International consortium for integrative genomics prediction

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

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

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

Publikacje

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

Autorzy: Nina Mars, Joni V. Lindbohm, Pietro della Briotta Parolo, Elisabeth Widén, Jaakko Kaprio, Aarno Palotie, FinnGen, Samuli Ripatti
Opublikowane w: AJHG, Numer Vol 109, Numer 12, 2022, Strona(/y) 2152-2162, ISSN 0002-9297
Wydawca: 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

Autorzy: 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
Opublikowane w: American Journal of Obstetrics and Gynecology, Numer 231, 2025, Strona(/y) 541.e1-541.e16, ISSN 0002-9378
Wydawca: Mosby Inc.
DOI: 10.1016/j.ajog.2024.02.303

A cross-disorder dosage sensitivity map of the human genome

Autorzy: 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
Opublikowane w: Cell, Numer 185, 2022, Strona(/y) 3041-3055, ISSN 1097-4172
Wydawca: Cell Press
DOI: 10.1016/j.cell.2022.06.036

Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases

Autorzy: 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.
Opublikowane w: Nature Medicine, Numer 29, 2023, Strona(/y) 209-218, ISSN 1546-170X
Wydawca: Nature
DOI: 10.1038/s41591-022-02122-5

Gene-Gene Interaction Detection with Deep Learning

Autorzy: Tianyu Cui, Khaoula El Mekkaoui, Jaakko Reinvall, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski
Opublikowane w: Communications Biology, Numer Vol 5, article 1238, 2022, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1101/2021.03.12.435063

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

Autorzy: 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
Opublikowane w: Viruses, Numer 14(6), 2022, ISSN 1999-4915
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061185

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

Autorzy: 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
Opublikowane w: Nature, Numer 5, 2022, Strona(/y) article 802, ISSN 0028-0836
Wydawca: 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

Autorzy: 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
Opublikowane w: Infectious Agents and Cancer, Numer 18, 2023, ISSN 1750-9378
Wydawca: BioMed Central
DOI: 10.1186/s13027-023-00561-4

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

Autorzy: Anthony Onoja, Nicola Picchiotti, Chiara Fallerini, Margherita Baldassarri, Francesca Fava, GEN-COVID Multicenter Study, Francesca Colombo, Francesca Chiaromonte, Alessandra Renieri, Simone Furini & Francesco Raimondi
Opublikowane w: Nature, Comm. Biology, Numer Vol 5, 2022, Strona(/y) Article 1133, ISSN 2399-3642
Wydawca: Nature
DOI: 10.1038/s42003-022-04073-6

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

Autorzy: 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
Opublikowane w: Cell Genomics, Numer Vol 3, Numer 1, 2023, ISSN 2666-979X
Wydawca: 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

Autorzy: 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
Opublikowane w: Journal of the American Heart Association, Numer 12, 2024, Strona(/y) No 15, ISSN 2047-9980
Wydawca: Wiley-Blackwell
DOI: 10.1161/jaha.122.029296

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

Autorzy: 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
Opublikowane w: Nature Medicine, Numer 27, 2021, Strona(/y) 1876-1884, ISSN 1078-8956
Wydawca: Nature Publishing Group
DOI: 10.1038/s41591-021-01549-6

Multitask Balanced and Recalibrated Network for Medical Code Prediction

Autorzy: Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
Opublikowane w: ACM Transactions on Intelligent Systems and Technology, Numer Vol 14, Numer 1, 2022, Strona(/y) 1-20, ISSN 2157-6904
Wydawca: Association for Computing Machinery (ACM)
DOI: 10.1145/3563041

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

Autorzy: 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
Opublikowane w: Frontiers in Genetics, Numer 14, 2023, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

