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

Project Information

FindingPheno

Grant agreement ID: 952914

DOI

10.3030/952914

Project closed

EC signature date 2 December 2020

Start date 1 March 2021

End date 31 August 2025

Funded under

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

Total cost

€ 5 793 085,00

EU contribution

€ 5 793 085,00

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

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

Documents, reports (8)

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

PDER agreed (updated annually or when needed)

PDER agreed updated annually or when needed

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

Publications

Peer reviewed articles (16)

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

Author(s): István Scheuring, Jacob A, Rasmussen, Davide Bozzi, Morten T Limborg
Published in: Frontiers in Microbiology, Issue 04. August, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.912806

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

Author(s): Adél Károlyi, István Scheuring
Published in: Journal of Evolutionary Biology, Issue 37, 2024, Page(s) 451-463, ISSN 1420-9101
Publisher: Oxford University Press (OUP)
DOI: 10.1093/jeb/voae029

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

Author(s): István Zachár, Gergely Boza
Published in: Frontiers in Ecology and Evolution, Issue 13 April, 2022, ISSN 2296-701X
Publisher: Frontiers Media
DOI: 10.3389/fevo.2022.798045

Assessing the safety of microbiome perturbations

Author(s): 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
Published in: Microbial Genomics, Issue 11, 2025, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.001405

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

Author(s): Ágnes Móréh, Ferenc Jordán, István Scheuring
Published in: Ecological Modelling, Issue 492, 2025, Page(s) 110735, ISSN 0304-3800
Publisher: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110735

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

Author(s): Ágnes Móréh, István Scheuring
Published in: Ecological Modelling, Issue 508, 2025, Page(s) 111238, ISSN 0304-3800
Publisher: 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

Author(s): Ali Mostafa Anwar, Akewak Jeba, Leo Lahti, Eleanor Coffey
Published in: bioRXiv, Issue February 08, 2025, 2025, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/2025.02.06.636801

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

Author(s): Dylan Feldner-Busztin ,Panos Firbas Nisantzis,Shelley Jane Edmunds ,Gergely Boza ,Fernando Racimo,Shyam Gopalakrishnan,Morten Tønsberg Limborg,Leo Lahti,Gonzalo G. de Polavieja
Published in: Bioinformatics, Issue Volume 39, Issue 2, February 2023, 2023, ISSN 1367-4811
Publisher: Oxford Press
DOI: 10.1093/bioinformatics/btad021

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

Author(s): Moein Khalighi; Didier Gonze; Karoline Faust; Guilhem Sommeria-Klein; Leo Lahti
Published in: PLOS Computational Biology, Issue 1553734X, 2022, Page(s) e1009396, ISSN 1553-734X
Publisher: 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

Author(s): Gergely Boza, György Barabás, István Scheuring, István Zachar
Published in: Scientific Reports, Issue 2022 January 17. Volume 13, 2022, Page(s) 1-15, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-27421-w

Elementary methods provide more replicable results in microbial differential abundance analysis

Author(s): Juho Pelto, Kari Auranen, Janne V Kujala, Leo Lahti
Published in: Briefings in Bioinformatics, Issue 26, 2025, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaf130

iSEEtree: interactive explorer for hierarchical data

Author(s): Giulio Benedetti, Ely Seraidarian, Theotime Pralas, Akewak Jeba, Tuomas Borman, Leo Lahti
Published in: Bioinformatics Advances, Issue 5, 2025, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbaf107

Gender differences in global antimicrobial resistance

Author(s): Mahkameh Salehi, Ville Laitinen, Shivang Bhanushali, Johan Bengtsson-Palme, Peter Collignon, John J. Beggs, Katariina Pärnänen, Leo Lahti
Published in: npj Biofilms and Microbiomes, Issue 11, 2025, ISSN 2055-5008
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41522-025-00715-9

Integration of polygenic and gut metagenomic risk prediction for common diseases

Author(s): 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
Published in: Nature Aging, Issue 4, 2024, Page(s) 584-594, ISSN 2662-8465
Publisher: 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

Author(s): Tamás Czárán, István Scheuring, István Zachar, Szabolcs Számadó
Published in: BMC Biology, Issue 22, 2024, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-024-01857-6

Learning and teaching biological data science in the Bioconductor community

Author(s): 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
Published in: PLOS Computational Biology, Issue 21, 2025, Page(s) e1012925, ISSN 1553-7358
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012925

Non-peer reviewed articles (2)

Biome-specific genome catalogues reveal functional potential of shallow sequencing

Author(s): Alejandra Escobar-Zepeda, Matti O. Ruuskanen, Martin Beracochea, Jennifer Lu, Dattatray Mongad, Lorna Richardson, Robert D. Finn, Leo Lahti
Published in: bioRXiv, 2025, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/2025.06.16.659887

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

Author(s): 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
Published in: bioRXiv, 2025, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/2025.07.03.659054

Other (1)

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

Author(s): Panos Firbas Nisantzis, Carolina Gonçalves, Gonzalo de Polavieja
Published in: bioRxiv, Issue February 23, 2025, 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.19.638643