International consortium for integrative genomics prediction

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Plan of data standards for genetic risk scores
Report of available data resources and plan for data harmonization strategy
Access to a biobank data set through implementation of local biobank APIs and cloud resources to support federated consortium access
Implementation of phenotype harmonization
Access to first INTERVENE consortium data sets available from EMBL-EBI and CSC Cloud services

Access to first INTERVENE consortium data sets available from EMBLEBI and CSC Cloud services

Report on the qualitative assessment of the public's perception of AI-based genetic scores

Report on the qualitative assessment of the public’s perception of AI-based genetic scores.

Genetic validation of disease endpoints
Review of the consortium partner biobank and data collections, including access policies

Review of the consortium partner biobank and data collections including access policies

Delivery of features supporting AI methods competition
Data coordination centre established
INTERVENE consortium AI algorithms supported by CSC HPC environment on synthetic data.

INTERVENE consortium AI algorithms supported by CSC HPC environment on synthetic data

Disease endpoint selection based on available resources and AI based methods

Publicaciones

Systematic comparison of family history and polygenic risk across 24 common diseases

Autores: Nina Mars, Joni V. Lindbohm, Pietro della Briotta Parolo, Elisabeth Widén, Jaakko Kaprio, Aarno Palotie, FinnGen, Samuli Ripatti
Publicado en: AJHG, Edición Vol 109, Edición 12, 2022, Página(s) 2152-2162, ISSN 0002-9297
Editor: University of Chicago Press
DOI: 10.1016/j.ajhg.2022.10.009

Periodic mobile application (eMOM) with self-tracking of glucose and lifestyle improves treatment of diet-controlled gestational diabetes without human guidance: a randomized controlled trial

Autores: Mikko Kyt, Shinji Hotta, Sari Niinist, Pekka Marttinen, Tuuli E. Korhonen, Lisa T. Markussen, Giulio Jacucci, Harri Sievnen, Henri Vh-Ypy, Ilkka Korhonen, Suvi Virtanen, Seppo Heinonen, Saila B. Koivusalo
Publicado en: American Journal of Obstetrics and Gynecology, Edición 231, 2025, Página(s) 541.e1-541.e16, ISSN 0002-9378
Editor: Mosby Inc.
DOI: 10.1016/j.ajog.2024.02.303

A cross-disorder dosage sensitivity map of the human genome

Autores: The members of the Estonian Biobank Research Team are Andres Metspalu, Reedik Mägi, Mari Nelis, Lili Milani, and Tõnu Esko. Ryan L. Collins, Joseph T. Glessner, Eleonora Porcu, ..., Shamil Sunyaev, Harrison Brand, Michael E. Ta
Publicado en: Cell, Edición 185, 2022, Página(s) 3041-3055, ISSN 1097-4172
Editor: Cell Press
DOI: 10.1016/j.cell.2022.06.036

Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases

Autores: Kiiskinen T, Helkkula P, Krebs K, Karjalainen J, Saarentaus E, Mars N, Lehisto A, Zhou W, Cordioli M, Jukarainen S, Rämö JT, Mehtonen J, Veerapen K, Räsänen M, Ruotsalainen S, Maasha M; FinnGen; Niiranen T, Tuomi T, Salomaa V, Kurki M, Pirinen M, Palotie A, Daly M, Ganna A, Havulinna AS, Milani L, Ripatti S.
Publicado en: Nature Medicine, Edición 29, 2023, Página(s) 209-218, ISSN 1546-170X
Editor: Nature
DOI: 10.1038/s41591-022-02122-5

Gene-Gene Interaction Detection with Deep Learning

Autores: Tianyu Cui, Khaoula El Mekkaoui, Jaakko Reinvall, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski
Publicado en: Communications Biology, Edición Vol 5, article 1238, 2022, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1101/2021.03.12.435063

Carriers of ADAMTS13 Rare Variants Are at High Risk of Life-Threatening COVID-19

Autores: Kristina Zguro,Margherita Baldassarri,Francesca Fava,Giada Beligni,Sergio Daga,Roberto Leoncini,Lucrezia Galasso,Michele Cirianni,Stefano Rusconi,...Giuseppe Marotta,Simone Furini,GEN-COVID Multicenter Study,Alessandra Renieri, Chiara Fallerini
Publicado en: Viruses, Edición 14(6), 2022, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061185

Inframe insertion and splice site variants in MFGE8 associate with protection against coronary atherosclerosis

Autores: Sanni E. Ruotsalainen, Ida Surakka, Nina Mars, Juha Karjalainen, Mitja Kurki, Masahiro Kanai, Kristi Krebs, Sarah Graham, Pashupati P. Mishra, Binisha H. Mishra, Juha Sinisalo, Priit Palta, Terho Lehtimäki, Olli Raitakari, Estonian Biobank Research Team, Lili Milani, The Biobank Japan Project, Yukinori Okada, FinnGen, Aarno Palotie, Elisabeth Widen, Mark J. Daly & Samuli Ripatt
Publicado en: Nature, Edición 5, 2022, Página(s) article 802, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s42003-022-03552-0

Polygenic risk scores for cervical HPV infection, neoplasia and cancer show potential for personalised screening: comparison of two methods

