International consortium for integrative genomics prediction

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

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

Deliverables

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

Publications

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

Author(s): Nina Mars, Joni V. Lindbohm, Pietro della Briotta Parolo, Elisabeth Widén, Jaakko Kaprio, Aarno Palotie, FinnGen, Samuli Ripatti
Published in: AJHG, Issue Vol 109, Issue 12, 2022, Page(s) 2152-2162, ISSN 0002-9297
Publisher: 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

Author(s): 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
Published in: American Journal of Obstetrics and Gynecology, Issue 231, 2025, Page(s) 541.e1-541.e16, ISSN 0002-9378
Publisher: Mosby Inc.
DOI: 10.1016/j.ajog.2024.02.303

A cross-disorder dosage sensitivity map of the human genome

Author(s): 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
Published in: Cell, Issue 185, 2022, Page(s) 3041-3055, ISSN 1097-4172
Publisher: Cell Press
DOI: 10.1016/j.cell.2022.06.036

Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases

Author(s): 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.
Published in: Nature Medicine, Issue 29, 2023, Page(s) 209-218, ISSN 1546-170X
Publisher: Nature
DOI: 10.1038/s41591-022-02122-5

Gene-Gene Interaction Detection with Deep Learning

Author(s): Tianyu Cui, Khaoula El Mekkaoui, Jaakko Reinvall, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski
Published in: Communications Biology, Issue Vol 5, article 1238, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1101/2021.03.12.435063

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

Author(s): 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
Published in: Viruses, Issue 14(6), 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14061185

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

Author(s): 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
Published in: Nature, Issue 5, 2022, Page(s) article 802, ISSN 0028-0836
Publisher: 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

Author(s): 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
Published in: Infectious Agents and Cancer, Issue 18, 2023, ISSN 1750-9378
Publisher: BioMed Central
DOI: 10.1186/s13027-023-00561-4

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

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

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

Author(s): 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
Published in: Cell Genomics, Issue Vol 3, Issue 1, 2023, ISSN 2666-979X
Publisher: 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

Author(s): 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
Published in: Journal of the American Heart Association, Issue 12, 2024, Page(s) No 15, ISSN 2047-9980
Publisher: Wiley-Blackwell
DOI: 10.1161/jaha.122.029296

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

Author(s): 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
Published in: Nature Medicine, Issue 27, 2021, Page(s) 1876-1884, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01549-6

Multitask Balanced and Recalibrated Network for Medical Code Prediction

Author(s): Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
Published in: ACM Transactions on Intelligent Systems and Technology, Issue Vol 14, Issue 1, 2022, Page(s) 1-20, ISSN 2157-6904
Publisher: Association for Computing Machinery (ACM)
DOI: 10.1145/3563041

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

Author(s): 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
Published in: Frontiers in Genetics, Issue 14, 2023, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

Polygenic scores in biomedical research

Author(s): Iftikhar J. Kullo, Cathryn M. Lewis, Michael Inouye, Alicia R. Martin, Samuli Ripatti & Nilanjan Chatterjee
Published in: Nature Reviews Genetics, Issue 23, 2022, Page(s) 524-532, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00470-z

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

Author(s): 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
Published in: Cell Reports Methods, Issue Vol 2,issue 2, 2022, ISSN 0346-251X
Publisher: Pergamon Press Ltd.
DOI: 10.1101/2021.04.19.440471

Genetic risk factors have a substantial impact on healthy life years

Author(s): Aki Havulinna; Sakari Jukarainen; Nina Mars
Published in: Nature Medicine, Issue 27, 2021, Page(s) 1876-1884, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1101/2022.01.25.22269831v1

Identifiable causal inference with noisy treatment and no side information

Author(s): Pllnen, A. and Marttinen, P.
Published in: Transactions on Machine Learning Research (TMLR), 2024, ISSN 1533-7928
Publisher: [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

Author(s): 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
Published in: Respiratory Research, Issue 24, 2023, Page(s) article no 158, ISSN 1465-9921
Publisher: BioMed Central
DOI: 10.1186/s12931-023-02458-7

TransferGWAS of T1-weighted brain MRI data from UK Biobank

Author(s): Alexander Rakowski, Remo Monti, Christoph Lippert
Published in: PLOS Genetics, Issue 20, 2024, Page(s) e1011332, ISSN 1553-7404
Publisher: Public Library of Science San Francisco, CA USA
DOI: 10.1371/journal.pgen.1011332

