Unified computational solutions to disentangle biological interactions in multi-omics data

Informacje na temat projektu

FindingPheno

Identyfikator umowy o grant: 952914

DOI

10.3030/952914

Projekt został zamknięty

Data podpisania przez KE 2 Grudnia 2020

Data rozpoczęcia 1 Marca 2021

Data zakończenia 31 Sierpnia 2025

Finansowanie w ramach

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Koszt całkowity

€ 5 793 085,00

Wkład UE

€ 5 793 085,00

Koordynowany przez

KOBENHAVNS UNIVERSITET
Denmark

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

Documents, reports (7)

Analysis of host-microbiome dynamics in gut microenvironment
Second Report on dissemination, training and networking activities in FindingPheno

Report on dissemination, training and networking activities in FindingPheno

Report on dissemination, training and networking activities in FindingPheno

Report on dissemination training and networking activities in FindingPheno

Plenary kick-off meeting, including minutes

Plenary kickoff meeting including minutes

Summary on challenges in curating public data to apply FindingPheno's solutions

Summary on challenges in curating public data to apply FindingPheno’s solutions

Knowledge resources for chicken, salmon and maize

Knowledge resources for chicken salmon and maize

Stakeholder Synergy Meeting

Websites, patent fillings, videos etc. (2)

Visual identity and project website for FindingPheno released
Dynamic model for multi-omic host-microbiome interactions

Publikacje

Peer reviewed articles (19)

A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis

Autorzy: István Scheuring, Jacob A, Rasmussen, Davide Bozzi, Morten T Limborg
Opublikowane w: Frontiers in Microbiology, Numer 04. August, 2022, ISSN 1664-302X
Wydawca: Frontiers Media
DOI: 10.3389/fmicb.2022.912806

Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon ( <i>Salmo salar</i> )

Autorzy: Aikaterini Katirtzoglou, Søren B. Hansen, Harald Sveier, Michael D. Martin, Jaelle C. Brealey, Morten T. Limborg
Opublikowane w: Epigenetics, Numer 19, 2024, ISSN 1559-2294
Wydawca: Landes Bioscience
DOI: 10.1080/15592294.2024.2392049

Cooperation in public goods game does not require assortment and depends on population density

Autorzy: Adél Károlyi, István Scheuring
Opublikowane w: Journal of Evolutionary Biology, Numer 37, 2024, Strona(/y) 451-463, ISSN 1420-9101
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/jeb/voae029

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Autorzy: Youwen Qin, Aki S. Havulinna, Yang Liu, Pekka Jousilahti, Scott C. Ritchie, Alex Tokolyi, Jon G. Sanders, Liisa Valsta, Marta Brożyńska, Qiyun Zhu, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Rohit Loomba, Susan Cheng, Mohit Jain, Teemu Niiranen, Leo Lahti, Rob Knight, Veikko Salomaa, Michael Inouye, Guillaume Méric
Opublikowane w: Nature Genetics, Numer 54, 2024, Strona(/y) 134-142, ISSN 1061-4036
Wydawca: Nature Publishing Group
DOI: 10.1038/s41588-021-00991-z

The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality

Autorzy: István Zachár, Gergely Boza
Opublikowane w: Frontiers in Ecology and Evolution, Numer 13 April, 2022, ISSN 2296-701X
Wydawca: Frontiers Media
DOI: 10.3389/fevo.2022.798045

Assessing the safety of microbiome perturbations

Autorzy: Aline Metris, Alan W. Walker, Alicia Showering, Andrea Doolan, Andrew J. McBain, Antonis Ampatzoglou, Barry Murphy, Catherine O'Neill, Colette Shortt, Elizabeth M. Darby, Gary Aldis, Greg G. Hillebrand, Helen L. Brown, Hilary P. Browne, Jay P. Tiesman, Joy Leng, Leo Lahti, Nicholas S. Jakubovics, Oliver Hasselwander, Robert D. Finn, Silvia Klamert, Tamas Korcsmaros, Lindsay J. Hall
Opublikowane w: Microbial Genomics, Numer 11, 2025, ISSN 2057-5858
Wydawca: Microbiology Society
DOI: 10.1099/mgen.0.001405

Effects of joint invasion: How co-invaders affect each other's success in model food webs?

Autorzy: Ágnes Móréh, Ferenc Jordán, István Scheuring
Opublikowane w: Ecological Modelling, Numer 492, 2025, Strona(/y) 110735, ISSN 0304-3800
Wydawca: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110735

Invaders’ trophic position and their direct and indirect relationship influence on resident food webs

Autorzy: Ágnes Móréh, István Scheuring
Opublikowane w: Ecological Modelling, Numer 508, 2025, Strona(/y) 111238, ISSN 0304-3800
Wydawca: Elsevier BV
DOI: 10.1016/j.ecolmodel.2025.111238

LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

Autorzy: Ali Mostafa Anwar, Akewak Jeba, Leo Lahti, Eleanor Coffey
Opublikowane w: bioRXiv, Numer February 08, 2025, 2025, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/2025.02.06.636801

Dealing with dimensionality: the application of machine learning to multi-omics data