Autores: Anna Tisler, Anneli Uuskla, Sven Erik Ojavee, Kristi Lll, null null, Andres Metspalu, Lili Milani, Tnu Esko, Reedik Mgi, Mari Nelis, Georgi Hudjashov, Triin Laisk
Publicado en: Infectious Agents and Cancer, Edición 18, 2023, ISSN 1750-9378
Editor: BioMed Central
DOI: 10.1186/s13027-023-00561-4

Contribution of schizophrenia polygenic burden to longitudinal phenotypic variance in 22q11.2 deletion syndrome

Autores: Maris Alver, Valentina Mancini, Kristi Läll, Maude Schneider, Luciana Romano, null null, Lili Milani, Mari Nelis, Reedik Mägi, Tõnu Esko, Andres Metspalu, Reedik Mägi, Emmanouil T. Dermitzakis, Stephan Eliez, Alexandre Reymond
Publicado en: Molecular Psychiatry, Edición 27, 2023, Página(s) 4191-4200, ISSN 1359-4184
Editor: Nature Publishing Group
DOI: 10.1038/s41380-022-01674-9

An explainable model of host genetic interactions linked to COVID-19 severity

Autores: Anthony Onoja, Nicola Picchiotti, Chiara Fallerini, Margherita Baldassarri, Francesca Fava, GEN-COVID Multicenter Study, Francesca Colombo, Francesca Chiaromonte, Alessandra Renieri, Simone Furini & Francesco Raimondi
Publicado en: Nature, Comm. Biology, Edición Vol 5, 2022, Página(s) Article 1133, ISSN 2399-3642
Editor: Nature
DOI: 10.1038/s42003-022-04073-6

Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Autores: Ying Wang, Shinichi Namba, Esteban Lopera, Sini Kerminen Kristin Tsuo, Kristi Läll, Masahiro Kanai, Wei Zhou, Kuan-Han Wu, Marie-Julie Favé, Laxmi Bhatta, Philip Awadalla, Ben Brumpton, Patrick Deelen, Kristian Hveem, Valeria Lo Faro, Reedik Mägi, Yoshinori Murakami, Serena Sanna, Jordan W. Smoller…Jibril Hirbo
Publicado en: Cell Genomics, Edición Vol 3, Edición 1, 2023, ISSN 2666-979X
Editor: Cell Press
DOI: 10.1101/2021.11.18.21266545

Using Polygenic Risk Scores for Prioritizing Individuals at Greatest Need of a Cardiovascular Disease Risk Assessment

Autores: Ryan Chung, Zhe Xu, Matthew Arnold, Samantha Ip, Hannah Harrison, Jessica Barrett, Lisa Pennells, Lois G. Kim, Emanuele Di Angelantonio, Ellie Paige, Scott C. Ritchie, Michael Inouye, Juliet A. Usher‐Smith, Angela M. Wood
Publicado en: Journal of the American Heart Association, Edición 12, 2024, Página(s) No 15, ISSN 2047-9980
Editor: Wiley-Blackwell
DOI: 10.1161/jaha.122.029296

Comprehensive Inherited Risk Estimation for Risk-Based Breast Cancer Screening in Women

Autores: Nina Mars, Sini Kerminen, Max Tamlander, Matti Pirinen, Eveliina Jakkula, Kirsimari Aaltonen, Tuomo Meretoja, Sirpa Heinävaara, Elisabeth Widén, Samuli Ripatti, Aarno Palotie, Mark Daly, Bridget Riley-Gills, Howard Jacob, Dirk Paul, Athena Matakidou, Adam Platt, Heiko Runz, Sally John, George Okafo, Nathan Lawless, Robert Plenge, Joseph Maranville, Mark McCarthy, Julie Hunkapiller, Margaret G. E
Publicado en: Journal of Clinical Oncology, Edición 42, 2024, Página(s) 1477-1487, ISSN 0732-183X
Editor: American Society of Clinical Oncology
DOI: 10.1200/jco.23.00295

Responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps

Autores: Adebowale Adeyemo, Mary K. Balaconis, Deanna R. Darnes, Segun Fatumo, Palmira Granados Moreno, Chani J. Hodonsky, Michael Inouye, Masahiro Kanai, Kazuto Kato, Bartha M. Knoppers, Anna C. F. Lewis, Alicia R. Martin, Mark I. McCarthy, Michelle N. Meyer, Yukinori Okada, J. Brent Richards, Lucas Richter, Samuli Ripatti, Charles N. Rotimi, Saskia C. Sanderson, Amy C. Sturm, Ricardo A. Verdugo, Elisabet
Publicado en: Nature Medicine, Edición 27, 2021, Página(s) 1876-1884, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/s41591-021-01549-6

Multitask Balanced and Recalibrated Network for Medical Code Prediction

Autores: Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
Publicado en: ACM Transactions on Intelligent Systems and Technology, Edición Vol 14, Edición 1, 2022, Página(s) 1-20, ISSN 2157-6904
Editor: Association for Computing Machinery (ACM)
DOI: 10.1145/3563041

Genetic determinants of plasma protein levels in the Estonian population

Autores: Anette Kalnapenkis, Maarja Jõeloo, Kaido Lepik, Viktorija Kukuškina, Mart Kals, Kaur Alasoo, null null, Andres Metspalu, Lili Milani, Mari Nelis, Georgi Hudjashov, Reedik Mägi, Tõnu Esko, Urmo Võsa
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-57966-3

Ethical layering in AI-driven polygenic risk scores—New complexities, new challenges

