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.
2025
Giulia Micoli, Kari Lavikka, Yilin Li, Anna Pirttikoski, Daria Afenteva, Wojciech Senkowski, Giovanni Marchi, Anna Vähärautio, Taru A. Muranen, Titta Joutsiniemi, Sakari Hietanen, Anni Virtanen, Krister Wennerberg, Johanna Hynninen, Jaana Oikkonen, Sampsa Hautaniemi. Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer. Cancer Discovery (2025) OF1–OF16.
Daria Afenteva, Rong Yu, Anna Rajavuori, Marina Salvadores, Inga-Maria Launonen, Kari Lavikka, Kaiyang Zhang, Anna Pirttikoski, Giovanni Marchi, Sanaz Jamalzadeh, Veli-Matti Isoviita, Yilin Li, Giulia Micoli, Erdogan Pekcan Erkan, Matias M. Falco, Daniela Ungureanu, Alexandra Lahtinen, Jaana Oikkonen, Sakari Hietanen, Anna Vähärautio, Inderpreet Sur, Anni Virtanen, Anniina Faärkkilä, Johanna Hynninen, Taru A. Muranen, Jussi Taipale, Sampsa Hautaniem. Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer. Cell Reports Medicine (2025).
Patricia Ferrer-Torres, Iván Galván-Femenía, Fran Supek. Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of DNA repair deficiencies. Genome Medicine (2025) 17.
Ahmed Khalil & Fran Supek. DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy. Nature Communications (2025) 16:4209.
Kari Lavikka, Altti Ilari Maarala, Jaana Oikkonen, Sampsa Hautaniemi. Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics. Bioinformatics (2025) 41(3).
Sebastian Lobentanzer, Shaohong Feng, Noah Bruderer, Andreas Maier, The BioChatter Consortium, Cankun Wang, Jan Baumbach, Jorge Abreu-Vicente, Nils Krehl, Qin Ma, Thomas Lemberger, Julio Saez-Rodriguez. A platform for the biomedical application of large language models. Nature Biotechnology (2025) 43:166–169.
Sara Potente, Diego Boscarino, Dino Paladin, Sergio Marchini, Luca Beltrame, Chiara Romualdi. SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline. Briefings in Bioinformatics (2025) 26(1).
Amanda Blick & Juli Mansnérus. Itsemääräämisoikeus ja innovatiiviset terapiat – kuka määrää? Defensor Legis (2025) 2:193-207.
2024
Inga-Maria Launonen, Iga Niemiec, María Hincapié-Otero, Erdogan Pekcan Erkan, Ada Junquera, Daria Afenteva, Matias M. Falco, Zhihan Liang, Matilda Salko, Foteini Chamchougia, Angela Szabo, Fernando Perez-Villatoro, Yilin Li, Giulia Micoli, Ashwini Nagaraj, Ulla-Maija Haltia, Essi Kahelin, Jaana Oikkonen, Johanna Hynninen, Anni Virtanen, Ajit J. Nirmal, Tuulia Vallius, Sampsa Hautaniemi, Peter K. Sorger, Anna Vähärautio, Anniina Färkkilä. Chemotherapy induces myeloid-driven spatiallyconfined T cell exhaustion in ovarian cancer. Cancer Cell (2024) 2045-2063.e10.
Pablo Rodriguez-Mier, Martin Garrido-Rodriguez, Attila Gabor, Julio Saez-Rodriguez. Unifying multi-sample network inference from prior knowledge and omics data with CORNETO. Nature Machine Intelligence (2024) 7: 1168–1186.
Anna Ray Laury, Shuyu Zheng, Niina Aho, Robin Fallegger, Satu Hänninen, Julio Saez-Rodriguez, Jovan Tanevski, Omar Youssef, Jing Tang, Olli Mikael Carpen. Opening the Black Box: Spatial Transcriptomics and the Relevance of Artificial Intelligence – Detected Prognostic Regions in High-Grade Serous Carcinoma. Modern Pathology (2024) 37: 100508.