Autorzy: Dylan Feldner-Busztin ,Panos Firbas Nisantzis,Shelley Jane Edmunds ,Gergely Boza ,Fernando Racimo,Shyam Gopalakrishnan,Morten Tønsberg Limborg,Leo Lahti,Gonzalo G. de Polavieja
Opublikowane w: Bioinformatics, Numer Volume 39, Numer 2, February 2023, 2023, ISSN 1367-4811
Wydawca: Oxford Press
DOI: 10.1093/bioinformatics/btad021

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Autorzy: Yu Gao, Yağmur Şimşek, Emma Gheysen, Tuomas Borman, Yi Li, Leo Lahti, Karoline Faust, Daniel Rios Garza
Opublikowane w: Methods in Ecology and Evolution, Numer 14, 2023, Strona(/y) 1967-1980, ISSN 2041-210X
Wydawca: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14129

Quantifying the impact of ecological memory on the dynamics of interacting communities

Autorzy: Moein Khalighi; Didier Gonze; Karoline Faust; Guilhem Sommeria-Klein; Leo Lahti
Opublikowane w: PLOS Computational Biology, Numer 1553734X, 2022, Strona(/y) e1009396, ISSN 1553-734X
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1009396

Eco-evolutionary modelling of microbial syntrophy indicates the robustness of cross-feeding over cross-facilitation

Autorzy: Gergely Boza, György Barabás, István Scheuring, István Zachar
Opublikowane w: Scientific Reports, Numer 2022 January 17. Volume 13, 2022, Strona(/y) 1-15, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-023-27421-w

Elementary methods provide more replicable results in microbial differential abundance analysis

Autorzy: Juho Pelto, Kari Auranen, Janne V Kujala, Leo Lahti
Opublikowane w: Briefings in Bioinformatics, Numer 26, 2025, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbaf130

iSEEtree: interactive explorer for hierarchical data

Autorzy: Giulio Benedetti, Ely Seraidarian, Theotime Pralas, Akewak Jeba, Tuomas Borman, Leo Lahti
Opublikowane w: Bioinformatics Advances, Numer 5, 2025, ISSN 2635-0041
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbaf107

Gender differences in global antimicrobial resistance

Autorzy: Mahkameh Salehi, Ville Laitinen, Shivang Bhanushali, Johan Bengtsson-Palme, Peter Collignon, John J. Beggs, Katariina Pärnänen, Leo Lahti
Opublikowane w: npj Biofilms and Microbiomes, Numer 11, 2025, ISSN 2055-5008
Wydawca: Springer Science and Business Media LLC
DOI: 10.1038/s41522-025-00715-9

Integration of polygenic and gut metagenomic risk prediction for common diseases

Autorzy: Yang Liu, Scott C. Ritchie, Shu Mei Teo, Matti O. Ruuskanen, Oleg Kambur, Qiyun Zhu, Jon Sanders, Yoshiki Vázquez-Baeza, Karin Verspoor, Pekka Jousilahti, Leo Lahti, Teemu Niiranen, Veikko Salomaa, Aki S. Havulinna, Rob Knight, Guillaume Méric, Michael Inouye
Opublikowane w: Nature Aging, Numer 4, 2024, Strona(/y) 584-594, ISSN 2662-8465
Wydawca: Springer Science and Business Media LLC
DOI: 10.1038/s43587-024-00590-7

Cue-driven microbial cooperation and communication: evolving quorum sensing with honest signaling

Autorzy: Tamás Czárán, István Scheuring, István Zachar, Szabolcs Számadó
Opublikowane w: BMC Biology, Numer 22, 2024, ISSN 1741-7007
Wydawca: BioMed Central
DOI: 10.1186/s12915-024-01857-6

Learning and teaching biological data science in the Bioconductor community

Autorzy: Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C. Culhane, Sean Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson
Opublikowane w: PLOS Computational Biology, Numer 21, 2025, Strona(/y) e1012925, ISSN 1553-7358
Wydawca: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012925

Other (2)

Inference of population genetics parameters using discriminator neural networks: an adversarial Monte Carlo approach

Autorzy: Graham Gower, Pablo Iáñez Picazo, Finn Lindgren, Fernando Racimo
Opublikowane w: Biorxiv, 2024
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.27.538386

C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data

Autorzy: Panos Firbas Nisantzis, Carolina Gonçalves, Gonzalo de Polavieja
Opublikowane w: bioRxiv, Numer February 23, 2025, 2025
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.19.638643

Non-peer reviewed articles (2)

Biome-specific genome catalogues reveal functional potential of shallow sequencing

Autorzy: Alejandra Escobar-Zepeda, Matti O. Ruuskanen, Martin Beracochea, Jennifer Lu, Dattatray Mongad, Lorna Richardson, Robert D. Finn, Leo Lahti
Opublikowane w: bioRXiv, 2025, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/2025.06.16.659887

Multi-omics time-series analysis in microbiome research: a systematic review

Autorzy: Moiz Khan Sherwani, Matti O. Ruuskanen, Dylan Feldner-Busztin, Panos Nisantzis Firbas, Gergely Boza, Ágnes Móréh, Tuomas Borman, Pande Putu Erawijantari, István Scheuring, Shyam Gopalakrishnan, Leo Lahti
Opublikowane w: bioRXiv, 2025, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/2025.07.03.659054