Autores: Fritzsche, M.-C., Akyüz, K., Cano Abadía, M., McLennan, S., Marttinen, P., Mayrhofer, M. T., & Buyx, A. M. (2023). Ethical layering in AI-driven polygenic risk scores—Fritzsche, M.-C., Akyüz, K., Cano Abadía, M., McLennan, S., Marttinen, P., Mayrhofer, M. T., & Buyx, A. M
Publicado en: Frontiers in Genetics, Edición 14, 2023, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

Polygenic scores in biomedical research

Autores: Iftikhar J. Kullo, Cathryn M. Lewis, Michael Inouye, Alicia R. Martin, Samuli Ripatti & Nilanjan Chatterjee
Publicado en: Nature Reviews Genetics, Edición 23, 2022, Página(s) 524-532, ISSN 1471-0056
Editor: Nature Publishing Group
DOI: 10.1038/s41576-022-00470-z

Multiparametric Platform for Profiling Lipid Trafficking in Human Leukocytes: Application for Hypercholesterolemia

Autores: Simon G. Pfisterer; Ivonne Brock; Ivonne Brock; Kristiina Kanerva; Kristiina Kanerva; Iryna Hlushchenko; Lassi Paavolainen; Pietari Ripatti; Mohammad Majharul Islam; Aija Kyttala; Maria Donata Di Taranto; Annalisa Scotto di Frega; Giuliana Fortunato; Johanna Kuusisto; Peter Horvath; Samuli Ripatti; Samuli Ripatti; Markku Laakso; Elina Ikonen; Elina Ikonen
Publicado en: Cell Reports Methods, Edición Vol 2,issue 2, 2022, ISSN 0346-251X
Editor: Pergamon Press Ltd.
DOI: 10.1101/2021.04.19.440471

Genetic risk factors have a substantial impact on healthy life years

Autores: Aki Havulinna; Sakari Jukarainen; Nina Mars
Publicado en: Nature Medicine, Edición 27, 2021, Página(s) 1876-1884, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1101/2022.01.25.22269831v1

Identifiable causal inference with noisy treatment and no side information

Autores: Pllnen, A. and Marttinen, P.
Publicado en: Transactions on Machine Learning Research (TMLR), 2024, ISSN 1533-7928
Editor: [Amherst Massachusetts]: OpenReview.net, 2022-

Ultra-rare RTEL1 gene variants associate with acute severity of COVID-19 and evolution to pulmonary fibrosis as a specific long COVID disorder

Autores: Laura Bergantini, Margherita Baldassarri, Miriana d’Alessandro, Giulia Brunelli, Gaia Fabbri, Kristina Zguro, Andrea Degl’Innocenti, GEN-COVID Multicenter study, Chiara Fallerini, Elena Bargagli & Alessandra Renieri
Publicado en: Respiratory Research, Edición 24, 2023, Página(s) article no 158, ISSN 1465-9921
Editor: BioMed Central
DOI: 10.1186/s12931-023-02458-7

TransferGWAS of T1-weighted brain MRI data from UK Biobank

Autores: Alexander Rakowski, Remo Monti, Christoph Lippert
Publicado en: PLOS Genetics, Edición 20, 2024, Página(s) e1011332, ISSN 1553-7404
Editor: Public Library of Science San Francisco, CA USA
DOI: 10.1371/journal.pgen.1011332

Pathogen-sugar interactions revealed by universal saturation transfer analysis

Autores: Charles J. Buchanan, Ben Gaunt, Peter J. Harrison, Yun Yang, Jiwei Liu, Aziz Khan, Andrew M. Giltrap, Audrey Le Bas, Philip N. Ward, Kapil Gupta, Maud Dumoux, Tiong Kit Tan, Lisa Schimaski, Sergio Daga, Nicola Picchiotti, Margherita Baldassarri, Elisa Benetti, Chiara Fallerini, Francesca Fava, Annarita Giliberti, Panagiotis I. Koukos, Matthew J. Davy, Abirami Lakshminarayanan, Xiaochao Xue, Georgi
Publicado en: Science, Edición 377, 2022, ISSN 0065-7085
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abm3125

<i>HLA‐DPB1*13:01</i> associates with enhanced, and <i>KIR2DS4*001</i> with diminished protection from developing severe <scp>COVID</scp>‐19

Autores: Ticiana D. J. Farias, Silvia Brugiapaglia, Susanna Croci, Paola Magistroni, Claudia Curcio, Kristina Zguro, Chiara Fallerini, Francesca Fava, Francesco Pettini, Katherine M. Kichula, Nicholas R. Pollock, Neus Font‐Porterias, William H. Palmer, Wesley M. Marin, Margherita Baldassarri, Mirella Bruttini, Jill A. Hollenbach, Audrey E. Hendricks, Ilaria Meloni, Francesco Novelli, null null, Alessandr
Publicado en: HLA, Edición 103, 2024, ISSN 2059-2302
Editor: Wiley
DOI: 10.1111/tan.15251

