Improved clinical decisions via integrating multiple data levels to overcome chemotherapy resistance in high-grade serous ovarian cancer

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Midterm report on the success of the vMTB in referring patients to one of the clinical trials.

Midterm report on the success of the vMTB in referring patients to one of the clinical trials. Report with an overview of recruited subjects and on potential recruiting problems or delays and measures to rectify them

Set-up prime-editing and barcoding for HGSOC cell lines

Set-up prime-editing and barcoding for HGSOC cell lines.

Project Office and Knowledge Management System up and running

Project Office and Knowledge Management System up and running Operational Project manager allocated for the project and external and internal websites done Members of Exploitation and Dissemination panels assigned Materials for project presentation produced

A panel of 3-5 isogenic pairs of HGSOC ovarian cancer cell lines where important oncogenic/drug resistance patient mutations are introduced by gene editing

A panel of 3-5 isogenic pairs of HGSOC ovarian cancer cell lines where important oncogenic/drug resistance patient mutations are introduced by gene editing.

Completion of UH retrospective HGSOC cohort

Completion of UH retrospective HGSOC cohort.

First study subject approvals package

First study subject approvals package Final version of observational study protocol approved by the local Ethics committee and the study protocol of the first observational part will be submitted to ClinicalTrialscov for registration

Midterm recruitment report

Midterm recruitment report. At the time point when 50% of the study population is expected to have been recruited.

Bayesian network method ready for dynamic multi-omics integration

Bayesian network method ready for dynamic multi-omics integration.

Set up of single-cell RNA-seq and cell hashing for HGSOC

Set up of singlecell RNAseq and cell hashing for HGSOC

Uniformly processed and stored multi-omics data available for the consortium

Uniformly processed and stored multi-omics data available for the consortium.

First study subject approvals package: Final version of clinical trial protocol

First study subject approvals package. Final version of clinical trial protocol: Study protocol approved by local Ethics committee, TUCH and FIMEA. Clinical trial protocol submitted to ClinicalTrials.cov for registration.

Preliminary report on regulatory issues in personalised medicine

Preliminary report on regulatory issues in personalised medicine.

Performance evaluation of the Predictor Tool

Performance evaluation of the Predictor Tool. The tool has been validated in independent HGSOC datasets.

Full design documentation for the eXplAIner software

Knowledge-base of associations between genomic indications and EMA approved drugs

Knowledge-base of associations between genomic indications and EMA approved drugs.

Fully functional, documented, and publicly available open-source eXplAIner app store

Fully functional, documented, and publicly available open-source eXplAIner app store.

Fully functional, documented, and publicly available open-source eXplAIner software

Fully functional, documented, and publicly available open-source eXplAIner software.

Data Management Plan

Data Management Plan A detailed and updated Data Management Plan available on the project website where the latest updated version will be available

Publications

TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening

Author(s): Miguel M. Álvarez, Josep Biayna & Fran Supek
Published in: Nature Communications, Issue 13(4520), 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-32285-1

Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

Author(s): Ignasi Toledano, Fran Supek, Ben Lehner
Published in: Nature Genetics, Issue 56, 2024, Page(s) 1914-1924, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-024-01878-5

Activation of invasion by oncogenic reprogramming of cholesterol metabolism via increased NPC1 expression and macropinocytosis

Author(s): Aikaterini Skorda, Anna Røssberg Lauridsen, Chengnan Wu, Jinrong Huang, Monika Mrackova, Nuggi Ingholt Winther, Vanessa Jank , Zsofia Sztupinszki, Robert Strauss , Mesut Bilgin, Kenji Maeda, Bin Liu, Yonglun Luo, Marja Jäättelä,Tuula Kallunki
Published in: Oncogene, 2023, ISSN 1476-5594
Publisher: Springer Nature Publishing Company
DOI: 10.1038/s41388-023-02771-x

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

Author(s): Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D Bader, Sylvie Baier, David B Blumenthal, Jing Chen, Maria L Elkjaer, Carlos Garcia-Hernandez, Mohamed Helmy, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Miles Mee, Mhaned Oubounyt, Chiara Past
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) W481-W488, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae388

