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

Información del proyecto

FindingPheno

Identificador del acuerdo de subvención: 952914

DOI

10.3030/952914

Proyecto cerrado

Fecha de la firma de la CE 2 Diciembre 2020

Fecha de inicio 1 Marzo 2021

Fecha de finalización 31 Agosto 2025

Financiado con arreglo a

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

Coste total

€ 5 793 085,00

Aportación de la UE

€ 5 793 085,00

Coordinado por

KOBENHAVNS UNIVERSITET
Denmark

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

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

Publicaciones

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

Autores: István Scheuring, Jacob A, Rasmussen, Davide Bozzi, Morten T Limborg
Publicado en: Frontiers in Microbiology, Edición 04. August, 2022, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2022.912806

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

Autores: Adél Károlyi, István Scheuring
Publicado en: Journal of Evolutionary Biology, Edición 37, 2024, Página(s) 451-463, ISSN 1420-9101
Editor: Oxford University Press (OUP)
DOI: 10.1093/jeb/voae029

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

Autores: István Zachár, Gergely Boza
Publicado en: Frontiers in Ecology and Evolution, Edición 13 April, 2022, ISSN 2296-701X
Editor: Frontiers Media
DOI: 10.3389/fevo.2022.798045

Assessing the safety of microbiome perturbations

Autores: 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
Publicado en: Microbial Genomics, Edición 11, 2025, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/mgen.0.001405

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

Autores: Ágnes Móréh, Ferenc Jordán, István Scheuring
Publicado en: Ecological Modelling, Edición 492, 2025, Página(s) 110735, ISSN 0304-3800
Editor: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110735

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

Autores: Ágnes Móréh, István Scheuring
Publicado en: Ecological Modelling, Edición 508, 2025, Página(s) 111238, ISSN 0304-3800
Editor: 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

Autores: Ali Mostafa Anwar, Akewak Jeba, Leo Lahti, Eleanor Coffey
Publicado en: bioRXiv, Edición February 08, 2025, 2025, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1101/2025.02.06.636801

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

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

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

Autores: Moein Khalighi; Didier Gonze; Karoline Faust; Guilhem Sommeria-Klein; Leo Lahti
Publicado en: PLOS Computational Biology, Edición 1553734X, 2022, Página(s) e1009396, ISSN 1553-734X
Editor: 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

Autores: Gergely Boza, György Barabás, István Scheuring, István Zachar
Publicado en: Scientific Reports, Edición 2022 January 17. Volume 13, 2022, Página(s) 1-15, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-27421-w

Elementary methods provide more replicable results in microbial differential abundance analysis

Autores: Juho Pelto, Kari Auranen, Janne V Kujala, Leo Lahti
Publicado en: Briefings in Bioinformatics, Edición 26, 2025, ISSN 1467-5463
Editor: Oxford University Press
DOI: 10.1093/bib/bbaf130

iSEEtree: interactive explorer for hierarchical data

Autores: Giulio Benedetti, Ely Seraidarian, Theotime Pralas, Akewak Jeba, Tuomas Borman, Leo Lahti
Publicado en: Bioinformatics Advances, Edición 5, 2025, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbaf107

Gender differences in global antimicrobial resistance

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

Integration of polygenic and gut metagenomic risk prediction for common diseases

Autores: 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
Publicado en: Nature Aging, Edición 4, 2024, Página(s) 584-594, ISSN 2662-8465
Editor: 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

Autores: Tamás Czárán, István Scheuring, István Zachar, Szabolcs Számadó
Publicado en: BMC Biology, Edición 22, 2024, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-024-01857-6

Learning and teaching biological data science in the Bioconductor community

Autores: 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
Publicado en: PLOS Computational Biology, Edición 21, 2025, Página(s) e1012925, ISSN 1553-7358
Editor: 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

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

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

Autores: 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
Publicado en: bioRXiv, 2025, ISSN 1367-4803
Editor: 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

Autores: Panos Firbas Nisantzis, Carolina Gonçalves, Gonzalo de Polavieja
Publicado en: bioRxiv, Edición February 23, 2025, 2025
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.19.638643