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. Single-cell transcriptomes identify patienttailored therapies for selective co-inhibition of cancer clones. Nature Communications (2024) 15:8579.
Anna Røssberg Lauridsen, Aikaterini Skorda, Nuggi Ingholt Winther, Marie Lund Bay, Tuula Kallunki. Why make it if you can take it: review on extracellular cholesterol uptake and its importance in breast and ovarian cancers. Journal of Experimental & Clinical Cancer Research (2024) 43:254.
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. Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit. GigaScience (2024) 13:1–15.
Marta Lovino, Elisa Ficarra, Loredana Martignetti. Integrated microRNA and proteome analysis of cancer datasets with MoPC. PLoS ONE (2024) 19(3).
Sebastian Lobentanzer, Pablo Rodriguez-Mier, Stefan Bauer, Julio Saez-Rodriguez. Molecular causality in the advent of foundation models. Molecular Systems Biology (2024).
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. PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures. Neoplasia (2024) 51.
Miquel Díaz Hernández, Waltter Roslin, Juli Mansnérus. Paving the Path for Sustainable and Responsible Off-Label Use of Pharmaceutical Products in Europe. European Journal of Health Law (2024).
Juli Mansnérus, Charlotta Bonsdorff, Petro Vornanen. Lääkkeiden off label -käyttö lapsipotilailla: lapsen osallisuuden oikeudelliset reunaehdot. Terveys ja lapsen oikeudet (2024) 7.
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. Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level. Scientific Reports (2024) 14:4322.
Sanaz Jamalzadeh, Jun Dai, Kari Lavikka, Yilin Li, Jing Jiang, Kaisa Huhtinen, Anni Virtanen, Jaana Oikkonen, Sakari Hietanen, Johanna Hynninen, Anna Vähärautio, Antti Häkkinen*, Sampsa Hautaniemi.* Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma. BMC Cancer (2024) 24:173.
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. HRD related signature 3 predicts clinical outcome in advanced tubo-ovarian high-grade serous carcinoma. Gynecologic Oncology (2024) 180:91-98.
Jenna H. Rannikko, Petri Bono, Johanna Hynninen, Maija Hollmén. Bexmarilimab Activates Human Tumor-Associated Macrophages to Support Adaptive Immune Responses in Interferon-Poor Immune Microenvironments. Cancer Immunology Research (2024) 12(1):48-59.
Marina Salvadores & Fran Supek. Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers. Nature Cancer (2024).
Valeria Ariotta, Eros Azzalini, Vincenzo Canzonieri, Sampsa Hautaniemi, Serena Boniny. Comparative Analysis of Gene Expression Analysis Methods for RNA in Situ Hybridization Images. The Journal of Molecular Diagnostics (2024) 26:931-942.
Daria Bulanova, Yevhen Akimov, Wojciech Senkowski, Jaana Oikkonen, Laura Gall-Mas, Sanna Timonen, Manar Elmadani, Johanna Hynninen, Sampsa Hautaniemi, Tero Aittokallio, Krister Wennerberg. A synthetic lethal dependency on casein kinase 2 in response to replication- perturbing therapeutics in RB1- deficient cancer cells. Science Advances (2024) 10:eadj1564.
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. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nature Cell Biology (2024) 26:1613-1622.
Elias Farr, Daniel Dimitrov, Christina Schmidt, Denes Turei, Sebastian Lobentanzer, Aurelien Dugourd, Julio Saez-Rodriguez. MetalinksDB: a f lexible and contextualizable resource of metabolite-protein interactions. Briefings in Bioinformatics (2024) 25(4).
Liangru Fei, Kaiyang Zhang, Sampsa Hautaniemi, Biswajyoti Sahu. Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach. STAR Protocols (2024) 5:103148.
Farzaneh Firoozbakht, Behnam Yousefi, Olga Tsoy, Jan Baumbach, Benno Schwikowski. Comparative evaluation of feature reduction methods for drug response prediction. Scientific Reports (2024) 14:30885.
