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ORCIDOla Spjuth
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- affiliation: Uppsala University, Sweden
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2020 – today
- 2024
[j55]Tianru Zhang
, Ankit Gupta, María Andreína Francisco Rodríguez, Ola Spjuth, Andreas Hellander, Salman Toor:
Data management of scientific applications in a reinforcement learning-based hierarchical storage system. Expert Syst. Appl. 237(Part B): 121443 (2024)- [j54]Staffan Arvidsson McShane, Ulf Norinder, Jonathan Alvarsson, Ernst Ahlberg, Lars Carlsson, Ola Spjuth:
CPSign: conformal prediction for cheminformatics modeling. J. Cheminformatics 16(1): 75 (2024) - [j53]Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J. Chem. Inf. Model. 64(4): 1172-1186 (2024) - 2023
- [j52]Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender:
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. J. Cheminformatics 15(1): 56 (2023) - [j51]Philip J. Harrison, Ankit Gupta, Jonne Rietdijk, Håkan Wieslander, Jordi Carreras Puigvert, Polina Georgiev, Carolina Wählby, Ola Spjuth, Ida-Maria Sintorn:
Evaluating the utility of brightfield image data for mechanism of action prediction. PLoS Comput. Biol. 19(7) (2023) - 2022
- [j50]Akshai P. Sreenivasan, Philip J. Harrison, Wesley Schaal, Damian J. Matuszewski, Kim Kultima, Ola Spjuth:
Predicting protein network topology clusters from chemical structure using deep learning. J. Cheminformatics 14(1): 47 (2022) - [j49]Nina Lukashina, Elena Kartysheva, Ola Spjuth, Elizaveta Virko, Aleksei Shpilman:
SimVec: predicting polypharmacy side effects for new drugs. J. Cheminformatics 14(1): 49 (2022) - [c15]Morgan Ekmefjord, Addi Ait-Mlouk, Sadi Alawadi, Mattias Åkesson, Prashant Singh, Ola Spjuth, Salman Toor, Andreas Hellander:
Scalable federated machine learning with FEDn. CCGRID 2022: 555-564 - 2021
- [j48]Jon E. T. Jakobsson, Ola Spjuth, Malin C. Lagerström:
scConnect: a method for exploratory analysis of cell-cell communication based on single-cell RNA-sequencing data. Bioinform. 37(20): 3501-3508 (2021) - [j47]Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth, Andrea Volkamer:
Assessing the calibration in toxicological in vitro models with conformal prediction. J. Cheminformatics 13(1): 35 (2021) - [j46]Ulf Norinder, Ola Spjuth, Fredrik Svensson:
Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning. J. Cheminformatics 13(1): 77 (2021) - [j45]Staffan Arvidsson McShane, Ernst Ahlberg, Tobias Noeske, Ola Spjuth:
Machine Learning Strategies When Transitioning between Biological Assays. J. Chem. Inf. Model. 61(7): 3722-3733 (2021) - [j44]Håkan Wieslander, Philip J. Harrison, Gabriel Skogberg, Sonya Jackson, Hakan Fridén, Johan Karlsson, Ola Spjuth, Carolina Wählby:
Deep Learning With Conformal Prediction for Hierarchical Analysis of Large-Scale Whole-Slide Tissue Images. IEEE J. Biomed. Health Informatics 25(2): 371-380 (2021) - [c14]Niharika Gauraha, Ola Spjuth:
Synergy conformal prediction. COPA 2021: 91-110 - [c13]Niharika Gauraha, Ola Spjuth:
Synergy Conformal Prediction for Regression. ICPRAM 2021: 212-221 - [i10]Morgan Ekmefjord, Addi Ait-Mlouk, Sadi Alawadi, Mattias Åkesson, Desislava Stoyanova, Ola Spjuth, Salman Toor, Andreas Hellander:
Scalable federated machine learning with FEDn. CoRR abs/2103.00148 (2021) - [i9]Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan W. Floden, Cédric Notredame, Pablo A. Moreno, Andreas Hellander, Payam Emami Khoonsari, Stephanie Herman, Kim Kultima, Samuel Lampa:
Approaches for containerized scientific workflows in cloud environments with applications in life science. F1000Research 10: 513 (2021) - 2020
- [j43]Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat:
Towards reproducible computational drug discovery. J. Cheminformatics 12(1): 9 (2020) - [j42]Laeeq Ahmed, Hiba Alogheli, Staffan Arvidsson McShane, Jonathan Alvarsson, Arvid Berg, Anders Larsson, Wesley Schaal, Erwin Laure, Ola Spjuth:
Predicting target profiles with confidence as a service using docking scores. J. Cheminformatics 12(1): 62 (2020) - [j41]Ulf Norinder, Ola Spjuth, Fredrik Svensson:
