Ola Spjuth
Professor at Department of Pharmaceutical Biosciences; Research; Pharmaceutical Bioinformatics
- Telephone:
- +46 18 471 46 81
- Mobile phone:
- +46 70 425 06 28
- E-mail:
- ola.spjuth@uu.se
- Visiting address:
- Biomedicinskt centrum BMC, Husargatan 3
- Postal address:
- Box 591
751 24 UPPSALA
- ORCID:
- 0000-0002-8083-2864
Short presentation
Research interests includes data-intensive and translational bioinformatics with a particular focus on how modern e-infrastructures enables the studying of complex phenomena, and predictive modeling in pharmacology, toxicology, and metabolism.
Keywords
- bioinformatics
- artificial intelligence
- machine learning
- pharmaceutical bioinformatics
- predictive modeling
- predictive toxicology
- predictive metabolism
- high-content imaging
- cell profiling
- cheminformatics
Biography
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.
Research
The Pharmaceutical Bioinformatics research group focuses on mathematical and statistical modeling, informatics and quantitative analysis of pharmacological systems. We develop methods, algorithms and software to study and model pharmaceutical interactions, and a key focus in the group is how predictive modeling, large-scale calculations and modern e-infrastructure (such as high-performance and cloud computing) can aid the drug discovery process; e.g. when studying drug toxicity, metabolism and resistance. We are involved in several national and international consortia and have a tight connection to the pharmaceutical industry, Uppsala University Hospital, and Science for Life Laboratory. See my research group website for more information ab

Publications
Selection of publications
Designing microplate layouts using artificial intelligence
Part of Artificial Intelligence in the Life Sciences, 2023
- DOI for Designing microplate layouts using artificial intelligence
- Download full text (pdf) of Designing microplate layouts using artificial intelligence
Part of Science of the Total Environment, 2022
- DOI for Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
- Download full text (pdf) of Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
Part of Communications Biology, 2022
- DOI for Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
- Download full text (pdf) of Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
Part of Nature Communications, 2022
- DOI for Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
- Download full text (pdf) of Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
A phenomics approach for antiviral drug discovery
Part of BMC Biology, 2021
- DOI for A phenomics approach for antiviral drug discovery
- Download full text (pdf) of A phenomics approach for antiviral drug discovery
Deep-learning models for lipid nanoparticle-based drug delivery
Part of Nanomedicine, p. 1097-1110, 2021
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021
- DOI for Predicting With Confidence: Using Conformal Prediction in Drug Discovery
- Download full text (pdf) of Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Machine Learning Strategies When Transitioning between Biological Assays
Part of Journal of Chemical Information and Modeling, p. 3722-3733, 2021
- DOI for Machine Learning Strategies When Transitioning between Biological Assays
- Download full text (pdf) of Machine Learning Strategies When Transitioning between Biological Assays
Recent publications
Cell Painting: a decade of discovery and innovation in cellular imaging.
Part of Nature Methods, p. 254-268, 2025
Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
Part of Nature Communications, 2025
- DOI for Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
- Download full text (pdf) of Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
Part of Expert systems with applications, p. 121443-121443, 2024
Part of Journal of Chemical Information and Modeling, p. 1172-1186, 2024
- DOI for Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
- Download full text (pdf) of Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
Part of Artificial Intelligence in the Life Sciences, 2024
- DOI for Federated learning for predicting compound mechanism of action based on image-data from cell painting
- Download full text (pdf) of Federated learning for predicting compound mechanism of action based on image-data from cell painting
All publications
Articles in journal
Cell Painting: a decade of discovery and innovation in cellular imaging.