LIANA+ provides an all-in-one framework for cell–cell communication inference

Author(s): Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, Julio Saez-Rodriguez
Published in: Nature Cell Biology, Issue 26, 2024, Page(s) 1613-1622, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-024-01469-w

Comparative Analysis of Gene Expression Analysis Methods for RNA in Situ Hybridization Images

Author(s): Valeria Ariotta, Eros Azzalini, Vincenzo Canzonieri, Sampsa Hautaniemi, Serena Bonin
Published in: The Journal of Molecular Diagnostics, Issue 26, 2024, Page(s) 931-942, ISSN 1525-1578
Publisher: American Society for Investigative Pathology
DOI: 10.1016/j.jmoldx.2024.06.010

DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy

Author(s): Ahmed Khalil, Fran Supek
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-59397-8

Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level

Author(s): Anna Perkiö, Barun Pradhan, Fatih Genc, Anna Pirttikoski, Sanna Pikkusaari, Erdogan Pekcan Erkan, Matias Marin Falco, Kaisa Huhtinen, Sara Narva, Johanna Hynninen, Liisa Kauppi, Anna Vähärautio
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-54113-w

POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching

Author(s): Susanna Holmström, Sampsa Hautaniemi, Antti Häkkinen
Published in: Bioinformatics, 2022, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac124

An overview of machine learning methods for monotherapy drug response prediction.

Author(s): Farzaneh Firoozbakht, Behnam Yousefi, Benno Schwikowski
Published in: Briefings in Bioinformatics, Issue 23:1, 2022, ISSN 1477-4054
Publisher: Oxford, United Kingdom
DOI: 10.1093/bib/bbab408

Cell cycle alterations associate with a redistribution of mutation rates across chromosomal domains in human cancers

Author(s): Marina Salvadores, Fran Supek
Published in: Nature Cancer, 2024, ISSN 2662-1347
Publisher: Nature Research
DOI: 10.1038/s43018-023-00707-8

Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks

Author(s): Martin Garrido-Rodriguez , Katharina Zirngibl, Olga Ivanova, Sebastian Lobentanzer, Julio Saez-Rodriguez
Published in: Molecular Systems Biology, Issue 18, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202211036

Bexmarilimab Activates Human Tumor-Associated Macrophages to Support Adaptive Immune Responses in Interferon-Poor Immune Microenvironments

Author(s): Jenna H. Rannikko, Petri Bono, Johanna Hynninen, Maija Hollmén
Published in: Cancer Immunol Res, Issue 12(1), 2024, Page(s) 48-59, ISSN 2326-6074
Publisher: American Association for Cancer Research
DOI: 10.1158/2326-6066.cir-23-0350

A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids

Author(s): Wojciech Senkowski, Laura Gall-Mas, Matías Marín Falco, Yilin Li, Kari Lavikka, Mette C. Kriegbaum, Jaana Oikkonen, Daria Bulanova, Elin J. Pietras, Karolin Voßgröne, Yan-Jun Chen, Erdogan Pekcan Erkan, Jun Dai, Anastasia Lundgren, Mia Kristine Grønning Høg, Ida Marie Larsen, Tarja Lamminen, Katja Kaipio, Jutta Huvila, Anni Virtanen, Lars Engelholm, Pernille Christiansen, Eric Santoni-Rugiu,
Published in: Developmental Cell, Issue 58, 2023, Page(s) 1106-1121.e7, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2023.04.012

QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability

Author(s): Sanaz Jamalzadeh, Antti Häkkinen, Noora Andersson, Kaisa Huhtinen, Anna Laury, Sakari Hietanen, Johanna Hynninen,Jaana Oikkonen, Olli Carpén, Anni Virtanen, Sampsa Hautaniemi
Published in: Laboratory Investigation, 2022, ISSN 1530-0307
Publisher: Nature Publishing Group
DOI: 10.1038/s41374-022-00743-5

The impact of rare germline variants on human somatic mutation processes

Author(s): Mischan Vali-Pour, Ben Lehner, Fran Supek
Published in: Nature Communications, Issue 13, 2022, Page(s) 3724, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31483-1

Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma

Author(s): Mai T.N. Nguyen, Anna Rajavuori, Kaisa Huhtinen, Sakari Hietanen, Johanna Hynninen, Jaana Oikkonen, Sampsa Hautaniemi
Published in: Biomedicine & Pharmacotherapy, Issue 168, 2023, ISSN 1950-6007
Publisher: Elsevier B.V
DOI: 10.1016/j.biopha.2023.115630

Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones

Author(s): Aleksandr Ianevski, Kristen Nader, Kyriaki Driva, Wojciech Senkowski, Daria Bulanova, Lidia Moyano-Galceran, Tanja Ruokoranta, Heikki Kuusanmäki, Nemo Ikonen, Philipp Sergeev, Markus Vähä-Koskela, Anil K. Giri, Anna Vähärautio, Mika Kontro, Kimmo Porkka, Esa Pitkänen, Caroline A. Heckman, Krister Wennerberg, Tero Aittokallio
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52980-5

A survey on data integration for multi-omics sample clustering

Author(s): Marta Lovino; Vincenzo Randazzo; Gabriele Ciravegna; Pietro Barbiero; Elisa Ficarra; Giansalvo Cirrincione
Published in: Neurocomputing, Issue 488, 2022, Page(s) 494-508, ISSN 0925-2312
Publisher: Elsevier BV
DOI: 10.1016/j.neucom.2021.11.094

A platform for the biomedical application of large language models

Author(s): Sebastian Lobentanzer, Shaohong Feng, Noah Bruderer, Andreas Maier, null null, Adrián G. Díaz, Amy Strange, Anis Ismail, Anton Kulaga, Aurelien Dugourd, Barbara Zdrazil, Bastien Chassagnol, Cyril Pommier, Daniele Lucarelli, Ellen M. McDonagh, Emma Verkinderen, Fernando M. Delgado-Chaves, Georg Fuellen, Hannah Sonntag, Jonatan Menger, Lionel Christiaen, Ludwig Geistlinger, Luna Zacharias Zetsche,
Published in: Nature Biotechnology, Issue 43, 2025, Page(s) 166-169, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-024-02534-3

A Subset of Secreted Proteins in Ascites Can Predict Platinum-Free Interval in Ovarian Cancer

Author(s): Molly J. Carroll, Katja Kaipio, Johanna Hynninen, Olli Carpen, Sampsa Hautaniemi, David Page, Pamela K. Kreeger
Published in: Cancers, Issue 14(17), 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174291

Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation

Author(s): David Mas-Ponte, Fran Supek
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 4393-4408, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae252

Integrated microRNA and proteome analysis of cancer datasets with MoPC

Author(s): Marta Lovino, Elisa Ficarra, Loredana Martignetti
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0289699, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0289699

Proton and alpha radiation-induced mutational profiles in human cells

Author(s): Tiffany M. Delhomme, Maia Munteanu, Manuela Buonanno, Veljko Grilj, Josep Biayna & Fran Supek
Published in: Scientific Reports, Issue 13(9791), 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-36845-3

A Graph-Based Multi-Scale Approach with Knowledge Distillation for WSI Classification

Author(s): Gianpaolo Bontempo; Federico Bolelli; Angelo Porrello; Simone Calderara; Elisa Ficarra
Published in: IEEE Transaction on medical imging, 2023, ISSN 0278-0062
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tmi.2023.3337549

Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma

Author(s): Sanaz Jamalzadeh, Jun Dai, Kari Lavikka, Yilin Li, Jing Jiang, Kaisa Huhtinen, Anni Virtanen, Jaana Oikkonen, Sakari Hietanen, Johanna Hynninen, Anna Vähärautio, Antti Häkkinen* and Sampsa Hautaniemi*
Published in: BMC Cancer, Issue 24:173, 2024, ISSN 1471-2407
Publisher: BioMed Central
DOI: 10.1186/s12885-024-11895-6

Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

Author(s): David Mas-Ponte, Marcel McCullough, Fran Supek
Published in: Clinical Science, Issue 136 (5), 2022, Page(s) 383–404, ISSN 1470-8736
Publisher: Portland Press Limited
DOI: 10.1042/cs20210682

Quantification of cell death and proliferation of patient-derived ovarian cancer organoids through 3D imaging and image analysis

