Farmaceutisk Bioinformatik
Beskrivning
Forskningsgruppen för farmaceutisk bioinformatik, som leds av professor Ola Spjuth, fokuserar på datadriven läkemedelsutveckling och studiers på kemikaliers toxicitet. Vi är ett tvärvetenskapligt team av forskare med en vision om att utveckla autonoma biologiska laboratorier där data driver beslut om vilka experiment som ska utföras härnäst, och där automatisering och AI-modellering är viktiga komponenter. Vi kombinerar datorbaserade och in vitro cellbaserade experiment, och har tillgång till ett robotiserat cellprofileringslaboratorium med modern IT-infrastruktur för att hantera och analysera storskalig data.


Exempel på våra tillämpningar inkluderar att studera verkningsmekanismer och säkerhet för nya kemiska föreningar, samt screening för nya läkemedel. Vi är speciellt intresserade av att utveckla och använda autonoma system som integrerar laboratorieutrustning med AI för iterativ upptäckt för att kunna angripa problem som tidigare inte var möjliga. Exempel på projekt inom denna kategori är att söka efter optimala individualiserade läkemedelskombinationer inom precisionsmedicin för cancer, samt att identifiera synergistiska kombinationer av miljökemikalier. Vi är involverade i flera nationella och internationella konsortier och har en nära koppling till läkemedelsindustrin, Akademiska sjukhuset i Uppsala och Science for Life Laboratory.

Publikationer
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
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 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
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
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
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
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
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
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
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
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
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 ATLA (Alternatives to Laboratory Animals), s. 39-54, 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
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
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 Xenobiotica, s. 113-118, 2022
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
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
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 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 Journal of Pharmaceutical Sciences, s. 2614-2619, 2022
Ingår i Journal of Pharmaceutical Sciences, s. 2645-2649, 2022
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
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
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 Proceedings of Machine Learning Research, s. 91-119, 2021
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
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
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
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
The machine learning life cycle and the cloud: implications for drug discovery.
Ingår i Expert Opinion on Drug Discovery, s. 1071-1079, 2021
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
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
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 Xenobiotica, s. 1366-1371, 2021
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 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 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
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
Deep-learning models for lipid nanoparticle-based drug delivery
Ingår i Nanomedicine, s. 1097-1110, 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
Ingår i F1000 Research, s. 513-513, 2021
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
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
Using Predicted Bioactivity Profiles to Improve Predictive Modeling
Ingår i Journal of Chemical Information and Modeling, s. 2830-2837, 2020
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 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
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