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 Pastrello, Alexander R. Pico, Rudolf T. Pillich, Julian M. Poschenrieder, Dexter Pratt, Nataša Pržulj, Sepideh Sadegh, Julio Saez-Rodriguez, Suryadipto Sarkar, Gideon Shaked, Ron Shamir, Nico Trummer, Ugur Turhan, Rui-Sheng Wang, Olga Zolotareva, Jan Baumbach. Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Research (2024) 52:W481–W488.
David Mas-Ponte & Fran Supek. Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation. Nucleic Acids Research (2024) 52:4393–4408.
Ignasi Toledano, Fran Supek, Ben Lehner. Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules. Nature Genetics (2024) 56:1914–1924.
2023
Wojciech Senkowski, Laura Gall-Mas, Matias Marin 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, Kaisa Huhtinen, Olli Carpén, Johanna Hynninen, Sampsa Hautaniemi, Anna Vähärautio, and Krister Wennerberg. A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids. Developmental Cell (2023) 58:1106–1121
Elizaveta Besedina & Fran Supek. Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations. Nature Communications (2023) 15:6139
Gianpaolo Bontempo, Federico Bolelli, Angelo Porrello, Simone Calderara, Elisa Ficarra. A Graph-Based Multi-Scale Approach with Knowledge Distillation for WSI Classification. IEEE Transaction on medical imaging (2023).
Gianpaolo Bontempo, Angelo Porrello, Federico Bolelli, Simone Calderara, Elisa Ficarra. DAS-MIL: Distilling Across Scales for MIL classification of histological WSIs. Medical Image Computing and Computer Assisted Intervention – MICCAI (2023) 14220:248-258
Gianpaolo Bontempo, Nicola Bartolini, Marta Lovino, Federico Bolelli, Anni Virtanen, Elisa Ficarra. Enhancing PFI Prediction with GDS-MIL: A Graph-based Dual Stream MIL Approach. International Conference on Image Analysis and Processing – ICIAP (2023) 14233:550-562
Gianpaolo Bontempo, Luca Lumetti, Angelo Porrello, Federico Bolelli, Simone Calderara, Elisa Ficarra. Buffer-MIL: Robust Multi-instance Learning with a Buffer-based Approach. Image Analysis and Processing – ICIAP (2023) 14234:1-12
Elena Pianfetti, Marta Lovino, Elisa Ficarra, Loredana Martignetti. MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge. BMC Bioinformatics (2023) 24.
Bruno Fito‑Lopez, Marina Salvadores, Miguel‑Martin Alvarez & Fran Supek. Prevalence, causes and impact of TP53‑loss phenocopying events in human tumors. BMC Biology (2023) 21(92).
Tiffany M. Delhomme, Maia Munteanu, Manuela Buonanno, Veljko Grilj, Josep Biayna & Fran Supek. Proton and alpha radiation‑induced mutational profiles in human cells. Scientifc Reports (2023) 13(9791).
Matteo Stefanini, Marta Lovino, Rita Cucchiara & Elisa Ficarra. Predicting gene and protein expression levels from DNA and protein sequences with Perceiver. Computer Methods and Programs in Biomedicine (2023) 234.
Aikaterini Skorda, Anna Røssberg Lauridsen, Kaisa Huhtinen, Alexandra Lahtinen, Wojciech Senkowski, Jaana Oikkonen, Johanna Hynninen, Sampsa Hautaniemi & Tuula Kallunki. Quantification of cell death and proliferation of patientderived ovarian cancer organoids through 3D imaging and image analysis. STAR Protocols (2023) 4(4).
Giovanni Marchi*, Anna Rajavuori*, Mai T N Nguyen, Kaisa Huhtinen, Sinikka Oksa, Sakari Hietanen, Sampsa Hautaniemi, Johanna Hynninen* & Jaana Oikkonen*. Extensive mutational ctDNA profiles reflect High-grade serous cancer tumors and reveal emerging mutations at recurrence. Translational Oncology (2023) 2(39).