Part of Nature Methods, p. 254-268, 2025
Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
Part of Nature Communications, 2025
- DOI for Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
- Download full text (pdf) of Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening
Part of Expert systems with applications, p. 121443-121443, 2024
Part of Journal of Chemical Information and Modeling, p. 1172-1186, 2024
- DOI for Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
- Download full text (pdf) of Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
Part of Artificial Intelligence in the Life Sciences, 2024
- DOI for Federated learning for predicting compound mechanism of action based on image-data from cell painting
- Download full text (pdf) of Federated learning for predicting compound mechanism of action based on image-data from cell painting
Part of Expert systems with applications, 2024
- DOI for Data management of scientific applications in a reinforcement learning-based hierarchical storage system
- Download full text (pdf) of 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
Part of Chemical Research in Toxicology, p. 1290-1305, 2024
- DOI for Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data
- Download full text (pdf) of Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data
CPSign: Conformal Prediction for Cheminformatics Modeling
Part of Journal of Cheminformatics, 2024
- DOI for CPSign: Conformal Prediction for Cheminformatics Modeling
- Download full text (pdf) of CPSign: Conformal Prediction for Cheminformatics Modeling
Artificial intelligence for high content imaging in drug discovery
Part of Current opinion in structural biology, 2024
- DOI for Artificial intelligence for high content imaging in drug discovery
- Download full text (pdf) of Artificial intelligence for high content imaging in drug discovery
Part of Frontiers in Toxicology, 2024
- DOI for New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project
- Download full text (pdf) of New approach methods to assess developmental and adult neurotoxicity for regulatory use: a PARC work package 5 project
Part of Molecular Biology of the Cell, 2024
- DOI for From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
- Download full text (pdf) of 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
Part of Artificial Intelligence in the Life Sciences, p. 100060-100060, 2023
Designing microplate layouts using artificial intelligence
Part of Artificial Intelligence in the Life Sciences, p. 100073-100073, 2023
Part of Journal of Cheminformatics, 2023
- DOI for Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
- Download full text (pdf) of 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
Part of PloS Computational Biology, 2023
- DOI for Evaluating the utility of brightfield image data for mechanism of action prediction
- Download full text (pdf) of Evaluating the utility of brightfield image data for mechanism of action prediction
Part of Frontiers in Toxicology, 2023
- DOI for Development of new approach methods for the identification and characterization of endocrine metabolic disruptors: a PARC project
- Download full text (pdf) of Development of new approach methods for the identification and characterization of endocrine metabolic disruptors: a PARC project
Part of ATLA (Alternatives to Laboratory Animals), p. 39-54, 2023
Designing microplate layouts using artificial intelligence
Part of Artificial Intelligence in the Life Sciences, 2023
- DOI for Designing microplate layouts using artificial intelligence
- Download full text (pdf) of Designing microplate layouts using artificial intelligence
Combining molecular and cell painting image data for mechanism of action prediction
Part of ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES, 2023
- DOI for Combining molecular and cell painting image data for mechanism of action prediction
- Download full text (pdf) of Combining molecular and cell painting image data for mechanism of action prediction
Disease phenotype prediction in multiple sclerosis
Part of iScience, 2023
- DOI for Disease phenotype prediction in multiple sclerosis
- Download full text (pdf) of Disease phenotype prediction in multiple sclerosis
Part of Journal of Pharmaceutical Sciences, p. 2645-2649, 2022
A method for Boolean analysis of protein interactions at a molecular level
Part of Nature Communications, 2022
- DOI for A method for Boolean analysis of protein interactions at a molecular level
- Download full text (pdf) of A method for Boolean analysis of protein interactions at a molecular level
Part of Science of the Total Environment, 2022
- DOI for Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
- Download full text (pdf) of Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
Part of Communications Biology, 2022
- DOI for Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
- Download full text (pdf) of Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
Part of Advanced biology, 2022
- DOI for An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
- Download full text (pdf) of An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
SimVec: predicting polypharmacy side effects for new drugs
Part of Journal of Cheminformatics, 2022
- DOI for SimVec: predicting polypharmacy side effects for new drugs
- Download full text (pdf) of SimVec: predicting polypharmacy side effects for new drugs
Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022
Part of Nature Communications, 2022
- DOI for Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
- Download full text (pdf) of Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening
Part of Cancer Informatics, p. 1-8, 2022
- DOI for Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening
- Download full text (pdf) of Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening
From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
Part of Scientific Data, 2022
- DOI for From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
- Download full text (pdf) of From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
Part of Xenobiotica, p. 113-118, 2022