Polygenic scores in biomedical research

Autorzy: Iftikhar J. Kullo, Cathryn M. Lewis, Michael Inouye, Alicia R. Martin, Samuli Ripatti & Nilanjan Chatterjee
Opublikowane w: Nature Reviews Genetics, Numer 23, 2022, Strona(/y) 524-532, ISSN 1471-0056
Wydawca: Nature Publishing Group
DOI: 10.1038/s41576-022-00470-z

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

Autorzy: 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
Opublikowane w: Cell Reports Methods, Numer Vol 2,issue 2, 2022, ISSN 0346-251X
Wydawca: Pergamon Press Ltd.
DOI: 10.1101/2021.04.19.440471

Genetic risk factors have a substantial impact on healthy life years

Autorzy: Aki Havulinna; Sakari Jukarainen; Nina Mars
Opublikowane w: Nature Medicine, Numer 27, 2021, Strona(/y) 1876-1884, ISSN 1078-8956
Wydawca: Nature Publishing Group
DOI: 10.1101/2022.01.25.22269831v1

Identifiable causal inference with noisy treatment and no side information

Autorzy: Pllnen, A. and Marttinen, P.
Opublikowane w: Transactions on Machine Learning Research (TMLR), 2024, ISSN 1533-7928
Wydawca: [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

Autorzy: 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
Opublikowane w: Respiratory Research, Numer 24, 2023, Strona(/y) article no 158, ISSN 1465-9921
Wydawca: BioMed Central
DOI: 10.1186/s12931-023-02458-7

TransferGWAS of T1-weighted brain MRI data from UK Biobank

Autorzy: Alexander Rakowski, Remo Monti, Christoph Lippert
Opublikowane w: PLOS Genetics, Numer 20, 2024, Strona(/y) e1011332, ISSN 1553-7404
Wydawca: Public Library of Science San Francisco, CA USA
DOI: 10.1371/journal.pgen.1011332

Pathogen-sugar interactions revealed by universal saturation transfer analysis

Autorzy: 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
Opublikowane w: Science, Numer 377, 2022, ISSN 0065-7085
Wydawca: 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

Autorzy: 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
Opublikowane w: HLA, Numer 103, 2024, ISSN 2059-2302
Wydawca: Wiley
DOI: 10.1111/tan.15251

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

Autorzy: 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,
Opublikowane w: Cell Reports Medicine, Numer 4, 2023, Strona(/y) 101152, ISSN 2666-3791
Wydawca: 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

Autorzy: Fanni Ojala, Mohamad R. Abdul Sater, Loren G. Miller, James A. McKinnell, Mary K. Hayden, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
Opublikowane w: PLOS Computational Biology, Numer 19, 2023, Strona(/y) e1010898, ISSN 1553-7358
Wydawca: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1010898

Informative Bayesian Neural Network Priors for Weak Signals

Autorzy: Tianyu Cui, Aki Havulinna, Pekka Marttinen, Samuel Kaski
Opublikowane w: Bayesian Anal., 2021, Strona(/y) 1-31 (2021), ISSN 1936-0975
Wydawca: Carnegie Mellon University
DOI: 10.1214/21-ba1291

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

Autorzy: 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
Opublikowane w: Nature Genetics, Numer 56, 2024, Strona(/y) 1989-1994, ISSN 1061-4036
Wydawca: 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.

Autorzy: Yu Xu, Dragana Vuckovic, Scott C. Ritchie, ..., John Danesh, Nicole Soranzo, Michael Inouye
Opublikowane w: Cell Genomics, Numer Vol 2, Numer 1, 2022, ISSN 2666-979X
Wydawca: Cell Press
DOI: 10.1016/j.xgen.2021.100086

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

Autorzy: 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
Opublikowane w: HGG advances,, Numer vol. 3, no. 4, 2022, Strona(/y) pp. 100133, ISSN 0346-251X
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.xhgg.2022.100133

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

Autorzy: Fritzsche, M., Akyüz, K., Abadía, M.C., McLennan, S., Marttinen, P. Mayrhofer, M.T., and Buyx, A.M.
Opublikowane w: Frontiers in Genetics, Numer Vol 4, 2023, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

