Publications

All the publications from the DECIDER project will be listed on this page. A link to the open access version will be provided if the publisher’s version is not directly open.

Juuli Raivola, Alice Dini, Hanna Karvonen, Emilia Piki, Kari Salokas, Wilhelmiina Niininen, Laura Kaleva, Kaiyang Zhang, Mariliina Arjama, Greta Gudoityte, Brinton Seashore-Ludlow, Markku Varjosalo, Olli Kallioniemi, Sampsa Hautaniemi, Astrid Murumägi & Daniela Ungureanu Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention. Cell Death and Disease (2022) 13: 714.

Molly J. Carroll, Katja Kaipio, Johanna Hynninen, Olli Carpen, Sampsa Hautaniemi, David Page & Pamela K. Kreeger A Subset of Secreted Proteins in Ascites Can Predict Platinum-Free Interval in Ovarian Cancer. Cancers (2022) 14: 4291.

Martin Garrido-Rodriguez, Katharina Zirngibl, Olga Ivanova, Sebastian Lobentanzer & Julio Saez-Rodriguez Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks. Molecular Systems Biology (2022) 18: e11036

Marta Lovino, Marilisa Montemurro, Venere S Barrese & Elisa Ficarra Identifying the oncogenic potential of gene fusions exploiting miRNAs. Journal of Biomedical Informatics (2022) 129

Marta Lovino, Vincenzo Randazzo, Gabriele Ciravegna , Pietro Barbiero, Elisa Ficarra & Giansalvo Cirrincione  A survey on data integration for multi-omics sample clustering. Neurocomputing (2022) 488: 494-508

David Mas-Ponte, Marcel McCullough & Fran Supek Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clinical Science (2022) 136 (5): 383–404

Susanna Holmström, Sampsa Hautaniemi & Antti Häkkinen POIBM: Batch correction of heterogeneous RNA-seq datasets through latent sample matching. Bioinformatics (2022), btac124

Kaiyang Zhang, Erdogan Pekcan Erkan, Sanaz Jamalzadeh, Jun Dai, Noora Andersson, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Olli Carpén, Sakari Hietanen, Jaana Oikkonen, Johanna Hynninen, Anni Virtanen, Antti Häkkinen, Sampsa Hautaniemi & Anna Vähärautio Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer. Science Advances (2022) 8, eabm1831

Sanaz Jamalzadeh, Antti Häkkinen, Noora Andersson, Kaisa Huhtinen, Anna Laury, Sakari Hietanen, Johanna Hynninen, Jaana Oikkonen, Olli Carpén, Anni Virtanen & Sampsa Hautaniemi QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability. Laboratory Investigation (2022)

Farzaneh Firoozbakht, Behnam Yousefi & Benno Schwikowski An overview of machine learning methods for monotherapy drug response prediction. Briefings in Bioinformatics (2022) 23:1

Anna Ray Laury, Sami Blom, Tuomas Ropponen, Anni Virtanen & Olli Mikael Carpén Artificial intelligence-based image analysis can predict outcome in high-grade serous carcinoma via histology alone. Nature Scientific Reports (2021) 11:19165