Author(s): Aikaterini Skorda, Anna Røssberg Lauridsen, Kaisa Huhtinen, Alexandra Lahtinen, Wojciech Senkowski, Jaana Oikkonen, Johanna Hynninen, Sampsa Hautaniemi. Tuula Kallunki
Published in: STAR Protocols, Issue 4(4), 2023, ISSN 2666-1667
Publisher: Elsevier B.V
DOI: 10.1016/j.xpro.2023.102683

A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells

Author(s): Daria Bulanova, Yevhen Akimov, Wojciech Senkowski, Jaana Oikkonen, Laura Gall-Mas, Sanna Timonen, Manar Elmadani, Johanna Hynninen, Sampsa Hautaniemi, Tero Aittokallio, Krister Wennerberg
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.adj1564

Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1 and GSTP1 in high-grade serous ovarian cancer.

Author(s): Feng Deng, Maren Laasik, Liina Salminen, Lauri Lapatto, Kaisa Huhtinen, Yilin Li, Sampsa Hautaniemi, Johanna Hynninen, Mikko Niemi, Rainer Lehtonen
Published in: Basic & Clinical Pharmacology & Toxicology, Issue 1-11, 2023, ISSN 1742-7843
Publisher: John Wiley & Sons, Inc.
DOI: 10.1111/bcpt.13866

Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention.

Author(s): 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
Published in: Cell Death and Disease, Issue 13, 2022, ISSN 2041-4889
Publisher: Nature Publishing Group
DOI: 10.1038/s41419-022-05161-5

Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of homologous recombination deficiency in tumors

Author(s): Fran Supek, Patricia Ferrer-Torres
Published in: Genome Medicine, Issue 17, 2024, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.21203/rs.3.rs-4833999/v1

Prevalence, causes and impact of TP53-loss phenocopying events in human tumors

Author(s): Bruno Fito-Lopez; Marina Salvadores; Miguel-Martin Alvarez; Fran Supek
Published in: BMC Biology, Issue 21(92), 2023, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-023-01595-1

Molecular causality in the advent of foundation models

Author(s): Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez
Published in: Molecular Systems Biology, Issue 20, 2024, Page(s) 848-858, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-024-00041-w

H&E image analysis pipeline for quantifying morphological features

Author(s): Valeria Ariotta, Oskari Lehtonen, Shams Salloum, Giulia Micoli, Kari Lavikka, Ville Rantanen, Johanna Hynninen, Anni Virtanen, Sampsa Hautaniemi
Published in: Journal of Pathology Informatics, Issue 14, 2023, ISSN 2153-3539
Publisher: Elsevier B.V
DOI: 10.1016/j.jpi.2023.100339

MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge

Author(s): Elena Pianfetti; Marta Lovino; Elisa Ficarra; Loredana Martignetti
Published in: BMC Bioinformatics, Issue 24, 2023, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05560-1

Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics

Author(s): Kari Lavikka, Altti Ilari Maarala, Jaana Oikkonen, Sampsa Hautaniemi
Published in: Bioinformatics, Issue 41, 2025, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaf091

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations

Author(s): Alessio Mascolini; Dario Cardamone; Francesco Ponzio; Santa Di Cataldo; Elisa Ficarra
Published in: BMC Bioinformatics, Issue 23(295), 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04845-1

Predicting gene and protein expression levels from DNA and protein sequences with Perceiver

Author(s): Matteo Stefanini; Marta Lovino; Rita Cucchiara; Elisa Ficarra
Published in: Computer Methods and Programs in Biomedicine, Issue 234, 2023, ISSN 1872-7565
Publisher: Elsevier B.V
DOI: 10.1101/2022.09.21.508821

Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes

Author(s): Sanna Pikkusaari, Manuela Tumiati, Anni Virtanen, Jaana Oikkonen, Yilin Li, Fernando Perez-Villatoro, Taru Muranen, Matilda Salko, Kaisa Huhtinen, Anna Kanerva, Heidi Koskela, Johanna Tapper, Riitta Koivisto-Korander, Titta Joutsiniemi, Ulla-Maija Haltia, Heini Lassus, Sampsa Hautaniemi, Anniina Färkkilä, Johanna Hynninen, Sakari Hietanen, Olli Carpen, Liisa Kauppi
Published in: Clinical Cancer Research, Issue 1557-3265, 2023, Page(s) OF1–OF14, ISSN 1557-3265
Publisher: American Association for Cancer Research
DOI: 10.1158/1078-0432.ccr-22-3156