Pathogen-sugar interactions revealed by universal saturation transfer analysis

Author(s): 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
Published in: Science, Issue 377, 2022, ISSN 0065-7085
Publisher: 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

Author(s): 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
Published in: HLA, Issue 103, 2024, ISSN 2059-2302
Publisher: Wiley
DOI: 10.1111/tan.15251

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

Author(s): 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,
Published in: Cell Reports Medicine, Issue 4, 2023, Page(s) 101152, ISSN 2666-3791
Publisher: 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

Author(s): Fanni Ojala, Mohamad R. Abdul Sater, Loren G. Miller, James A. McKinnell, Mary K. Hayden, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
Published in: PLOS Computational Biology, Issue 19, 2023, Page(s) e1010898, ISSN 1553-7358
Publisher: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1010898

Informative Bayesian Neural Network Priors for Weak Signals

Author(s): Tianyu Cui, Aki Havulinna, Pekka Marttinen, Samuel Kaski
Published in: Bayesian Anal., 2021, Page(s) 1-31 (2021), ISSN 1936-0975
Publisher: Carnegie Mellon University
DOI: 10.1214/21-ba1291

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

Author(s): 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
Published in: Nature Genetics, Issue 56, 2024, Page(s) 1989-1994, ISSN 1061-4036
Publisher: 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.

Author(s): Yu Xu, Dragana Vuckovic, Scott C. Ritchie, ..., John Danesh, Nicole Soranzo, Michael Inouye
Published in: Cell Genomics, Issue Vol 2, Issue 1, 2022, ISSN 2666-979X
Publisher: Cell Press
DOI: 10.1016/j.xgen.2021.100086

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

Author(s): 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
Published in: HGG advances,, Issue vol. 3, no. 4, 2022, Page(s) pp. 100133, ISSN 0346-251X
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.xhgg.2022.100133

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

Author(s): Fritzsche, M., Akyüz, K., Abadía, M.C., McLennan, S., Marttinen, P. Mayrhofer, M.T., and Buyx, A.M.
Published in: Frontiers in Genetics, Issue Vol 4, 2023, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2023.1098439

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

Author(s): 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
Published in: Cell Genomics, Issue 2, Issue 4, 2022, ISSN 2666-979X
Publisher: CellPress
DOI: 10.1038/s41467-022-29143-5

A Unified Review of Deep Learning for Automated Medical Coding

Author(s): Shaoxiong Ji, Xiaobo Li, Wei Sun, Hang Dong, Ara Taalas, Yijia Zhang, Honghan Wu, Esa Pitknen, Pekka Marttinen
Published in: ACM Computing Surveys, Issue 56, 2024, Page(s) 1-41, ISSN 0360-0300
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3664615

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

Author(s): 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
Published in: Cell Genomics, Issue Apr 13; 2(4), 2023, ISSN 2666-979X
Publisher: Cell Press
DOI: 10.1016/j.xgen.2022.100118

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

Author(s): Tuukka Holster, Shaoxiong Ji, Pekka Marttinen
Published in: The European Journal of Health Economics, Issue 25, 2024, Page(s) 1117-1131, ISSN 1618-7598
Publisher: Springer Verlag
DOI: 10.1007/s10198-023-01656-w

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

Author(s): Remo Monti, Pia Rautenstrauch, Mahsa Ghanbari, Alva Rani James, Uwe Ohler, Stefan Konigorski, Christoph Lippert
Published in: Nature Communications, Issue Vol 13, article 5332, 2022, Page(s) 1-16, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.05.27.444972

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

Author(s): Kristina Zguro, Chiara Fallerini, Francesca Fava, Simone Furini & Alessandra Renieri
Published in: EJHG, Issue Vol 30, 2022, Page(s) 899-907, ISSN 1018-4813
Publisher: Natue Publishing Group
DOI: 10.1038/s41431-022-01121-x

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

Author(s): Ji, Shaoxiong; Gao, Ya; Marttinen, Pekka
Published in: Arxiv, Issue 6, 2023, ISSN 2331-8422
Publisher: Cornell University
DOI: 10.48550/arxiv.2301.10451

Metadata-guided feature disentanglement for functional genomics

Author(s): Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert
Published in: Bioinformatics, Issue 40, 2024, Page(s) ii4-ii10, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btae403

Challenges and Opportunities for Developing More Generalizable Polygenic Risk Scores