Using Predicted Bioactivity Profiles to Improve Predictive Modeling. J. Chem. Inf. Model. 60(6): 2830-2837 (2020) - [j40]Ulf Norinder, Ola Spjuth, Fredrik Svensson:
Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling". J. Chem. Inf. Model. 60(12): 6722 (2020) - [c12]Oliver Stein, Ben Blamey, Johan Karlsson, Alan Sabirsh, Ola Spjuth, Andreas Hellander, Salman Toor:
Smart Resource Management for Data Streaming using an Online Bin-packing Strategy. IEEE BigData 2020: 2207-2216 - [i8]Oliver Stein, Ben Blamey, Johan Karlsson, Alan Sabirsh, Ola Spjuth, Andreas Hellander, Salman Toor:
Smart Resource Management for Data Streaming using an Online Bin-packing Strategy. CoRR abs/2001.10865 (2020)
2010 – 2019
- 2019
- [j39]Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack, Marco Capuccini, Joachim Burman, Kim Kultima, Ola Spjuth:
Container-based bioinformatics with Pachyderm. Bioinform. 35(5): 839-846 (2019) - [j38]Payam Emami Khoonsari, Pablo A. Moreno, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne A. Thévenot, Michael van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth:
Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinform. 35(19): 3752-3760 (2019) - [j37]Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth:
SciPipe - Turning Scientific Workflows into Computer Programs. Comput. Sci. Eng. 21(3): 109-113 (2019) - [j36]Marco Capuccini, Anders Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Toor, Ola Spjuth:
On-demand virtual research environments using microservices. PeerJ Comput. Sci. 5: e232 (2019) - [c11]Niharika Gauraha, Fabian Söderdahl, Ola Spjuth:
Split knowledge transfer in learning under privileged information framework. COPA 2019: 43-52 - [c10]Ola Spjuth, Robin Carrión Brännström, Lars Carlsson, Niharika Gauraha:
Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets. COPA 2019: 53-65 - [i7]Ola Spjuth, Robin Carrión Brännström, Lars Carlsson, Niharika Gauraha:
Combining Prediction Intervals on Multi-Source Non-Disclosed Regression Datasets. CoRR abs/1908.05571 (2019) - 2018
- [j35]Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Zubair Toor, Wesley Schaal, Erwin Laure, Ola Spjuth:
Efficient iterative virtual screening with Apache Spark and conformal prediction. J. Cheminformatics 10(1): 8:1-8:8 (2018) - [j34]Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson, Ola Spjuth:
A confidence predictor for logD using conformal regression and a support-vector machine. J. Cheminformatics 10(1): 17:1-17:10 (2018) - [j33]Ola Spjuth:
Novel applications of Machine Learning in cheminformatics. J. Cheminformatics 10(1): 46:1-46:2 (2018) - [j32]Alexander Kensert, Jonathan Alvarsson, Ulf Norinder, Ola Spjuth:
Evaluating parameters for ligand-based modeling with random forest on sparse data sets. J. Cheminformatics 10(1): 49:1-49:10 (2018) - [j31]Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender:
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. J. Chem. Inf. Model. 58(5): 1132-1140 (2018) - [c9]Niharika Gauraha, Lars Carlsson, Ola Spjuth:
Conformal prediction in learning under privileged information paradigm with applications in drug discovery. COPA 2018: 147-156 - [i6]Niharika Gauraha, Lars Carlsson, Ola Spjuth:
Conformal Prediction in Learning Under Privileged Information Paradigm with Applications in Drug Discovery. CoRR abs/1803.11136 (2018) - [i5]Niharika Gauraha, Ola Spjuth:
conformalClassification: A Conformal Prediction R Package for Classification. CoRR abs/1804.05494 (2018) - [i4]Marco Capuccini, Anders Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Zubair Toor, Ola Spjuth:
KubeNow: an On-Demand Cloud-Agnostic Platform for Microservices-Based Research Environments. CoRR abs/1805.06180 (2018) - [i3]Ola Spjuth, Lars Carlsson, Niharika Gauraha:
Aggregating Predictions on Multiple Non-disclosed Datasets using Conformal Prediction. CoRR abs/1806.04000 (2018) - [i2]Marco Capuccini, Salman Zubair Toor, Staffan Arvidsson, Ola Spjuth:
