Machine learned-based visualization of the diversity of grapevine genomes worldwide and in Armenia using SOMmelier
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BiBTeXIn the proposed study three major issues have been addressed: Firstly, the diversity of grapevine accessions worldwide and particularly in Armenia, a small country located in the largely volcanic Armenian Highlands, is incredibly rich in cultivated and especially wild grapes; secondly, the information hidden in their (whole) genomes, e.g., about the domestication history of grapevine over the last 11,000 years and phenotypic traits such as cultivar utilization and a putative resistance against powdery mildew, and, thirdly machine learning methods to extract and to visualize this information in an easy to percept way. We shortly describe the Self Origanizing Maps (SOM) portrayal method called “SOMmelier” (as the vine-genome “waiter”) and illustrate its power by applying it to whole genome data of hundreds of grapevine accessions. We also give a short outlook on possible future directions of machine learning in grapevine transcriptomics and ampelogaphy.
SEEK ID: https://armlifebank.am/publications/34
DOI: 10.1051/bioconf/20236801009
Projects: Armenian Wine Genome Program, Functional Genomics of Vine
Publication type: Journal
Journal: BIO Web of Conferences
Publisher: EDP Sciences
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Created: 10th Jul 2025 at 11:04
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Projects: Sex-specific differences in long-term gamma and simGCRsim-associated alterations in deferential gene expression in the heart tissue, Functional Genomics of Vine, Molecular Profiling of Cancer Metastases, Study of the molecular mechanisms of familial Mediterranean fever using genetic engineering and functional genomics, Mental disorders and aging brain, Omics-Based Insights into Human Long-Term Exposure to Environmental Metals, Biological pathway activity analysis, ML approaches for omic data analysis, Tools for Telomere Biology, Armenian Wine Genome Program, Molecular characterization of cancers with long-read RNA sequencing, Low dose radiation risks: present research and future perspectives
Institutions: Institute of Molecular Biology NAS RA, Armenian Bioinformatics Institute
https://orcid.org/0000-0002-6851-1056
Projects: Functional Genomics of Vine, Molecular Profiling of Cancer Metastases, Biological pathway activity analysis, Mental disorders and aging brain, ML approaches for omic data analysis, Armenian Wine Genome Program
Institutions: Armenian Bioinformatics Institute, Interdisciplinary Center for Bioinformatics (IZBI)
https://orcid.org/0000-0002-2242-4678
Projects: Study of the molecular mechanisms of familial Mediterranean fever using genetic engineering and functional genomics, Development of induced pluripotent stem cell bank of patients with Familial Mediterranean Fever, Molecular Profiling of Cancer Metastases, Sex-specific differences in long-term gamma and simGCRsim-associated alterations in deferential gene expression in the heart tissue, Molecular characterization of cancers with long-read RNA sequencing, ML approaches for omic data analysis, Mental disorders and aging brain, Armenian Wine Genome Program, Functional Genomics of Vine
Institutions: Russian-Armenian University
https://orcid.org/0009-0009-7992-1366
Tomas Konecny obtained his bachelor's and master's degrees in Molecular Biology and Genetics at Masaryk University, Czech Republic. He began a PhD in Molecular and Cell Biology at the University of South Bohemia. In 2023, Tomas switched to bioinformatics and started a PhD at Leipzig University, Germany. He is currently a bioinformatician at the Armenian Bioinformatics Institute and the Interdisciplinary Centre for Bioinformatics, Leipzig. His research focuses on grapevine response to climate ...
The Plant Genomics Programme focuses on the comprehensive characterization of plant genetic resources, aiming to understand the factors that shape genetic variation across plant genomes and drive phenotypic diversity in traits of adaptive and economic importance. The research explores the genetic architecture of plant adaptation to changing climatic conditions and investigates the genomic determinants of genetic diversity. A key objective is the integration of multi-omics data into innovative ...
Projects: Functional Genomics of Vine, Armenian Wine Genome Program
Web page: Not specified
Principal Investigator: Prof. Hans Binder
University: University of Leipzig
Research Group: Kristina Margaryan, Maria Nikoghosyan, Tomas Konecny, Anush Baloyan, Hripsime Gasoyan, Emma Hovhannisyan, Levon Galstyan, Duan Shengchang
Duration: 2023-2027
Co-implementing and hosting partner: Armenian Bioinformatics Institute (ABI) and Institute of Molecular Biology
Project Importance The cultivated grape (Vitis vinifera) has become the world’s leading fruit crop. Grape is unique not only because it is ...
Programme: Plant Genomics & Bioinformatics
Public web page: https://www.fast.foundation/en/program/847/2022/new_tab/6586/6677
Programme: Plant Genomics & Bioinformatics
Public web page: Not specified