Predicting protein network topology clusters from chemical structure using deep learning
Part of Journal of Cheminformatics, 2022
- DOI for Predicting protein network topology clusters from chemical structure using deep learning
- Download full text (pdf) of Predicting protein network topology clusters from chemical structure using deep learning
Part of IEEE journal of biomedical and health informatics, p. 371-380, 2021
- DOI for Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images
- Download full text (pdf) of Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images
Part of F1000 Research, p. 513-513, 2021
A phenomics approach for antiviral drug discovery
Part of BMC Biology, 2021
- DOI for A phenomics approach for antiviral drug discovery
- Download full text (pdf) of A phenomics approach for antiviral drug discovery
Deep-learning models for lipid nanoparticle-based drug delivery
Part of Nanomedicine, p. 1097-1110, 2021
Part of Molecules, 2021
- DOI for Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology
- Download full text (pdf) of Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology
Part of International Journal of Molecular Sciences, 2021
- DOI for Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
- Download full text (pdf) of Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
Part of Xenobiotica, p. 1095-1100, 2021
- DOI for Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma
- Download full text (pdf) of Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma
Part of Xenobiotica, p. 1366-1371, 2021
Machine Learning Strategies When Transitioning between Biological Assays
Part of Journal of Chemical Information and Modeling, p. 3722-3733, 2021
- DOI for Machine Learning Strategies When Transitioning between Biological Assays
- Download full text (pdf) of Machine Learning Strategies When Transitioning between Biological Assays
Part of GigaScience, p. 1-14, 2021
- DOI for Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
- Download full text (pdf) of Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
Part of Bioinformatics, p. 3501-3508, 2021
- DOI for scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data
- Download full text (pdf) of scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data
The machine learning life cycle and the cloud: implications for drug discovery.
Part of Expert Opinion on Drug Discovery, p. 1071-1079, 2021
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
Part of Journal of Cheminformatics, 2021
- DOI for Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
- Download full text (pdf) of Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning
Assessing the calibration in toxicological in vitro models with conformal prediction
Part of Journal of Cheminformatics, 2021
- DOI for Assessing the calibration in toxicological in vitro models with conformal prediction
- Download full text (pdf) of Assessing the calibration in toxicological in vitro models with conformal prediction
Metabolomics: The Stethoscope for the Twenty-First Century
Part of Medical principles and practice, p. 301-310, 2021
- DOI for Metabolomics: The Stethoscope for the Twenty-First Century
- Download full text (pdf) of Metabolomics: The Stethoscope for the Twenty-First Century
ELIXIR and Toxicology: a community in development
Part of F1000 Research, p. 1129-1129, 2021
- DOI for ELIXIR and Toxicology: a community in development
- Download full text (pdf) of ELIXIR and Toxicology: a community in development
Part of Proceedings of Machine Learning Research, p. 91-119, 2021
Using Predicted Bioactivity Profiles to Improve Predictive Modeling
Part of Journal of Chemical Information and Modeling, p. 2830-2837, 2020
MaRe: Processing Big Data with application containers on Apache Spark
Part of GigaScience, 2020
- DOI for MaRe: Processing Big Data with application containers on Apache Spark
- Download full text (pdf) of MaRe: Processing Big Data with application containers on Apache Spark
Predicting target profiles with confidence as a service using docking scores
Part of Journal of Cheminformatics, 2020
- DOI for Predicting target profiles with confidence as a service using docking scores
- Download full text (pdf) of Predicting target profiles with confidence as a service using docking scores
Part of SLAS Discovery, p. 466-475, 2019
- DOI for Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes
- Download full text (pdf) of Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes
Container-based bioinformatics with Pachyderm
Part of Bioinformatics, p. 839-846, 2019
PhenoMeNal: Processing and analysis of metabolomics data in the cloud
Part of GigaScience, 2019
On-demand virtual research environments using microservices
Part of PeerJ Computer Science, 2019
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Part of GigaScience, 2019
- DOI for SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
- Download full text (pdf) of SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Part of Scientific Reports, 2019
- DOI for Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects
- Download full text (pdf) of Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects
Interoperable and scalable data analysis with microservices: Applications in metabolomics
Part of Bioinformatics, p. 3752-3760, 2019
- DOI for Interoperable and scalable data analysis with microservices: Applications in metabolomics
- Download full text (pdf) of Interoperable and scalable data analysis with microservices: Applications in metabolomics
Part of Cells, 2019
- DOI for Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis
- Download full text (pdf) of Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis
SciPipe - Turning Scientific Workflows into Computer Programs
Part of Computing in science & engineering (Print), p. 109-113, 2019
- DOI for SciPipe - Turning Scientific Workflows into Computer Programs
- Download full text (pdf) of SciPipe - Turning Scientific Workflows into Computer Programs
Part of Journal of Chemical Information and Modeling, p. 1132-1140, 2018
Part of Theranostics, p. 4477-4490, 2018
- DOI for Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.
