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Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis

Deliverables

Knowledge Management System up and running

Knowledge Management System up and running

Project Office with Operational Project Manager in place and Project Management Committee

Project Office with Operational Project Manager in place and Project Management Committee

Project presentation produced

Project presentation produced

A workflow for obtaining consents from advanced HGS-OvCa patients, and for collecting samples from the patients

A workflow for obtaining consents from advanced HGS-OvCa patients, and for collecting samples from the patients

Evaluation of flow cytometry and imaging-based clonal drug response assays

Evaluation of flow cytometry and imaging-based clonal drug response assays

One or more software components that automate import and integration of modelling data into Cytoscape

One or more software components that automate import and integration of modelling data into Cytoscape

Publications

Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer

Author(s): Emilia Kozłowska, Anniina Färkkilä, Tuulia Vallius, Olli Carpén, Jukka Kemppainen, Seija Grénman, Rainer Lehtonen, Johanna Hynninen, Sakari Hietanen, Sampsa Hautaniemi
Published in: Cancer Research, Issue 78/14, 2018, Page(s) 4036-4044, ISSN 0008-5472
DOI: 10.1158/0008-5472.can-17-3746

Clinical Value of 18 F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer

Author(s): J. Hynninen, M. Laasik, T. Vallius, J. Kemppainen, S. Grönroos, J. Virtanen, J. Casado, S. Hautaniemi, S. Grenman, M. Seppänen, A. Auranen
Published in: Clinical Oncology, Issue 30/8, 2018, Page(s) 507-514, ISSN 0936-6555
DOI: 10.1016/j.clon.2018.04.007

Identifying differentially methylated sites in samples with varying tumor purity

Author(s): Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Published in: Bioinformatics, Issue 34/18, 2018, Page(s) 3078-3085, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty310

Network module identification—A widespread theoretical bias and best practices

Author(s): Iryna Nikolayeva, Oriol Guitart Pla, Benno Schwikowski
Published in: Methods, Issue 132, 2018, Page(s) 19-25, ISSN 1046-2023
DOI: 10.1016/j.ymeth.2017.08.008

Behavior of FDG-avid supradiaphragmatic lymph nodes in PET/CT throughout primary therapy in advanced serous epithelial ovarian cancer: a prospective study

Author(s): Maren Laasik, Jukka Kemppainen, Annika Auranen, Sakari Hietanen, Seija Grénman, Marko Seppänen, Johanna Hynninen
Published in: Cancer Imaging, Issue 19/1, 2019, ISSN 1470-7330
DOI: 10.1186/s40644-019-0215-7

Anduril 2: upgraded large-scale data integration framework

Author(s): Alejandra Cervera, Ville Rantanen, Kristian Ovaska, Marko Laakso, Javier Nuñez-Fontarnau, Amjad Alkodsi, Julia Casado, Chiara Facciotto, Antti Häkkinen, Riku Louhimo, Sirkku Karinen, Kaiyang Zhang, Kari Lavikka, Lauri Lyly, Maninder Pal Singh, Sampsa Hautaniemi
Published in: Bioinformatics, Issue 35/19, 2019, Page(s) 3815-3817, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz133

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

Author(s): Jaana Oikkonen, Kaiyang Zhang, Liina Salminen, Ingrid Schulman, Kari Lavikka, Noora Andersson, Erika Ojanperä, Sakari Hietanen, Seija Grénman, Rainer Lehtonen, Kaisa Huhtinen, Olli Carpén, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Published in: JCO Precision Oncology, Issue 3, 2019, Page(s) 1-12, ISSN 2473-4284
DOI: 10.1200/po.18.00343

Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses

Author(s): Veli-Matti Isoviita, Liina Salminen, Jimmy Azar, Rainer Lehtonen, Pia Roering, Olli Carpén, Sakari Hietanen, Seija Grénman, Johanna Hynninen, Anniina Färkkilä, Sampsa Hautaniemi
Published in: JCO Clinical Cancer Informatics, Issue 3, 2019, Page(s) 1-16, ISSN 2473-4276
DOI: 10.1200/cci.18.00132

Virtual clinical trials identify effective combination therapies in ovarian cancer

Author(s): Emilia Kozłowska, Tuulia Vallius, Johanna Hynninen, Sakari Hietanen, Anniina Färkkilä, Sampsa Hautaniemi
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
DOI: 10.1038/s41598-019-55068-z

Improved detection of differentially represented DNA barcodes for high‐throughput clonal phenomics

Author(s): Yevhen Akimov, Daria Bulanova, Sanna Timonen, Krister Wennerberg, Tero Aittokallio
Published in: Molecular Systems Biology, Issue 16/3, 2020, ISSN 1744-4292
DOI: 10.15252/msb.20199195

qSNE: Quadratic rate t-SNE optimizer with automatic parameter tuning for large data sets

Author(s): Antti Häkkinen, Juha Koiranen, Julia Casado, Katja Kaipio, Oskari Lehtonen, Eleonora Petrucci, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Luca Pasquini, Mauro Biffoni, Rainer Lehtonen, Sampsa Hautaniemi
Published in: Bioinformatics, 2020, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btaa637

Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues

Author(s): Eros Azzalini, Eleonora De Martino, Paolo Fattorini, Vincenzo Canzonieri, Giorgio Stanta, Serena Bonin
Published in: International Journal of Molecular Sciences, Issue 20/19, 2019, Page(s) 4819, ISSN 1422-0067
DOI: 10.3390/ijms20194819