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 Probul, Benno Schwikowski, Bünyamin Sen, Maximilian T. Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith A. H. Wodke & Julio Saez-Rodriguez. Democratizing knowledge representation with BioCypher. Nature Biotechnology (2023) 41:1056–1059.
Valeria Ariotta*, Oskari Lehtonen*, Shams Salloum, Giulia Micoli, Kari Lavikka, Ville Rantanen, Johanna Hynninen, Anni Virtanen & Sampsa Hautaniemi. H&E image analysis pipeline for quantifying morphological features. Journal of Pathology Informatics (2023) 14.
Mai T.N. Nguyen, Anna Rajavuori, Kaisa Huhtinen, Sakari Hietanen, Johanna Hynninen, Jaana Oikkonen & Sampsa Hautaniemi. Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma. Biomedicine & Pharmacotherapy (2023) 168.
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. ROR1-STAT3 signaling contributes to ovarian cancer intra-tumor heterogeneity. Cell Death Discovery (2023) 9(222).
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. Activation of invasion by oncogenic reprogramming of cholesterol metabolism via increased NPC1 expression and macropinocytosis. Oncogene (2023)
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.* Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma. Cancer Cell (2023) 41:1103–1117.
Waltter Roslin & Juli Mansnérus. From the integrity of potency assays to safe clinical intervention: Legal perspectives. from J. Burns (Ed.), Potency Assays for Advanced Stem Cell Therapy Medicinal Products (2023) 1:151-163 (Part of the book series: Advances in Experimental Medicine and Biology, AEMB, vol. 1420).
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 Carpén & Liisa Kauppi. Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Clinical Cancer Research (2023) OF1–OF14.
Feng Deng, Maren Laasik, Liina Salminen, Lauri Lapatto, Kaisa Huhtinen, Yilin Li, Sampsa Hautaniemi, Johanna Hynninen, Mikko Niemi & Rainer Lehtonen. Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1 and GSTP1 in high-grade serous ovarian cancer. Basic & Clinical Pharmacology & Toxicology (2023) 1–11.
2022
Federica Citarrella; Gianpaolo Bontempo; Marta Lovino; Elisa Ficarra. FusionFlow: An Integrated System Workflow for Gene Fusion Detection in Genomic Samples. New Trends in Database and Information Systems (2022), Part of the book series: Communications in Computer and Information Science (CCIS, vol. 1652)
Miguel M. Álvarez, Josep Biayna & Fran Supek. TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening. Nature Communications (2022) 13(4520).
Jurica Levatić, Marina Salvadores, Francisco Fuster-Tormo & Fran Supek. Mutational signatures are markers of drug sensitivity of cancer cells. Nature Communications (2022) 13.
Aikaterini Skorda, Marie Lund Bay, Sampsa Hautaniemi, Alexandra Lahtinen & Tuula Kallunki. Kinase Inhibitors in the Treatment of Ovarian Cancer: Current State and Future Promises. Cancers (2022) 14(24):6257.
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. Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. NPJ Precision Oncology (2022) 6(1):96.
Alessio Mascolini, Dario Cardamone, Francesco Ponzio, Santa Di Cataldo, Elisa Ficarra. Exploiting generative self‑supervised learning for the assessment of biological images with lack of annotations. BMC Bioinformatics (2022) 23:295.
Vittorio Pipoli, Mattia Cappelli, Alessandro Palladini, Carlo Pelusoa, Marta Lovino, Elisa Ficarra. Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers. Computer Methods and Programs in Biomedicine (2022) 225
Mischan Vali-Pour, Ben Lehner, Fran Supek. The impact of rare germline variants on human somatic mutation processes. Nature Communications (2022) 13:3724
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
2021
Anna Laury, Sami Blom, Tuomas Ropponen, Anni Virtanen & Olli Carpén. Artificial intelligence-based image analysis can predict outcome in high-grade serous carcinoma via histology alone. Nature Scientific Reports (2021) 11:19165