- Download full text (pdf) of Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.
Predicting off-target binding profiles with confidence using Conformal Prediction
Part of Frontiers in Pharmacology, 2018
- DOI for Predicting off-target binding profiles with confidence using Conformal Prediction
- Download full text (pdf) of Predicting off-target binding profiles with confidence using Conformal Prediction
Part of GigaScience, 2018
- DOI for Tracking the NGS revolution: managing life science research on shared high-performance computing clusters
- Download full text (pdf) of 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
Part of Journal of Cheminformatics, 2018
- DOI for Evaluating parameters for ligand-based modeling with random forest on sparse data sets
- Download full text (pdf) of Evaluating parameters for ligand-based modeling with random forest on sparse data sets
Efficient iterative virtual screening with Apache Spark and conformal prediction
Part of Journal of Cheminformatics, 2018
A confidence predictor for logD using conformal regression and a support-vector machine
Part of Journal of Cheminformatics, 2018
- DOI for A confidence predictor for logD using conformal regression and a support-vector machine
- Download full text (pdf) of A confidence predictor for logD using conformal regression and a support-vector machine
Novel applications of Machine Learning in cheminformatics
Part of Journal of Cheminformatics, 2018
- DOI for Novel applications of Machine Learning in cheminformatics
- Download full text (pdf) of Novel applications of Machine Learning in cheminformatics
Part of Abstracts of Papers of the American Chemical Society, 2018
Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms
Part of Toxicology Letters, 2018
Part of Toxicology Letters, 2018
Towards Predicting the Cytochrome P450 Modulation: From QSAR to proteochemometric modeling.
Part of Current drug metabolism, p. 540-555, 2017
The future of metabolomics in ELIXIR.
Part of F1000 Research, 2017
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Part of Journal of Biomedical Semantics, 2017
- DOI for RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
- Download full text (pdf) of RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Large-scale virtual screening on public cloud resources with Apache Spark
Part of Journal of Cheminformatics, 2017
Part of Journal of Cheminformatics, 2017
- DOI for The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
- Download full text (pdf) of The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Part of Metabolomics, 2017
- DOI for Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.
- Download full text (pdf) of Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions.
Part of JAMIA Journal of the American Medical Informatics Association, p. 950-957, 2017
- DOI for E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
- Download full text (pdf) of E-Science technologies in a workflow for personalized medicine using cancer screening as a case study
Origin of aromatase inhibitory activity via proteochemometric modeling
Part of PeerJ, 2016
- DOI for Origin of aromatase inhibitory activity via proteochemometric modeling
- Download full text (pdf) of Origin of aromatase inhibitory activity via proteochemometric modeling
Recommendations on e-infrastructures for next-generation sequencing
Part of GigaScience, 2016
Large-scale ligand-based predictive modelling using support vector machines
Part of Journal of Cheminformatics, 2016
- DOI for Large-scale ligand-based predictive modelling using support vector machines
- Download full text (pdf) of Large-scale ligand-based predictive modelling using support vector machines
XMetDB: an open access database for xenobiotic metabolism
Part of Journal of Cheminformatics, 2016
- DOI for XMetDB: an open access database for xenobiotic metabolism
- Download full text (pdf) of XMetDB: an open access database for xenobiotic metabolism
Part of Journal of Cheminformatics, 2016
- DOI for Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
- Download full text (pdf) of Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles
Part of European Journal of Human Genetics, p. 521-528, 2016
- DOI for Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
- Download full text (pdf) of 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
Part of Bioinformatics and Biology Insights, p. 125-128, 2015