Author(s): Ying Wang, Kristin Tsuo, Masahiro Kanai, Benjamin M. Neale, Alicia R. Martin
Published in: Annual Rev of Biomed. Data Science, Issue Vol 5, 2022, Page(s) 293-320, ISSN 2574-3414
Publisher: Annual Reviews
DOI: 10.1146/annurev-biodatasci-111721-074830

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

Author(s): 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
Published in: Trials, Issue 25, 2024, ISSN 1745-6215
Publisher: BioMed Central
DOI: 10.1186/s13063-024-08356-7

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

Author(s): Natàlia Pujol-Gualdo, Kristi Läll, Maarja Lepamets, Estonian Biobank Research Team, Henna-Riikka Rossi, Riikka K. Arffman, Terhi T. Piltonen, Reedik Mäg, Triin Laisk
Published in: Nature Communications, Issue Vol 13, 2022, Page(s) article: 3584, ISSN 2041-1723
Publisher: 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

Author(s): Jiwoo Lee, Tuomo Kiiskinen, Nina Mars, Sakari Jukarainen, Erik Ingelsson, Benjamin Neale, Samuli Ripatti, Pradeep Natarajan, and Andrea Ganna
Published in: Circulation: Genomic and Precision Medicine, Issue Vol. 14, No. 4, 2021, ISSN 0009-7322
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circgen.120.003283

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

Author(s): 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.
Published in: Nature Human Behaviour, Issue Vol 7, 2023, Page(s) 1069-1083, ISSN 1476-4687
Publisher: 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

Author(s): Shinji Hotta, Mikko Kyt, Saila Koivusalo, Seppo Heinonen, Pekka Marttinen
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0298506, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0298506

COVID-19: a challenge and an opportunity

Author(s): Alessandra Renieri
Published in: EJHG, Issue Vol 30, 2022, Page(s) 870-871, ISSN 1018-4813
Publisher: Natue Publishing Group
DOI: 10.1038/s41431-022-01142-6

The human genetic epidemiology of COVID-19

Author(s): Mari Niemi, Mark Daly, Andrea Ganna
Published in: Nature Reviews: Genetics, Issue Vol 23, 2022, Page(s) 533-546, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00478-5

Population Heterogeneity and Selection of Coronary Artery Disease Polygenic Scores

Author(s): 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
Published in: Journal of Personalized Medicine, Issue 14, 2025, Page(s) 1025, ISSN 2075-4426
Publisher: Basel MDPI AG 2011-
DOI: 10.3390/jpm14101025

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

Author(s): 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
Published in: Cells, Issue 11(24), 2022, Page(s) 4096, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells11244096

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

Author(s): 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
Published in: AJHG, Issue Vol 109, Issue 10, 2022, Page(s) 1727-1741, ISSN 0002-9297
Publisher: 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

Author(s): Gabriele Martelloni, Alessio Turchi, Chiara Fallerini, Andrea Degl’Innocenti, Margherita Baldassarri, Simona Olmi, Simone Furini, Alessandra Renieri, null null
Published in: Frontiers in Genetics, Issue 15, 2024, ISSN 1664-8021
Publisher: 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

Author(s): Max Tamlander, Nina Mars, Matti Pirinen, FinnGen, Elisabeth Widén & Samuli Ripatti
Published in: Comm. Biology, Issue Vol 5, 2022, Page(s) 158, ISSN 2399-3642
Publisher: Nature
DOI: 10.1038/s42003-021-02996-0

Reducing noisy annotations for depression estimation from facial images

Author(s): Lang He, Prayag Tiwari, Chonghua Lv, WenShuai Wu, Liyong Guo
Published in: Neural Networks, Issue Vol 153, 2022, Page(s) 120-129, ISSN 0893-6080
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2022.05.025

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

Author(s): Kumar, Y., Ilin, A., Salo, H., Kulathinal, S., Leinonen, M.K., and Marttinen, P.
Published in: IEEE Transactions on artificial intelligence, Issue Vol 5, No 8, 2024, ISSN 2691-4581
Publisher: 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

Author(s): 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
Published in: European Heart Journal, Issue 43, issue 18, 2022, Page(s) 1715-1727, ISSN 0195-668X
Publisher: Oxford University Press
DOI: 10.1093/eurheartj/ehac056

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

Author(s): Pyry, Helkkula; Tuomo, Kiiskinen; Aki S, Havulinna; Juha, Karjalainen; Seppo, Koskinen; Veikko, Salomaa; Mark J, Daly; Aarno, Palotie; Ida, Surakka; Samuli, Ripatti
Published in: PLoS Genetics, Issue 11, 2021, ISSN 1553-7404
Publisher: 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