CYP19A1 mediates severe SARS-CoV-2 disease outcome in males

Autores: Stephanie Stanelle-Bertram, Sebastian Beck, Nancy Kouassi Mounogou, Berfin Schaumburg, Fabian Stoll, Amirah Al Jawazneh, Zoé Schmal, Tian Bai, Martin Zickler, Georg Beythien, Kathrin Becker, Madeleine de la Roi, Fabian Heinrich, Claudia Schulz, Martina Sauter, Susanne Krasemann, Philine Lange, Axel Heinemann, Debby van Riel, Lonneke Leijten, Lisa Bauer, Thierry P.P. van den Bosch, Boaz Lopuhaä,
Publicado en: Cell Reports Medicine, Edición 4, 2023, Página(s) 101152, ISSN 2666-3791
Editor: Cell Press Elsevier Inc.
DOI: 10.1016/j.xcrm.2023.101152

Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization

Autores: Fanni Ojala, Mohamad R. Abdul Sater, Loren G. Miller, James A. McKinnell, Mary K. Hayden, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
Publicado en: PLOS Computational Biology, Edición 19, 2023, Página(s) e1010898, ISSN 1553-7358
Editor: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1010898

Informative Bayesian Neural Network Priors for Weak Signals

Autores: Tianyu Cui, Aki Havulinna, Pekka Marttinen, Samuel Kaski
Publicado en: Bayesian Anal., 2021, Página(s) 1-31 (2021), ISSN 1936-0975
Editor: Carnegie Mellon University
DOI: 10.1214/21-ba1291

Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization

Autores: Samuel A. Lambert, Benjamin Wingfield, Joel T. Gibson, Laurent Gil, Santhi Ramachandran, Florent Yvon, Shirin Saverimuttu, Emily Tinsley, Elizabeth Lewis, Scott C. Ritchie, Jingqin Wu, Rodrigo Cánovas, Aoife McMahon, Laura W. Harris, Helen Parkinson, Michael Inouye
Publicado en: Nature Genetics, Edición 56, 2024, Página(s) 1989-1994, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-024-01937-x

Machine learning optimized polygenic scores for blood cell traits identify sex-specific trajectories and genetic correlations with disease.

Autores: Yu Xu, Dragana Vuckovic, Scott C. Ritchie, ..., John Danesh, Nicole Soranzo, Michael Inouye
Publicado en: Cell Genomics, Edición Vol 2, Edición 1, 2022, ISSN 2666-979X
Editor: Cell Press
DOI: 10.1016/j.xgen.2021.100086

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations

Autores: Maarja Lepamets; Chiara Auwerx; Margit Nõukas; Annique Claringbould; Eleonora Porcu; Mart Kals; Tuuli Jürgenson; Andrew Paul Morris; Urmo Võsa; Murielle Bochud; Silvia Stringhini; Cisca Wijmenga; Lude Franke; Hedi Peterson; Jaak Vilo; Kaido Lepik; Reedik Mägi; Zoltán Kutalik
Publicado en: HGG advances,, Edición vol. 3, no. 4, 2022, Página(s) pp. 100133, ISSN 0346-251X
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.xhgg.2022.100133

Ethical layering in AI-driven polygenic risk scores – new complexities, new challenges

Autores: Fritzsche, M., Akyüz, K., Abadía, M.C., McLennan, S., Marttinen, P. Mayrhofer, M.T., and Buyx, A.M.
Publicado en: Frontiers in Genetics, Edición Vol 4, 2023, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

Patterns of item nonresponse behaviour to survey questionnaires are systematic and associated with genetic loci

Autores: Gianmarco Mignogna, Caitlin E. Carey, Robbee Wedow, Nikolas Baya, Mattia Cordioli, Nicola Pirastu, Rino Bellocco, Kathryn Fiuza Malerbi, Michel G. Nivard, Benjamin M. Neale, Raymond K. Walters, Andrea Ganna
Publicado en: Nature Human Behaviour, Edición 7, 2023, Página(s) 1371-1387, ISSN 2397-3374
Editor: Nature Publishing
DOI: 10.1038/s41562-023-01632-7

Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci

Autores: Nina Mars, Sini Kerminen, Yen-Chen A. Feng, Masahiro Kanai, Kristi Läll, Laurent F. Thomas, Anne Heidi Skogholt, Pietro della Briotta Parolo, The Biobank Japan Project, FinnGen, Benjamin M. Neale, Jordan W. Smoller, Maiken E. Gabrielsen, Kristian Hveem, Reedik Mägi, Koichi Matsuda, Yukinori Okada, Matti Pirinen, Aarno Palotie, Andrea Ganna, Alicia R. Martin
Publicado en: Cell Genomics, Edición 2, Edición 4, 2022, ISSN 2666-979X
Editor: CellPress
DOI: 10.1038/s41467-022-29143-5

A Unified Review of Deep Learning for Automated Medical Coding

Autores: Shaoxiong Ji, Xiaobo Li, Wei Sun, Hang Dong, Ara Taalas, Yijia Zhang, Honghan Wu, Esa Pitknen, Pekka Marttinen
Publicado en: ACM Computing Surveys, Edición 56, 2024, Página(s) 1-41, ISSN 0360-0300
Editor: Association for Computing Machinary, Inc.
DOI: 10.1145/3664615

Genome-wide risk prediction of common diseases across ancestries in one million people.