ROR1-STAT3 signaling contributes to ovarian cancer intra-tumor heterogeneity

Author(s): Emilia Piki, Alice Dini, Juuli Raivola, Kari Salokas, Kaiyang Zhang, Markku Varjosalo, Teijo Pellinen, Katja Välimäki, Kristina Tabor Veskimäe, Synnöve Staff, Sampsa Hautaniemi, Astrid Murumägi, Daniela Ungureanu
Published in: Cell Death Discovery, Issue 9 (222), 2023, ISSN 2058-7716
Publisher: Nature Publishing Group
DOI: 10.1038/s41420-023-01527-6

Author(s): Heidi Koskela, Yilin Li, Titta Joutsiniemi, Taru Muranen, Veli-Matti Isoviita, Kaisa Huhtinen, Giulia Micoli, Kari Lavikka, Giovanni Marchi, Sakari Hietanen, Anni Virtanen, Sampsa Hautaniemi, Jaana Oikkonen, Johanna Hynninen
Published in: Gynecologic Oncology, Issue 180, 2024, Page(s) 91-98, ISSN 1095-6859
Publisher: Elsevier B.V
DOI: 10.1016/j.ygyno.2023.11.027

Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach

Author(s): Liangru Fei, Kaiyang Zhang, Sampsa Hautaniemi, Biswajyoti Sahu
Published in: STAR Protocols, Issue 5, 2025, Page(s) 103148, ISSN 2666-1667
Publisher: Elsevier BV
DOI: 10.1016/j.xpro.2024.103148

Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

Author(s): Kari Lavikka, Jaana Oikkonen, Yilin Li, Taru Muranen, Giulia Micoli, Giovanni Marchi, Alexandra Lahtinen, Kaisa Huhtinen, Rainer Lehtonen, Sakari Hietanen, Johanna Hynninen, Anni Virtanen, Sampsa Hautaniemi
Published in: GigaScience, Issue 13, 2024, ISSN 2047-217X
Publisher: Oxford Academic
DOI: 10.1093/gigascience/giae040

Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma

Author(s): Alexandra Lahtinen; Kari Lavikka; Anni Virtanen; Yilin Li; Sanaz Jamalzadeh; Aikaterini Skorda; Anna Røssberg Lauridsen; Kaiyang Zhang; Giovanni Marchi; Veli-Matti Isoviita; Valeria Ariotta; Oskari Lehtonen; Taru A. Muranen; Kaisa Huhtinen; Olli Carpén; Sakari Hietanen; Wojciech Senkowski; Tuula Kallunki; Antti Häkkinen; Johanna Hynninen; Jaana Oikkonen; Sampsa Hautaniemi
Published in: Cancer Cell, Issue 41, 2023, Page(s) 1103–1117, ISSN 1878-3686
Publisher: Elsevier B.V
DOI: 10.1016/j.ccell.2023.04.017

Kinase Inhibitors in the Treatment of Ovarian Cancer: Current State and Future Promises

Author(s): Aikaterini Skorda, Marie Lund Bay, Sampsa Hautaniemi, Alexandra Lahtinen, Tuula Kallunki
Published in: Cancers, Issue 14(24), 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14246257

Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer

Author(s): 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
Published in: Science Advances, Issue eabm1831, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abm1831

Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations

Author(s): Elizaveta Besedina, Fran Supek
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-50552-1

Identifying the oncogenic potential of gene fusions exploiting miRNAs

Author(s): Marta Lovino, Marilisa Montemurro, Venere S Barrese, Elisa Ficarra
Published in: Journal of Biomedical Informatics, Issue 129, 2022, ISSN 1532-0464
Publisher: Academic Press
DOI: 10.1016/j.jbi.2022.104057

Artificial intelligence-based image analysis can predict outcome in high-grade serous carcinoma via histology alone

Author(s): Anna Ray Laury, Sami Blom, Tuomas Ropponen, Anni Virtanen, Olli Mikael Carpén
Published in: Scientific Reports, Issue 11/1, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-98480-0