Part of GigaScience, 2015
- DOI for A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
- Download full text (pdf) of A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
Privacy-Preservation for Publishing Sample Availability Data with Personal Identifiers
Part of Journal of medical and bioengineering, p. 117-125, 2015
Scaling predictive modeling in drug development with cloud computing
Part of Journal of Chemical Information and Modeling, p. 19-25, 2015
Part of ATLA (Alternatives to Laboratory Animals), p. 325-332, 2015
Ligand-Based Target Prediction with Signature Fingerprints
Part of Journal of Chemical Information and Modeling, p. 2647-2653, 2014
Part of Journal of Chemical Information and Modeling, p. 3211-3217, 2014
Automated QuantMap for rapid quantitative molecular network topology analysis
Part of Bioinformatics, p. 2369-2370, 2013
- DOI for Automated QuantMap for rapid quantitative molecular network topology analysis
- Download full text (pdf) of Automated QuantMap for rapid quantitative molecular network topology analysis
On Mechanisms of Reactive Metabolite Formation from Drugs
Part of Mini-Reviews in medical chemistry, p. 720-729, 2013
Applications of the InChI in cheminformatics with the CDK and Bioclipse
Part of Journal of Cheminformatics, 2013
- DOI for Applications of the InChI in cheminformatics with the CDK and Bioclipse
- Download full text (pdf) of Applications of the InChI in cheminformatics with the CDK and Bioclipse
Part of GigaScience, p. 1-10, 2013
- DOI for Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data
- Download full text (pdf) of 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
Part of Bioinformatics, p. 286-289, 2013
A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
Part of PLOS ONE, 2013
- DOI for A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
- Download full text (pdf) of A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms
WhichCyp: Prediction of Cytochromes P450 Inhibition
Part of Bioinformatics, p. 2051-2052, 2013
The ChEMBL database as linked open data
Part of Journal of Cheminformatics, p. 23, 2013
- DOI for The ChEMBL database as linked open data
- Download full text (pdf) of The ChEMBL database as linked open data
Toxicology Ontology Perspectives
Part of ALTEX. Alternatives zu Tierexperimenten, p. 139-156, 2012
Food for thought...: A toxicology ontology roadmap
Part of ALTEX. Alternatives zu Tierexperimenten, p. 129-137, 2012
Accessing, using, and creating chemical property databases for computational toxicology modeling
Part of Methods in molecular biology (Clifton, N.J.), p. 221-241, 2012
Model building in Bioclipse Decision Support applied to open datasets
Part of Toxicology Letters, 2012
A novel infrastructure for chemical safety predictions with focus on human health
Part of Toxicology Letters, 2012
UPPNEX: A solution for next generation sequencing data management and analysis
Part of EMBnet.journal, p. 44-44, 2012
Computational toxicology using OpenTox & Bioclipse
Part of Toxicology Letters, 2012
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
Part of Journal of Cheminformatics, p. 37, 2011
Linking the Resource Description Framework to cheminformatics and proteochemometrics
Part of Journal of Biomedical Semantics, p. 6, 2011
Integrated Decision Support for Assessing Chemical Liabilities
Part of Journal of chemical information and modeling, p. 1840-1847, 2011
Computational toxicology using the OpenTox application programming interface and Bioclipse
Part of BMC Research Notes, p. 487, 2011
Part of BMC Bioinformatics, 2011
- DOI for Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
- Download full text (pdf) of Brunn: an open source laboratory information system for microplates with a graphical plate layout design process
Part of Bioinformatics, p. 1719-1720, 2011
Part of BMC Bioinformatics, p. 362, 2010
Towards interoperable and reproducible QSAR analyses: Exchange of data sets
Part of Journal of Cheminformatics, 2010
- DOI for Towards interoperable and reproducible QSAR analyses: Exchange of data sets
- Download full text (pdf) of Towards interoperable and reproducible QSAR analyses: Exchange of data sets
An eScience-Bayes strategy for analyzing omics data
Part of BMC Bioinformatics, p. 282, 2010
Part of PLoS ONE, 2010
Bioclipse 2: Towards integrated biocheminformatics
Part of EMBnet.news, p. 25-27, 2009
Bioclipse 2.0: Life Science setzt auf die Staerken von Eclipse.