Autores: Nina Mars, Sini Kerminen, Yen-Chen A. Feng, Masahiro Kanai, Kristi Läll, Laurent F. Thomas, Anne Heidi Skogholt, Pietro della Briotta Parolo, The Biobank Japan Project, FinnGen, Benjamin M. Neale, Jordan W. Smoller, Maiken E. Gabrielsen, Kristian Hveem, Reedik Mägi, Koichi Matsuda, Yukinori Okada, Matti Pirinen, Aarno Palotie, Andrea Ganna, Alicia R. Martin
Publicado en: Cell Genomics, Edición Apr 13; 2(4), 2023, ISSN 2666-979X
Editor: Cell Press
DOI: 10.1016/j.xgen.2022.100118

Risk adjustment for regional healthcare funding allocations with ensemble methods: an empirical study and interpretation

Autores: Tuukka Holster, Shaoxiong Ji, Pekka Marttinen
Publicado en: The European Journal of Health Economics, Edición 25, 2024, Página(s) 1117-1131, ISSN 1618-7598
Editor: Springer Verlag
DOI: 10.1007/s10198-023-01656-w

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes

Autores: Remo Monti, Pia Rautenstrauch, Mahsa Ghanbari, Alva Rani James, Uwe Ohler, Stefan Konigorski, Christoph Lippert
Publicado en: Nature Communications, Edición Vol 13, article 5332, 2022, Página(s) 1-16, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2021.05.27.444972

Host genetic basis of COVID-19: from methodologies to genes

Autores: Kristina Zguro, Chiara Fallerini, Francesca Fava, Simone Furini & Alessandra Renieri
Publicado en: EJHG, Edición Vol 30, 2022, Página(s) 899-907, ISSN 1018-4813
Editor: Natue Publishing Group
DOI: 10.1038/s41431-022-01121-x

Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection

Autores: Ji, Shaoxiong; Gao, Ya; Marttinen, Pekka
Publicado en: Arxiv, Edición 6, 2023, ISSN 2331-8422
Editor: Cornell University
DOI: 10.48550/arxiv.2301.10451

Socio-demographic and genetic risk factors for drug adherence and persistence across 5 common medication classes

Autores: Mattia Cordioli, Andrea Corbetta, Hanna Maria Kariis, Sakari Jukarainen, Pekka Vartiainen, Tuomo Kiiskinen, Matteo Ferro, null null, Markus Perola, Samuli Ripatti, Andrea Ganna, null null, Andres Metspalu, Lili Milani, Tõnu Esko, Reedik Mägi, Mari Nelis, Georgi Hudjashov, Markus Perola, Mikko Niemi, Samuli Ripatti, Kelli Lehto, Lili Milani, Andrea Ganna
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-024-53556-z

Metadata-guided feature disentanglement for functional genomics

Autores: Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Publicado en: Bioinformatics, Edición 40, 2024, Página(s) ii4-ii10, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btae403

Genome-wide polygenic risk scores for colorectal cancer have implications for risk-based screening

Autores: Max Tamlander, Bradley Jermy, Toni T. Seppälä, Martti Färkkilä, null null, Elisabeth Widén, Samuli Ripatti, Nina Mars
Publicado en: British Journal of Cancer, Edición 130, 2024, Página(s) 651-659, ISSN 0007-0920
Editor: Nature Publishing Group
DOI: 10.1038/s41416-023-02536-z

Challenges and Opportunities for Developing More Generalizable Polygenic Risk Scores

Autores: Ying Wang, Kristin Tsuo, Masahiro Kanai, Benjamin M. Neale, Alicia R. Martin
Publicado en: Annual Rev of Biomed. Data Science, Edición Vol 5, 2022, Página(s) 293-320, ISSN 2574-3414
Editor: Annual Reviews
DOI: 10.1146/annurev-biodatasci-111721-074830

Digital endpoints in clinical trials: emerging themes from a multi-stakeholder Knowledge Exchange event

Autores: Mia S. Tackney, Amber Steele, Joseph Newman, Marie-Christine Fritzsche, Federica Lucivero, Zarnie Khadjesari, Jennifer Lynch, Rosemary A. Abbott, Vicki S. Barber, James R. Carpenter, Bethan Copsey, Elin H. Davies, William G. Dixon, Lisa Fox, Javier González, Jessica Griffiths, Chloe H. L. Hinchliffe, Magdalena A. Kolanko, Dylan McGagh, Aryelly Rodriguez, George Roussos, Karen B. E. So, Louise Sta
Publicado en: Trials, Edición 25, 2024, ISSN 1745-6215
Editor: BioMed Central
DOI: 10.1186/s13063-024-08356-7

Advancing our understanding of genetic risk factors and potential personalized strategies for pelvic organ prolapse

Autores: Natàlia Pujol-Gualdo, Kristi Läll, Maarja Lepamets, Estonian Biobank Research Team, Henna-Riikka Rossi, Riikka K. Arffman, Terhi T. Piltonen, Reedik Mäg, Triin Laisk
Publicado en: Nature Communications, Edición Vol 13, 2022, Página(s) article: 3584, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31188-5

Clinical Conditions and Their Impact on Utility of Genetic Scores for Prediction of Acute Coronary Syndrome

Autores: Jiwoo Lee, Tuomo Kiiskinen, Nina Mars, Sakari Jukarainen, Erik Ingelsson, Benjamin Neale, Samuli Ripatti, Pradeep Natarajan, and Andrea Ganna
Publicado en: Circulation: Genomic and Precision Medicine, Edición Vol. 14, No. 4, 2021, ISSN 0009-7322
Editor: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circgen.120.003283

Nationwide health, socio-economic and genetic predictors of COVID-19 vaccination status in Finland

