bioengineering
Artiklar, forskningsöversikt
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
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
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
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
Ingår i Biology Direct, 2015
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand
Ingår i Basic & Clinical Pharmacology & Toxicology, s. 50-58, 2014
Open source drug discovery with Bioclipse
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
Böcker
Introduction to Pharmaceutical Bioinformatics
Oakleaf Academic, 2010
Doktorsavhandlingar, sammanläggning
Kapitel i böcker, delar av antologi
Ingår i Data Integration in the Life Sciences, s. 32-40, Springer International Publishing, 2014
Chemoinformatics taking Biology into Account: Proteochemometrics
Ingår i Computational Approaches in Cheminformatics and Bioinformatics, John Wiley & Sons, 2012
Collaborative Cheminformatics Applications
Ingår i Collaborative Computational Technologies for Biomedical Research, John Wiley & Sons, 2011
Konferensbidrag
Is brightfield all you need for MoA prediction?
2022
Scalable federated machine learning with FEDn
Ingår i 2022 22nd IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2022), s. 555-564, 2022
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
- Ladda ner fulltext 2 (pdf) av Synergy Conformal Prediction
Synergy Conformal Prediction for Regression
Ingår i Proceedings of the 10th international conference on pattern recognition applications and methods (icpram), s. 212-221, 2021
A Constraint Programming Approach to Microplate Layout Design
s. 1-3, 2020
Smart Resource Management for Data Streaming using an Online Bin-packing Strategy
Ingår i 2020 IEEE International Conference on Big Data (Big Data), s. 2207-2216, 2020
Split knowledge transfer in learning under privileged information framework
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
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
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
Ingår i Proc. 13th International Conference on e-Science, s. 219-227, 2017
Conformal prediction in Spark: Large-scale machine learning with confidence
Ingår i Proc. 2nd International Symposium on Big Data Computing, s. 61-67, 2015
Interpretation of Conformal Prediction Classification Models
Ingår i STATISTICAL LEARNING AND DATA SCIENCES, s. 323-334, 2015
HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis using Hadoop
Ingår i Proc. 10th International Conference on e-Science, s. 317-323, 2014
NGS data management and analysis for hundreds of projects: Experiences from Sweden
Ingår i NGS Data after the Gold Rush, 2013
Manuskript (preprint)
Synergy Conformal Prediction for Regression
Robust Knowledge Transfer in Learning Under Privileged Information Framework
Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
AROS: Open Source Lab Automation Enables Fully Automated CellPainting
Pharmaceutical Bioinformatics Primer