MaRe: Container-Based Parallel Computing with Data Locality. CoRR abs/1808.02318 (2018) - 2017
- [j30]Samuel Lampa, Egon L. Willighagen, Pekka Kohonen, Ali King, Denny Vrandecic, Roland Grafstrom, Ola Spjuth:
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management. J. Biomed. Semant. 8(1): 35:1-35:13 (2017) - [j29]Ola Spjuth, Andreas Karlsson, Mark Clements, Keith Humphreys, Emma Ivansson, Jim Dowling, Martin Eklund, Alexandra Jauhiainen, Kamila Czene, Henrik Gronberg, Pär Sparén, Fredrik Wiklund, Abbas Cheddad, þorgerður Pálsdóttir, Mattias Rantalainen, Linda Abrahamsson, Erwin Laure, Jan-Eric Litton, Juni Palmgren:
E-Science technologies in a workflow for personalized medicine using cancer screening as a case study. J. Am. Medical Informatics Assoc. 24(5): 950-957 (2017) - [j28]Marco Capuccini, Laeeq Ahmed, Wesley Schaal, Erwin Laure, Ola Spjuth:
Large-scale virtual screening on public cloud resources with Apache Spark. J. Cheminformatics 9(1): 15:1-15:6 (2017) - [j27]Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck:
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminformatics 9(1): 33:1-33:19 (2017) - [j26]Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomás Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. A. Evelo, Rajarshi Guha, Christoph Steinbeck:
Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J. Cheminformatics 9(1): 53 (2017) - [c8]Staffan Arvidsson, Ola Spjuth, Lars Carlsson, Paolo Toccaceli:
Prediction of Metabolic Transformations using Cross Venn-ABERS Predictors. COPA 2017: 118-131 - [c7]Salman Zubair Toor, Mathias Lindberg, Ingemar Falman, Andreas Vallin, Olof Mohill, Pontus Freyhult, Linus Nilsson, Martin Agback, Lars Viklund, Henric Zazzik, Ola Spjuth, Marco Capuccini, Joakim Moller, Donal Murtagh, Andreas Hellander:
SNIC Science Cloud (SSC): A National-Scale Cloud Infrastructure for Swedish Academia. eScience 2017: 219-227 - [c6]Marco Capuccini, Anders Larsson, Salman Zubair Toor, Ola Spjuth:
KubeNow: A Cloud Agnostic Platform for Microservice-Oriented Applications. ICCSW 2017: 9:1-9:2 - [i1]Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata P. Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck:
The future of metabolomics in ELIXIR. F1000Research 6: 1649- (2017) - 2016
- [j25]Jonathan Alvarsson, Samuel Lampa, Wesley Schaal, Claes R. Andersson, Jarl E. S. Wikberg, Ola Spjuth:
Large-scale ligand-based predictive modelling using support vector machines. J. Cheminformatics 8(1): 39:1-39:9 (2016) - [j24]Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. A. Evelo, Nina Jeliazkova:
XMetDB: an open access database for xenobiotic metabolism. J. Cheminformatics 8(1): 47:1-47:8 (2016) - [j23]Samuel Lampa, Jonathan Alvarsson, Ola Spjuth:
Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. J. Cheminformatics 8(1): 67:1-67:12 (2016) - 2015
- [j22]Behrooz Torabi Moghadam, Jonathan Alvarsson, Marcus Holm, Martin Eklund, Lars Carlsson, Ola Spjuth:
Scaling Predictive Modeling in Drug Development with Cloud Computing. J. Chem. Inf. Model. 55(1): 19-25 (2015) - [c5]Marco Capuccini, Lars Carlsson, Ulf Norinder, Ola Spjuth:
Conformal Prediction in Spark: Large-Scale Machine Learning with Confidence. BDC 2015: 61-67 - [c4]Ernst Ahlberg, Ola Spjuth, Catrin Hasselgren, Lars Carlsson:
Interpretation of Conformal Prediction Classification Models. SLDS 2015: 323-334 - 2014
- [j21]Jonathan Alvarsson, Martin Eklund, Ola Engkvist, Ola Spjuth, Lars Carlsson, Jarl E. S. Wikberg, Tobias Noeske:
Ligand-Based Target Prediction with Signature Fingerprints. J. Chem. Inf. Model. 54(10): 2647-2653 (2014) - [j20]Jonathan Alvarsson, Martin Eklund, Claes R. Andersson, Lars Carlsson, Ola Spjuth, Jarl E. S. Wikberg:
Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines. J. Chem. Inf. Model. 54(11): 3211-3217 (2014) - [c3]Ola Spjuth, Jani Heikkinen, Jan-Eric Litton, Juni Palmgren, Maria Krestyaninova:
Data Integration between Swedish National Clinical Health Registries and Biobanks Using an Availability System. DILS 2014: 32-40 - [c2]Alexey Siretskiy, Ola Spjuth:
HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis Using Hadoop. eScience 2014: 317-323 - 2013