Autores: Hartonen T*, Jermy B*, Sõnajalg H, Vartiainen P, Krebs K, Vabalas A, FinnGen, Estonian Biobank Research Team, Leino T, Nohynek H, Sivelä J, Mägi R, Daly MJ, Ollila HM, Milani L, Perola M, Ripatti S, Ganna A.
Publicado en: Nature Human Behaviour, Edición Vol 7, 2023, Página(s) 1069-1083, ISSN 1476-4687
Editor: Nature
DOI: 10.1038/s41562-023-01591-z

Optimizing postprandial glucose prediction through integration of diet and exercise: Leveraging transfer learning with imbalanced patient data

Autores: Shinji Hotta, Mikko Kyt, Saila Koivusalo, Seppo Heinonen, Pekka Marttinen
Publicado en: PLOS ONE, Edición 19, 2024, Página(s) e0298506, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0298506

GWAS meta-analyses clarify the genetics of cervical phenotypes and inform risk stratification for cervical cancer

Autores: Mariann Koel, Urmo Võsa, Maarja Jõeloo, Kristi Läll, Natàlia P Gualdo, Hannele Laivuori, Susanna Lemmelä, null null, Mark Daly, Priit Palta, Reedik Mägi, Triin Laisk
Publicado en: Human Molecular Genetics, Edición 32, 2023, Página(s) 2103-2116, ISSN 0964-6906
Editor: Oxford University Press
DOI: 10.1093/hmg/ddad043

COVID-19: a challenge and an opportunity

Autores: Alessandra Renieri
Publicado en: EJHG, Edición Vol 30, 2022, Página(s) 870-871, ISSN 1018-4813
Editor: Natue Publishing Group
DOI: 10.1038/s41431-022-01142-6

The human genetic epidemiology of COVID-19

Autores: Mari Niemi, Mark Daly, Andrea Ganna
Publicado en: Nature Reviews: Genetics, Edición Vol 23, 2022, Página(s) 533-546, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41576-022-00478-5

Population Heterogeneity and Selection of Coronary Artery Disease Polygenic Scores

Autores: Carla Debernardi, Angelo Savoca, Alessandro De Gregorio, Elisabetta Casalone, Miriam Rosselli, Elton Jalis Herman, Cecilia Di Primio, Rosario Tumino, Sabina Sieri, Paolo Vineis, Salvatore Panico, Carlotta Sacerdote, Diego Ardissino, Rosanna Asselta, Giuseppe Matullo
Publicado en: Journal of Personalized Medicine, Edición 14, 2025, Página(s) 1025, ISSN 2075-4426
Editor: Basel MDPI AG 2011-
DOI: 10.3390/jpm14101025

Gain- and Loss-of-Function CFTR Alleles Are Associated with COVID-19 Clinical Outcomes

Autores: Margherita Baldassarri, Kristina Zguro, Valeria Tomati, Cristina Pastorino, Francesca Fava, Susanna Croci, Mirella Bruttini, Nicola Picchiotti, Simone Furini 2,GEN-COVID, Nicoletta Pedemonte, Chiara Gabbi, Alessandra Renieri, Chiara Fallerini
Publicado en: Cells, Edición 11(24), 2022, Página(s) 4096, ISSN 2073-4409
Editor: MDPI
DOI: 10.3390/cells11244096

Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk

Autores: Xianyong Yin; Debraj Bose; Annie Kwon; Sarah C. Hanks; Anne U. Jackson; Heather M. Stringham; Ryan Welch; Anniina Oravilahti; Lilian Fernandes Silva; Adam E. Locke; Christian Fuchsberger; Susan K. Service; Michael R. Erdos; Lori L. Bonnycastle; Johanna Kuusisto; Nathan O. Stitziel; Ira M. Hall; Jean Morrison; Samuli Ripatti; Aarno Palotie; Nelson B. Freimer; Francis S. Collins; Karen L. Mohlke; La
Publicado en: AJHG, Edición Vol 109, Edición 10, 2022, Página(s) 1727-1741, ISSN 0002-9297
Editor: University of Chicago Press
DOI: 10.1016/j.ajhg.2022.08.007

Host genetics and COVID-19 severity: increasing the accuracy of latest severity scores by Boolean quantum features

Autores: Gabriele Martelloni, Alessio Turchi, Chiara Fallerini, Andrea Degl’Innocenti, Margherita Baldassarri, Simona Olmi, Simone Furini, Alessandra Renieri, null null
Publicado en: Frontiers in Genetics, Edición 15, 2024, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2024.1362469

Quantifying the causal impact of biological risk factors on healthcare costs

Autores: Jiwoo Lee, Sakari Jukarainen, Antti Karvanen, Padraig Dixon, Neil M. Davies, George Davey Smith, Pradeep Natarajan, Andrea Ganna
Publicado en: Nature Communications, Edición 14, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-41394-4

Integration of questionnaire-based risk factors improves polygenic risk scores for human coronary heart disease and type 2 diabetes

Autores: Max Tamlander, Nina Mars, Matti Pirinen, FinnGen, Elisabeth Widén & Samuli Ripatti
Publicado en: Comm. Biology, Edición Vol 5, 2022, Página(s) 158, ISSN 2399-3642
Editor: Nature
DOI: 10.1038/s42003-021-02996-0

Reducing noisy annotations for depression estimation from facial images

Autores: Lang He, Prayag Tiwari, Chonghua Lv, WenShuai Wu, Liyong Guo
Publicado en: Neural Networks, Edición Vol 153, 2022, Página(s) 120-129, ISSN 0893-6080
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2022.05.025