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

Autorzy: 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
Opublikowane w: Cell Genomics, Numer 2, Numer 4, 2022, ISSN 2666-979X
Wydawca: CellPress
DOI: 10.1038/s41467-022-29143-5

A Unified Review of Deep Learning for Automated Medical Coding

Autorzy: Shaoxiong Ji, Xiaobo Li, Wei Sun, Hang Dong, Ara Taalas, Yijia Zhang, Honghan Wu, Esa Pitknen, Pekka Marttinen
Opublikowane w: ACM Computing Surveys, Numer 56, 2024, Strona(/y) 1-41, ISSN 0360-0300
Wydawca: Association for Computing Machinary, Inc.
DOI: 10.1145/3664615

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

Autorzy: 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
Opublikowane w: Cell Genomics, Numer Apr 13; 2(4), 2023, ISSN 2666-979X
Wydawca: Cell Press
DOI: 10.1016/j.xgen.2022.100118

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

Autorzy: Tuukka Holster, Shaoxiong Ji, Pekka Marttinen
Opublikowane w: The European Journal of Health Economics, Numer 25, 2024, Strona(/y) 1117-1131, ISSN 1618-7598
Wydawca: Springer Verlag
DOI: 10.1007/s10198-023-01656-w

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

Autorzy: Remo Monti, Pia Rautenstrauch, Mahsa Ghanbari, Alva Rani James, Uwe Ohler, Stefan Konigorski, Christoph Lippert
Opublikowane w: Nature Communications, Numer Vol 13, article 5332, 2022, Strona(/y) 1-16, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/2021.05.27.444972

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

Autorzy: Kristina Zguro, Chiara Fallerini, Francesca Fava, Simone Furini & Alessandra Renieri
Opublikowane w: EJHG, Numer Vol 30, 2022, Strona(/y) 899-907, ISSN 1018-4813
Wydawca: Natue Publishing Group
DOI: 10.1038/s41431-022-01121-x

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

Autorzy: Ji, Shaoxiong; Gao, Ya; Marttinen, Pekka
Opublikowane w: Arxiv, Numer 6, 2023, ISSN 2331-8422
Wydawca: Cornell University
DOI: 10.48550/arxiv.2301.10451

Metadata-guided feature disentanglement for functional genomics

Autorzy: Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Opublikowane w: Bioinformatics, Numer 40, 2024, Strona(/y) ii4-ii10, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btae403

Challenges and Opportunities for Developing More Generalizable Polygenic Risk Scores

Autorzy: Ying Wang, Kristin Tsuo, Masahiro Kanai, Benjamin M. Neale, Alicia R. Martin
Opublikowane w: Annual Rev of Biomed. Data Science, Numer Vol 5, 2022, Strona(/y) 293-320, ISSN 2574-3414
Wydawca: Annual Reviews
DOI: 10.1146/annurev-biodatasci-111721-074830

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

Autorzy: 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
Opublikowane w: Trials, Numer 25, 2024, ISSN 1745-6215
Wydawca: BioMed Central
DOI: 10.1186/s13063-024-08356-7

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

Autorzy: Natàlia Pujol-Gualdo, Kristi Läll, Maarja Lepamets, Estonian Biobank Research Team, Henna-Riikka Rossi, Riikka K. Arffman, Terhi T. Piltonen, Reedik Mäg, Triin Laisk
Opublikowane w: Nature Communications, Numer Vol 13, 2022, Strona(/y) article: 3584, ISSN 2041-1723
Wydawca: 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

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

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

Autorzy: 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.
Opublikowane w: Nature Human Behaviour, Numer Vol 7, 2023, Strona(/y) 1069-1083, ISSN 1476-4687
Wydawca: 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