- [j19]Ola Spjuth, Valentin Georgiev, Lars Carlsson, Jonathan Alvarsson, Arvid Berg, Egon L. Willighagen, Jarl E. S. Wikberg, Martin Eklund:
Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinform. 29(2): 286-289 (2013) - [j18]Michal Rostkowski, Ola Spjuth, Patrik Rydberg:
WhichCyp: prediction of cytochromes P450 inhibition. Bioinform. 29(16): 2051-2052 (2013) - [j17]Wesley Schaal, Ulf Hammerling, Mats G. Gustafsson, Ola Spjuth:
Automated QuantMap for rapid quantitative molecular network topology analysis. Bioinform. 29(18): 2369-2370 (2013) - [j16]Ola Spjuth, Arvid Berg, Samuel E. Adams, Egon L. Willighagen:
Applications of the InChI in cheminformatics with the CDK and Bioclipse. J. Cheminformatics 5: 14 (2013) - [j15]Egon L. Willighagen, Andra Waagmeester, Ola Spjuth, Peter Ansell, Antony J. Williams, Valery Tkachenko, Janna Hastings, Bin Chen, David J. Wild:
The ChEMBL database as linked open data. J. Cheminformatics 5: 23 (2013) - [c1]Laeeq Ahmed, Åke Edlund, Erwin Laure, Ola Spjuth:
Using Iterative MapReduce for Parallel Virtual Screening. CloudCom (2) 2013: 27-32 - 2011
- [j14]Ola Spjuth, Martin Eklund, Maris Lapins, Muhammad Junaid, Jarl E. S. Wikberg:
Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre. Bioinform. 27(12): 1719-1720 (2011) - [j13]Egon L. Willighagen, Jonathan Alvarsson, Annsofie Andersson, Martin Eklund, Samuel Lampa, Maris Lapins, Ola Spjuth, Jarl E. S. Wikberg:
Linking the Resource Description Framework to cheminformatics and proteochemometrics. J. Biomed. Semant. 2(S-1): S6 (2011) - [j12]Jonathan Alvarsson, Claes R. Andersson, Ola Spjuth, Rolf Larsson, Jarl E. S. Wikberg:
Brunn: An open source laboratory information system for microplates with a graphical plate layout design process. BMC Bioinform. 12: 179 (2011) - [j11]Noel M. O'Boyle, Rajarshi Guha, Egon L. Willighagen, Sam E. Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V. Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Andrew S. I. D. Lang, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jérôme Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, Peter Murray-Rust:
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. J. Cheminformatics 3: 37 (2011) - [j10]Ola Spjuth, Martin Eklund, Ernst Ahlberg Helgee, Scott Boyer, Lars Carlsson:
Integrated Decision Support for Assessing Chemical Liabilities. J. Chem. Inf. Model. 51(8): 1840-1847 (2011) - 2010
- [j9]Martin Eklund, Ola Spjuth, Jarl E. S. Wikberg:
An eScience-Bayes strategy for analyzing omics data. BMC Bioinform. 11: 282 (2010) - [j8]Lars Carlsson, Ola Spjuth, Samuel E. Adams, Robert C. Glen, Scott Boyer:
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse. BMC Bioinform. 11: 362 (2010) - [j7]Ola Spjuth, Egon L. Willighagen, Rajarshi Guha, Martin Eklund, Jarl E. S. Wikberg:
Towards interoperable and reproducible QSAR analyses: Exchange of datasets. J. Cheminformatics 2: 5 (2010)
2000 – 2009
- 2009
- [j6]Johannes Wagener, Ola Spjuth, Egon L. Willighagen, Jarl E. S. Wikberg:
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. BMC Bioinform. 10: 279 (2009) - [j5]Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain M. Torrance, Johannes Wagener, Egon L. Willighagen, Christoph Steinbeck, Jarl E. S. Wikberg:
Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinform. 10: 397 (2009) - 2008
- [j4]Martin Eklund, Ola Spjuth, Jarl E. S. Wikberg:
The C1C2: A framework for simultaneous model selection and assessment. BMC Bioinform. 9 (2008) - [j3]Maris Lapins, Martin Eklund, Ola Spjuth, Peteris Prusis, Jarl E. S. Wikberg:
Proteochemometric modeling of HIV protease susceptibility. BMC Bioinform. 9 (2008) - 2007
- [j2]Ola Spjuth, Tobias Helmus, Egon L. Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E. S. Wikberg:
Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinform. 8 (2007) - 2006
- [j1]Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, Henryk Jan Komorowski:
The LCB Data Warehouse. Bioinform. 22(8): 1024-1026 (2006)
Coauthor Index
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