Self-Supervised Forecasting in Electronic Health Records with Attention-Free Models

Autores: Kumar, Y., Ilin, A., Salo, H., Kulathinal, S., Leinonen, M.K., and Marttinen, P.
Publicado en: IEEE Transactions on artificial intelligence, Edición Vol 5, No 8, 2024, ISSN 2691-4581
Editor: Piscataway, NJ Institute of Electrical and Electronics Engineers, Inc. IEEE Computational Intelligence Society [2020]-

Estimation of recurrent atherosclerotic cardiovascular event risk in patients with established cardiovascular disease: the updated SMART2 algorithm

Autores: Steven H J Hageman, Ailsa J McKay, Peter Ueda, Laura H Gunn, Tomas Jernberg, Emil Hagström, Deepak L Bhatt, Ph. Gabriel Steg, Kristi Läll, Reedik Mägi, ...Kausik K Ray, Jannick A N Dorresteijn, Frank L J Visseren on behalf of the UCC-SMART Study Group and the ESC Cardiovascular Risk Collaboration
Publicado en: European Heart Journal, Edición 43, issue 18, 2022, Página(s) 1715-1727, ISSN 0195-668X
Editor: Oxford University Press
DOI: 10.1093/eurheartj/ehac056

ANGPTL8 protein-truncating variant associated with lower serum triglycerides and risk of coronary disease.

Autores: Pyry, Helkkula; Tuomo, Kiiskinen; Aki S, Havulinna; Juha, Karjalainen; Seppo, Koskinen; Veikko, Salomaa; Mark J, Daly; Aarno, Palotie; Ida, Surakka; Samuli, Ripatti
Publicado en: PLoS Genetics, Edición 11, 2021, ISSN 1553-7404
Editor: San Francisco, CA Public Library of Science ©2005-
DOI: 10.1371/journal.pgen.1009501

Deformation equivariant cross-modality image synthesis with paired non-aligned training data

Autores: Joel Honkamaa, Umair Khan, Sonja Koivukoski, Mira Valkonen, Leena Latonen, Pekka Ruusuvuori, Pekka Marttinen
Publicado en: Medical Image Analysis, Edición 90, 2024, Página(s) 102940, ISSN 1361-8415
Editor: Elsevier BV
DOI: 10.1016/j.media.2023.102940

SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration

Autores: Joel Honkamaa, Pekka Marttinen
Publicado en: Machine Learning for Biomedical Imaging, Edición 2, 2025, Página(s) 2148-2194, ISSN 2766-905X
Editor: Melba
DOI: 10.59275/j.melba.2024-276b

Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning

Autores: Remo Monti, Lisa Eick, Georgi Hudjashov, Kristi Läll, Stavroula Kanoni, Brooke N. Wolford, Benjamin Wingfield, Oliver Pain, Sophie Wharrie, Bradley Jermy, Aoife McMahon, Tuomo Hartonen, Henrike Heyne, Nina Mars, Samuel Lambert, Kristian Hveem, Michael Inouye, David A. van Heel, Reedik Mägi, Pekka Marttinen, Samuli Ripatti, Andrea Ganna, Christoph Lippert
Publicado en: The American Journal of Human Genetics, Edición 111, 2025, Página(s) 1431-1447, ISSN 0002-9297
Editor: University of Chicago Press
DOI: 10.1016/j.ajhg.2024.06.003

Multitask Recalibrated Aggregation Network for Medical Code Prediction

Autores: Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
Publicado en: Lecture Notes in Computer Science, Machine Learning and Knowledge Discovery in Databases. Applied Data Science Track, 2023, Página(s) 367-383
Editor: Springer International Publishing
DOI: 10.1007/978-3-030-86514-6_23

Generating Code World Models with Large Language Models Guided by Monte Carlo Tree Search

Autores: Dainese, N.*, Merler, M.*, Alakuijala, M., and Marttinen, P.
Publicado en: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2024
Editor: Cornell University

Incorporating functional summary information in Bayesian neural networks using a Dirichlet process likelihood approach

Autores: Raj, V., Cui, T., Heinonen, M., and Marttinen, P.
Publicado en: The Proceedings of 26th International Conference on Artificial Intelligence and Statistics, PMLR 206:6741-6763. (AISTATS 2023), 2023, Página(s) PMLR 206:6741-6763
Editor: PMLR

Temporal causal mediation through a point process: direct and indirect effects of healthcare interventions

Autores: Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietilinen, K., and Marttinen, P.
Publicado en: 37th Conference on Neural Information Processing Systems (NeurIPS 2023), 2023
Editor: NeurIOS 2023

Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection

Autores: Gao, Y., Ji, S., and Marttinen, P.
Publicado en: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), 2024, Página(s) 9787-9798
Editor: ACL Anthology

Mixture of Coupled HMMs for Robust Modeling of Multivariate Healthcare Time Series

Autores: Poyraz, O. and Marttinen, P.
Publicado en: Proceedings of the 3rd Machine Learning for Health Symposium 2023, PMLR, Edición 225, 2023, Página(s) 461-479
Editor: Machine Learning for Health

Contextualized graph embeddings for adverse drug event detection

Autores: Gao, Y., Ji, S., Zhang, T., Tiwari, P., and Marttinen, P.
Publicado en: The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2022), 2022
Editor: Springer
DOI: 10.1007/978-3-031-26390-3_35