Part of Eclipse Magazine, 2009
Bioclipse 2: A scriptable integration platform for the life sciences
Part of BMC Bioinformatics, p. 397, 2009
- DOI for Bioclipse 2: A scriptable integration platform for the life sciences
- Download full text (pdf) of Bioclipse 2: A scriptable integration platform for the life sciences
Part of BMC Bioinformatics, p. 279, 2009
The C1C2: a framework for simultaneous model selection and assessment
Part of BMC Bioinformatics, p. 360, 2008
Proteochemometric modeling of HIV protease susceptibility
Part of BMC Bioinformatics, p. 181, 2008
Bioclipse: an open source workbench for chemo- and bioinformatics
Part of BMC Bioinformatics, p. 59, 2007
- DOI for Bioclipse: an open source workbench for chemo- and bioinformatics
- Download full text (pdf) of Bioclipse: an open source workbench for chemo- and bioinformatics
Eine visuelle Open-Source-Platform für Chemo- und Bioinformatik
Part of JAVAmagazin, 2006
Part of Bioinformatics, p. 1024-1026, 2006
Using Bioclipse to integrate bioinformatics functionality
Part of EMBnet.news, p. 5-11, 2005
An Information System for Proteochemometrics
Part of CDK News, p. 54-56, 2005
Using Iterative MapReduce for Parallel Virtual Screening
Part of Journal of medical and bioengineering
Articles, review/survey
Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Part of Journal of Pharmaceutical Sciences, p. 42-49, 2021
- DOI for Predicting With Confidence: Using Conformal Prediction in Drug Discovery
- Download full text (pdf) of Predicting With Confidence: Using Conformal Prediction in Drug Discovery
Towards reproducible computational drug discovery
Part of Journal of Cheminformatics, 2020
- DOI for Towards reproducible computational drug discovery
- Download full text (pdf) of Towards reproducible computational drug discovery
Deep Learning in Image Cytometry: A Review
Part of Cytometry Part A, p. 366-380, 2019
- DOI for Deep Learning in Image Cytometry: A Review
- Download full text (pdf) of Deep Learning in Image Cytometry: A Review
Experiences with workflows for automating data-intensive bioinformatics
Part of Biology Direct, 2015
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand
Part of Basic & Clinical Pharmacology & Toxicology, p. 50-58, 2014
Open source drug discovery with Bioclipse
Part of Current Topics in Medicinal Chemistry, p. 1980-1986, 2012
- DOI for Open source drug discovery with Bioclipse
- Download full text (pdf) of Open source drug discovery with Bioclipse
Books
Introduction to Pharmaceutical Bioinformatics
Oakleaf Academic, 2010
Chapters in book
Part of Data Integration in the Life Sciences, p. 32-40, Springer International Publishing, 2014
Chemoinformatics taking Biology into Account: Proteochemometrics
Part of Computational Approaches in Cheminformatics and Bioinformatics, John Wiley & Sons, 2012
Collaborative Cheminformatics Applications
Part of Collaborative Computational Technologies for Biomedical Research, John Wiley & Sons, 2011
Comprehensive doctoral thesis
Conference papers
Is brightfield all you need for MoA prediction?
2022
Scalable federated machine learning with FEDn
Part of 2022 22nd IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2022), p. 555-564, 2022
Part of Proceedings of the Tenth Symposium on Conformal and Probabilistic Prediction and Applications, p. 91-110, 2021
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Synergy Conformal Prediction for Regression
Part of Proceedings of the 10th international conference on pattern recognition applications and methods (icpram), p. 212-221, 2021
A Constraint Programming Approach to Microplate Layout Design
p. 1-3, 2020
Smart Resource Management for Data Streaming using an Online Bin-packing Strategy
Part of 2020 IEEE International Conference on Big Data (Big Data), p. 2207-2216, 2020
Split knowledge transfer in learning under privileged information framework
Part of Proceedings of the Eighth Symposium on Conformal and Probabilistic Prediction and Applications, p. 43-52, 2019
Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets
Part of Proceedings of the Eighth Symposium on Conformal and Probabilistic Prediction and Applications, p. 53-65, 2019
Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors
Part of Conformal and Probabilistic Prediction with Applications (COPA) 2017, p. 118-131, 2017
SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia
Part of Proc. 13th International Conference on e-Science, p. 219-227, 2017
Conformal prediction in Spark: Large-scale machine learning with confidence
Part of Proc. 2nd International Symposium on Big Data Computing, p. 61-67, 2015
Interpretation of Conformal Prediction Classification Models
Part of STATISTICAL LEARNING AND DATA SCIENCES, p. 323-334, 2015
HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis using Hadoop
Part of Proc. 10th International Conference on e-Science, p. 317-323, 2014
NGS data management and analysis for hundreds of projects: Experiences from Sweden
Part of NGS Data after the Gold Rush, 2013
Manuscripts (preprints)
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