Ola Spjuth

Andreas Hellander

Salman Toor

Expert Syst. Appl., March, 2024

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank.

[BibT_eX]

[DOI]

Srijit Seal

Layla Hosseini-Gerami

Miguel García-Ortegón

Shantanu Singh

Andreas Bender

Anne E. Carpenter

J. Chem. Inf. Model., February, 2024

2023

Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data.

[BibT_eX]

[DOI]

Jordi Carreras Puigvert

Andreas Bender

J. Cheminformatics, December, 2023

Evaluating the utility of brightfield image data for mechanism of action prediction.

[BibT_eX]

[DOI]

Jordi Carreras Puigvert

PLoS Comput. Biol., 2023

2022

Predicting protein network topology clusters from chemical structure using deep learning.

[BibT_eX]

[DOI]

Akshai P. Sreenivasan

Philip J. Harrison

Wesley Schaal

Damian J. Matuszewski

Kim Kultima

Staffan Arvidsson McShane

J. Cheminformatics, 2022

SimVec: predicting polypharmacy side effects for new drugs.

[BibT_eX]

[DOI]

J. Cheminformatics, 2022

Scalable federated machine learning with FEDn.

[BibT_eX]

[DOI]

Proceedings of the 22nd IEEE International Symposium on Cluster, 2022

2021

Deep Learning With Conformal Prediction for Hierarchical Analysis of Large-Scale Whole-Slide Tissue Images.

[BibT_eX]

[DOI]

IEEE J. Biomed. Health Informatics, 2021

Machine Learning Strategies When Transitioning between Biological Assays.

[BibT_eX]

[DOI]

Ernst Ahlberg

Tobias Noeske

J. Chem. Inf. Model., 2021

Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning.

[BibT_eX]

[DOI]

J. Cheminformatics, 2021

Assessing the calibration in toxicological in vitro models with conformal prediction.

[BibT_eX]

[DOI]

Andrea Morger

Staffan Arvidsson McShane

J. Cheminformatics, 2021

Approaches for containerized scientific workflows in cloud environments with applications in life science.

[BibT_eX]

[DOI]

Payam Emami Khoonsari

Stephanie Herman

Kim Kultima

Samuel Lampa

F1000Research, 2021

Scalable federated machine learning with FEDn.

[BibT_eX]

[DOI]

CoRR, 2021

scConnect: a method for exploratory analysis of cell-cell communication based on single-cell RNA-sequencing data.

[BibT_eX]

[DOI]

Jon E. T. Jakobsson

Malin C. Lagerström

Bioinform., 2021

Synergy Conformal Prediction for Regression.

[BibT_eX]

[DOI]

Proceedings of the 10th International Conference on Pattern Recognition Applications and Methods, 2021

Synergy conformal prediction.

[BibT_eX]

[DOI]

Proceedings of the Conformal and Probabilistic Prediction and Applications, 2021

2020

Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling".

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2020

Using Predicted Bioactivity Profiles to Improve Predictive Modeling.

[BibT_eX]

[DOI]

Staffan Arvidsson McShane

J. Chem. Inf. Model., 2020

Towards reproducible computational drug discovery.

[BibT_eX]

[DOI]

J. Cheminformatics, 2020

Predicting target profiles with confidence as a service using docking scores.

[BibT_eX]

[DOI]

Laeeq Ahmed

Hiba Alogheli

J. Cheminformatics, 2020

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy.

[BibT_eX]

[DOI]

Proceedings of the 2020 IEEE International Conference on Big Data (IEEE BigData 2020), 2020

2019

On-demand virtual research environments using microservices.

[BibT_eX]

[DOI]

PeerJ Comput. Sci., 2019

SciPipe - Turning Scientific Workflows into Computer Programs.

[BibT_eX]

[DOI]

Comput. Sci. Eng., 2019

Container-based bioinformatics with Pachyderm.

[BibT_eX]

[DOI]

Jon Ander Novella

Payam Emami Khoonsari

Bioinform., 2019

Interoperable and scalable data analysis with microservices: applications in metabolomics.

[BibT_eX]

[DOI]

Bioinform., 2019

Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets.

[BibT_eX]

[DOI]

Robin Carrión Brännström

Proceedings of the Conformal and Probabilistic Prediction and Applications, 2019

Split knowledge transfer in learning under privileged information framework.

[BibT_eX]

[DOI]

Fabian Söderdahl

Proceedings of the Conformal and Probabilistic Prediction and Applications, 2019

2018

Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty.

[BibT_eX]

[DOI]

Natália Aniceto

Isidro Cortes-Ciriano

Andreas Bender

J. Chem. Inf. Model., 2018

Novel applications of Machine Learning in cheminformatics.

[BibT_eX]

[DOI]

J. Cheminformatics, 2018

A confidence predictor for logD using conformal regression and a support-vector machine.

[BibT_eX]

[DOI]

J. Cheminformatics, 2018

Evaluating parameters for ligand-based modeling with random forest on sparse data sets.

[BibT_eX]

[DOI]

J. Cheminformatics, 2018

Efficient iterative virtual screening with Apache Spark and conformal prediction.

[BibT_eX]

[DOI]

J. Cheminformatics, 2018

MaRe: Container-Based Parallel Computing with Data Locality.