HAPNEST: An efficient tool for generating large-scale genetics datasets from limited training data

Autores: Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J O'Connor, Samuel Kaski, Pekka Marttinen, Pier Palamara, Christoph Lippert, Andrea Ganna
Publicado en: NeurIPS 2022 Workshop on Synthetic Data for Empowering ML Research, 2022, Página(s) 1-7
Editor: NeurIPS

Nonparametric modeling of the composite effect of multiple nutrients on blood glucose dynamics

Autores: Odnoblyudova, A., Hzl, C., John, S.T., Cognolato, A., Juuti, A., Srkk, S., Pietilinen, K., and Marttinen, P.
Publicado en: Proceedings of Machine Learning Research, Edición 225, 2023, Página(s) 428-444
Editor: Machine Learning for Health (ML4H) 2023

Improving Medical Multi-modal Contrastive Learning with Expert Annotations

Autores: Kumar, Y. and Marttinen, P.
Publicado en: The 18th European Conference on Computer Vision (ECCV 2024), 2024
Editor: Cornell University
DOI: 10.48550/arxiv.2403.10153

VMS: Interactive Visualization to Support the Sensemaking and Selection of Predictive Models

Autores: Chen He, Vishnu Raj, Hans Moen, Tommi Grhn, Chen Wang, Laura-Maria Peltonen, Saila Koivusalo, Pekka Marttinen, Giulio Jacucci
Publicado en: Proceedings of the 29th International Conference on Intelligent User Interfaces, 2024, Página(s) 229-244
Editor: ACM
DOI: 10.1145/3640543.3645151

Causal Modeling of Policy Interventions From Treatment–Outcome Sequences

Autores: Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietiläinen, K., and Marttinen, P.
Publicado en: The 40th International Conference on Machine Learning (ICML 2023), 2023
Editor: unkonwn

Deconfounded Representation Similarity for Comparison of Neural Networks

Autores: Cui, T., Kumar, Y., Marttinen, P., and Kaski, S.
Publicado en: 2022, ISBN 9781713871088
Editor: NeurIPS Proceedings

Patient Outcome and Zero-shot Diagnosis Prediction with Hypernetwork-guided Multitask Learning

Autores: Ji, Shaoxiong; Marttinen, Pekka
Publicado en: The 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2023)., Edición 1, 2023, Página(s) 589-598
Editor: EACL
DOI: 10.48550/arxiv.2109.03062

A Critical Look at the Consistency of Causal Estimation with Deep Latent Variable Models

Autores: Severi Rissanen, Pekka Marttinen
Publicado en: 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021
Editor: NeurIPS 2021

Query-Guided Self-Supervised Summarization of Nursing Notes

Autores: Gao, Y., Moen, H., Koivusalo, S., Koskinen, M., and Marttinen, P.
Publicado en: Proceedings of the Machine Learning for Health Symposium (ML4H 2024), 2024
Editor: Cornell University

Characterizing personalized effects of family information on disease risk using graph representation learning

Autores: Wharrie, S., Yang, Z., Ganna, A., & Kaski, S.
Publicado en: Proceedings of Machine Learning Research, 2023
Editor: unknown

Kernel Language Entropy: Fine-grained Uncertainty Quantification for LLMs from Semantic Similarities

Autores: Nikitin, A., Kossen, J., Gal, Y., and Marttinen, P.
Publicado en: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2023
Editor: Cornell University

A Unified Review of Deep Learning for Automated Medical Coding

Autores: Ji, Shaoxiong; Sun, Wei; Li, Xiaobo; Dong, Hang; Taalas, Ara; Zhang, Yijia; Wu, Honghan; Pitkänen, Esa; Marttinen, Pekka
Publicado en: J of ACM, Edición Vol 37, no 4, article 111, 2022, ISSN 0004-5411
Editor: Association for Computing Machinary, Inc.
DOI: 10.48550/arxiv.2201.02797

Deep learning-based prediction of one-year mortality in Finland is an accurate but unfair aging marker

Autores: Andrius Vabalas, Tuomo Hartonen, Pekka Vartiainen, Sakari Jukarainen, Essi Viippola, Rodosthenis S. Rodosthenous, Aoxing Liu, Sara Hägg, Markus Perola, Andrea Ganna
Publicado en: Nature Aging, Edición 4, 2024, Página(s) 1014-1027, ISSN 2662-8465
Editor: University of Helsinki
DOI: 10.1038/s43587-024-00657-5

A unified framework for estimating country-specific cumulative incidence for 18 diseases stratified by polygenic risk

Autores: Bradley Jermy, Kristi Läll, Brooke Wolford, Ying Wang, Kristina Zguro, Yipeng Cheng, Masahiro Kanai, Stavroula Kanoni, Zhiyu Yang, Tuomo Hartonen, Remo Monti, Julian Wanner, Omar Youssef, Estonian Biobank research team, FinnGen, Christoph Lippert, David van Heel, Yukinori Okada, Daniel L.McCartney, Caroline Hayward, Riccardo E. Marioni, Simone Furini, Alessandra Renieri, Alicia R. Martin, Benjami
Publicado en: Nature Communications, Edición 15: 5007, 2024, ISSN 1476-4687
Editor: Nature
DOI: 10.1101/2023.06.12.23291186

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