Autorzy: Shinji Hotta, Mikko Kyt, Saila Koivusalo, Seppo Heinonen, Pekka Marttinen
Opublikowane w: PLOS ONE, Numer 19, 2024, Strona(/y) e0298506, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0298506

COVID-19: a challenge and an opportunity

Autorzy: Alessandra Renieri
Opublikowane w: EJHG, Numer Vol 30, 2022, Strona(/y) 870-871, ISSN 1018-4813
Wydawca: Natue Publishing Group
DOI: 10.1038/s41431-022-01142-6

The human genetic epidemiology of COVID-19

Autorzy: Mari Niemi, Mark Daly, Andrea Ganna
Opublikowane w: Nature Reviews: Genetics, Numer Vol 23, 2022, Strona(/y) 533-546, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41576-022-00478-5

Population Heterogeneity and Selection of Coronary Artery Disease Polygenic Scores

Autorzy: 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
Opublikowane w: Journal of Personalized Medicine, Numer 14, 2025, Strona(/y) 1025, ISSN 2075-4426
Wydawca: Basel MDPI AG 2011-
DOI: 10.3390/jpm14101025

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

Autorzy: 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
Opublikowane w: Cells, Numer 11(24), 2022, Strona(/y) 4096, ISSN 2073-4409
Wydawca: MDPI
DOI: 10.3390/cells11244096

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

Autorzy: 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
Opublikowane w: AJHG, Numer Vol 109, Numer 10, 2022, Strona(/y) 1727-1741, ISSN 0002-9297
Wydawca: 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

Autorzy: Gabriele Martelloni, Alessio Turchi, Chiara Fallerini, Andrea Degl’Innocenti, Margherita Baldassarri, Simona Olmi, Simone Furini, Alessandra Renieri, null null
Opublikowane w: Frontiers in Genetics, Numer 15, 2024, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2024.1362469

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

Autorzy: Max Tamlander, Nina Mars, Matti Pirinen, FinnGen, Elisabeth Widén & Samuli Ripatti
Opublikowane w: Comm. Biology, Numer Vol 5, 2022, Strona(/y) 158, ISSN 2399-3642
Wydawca: Nature
DOI: 10.1038/s42003-021-02996-0

Reducing noisy annotations for depression estimation from facial images

Autorzy: Lang He, Prayag Tiwari, Chonghua Lv, WenShuai Wu, Liyong Guo
Opublikowane w: Neural Networks, Numer Vol 153, 2022, Strona(/y) 120-129, ISSN 0893-6080
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2022.05.025

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

Autorzy: Kumar, Y., Ilin, A., Salo, H., Kulathinal, S., Leinonen, M.K., and Marttinen, P.
Opublikowane w: IEEE Transactions on artificial intelligence, Numer Vol 5, No 8, 2024, ISSN 2691-4581
Wydawca: 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

Autorzy: 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
Opublikowane w: European Heart Journal, Numer 43, issue 18, 2022, Strona(/y) 1715-1727, ISSN 0195-668X
Wydawca: Oxford University Press
DOI: 10.1093/eurheartj/ehac056

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

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

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

Autorzy: Joel Honkamaa, Pekka Marttinen
Opublikowane w: Machine Learning for Biomedical Imaging, Numer 2, 2025, Strona(/y) 2148-2194, ISSN 2766-905X
Wydawca: 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

Autorzy: 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
Opublikowane w: The American Journal of Human Genetics, Numer 111, 2025, Strona(/y) 1431-1447, ISSN 0002-9297
Wydawca: University of Chicago Press
DOI: 10.1016/j.ajhg.2024.06.003

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

Autorzy: Dainese, N.*, Merler, M.*, Alakuijala, M., and Marttinen, P.
Opublikowane w: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2024
Wydawca: Cornell University

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

Autorzy: Raj, V., Cui, T., Heinonen, M., and Marttinen, P.
Opublikowane w: The Proceedings of 26th International Conference on Artificial Intelligence and Statistics, PMLR 206:6741-6763. (AISTATS 2023), 2023, Strona(/y) PMLR 206:6741-6763
Wydawca: PMLR