SAMURAI: Shallow Analysis of copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline

Author(s): Sara Potente, Diego Boscarino, Dino Paladin, Sergio Marchini, Luca Beltrame, Chiara Romualdi
Published in: Briefings in Bioinformatics, Issue 26(1), 2025, ISSN 1477-4054
Publisher: Oxford Academic
DOI: 10.1101/2024.09.30.615766

Mutational signatures are markers of drug sensitivity of cancer cells

Author(s): Levatić, Jurica; Salvadores, Marina; Fuster-Tormo, Francisco; Supek, Fran; Universitat Autònoma de Barcelona
Published in: Nature Communications, Issue 13, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.05.19.444811

PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures

Author(s): Heidi Rausio, Alejandra Cervera, Vanina D. Heuser, Gun West, Jaana Oikkonen, Elena Pianfetti, Marta Lovino, Elisa Ficarra, Pekka Taimen, Johanna Hynninen, Rainer Lehtonen, Sampsa Hautaniemi, Olli Carpén, Kaisa Huhtinen
Published in: Neoplasia, Issue 51, 2024, ISSN 1476-5586
Publisher: Elsevier B.V
DOI: 10.1016/j.neo.2024.100987

Democratizing knowledge representation with BioCypher

Author(s): Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent J. Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Doğan, Johann Dreo, Ian Dunham, Elias Farr, Adrià Fernandez-Torras, Benjamin M. Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas P
Published in: Nature Biotechnology, Issue 41, 2023, Page(s) 1056–1059, ISSN 1546-1696
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01848-y

Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer.

Author(s): "Fernando Perez-Villatoro, Jaana Oikkonen, Julia Casado, Anastasiya Chernenko, Doga C. Gulhan, Manuela Tumiati, Yilin Li, Kari Lavikka, Sakari Hietanen, Johanna Hynninen, Ulla-Maija Haltia, Jaakko S. Tyrmi, Hannele Laivuori, Panagiotis A. Konstantinopoulos, Sampsa Hautaniemi, Liisa Kauppi, Anniina Färkkilä """
Published in: NPJ Precision Oncology, Issue 6(1), 2022, Page(s) 96, ISSN 2397-768X
Publisher: Nature Publishing Group
DOI: 10.1038/s41698-022-00339-8

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

Author(s): Elias Farr, Daniel Dimitrov, Christina Schmidt, Denes Turei, Sebastian Lobentanzer, Aurelien Dugourd, Julio Saez-Rodriguez
Published in: Briefings in Bioinformatics, Issue 25, 2024, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbae347

Extensive mutational ctDNA profiles reflect High-grade serous cancer tumors and reveal emerging mutations at recurrence

Author(s): Giovanni Marchi, Anna Rajavuori, Mai T N Nguyen, Kaisa Huhtinen, Sinikka Oksa, Sakari Hietanen, Sampsa Hautaniemi, Johanna Hynninen, Jaana Oikkonen
Published in: Translational Oncology, Issue 2(39), 2023, ISSN 1944-7124
Publisher: Elsevier B.V
DOI: 10.1016/j.tranon.2023.101814

Paving the Path for Sustainable and Responsible Off-Label Use of Pharmaceutical Products in Europe

Author(s): Miquel Díaz Hernández; Waltter Roslin; Juli Mansnérus
Published in: European Journal of Health Law, Issue 31(2), 2024, Page(s) 129–152, ISSN 1571-8093
Publisher: Brill
DOI: 10.1163/15718093-bja10123

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

Author(s): Vittorio Pipoli; Mattia Cappelli; Alessandro Palladini; Carlo Peluso; Marta Lovino; Elisa Ficarra
Published in: Computer Methods and Programs in Biomedicine, Issue 225, 2022, ISSN 1872-7565
Publisher: Elsevier B.V
DOI: 10.1016/j.cmpb.2022.107035

Comparative evaluation of feature reduction methods for drug response prediction

Author(s): Farzaneh Firoozbakht, Behnam Yousefi, Olga Tsoy, Jan Baumbach, Benno Schwikowski
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-81866-1

Why make it if you can take it: review on extracellular cholesterol uptake and its importance in breast and ovarian cancers

Author(s): Anna Røssberg Lauridsen, Aikaterini Skorda, Nuggi Ingholt Winther, Marie Lund Bay, Tuula Kallunki
Published in: Journal of Experimental & Clinical Cancer Research, Issue 43, 2024, ISSN 1756-9966
Publisher: BioMed Central
DOI: 10.1186/s13046-024-03172-y

From the integrity of potency assays to safe clinical intervention: Legal perspectives.

