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

Informazioni relative al progetto

FindingPheno

ID dell’accordo di sovvenzione: 952914

DOI

10.3030/952914

Progetto chiuso

Data della firma CE 2 Dicembre 2020

Data di avvio 1 Marzo 2021

Data di completamento 31 Agosto 2025

Finanziato da

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

Costo totale

€ 5 793 085,00

Contributo UE

€ 5 793 085,00

Coordinato da

KOBENHAVNS UNIVERSITET
Denmark

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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

Pubblicazioni

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

Autori: István Scheuring, Jacob A, Rasmussen, Davide Bozzi, Morten T Limborg
Pubblicato in: Frontiers in Microbiology, Numero 04. August, 2022, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2022.912806

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

Autori: Adél Károlyi, István Scheuring
Pubblicato in: Journal of Evolutionary Biology, Numero 37, 2024, Pagina/e 451-463, ISSN 1420-9101
Editore: Oxford University Press (OUP)
DOI: 10.1093/jeb/voae029

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

Autori: István Zachár, Gergely Boza
Pubblicato in: Frontiers in Ecology and Evolution, Numero 13 April, 2022, ISSN 2296-701X
Editore: Frontiers Media
DOI: 10.3389/fevo.2022.798045

Assessing the safety of microbiome perturbations

Autori: 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
Pubblicato in: Microbial Genomics, Numero 11, 2025, ISSN 2057-5858
Editore: Microbiology Society
DOI: 10.1099/mgen.0.001405

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

Autori: Ágnes Móréh, Ferenc Jordán, István Scheuring
Pubblicato in: Ecological Modelling, Numero 492, 2025, Pagina/e 110735, ISSN 0304-3800
Editore: Elsevier BV
DOI: 10.1016/j.ecolmodel.2024.110735

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

Autori: Ágnes Móréh, István Scheuring
Pubblicato in: Ecological Modelling, Numero 508, 2025, Pagina/e 111238, ISSN 0304-3800
Editore: 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

Autori: Ali Mostafa Anwar, Akewak Jeba, Leo Lahti, Eleanor Coffey
Pubblicato in: bioRXiv, Numero February 08, 2025, 2025, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1101/2025.02.06.636801

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

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

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

Autori: Moein Khalighi; Didier Gonze; Karoline Faust; Guilhem Sommeria-Klein; Leo Lahti
Pubblicato in: PLOS Computational Biology, Numero 1553734X, 2022, Pagina/e e1009396, ISSN 1553-734X
Editore: 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

Autori: Gergely Boza, György Barabás, István Scheuring, István Zachar
Pubblicato in: Scientific Reports, Numero 2022 January 17. Volume 13, 2022, Pagina/e 1-15, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-023-27421-w

Elementary methods provide more replicable results in microbial differential abundance analysis

Autori: Juho Pelto, Kari Auranen, Janne V Kujala, Leo Lahti
Pubblicato in: Briefings in Bioinformatics, Numero 26, 2025, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbaf130

iSEEtree: interactive explorer for hierarchical data

Autori: Giulio Benedetti, Ely Seraidarian, Theotime Pralas, Akewak Jeba, Tuomas Borman, Leo Lahti
Pubblicato in: Bioinformatics Advances, Numero 5, 2025, ISSN 2635-0041
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbaf107

Gender differences in global antimicrobial resistance

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

Integration of polygenic and gut metagenomic risk prediction for common diseases

Autori: 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
Pubblicato in: Nature Aging, Numero 4, 2024, Pagina/e 584-594, ISSN 2662-8465
Editore: 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

Autori: Tamás Czárán, István Scheuring, István Zachar, Szabolcs Számadó
Pubblicato in: BMC Biology, Numero 22, 2024, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-024-01857-6

Learning and teaching biological data science in the Bioconductor community

Autori: 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
Pubblicato in: PLOS Computational Biology, Numero 21, 2025, Pagina/e e1012925, ISSN 1553-7358
Editore: 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

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

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

Autori: 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
Pubblicato in: bioRXiv, 2025, ISSN 1367-4803
Editore: 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

Autori: Panos Firbas Nisantzis, Carolina Gonçalves, Gonzalo de Polavieja
Pubblicato in: bioRxiv, Numero February 23, 2025, 2025
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.19.638643