Author

Mattias Rantalainen

Karolinska InstitutetORCID 0000-0002-7740-2986Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Trung Nghia VuiD· 2 shared Alain Bols· 1 shared Albin ÖsterroosiD· 1 shared Anders UlléniD· 1 shared Anna Bohlin· 1 shared Annemie RutteniD· 1 shared Barbara Anna Henk BrouwersiD· 1 shared Bram De LaereiD· 1 shared

Activity by Year

2016-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersBioinformatics

Trung Nghia VuORCID

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Author profile →

4 papers

Recent·Most cited

Pathway activation model for personalized prediction of drug synergy

Quang Thinh Trac, Yue Huang, Tom Erkers, Päivi Östling, Anna Bohlin, Albin Österroos, Mattias Vesterlund, Rozbeh Jafari, Ioannis Siavelis, Helena Bäckvall, Santeri Kiviluoto, Lukas M. Orre, Mattias Rantalainen, Janne Lehtiö, Sören Lehmann, , Trung Nghia Vu

This paper introduces DIPx, a model predicting drug synergy using pathway activation scores, showing better performance than existing methods on both known and novel drug combinations.

eLife · Jun 3, 2025Peer-reviewedBioinformatics

Ensembles for improved detection of invasive breast cancer in histological images

Leslie Solorzano, Stephanie Robertson, Johan Hartman, Mattias Rantalainen

This paper compares single and ensemble CNN models for detecting invasive breast cancer in histological images, finding ensembles improve accuracy across internal and external datasets.

bioRxiv · Apr 13, 2023 · PreprintBioinformatics

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Markus Mayrhofer, Bram De Laere, Tom Whitington, Peter Van Oyen, Christophe Ghysel, J Ampe, Piet Ost, Wim Demey, Lucien Hoekx, Dirk L. A. L. Schrijvers, Barbara Anna Henk Brouwers, Willem Lybaert, Els Grieta Everaert, Daan Joost De Maeseneer, Michiel Hendrik Strijbos, , Johan Lindberg

This study profiles cell-free DNA in metastatic prostate cancer patients, identifying genomic alterations, microsatellite instability, and clonal hematopoiesis as potential biomarkers.

Genome Medicine · Nov 19, 2018Peer-reviewedGenomics

Isoform-level gene expression patterns in single-cell RNA-sequencing data

Trung Nghia Vu, Quin F Wills, Krishna R Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Mattias Rantalainen

This study introduces ISOP, a method for analyzing isoform-level expression patterns in single-cell RNA-seq data, revealing common isoform preferences and heterogeneity in breast cancer cells.

bioRxiv · Jan 16, 2016Bioinformatics