[BibT_eX]

[DOI]

CoRR, 2018

Aggregating Predictions on Multiple Non-disclosed Datasets using Conformal Prediction.

[BibT_eX]

[DOI]

CoRR, 2018

KubeNow: an On-Demand Cloud-Agnostic Platform for Microservices-Based Research Environments.

[BibT_eX]

[DOI]

CoRR, 2018

conformalClassification: A Conformal Prediction R Package for Classification.

[BibT_eX]

[DOI]

CoRR, 2018

Conformal prediction in learning under privileged information paradigm with applications in drug discovery.

[BibT_eX]

[DOI]

Proceedings of the 7th Symposium on Conformal and Probabilistic Prediction and Applications, 2018

2017

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

[BibT_eX]

[DOI]

J. Cheminformatics, 2017

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

[BibT_eX]

[DOI]

J. Cheminformatics, 2017

Large-scale virtual screening on public cloud resources with Apache Spark.

[BibT_eX]

[DOI]

J. Cheminformatics, 2017

E-Science technologies in a workflow for personalized medicine using cancer screening as a case study.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2017

The future of metabolomics in ELIXIR.

[BibT_eX]

[DOI]

F1000Research, 2017

RDFIO: extending Semantic MediaWiki for interoperable biomedical data management.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2017

KubeNow: A Cloud Agnostic Platform for Microservice-Oriented Applications.

[BibT_eX]

[DOI]

Proceedings of the 2017 Imperial College Computing Student Workshop, 2017

SNIC Science Cloud (SSC): A National-Scale Cloud Infrastructure for Swedish Academia.

[BibT_eX]

[DOI]

Proceedings of the 13th IEEE International Conference on e-Science, 2017

Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors.

[BibT_eX]

[DOI]

Proceedings of the Conformal and Probabilistic Prediction and Applications, 2017

2016

XMetDB: an open access database for xenobiotic metabolism.

[BibT_eX]

[DOI]

J. Cheminformatics, 2016

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.

[BibT_eX]

[DOI]

Samuel Lampa

Jonathan Alvarsson

J. Cheminformatics, 2016

Large-scale ligand-based predictive modelling using support vector machines.

[BibT_eX]

[DOI]

J. Cheminformatics, 2016

2015

Scaling Predictive Modeling in Drug Development with Cloud Computing.

[BibT_eX]

[DOI]

Behrooz Torabi Moghadam

J. Chem. Inf. Model., 2015

Interpretation of Conformal Prediction Classification Models.

[BibT_eX]

[DOI]

Proceedings of the Statistical Learning and Data Sciences - Third International Symposium, 2015

Conformal Prediction in Spark: Large-Scale Machine Learning with Confidence.

[BibT_eX]

[DOI]

Proceedings of the 2nd IEEE/ACM International Symposium on Big Data Computing, 2015

2014

Ligand-Based Target Prediction with Signature Fingerprints.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2014

HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis Using Hadoop.

[BibT_eX]

[DOI]

Alexey Siretskiy

Proceedings of the 10th IEEE International Conference on e-Science, 2014

Data Integration between Swedish National Clinical Health Registries and Biobanks Using an Availability System.

[BibT_eX]

[DOI]

Proceedings of the Data Integration in the Life Sciences - 10th International Conference, 2014

2013

The ChEMBL database as linked open data.

[BibT_eX]

[DOI]

J. Cheminformatics, 2013

Applications of the InChI in cheminformatics with the CDK and Bioclipse.

[BibT_eX]

[DOI]

J. Cheminformatics, 2013

Bioclipse-R: integrating management and visualization of life science data with statistical analysis.

[BibT_eX]

[DOI]

Bioinform., 2013

Automated QuantMap for rapid quantitative molecular network topology analysis.

[BibT_eX]

[DOI]

Bioinform., 2013

WhichCyp: prediction of cytochromes P450 inhibition.

[BibT_eX]

[DOI]

Michal Rostkowski

Patrik Rydberg

Bioinform., 2013

Using Iterative MapReduce for Parallel Virtual Screening.

[BibT_eX]

[DOI]

Proceedings of the IEEE 5th International Conference on Cloud Computing Technology and Science, 2013

2011

Integrated Decision Support for Assessing Chemical Liabilities.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2011

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.

[BibT_eX]

[DOI]

J. Cheminformatics, 2011

Brunn: An open source laboratory information system for microplates with a graphical plate layout design process.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

Linking the Resource Description Framework to cheminformatics and proteochemometrics.

[BibT_eX]

[DOI]

J. Biomed. Semant., 2011

Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

[BibT_eX]

[DOI]

J. Cheminformatics, 2010

An eScience-Bayes strategy for analyzing omics data.

[BibT_eX]

[DOI]

Martin Eklund

Jarl E. S. Wikberg

BMC Bioinform., 2010

Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

2009

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

[BibT_eX]

[DOI]

BMC Bioinform., 2009

Bioclipse 2: A scriptable integration platform for the life sciences.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

2008

Proteochemometric modeling of HIV protease susceptibility.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

The C1C2: A framework for simultaneous model selection and assessment.

[BibT_eX]

[DOI]

Martin Eklund