Author(s): Waltter Roslin, Juli Mansnérus
Published in: Potency Assays for Advanced Stem Cell Therapy Medicinal Products, Issue 1, 2023, Page(s) 151-163, ISBN 978-3-031-30039-4
Publisher: Springer Publishing Company
DOI: 10.1007/978-3-031-30040-0_10

Lääkkeiden off label -käyttö lapsipotilailla: lapsen osallisuuden oikeudelliset reunaehdot

Author(s): Juli Mansnérus, Charlotta Bonsdorff, Petro Vornanen
Published in: Terveys ja lapsen oikeudet, Issue 2023:7, 2023, Page(s) 190-203, ISBN 978-952-400-747-4
Publisher: Office of the Ombudsman for Children

FusionFlow: An Integrated System Workflow for Gene Fusion Detection in Genomic Samples

Author(s): Federica Citarrella; Gianpaolo Bontempo; Marta Lovino; Elisa Ficarra
Published in: New Trends in Database and Information Systems, 2022, ISBN 978-3-031-15743-1
Publisher: Springer Publishing Company
DOI: 10.1007/978-3-031-15743-1_8

Enhancing PFI Prediction with GDS-MIL: A Graph-based Dual Stream MIL Approach

Author(s): Gianpaolo Bontempo, Nicola Bartolini, Marta Lovino, Federico Bolelli, Anni Virtanen, Elisa Ficarra
Published in: Lecture Notes in Computer Science, Issue 14233, 2023, Page(s) 550-562, ISSN 1611-3349
Publisher: Springer
DOI: 10.1007/978-3-031-43148-7_46

ClusterFix: A Cluster-Based Debiasing Approach without Protected-Group Supervision

Author(s): Giacomo Capitani, Federico Bolelli, Angelo Porrello, Simone Calderara, Elisa Ficarra
Published in: 2024 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), Issue 30, 2024, Page(s) 4858-4867
Publisher: IEEE
DOI: 10.1109/wacv57701.2024.00480

DAS-MIL: Distilling Across Scales for MIL Classification of Histological WSIs

Author(s): Bontempo, Gianpaolo; Porrello, Angelo; Bolelli, Federico; Calderara, Simone; Ficarra, Elisa
Published in: Lecture Notes in Computer Science, Issue 14220, 2023, Page(s) 248-258, ISSN 1611-3349
Publisher: Springer
DOI: 10.1007/978-3-031-43907-0_24

Buffer-MIL: Robust Multi-instance Learning with a Buffer-based Approach

Author(s): Gianpaolo Bontempo, Luca Lumetti, Angelo Porrello, Federico Bolelli, Simone Calderara, Elisa Ficarra
Published in: Lecture Notes in Computer Science, Issue 14234, 2023, Page(s) 1-12, ISSN 1611-3349
Publisher: Springer
DOI: 10.1007/978-3-031-43153-1_1

Computational investigation of cancer transcriptomics

Author(s): Kaiyang Zhang
Published in: 2024, ISBN 978-951-51-9817-4
Publisher: University of Helsinki

More than meets the eye? : Artificial intelligence-directed spatial transcriptomics of high grade serous carcinoma

Author(s): Anna Laury
Published in: 2024, ISBN 978-952-84-0323-4
Publisher: University o Helsinki

Transcriptome-based characterization of treatment resistance mechanisms in high-grade serous carcinoma

Author(s): Sanaz Jamalzadeh
Published in: 2024, ISBN 978-951-51-9735-1
Publisher: University of Helsinki

Itsemääräämisoikeus ja innovatiiviset terapiat – kuka määrää?

Author(s): Amanda Blick, Juli Mansnérus
Published in: Defensor Legis, Issue 2, 2025, Page(s) 193-207, ISSN 0356-262X
Publisher: Suomen asianajajaliitto

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