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

Autorzy: Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietilinen, K., and Marttinen, P.
Opublikowane w: 37th Conference on Neural Information Processing Systems (NeurIPS 2023), 2023
Wydawca: NeurIOS 2023

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

Autorzy: Gao, Y., Ji, S., and Marttinen, P.
Opublikowane w: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), 2024, Strona(/y) 9787-9798
Wydawca: ACL Anthology

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

Autorzy: Poyraz, O. and Marttinen, P.
Opublikowane w: Proceedings of the 3rd Machine Learning for Health Symposium 2023, PMLR, Numer 225, 2023, Strona(/y) 461-479
Wydawca: Machine Learning for Health

Contextualized graph embeddings for adverse drug event detection

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

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

Autorzy: 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
Opublikowane w: NeurIPS 2022 Workshop on Synthetic Data for Empowering ML Research, 2022, Strona(/y) 1-7
Wydawca: NeurIPS

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

Autorzy: Odnoblyudova, A., Hzl, C., John, S.T., Cognolato, A., Juuti, A., Srkk, S., Pietilinen, K., and Marttinen, P.
Opublikowane w: Proceedings of Machine Learning Research, Numer 225, 2023, Strona(/y) 428-444
Wydawca: Machine Learning for Health (ML4H) 2023

Improving Medical Multi-modal Contrastive Learning with Expert Annotations

Autorzy: Kumar, Y. and Marttinen, P.
Opublikowane w: The 18th European Conference on Computer Vision (ECCV 2024), 2024
Wydawca: Cornell University
DOI: 10.48550/arxiv.2403.10153

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

Autorzy: Chen He, Vishnu Raj, Hans Moen, Tommi Grhn, Chen Wang, Laura-Maria Peltonen, Saila Koivusalo, Pekka Marttinen, Giulio Jacucci
Opublikowane w: Proceedings of the 29th International Conference on Intelligent User Interfaces, 2024, Strona(/y) 229-244
Wydawca: ACM
DOI: 10.1145/3640543.3645151

Causal Modeling of Policy Interventions From Treatment–Outcome Sequences

Autorzy: Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietiläinen, K., and Marttinen, P.
Opublikowane w: The 40th International Conference on Machine Learning (ICML 2023), 2023
Wydawca: unkonwn

Deconfounded Representation Similarity for Comparison of Neural Networks

Autorzy: Cui, T., Kumar, Y., Marttinen, P., and Kaski, S.
Opublikowane w: 2022, ISBN 9781713871088
Wydawca: NeurIPS Proceedings

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

Autorzy: Ji, Shaoxiong; Marttinen, Pekka
Opublikowane w: The 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2023)., Numer 1, 2023, Strona(/y) 589-598
Wydawca: EACL
DOI: 10.48550/arxiv.2109.03062

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

Autorzy: Severi Rissanen, Pekka Marttinen
Opublikowane w: 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021
Wydawca: NeurIPS 2021

Query-Guided Self-Supervised Summarization of Nursing Notes

Autorzy: Gao, Y., Moen, H., Koivusalo, S., Koskinen, M., and Marttinen, P.
Opublikowane w: Proceedings of the Machine Learning for Health Symposium (ML4H 2024), 2024
Wydawca: Cornell University

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

Autorzy: Wharrie, S., Yang, Z., Ganna, A., & Kaski, S.
Opublikowane w: Proceedings of Machine Learning Research, 2023
Wydawca: unknown

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

Autorzy: Nikitin, A., Kossen, J., Gal, Y., and Marttinen, P.
Opublikowane w: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2023
Wydawca: Cornell University

A Unified Review of Deep Learning for Automated Medical Coding

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

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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 15: 5007, 2024, ISSN 1476-4687
Wydawca: Nature
DOI: 10.1101/2023.06.12.23291186

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