Author(s): Joel Honkamaa, Pekka Marttinen
Published in: Machine Learning for Biomedical Imaging, Issue 2, 2025, Page(s) 2148-2194, ISSN 2766-905X
Publisher: 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

Author(s): 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
Published in: The American Journal of Human Genetics, Issue 111, 2025, Page(s) 1431-1447, ISSN 0002-9297
Publisher: 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

Author(s): Dainese, N.*, Merler, M.*, Alakuijala, M., and Marttinen, P.
Published in: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2024
Publisher: Cornell University

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

Author(s): Raj, V., Cui, T., Heinonen, M., and Marttinen, P.
Published in: The Proceedings of 26th International Conference on Artificial Intelligence and Statistics, PMLR 206:6741-6763. (AISTATS 2023), 2023, Page(s) PMLR 206:6741-6763
Publisher: PMLR

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

Author(s): Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietilinen, K., and Marttinen, P.
Published in: 37th Conference on Neural Information Processing Systems (NeurIPS 2023), 2023
Publisher: NeurIOS 2023

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

Author(s): Gao, Y., Ji, S., and Marttinen, P.
Published in: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), 2024, Page(s) 9787-9798
Publisher: ACL Anthology

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

Author(s): Poyraz, O. and Marttinen, P.
Published in: Proceedings of the 3rd Machine Learning for Health Symposium 2023, PMLR, Issue 225, 2023, Page(s) 461-479
Publisher: Machine Learning for Health

Contextualized graph embeddings for adverse drug event detection

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

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

Author(s): 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
Published in: NeurIPS 2022 Workshop on Synthetic Data for Empowering ML Research, 2022, Page(s) 1-7
Publisher: NeurIPS

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

Author(s): Odnoblyudova, A., Hzl, C., John, S.T., Cognolato, A., Juuti, A., Srkk, S., Pietilinen, K., and Marttinen, P.
Published in: Proceedings of Machine Learning Research, Issue 225, 2023, Page(s) 428-444
Publisher: Machine Learning for Health (ML4H) 2023

Improving Medical Multi-modal Contrastive Learning with Expert Annotations

Author(s): Kumar, Y. and Marttinen, P.
Published in: The 18th European Conference on Computer Vision (ECCV 2024), 2024
Publisher: Cornell University
DOI: 10.48550/arxiv.2403.10153

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

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

Causal Modeling of Policy Interventions From Treatment–Outcome Sequences

Author(s): Hizli, C., John, S.T., Juuti, A., Saarinen, T., Pietiläinen, K., and Marttinen, P.
Published in: The 40th International Conference on Machine Learning (ICML 2023), 2023
Publisher: unkonwn

Deconfounded Representation Similarity for Comparison of Neural Networks

Author(s): Cui, T., Kumar, Y., Marttinen, P., and Kaski, S.
Published in: 2022, ISBN 9781713871088
Publisher: NeurIPS Proceedings

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

Author(s): Ji, Shaoxiong; Marttinen, Pekka
Published in: The 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2023)., Issue 1, 2023, Page(s) 589-598
Publisher: EACL
DOI: 10.48550/arxiv.2109.03062

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

Author(s): Severi Rissanen, Pekka Marttinen
Published in: 35th Conference on Neural Information Processing Systems (NeurIPS 2021), 2021
Publisher: NeurIPS 2021

Query-Guided Self-Supervised Summarization of Nursing Notes

Author(s): Gao, Y., Moen, H., Koivusalo, S., Koskinen, M., and Marttinen, P.
Published in: Proceedings of the Machine Learning for Health Symposium (ML4H 2024), 2024
Publisher: Cornell University

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

Author(s): Wharrie, S., Yang, Z., Ganna, A., & Kaski, S.
Published in: Proceedings of Machine Learning Research, 2023
Publisher: unknown

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

Author(s): Nikitin, A., Kossen, J., Gal, Y., and Marttinen, P.
Published in: Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2023
Publisher: Cornell University

A Unified Review of Deep Learning for Automated Medical Coding

Author(s): Ji, Shaoxiong; Sun, Wei; Li, Xiaobo; Dong, Hang; Taalas, Ara; Zhang, Yijia; Wu, Honghan; Pitkänen, Esa; Marttinen, Pekka
Published in: J of ACM, Issue Vol 37, no 4, article 111, 2022, ISSN 0004-5411
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue 15: 5007, 2024, ISSN 1476-4687
Publisher: Nature
DOI: 10.1101/2023.06.12.23291186

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