Latest publications
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An Open-Source Modular Framework for Automated Pipetting and Imaging Applications
Part of Advanced biology, 2022.
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Predicting protein network topology clusters from chemical structure using deep learning
Part of Journal of Cheminformatics, 2022.
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Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
Part of Communications Biology, 2022.
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The Impact of Reference Data Selection for the Prediction Accuracy of Intrinsic Hepatic Metabolic Clearance
Part of Journal of Pharmaceutical Sciences, p. 2645-2649, 2022.
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In Silico Predictions of the Gastrointestinal Uptake of Macrocycles in Man Using Conformal Prediction Methodology
Part of Journal of Pharmaceutical Sciences, p. 2614-2619, 2022.
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In silico predictions of the human pharmacokinetics/toxicokinetics of 65 chemicals from various classes using conformal prediction methodology
Part of Xenobiotica, p. 113-118, 2022.
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Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
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
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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
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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
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Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
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
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Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology
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
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Machine Learning Strategies When Transitioning between Biological Assays
Part of Journal of Chemical Information and Modeling, p. 3722-3733, 2021.
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Deep-learning models for lipid nanoparticle-based drug delivery
Part of Nanomedicine, p. 1097-1110, 2021.
DOI for Deep-learning models for lipid nanoparticle-based drug delivery
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scConnect: a method for exploratory analysis of cell–cell communication based on single-cell RNA-sequencing data
Part of Bioinformatics, p. 3501-3508, 2021.
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Comparison between lab variability and in silico prediction errors for the unbound fraction of drugs in human plasma
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
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In silico prediction of volume of distribution of drugs in man using conformal prediction performs on par with animal data-based models
Part of Xenobiotica, p. 1366-1371, 2021.
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The machine learning life cycle and the cloud: implications for drug discovery.
Part of Expert Opinion on Drug Discovery, p. 1071-1079, 2021.
DOI for The machine learning life cycle and the cloud: implications for drug discovery.
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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 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
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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
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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
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Metabolomics: The Stethoscope for the Twenty-First Century
Part of Medical principles and practice, p. 301-310, 2021.
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Synergy Conformal Prediction
Part of Proceedings of Machine Learning Research, p. 91-119, 2021.
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Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images
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
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Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
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
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ELIXIR and Toxicology: a community in development
Part of F1000 Research, p. 1129-1129, 2021.
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Predicting target profiles with confidence as a service using docking scores
Part of Journal of Cheminformatics, 2020.
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Using Predicted Bioactivity Profiles to Improve Predictive Modeling
Part of Journal of Chemical Information and Modeling, p. 2830-2837, 2020.
DOI for Using Predicted Bioactivity Profiles to Improve Predictive Modeling
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Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes
Part of SLAS discovery : advancing life sciences R & D, 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
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Container-based bioinformatics with Pachyderm
Part of Bioinformatics, p. 839-846, 2019.
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SciPipe - Turning Scientific Workflows into Computer Programs
Part of Computing in science & engineering (Print), p. 109-113, 2019.
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On-demand virtual research environments using microservices
Part of PeerJ Computer Science, 2019.
DOI for On-demand virtual research environments using microservices
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Biochemical Differences in Cerebrospinal Fluid between Secondary Progressive and Relapsing-Remitting Multiple Sclerosis
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
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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
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Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects
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
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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
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Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty
Part of Journal of Chemical Information and Modeling, p. 1132-1140, 2018.
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Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms
Part of Toxicology Letters, p. S203-S203, 2018.
DOI for Exploring the usefulness of morphological profiling of cells to study toxicity mechanisms
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OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration and in silico analysis and modelling in risk assessment
Part of Toxicology Letters, p. S104-S104, 2018.
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OpenRiskNet, an open e-infrastructure to support data sharing, knowledge integration, in silico analysis and modelling in risk assessment
Part of Abstracts of Papers of the American Chemical Society, 2018.
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Integration of magnetic resonance imaging and protein and metabolite CSF measurements to enable early diagnosis of secondary progressive multiple sclerosis.
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.
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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
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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
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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
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Efficient iterative virtual screening with Apache Spark and conformal prediction
Part of Journal of Cheminformatics, 2018.
DOI for Efficient iterative virtual screening with Apache Spark and conformal prediction