Tomas Konecny

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About Tomas Konecny:

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 change and molecular mechanisms of colorectal cancer. Tomas has expertise in molecular biology, genetics, epigenetics, and programming in Python, R, and Bash.

SEEK ID: https://armlifebank.am/people/26

Location: Armenia

ORCID: https://orcid.org/0000-0003-2311-6092

Joined: 16th May 2025

Expertise: Not specified

Tools: Genomics, Molecular Biology, Python, R, Transcriptomics, Cell biology

Their tags

bud dormancy C800_CRC climate change grapevine SOM machine learning stilbenoid stilbenoid biosynthesis thiamine thiamine biosynthesis transcriptome portrayal Transcriptomics water(-deficient) stress

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Plant Genomics & Bioinformatics

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

Bioinformatics Tools for Analysis of Big Genomic Data

This Programme focuses on the development, implementation, and application of bioinformatics tools for the analysis of large-scale genomic datasets. It aims to facilitate the processing, integration, and interpretation of high-throughput sequencing data, including whole-genome, transcriptome, and epigenome analyses. The Programme encompasses computational approaches for variant discovery, gene expression profiling, network biology, and multi-omics data integration.

Projects: Biological pathway activity analysis, ML approaches for omic data analysis, Tools for Telomere Biology

Web page: Not specified

Cancer Omics

This Programme offers a comprehensive summary of various projects focused on deciphering the intricate molecular mechanisms of cancer development, progression, and response to treatments, utilizing bioinformatics, computational biology, and machine learning. These are multi-laboratory efforts carried out across several research institutions, supported by various grant programs.

Projects: Molecular Profiling of Cancer Metastases, Molecular characterization of cancers with long-read RNA sequencing, Multi-Omics Molecular Diversity of Cancers

Web page: Not specified

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Functional Genomics of Vine

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

Organisms: Grapevine

Molecular Profiling of Cancer Metastases

Together with the scientists at Agenus, a US-based biotech company specializing in innovative forms of cancer treatment, including the discovery and development of immuno-oncology therapies, ABI has formed a team of students and researchers to study cancer metastases and identify potential biomarkers and targets for cancer immunotherapies. This collaboration is also part of our long-term vision of supporting biotech developments in Armenia. The team discovers transcriptomics heterogeneity of Liver ...

Programme: Cancer Omics

Public web page: https://abi.am/research/research-labs/agenus-lab/

Start date: 21st Feb 2024

Organisms: Human

ML approaches for omic data analysis

This project focuses on developing and applying machine learning (ML) methodologies to analyze complex omic datasets, including genomics, transcriptomics, proteomics, and metabolomics. By leveraging advanced ML techniques, the project aims to uncover novel biological insights, identify biomarkers, and enhance our understanding of molecular mechanisms underlying various diseases. The initiative is a collaborative effort maintained by the Institute of Molecular Biology NAS RA (IMB), ...

Programme: Bioinformatics Tools for Analysis of Big Genomic Data

Public web page: Not specified

Organisms: Not specified

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Armenian Bioinformatics Institute

Country: Armenia

City: Yerevan

Web page: https://www.abi.am

Institute of Molecular Biology NAS RA

Country: Armenia

City: Yerevan

Web page: https://molbiol.sci.am

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Annual Transcriptomic Trajectory of Grapevine Buds Reveals the Coordinated Regulation of Thiamine and Stilbenoid Biosynthesis During Winter Dormancy

Functional Genomics of Vine

Bud dormancy is a critical survival strategy for perennial plants in temperate climates to endure winter, involving complex transcriptional reprogramming. While previous studies have investigated gene expression during discrete phases of the grapevine bud annual cycle, a holistic understanding requires an integrated, season-wide analysis. We conducted a meta-analysis by combining and reexamining the transcriptomic data from two seminal studies on grapevine bud development. Using Self-Organizing ...

Creator: Tomas Konecny

Submitter: Tomas Konecny

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 28th Aug 2025 at 10:45

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Showing 5 out of a possible 11 Publications Advanced Publications list for this Person with search and filtering

Transcriptomic profiling identifies immunotherapy-responsive phenotypes in microsatellite-stable metastatic colorectal cancer.

Molecular Profiling of Cancer Metastases

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Abstract (Expand)

Conventional immune checkpoint inhibitors (ICIs) remain largely ineffective in microsatellite-stable metastatic colorectal cancer (MSS mCRC), where low tumor immunogenicity and molecular heterogeneity …

Authors: T. Konecny, N. Zadirako, A. Grigoryan, M. Tamazyan, S. Mnatsakanyan, L. Stepanyan, H. Loeffler-Wirth, S. Bourdelais, G. Mednick, C. Delepine, D. Chand, H. Binder

Date Published: 16th Jun 2026

Publication Type: Journal

PubMed ID: 42298180

Citation: Oncogene. 2026 Jun 16. doi: 10.1038/s41388-026-03861-2.

Created: 24th Jun 2026 at 07:29

Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma.

Molecular Profiling of Cancer Metastases

Abstract (Expand)

Lymph node (LN) function requires the organization of cells into higher-order spatial units. However, the principles governing LN architecture in health and disease remain poorly understood. Here, we …

Authors: F. Czernilofsky, A. Mathioudaki, L. Jopp-Saile, R. Lutz, D. Vonficht, X. Wang, C. Schniederjohann, H. Voehringer, T. Roider, M. A. Baertsch, C. Rodemer, H. Loffler-Wirth, M. Grau, D. Fitzgerald, J. Mammen, J. Kosla, N. Liebers, P. M. Bruch, D. Ordonez-Rueda, A. Brobeil, G. Mechtersheimer, C. Pabst, C. Muller-Tidow, A. Trumpp, M. Seifert, F. Neumann, M. Heikenwalder, V. Benes, W. Huber, J. Distler, G. Lenz, H. Binder, R. Siebert, G. P. Nolan, M. Gerstung, J. B. Zaugg, D. Hubschmann, S. Haas, S. Dietrich

Date Published: 31st Mar 2026

Publication Type: Journal

PubMed ID: 41882179

Citation: Nat Cancer. 2026 Mar;7(3):538-552. doi: 10.1038/s43018-026-01136-z. Epub 2026 Mar 25.

Created: 24th Jun 2026 at 14:03

Spotting a unicorn: spatial transcriptome analysis of the eyelid reveals gene regulatory networks enriched in Moll glands.

ML approaches for omic data analysis

Abstract (Expand)

Moll glands, found in the margin of the eyelid next to the base of the eyelashes, are likely to play an important role in maintaining the tear film and therefore in securing adequate visual function. …

Authors: T. Konecny, H. Binder, U. Hampel, F. Hansmann, H. Pfannkuche, M. R. Schneider

Date Published: 1st Mar 2026

Publication Type: Journal

PubMed ID: 41903186

Citation: Brief Bioinform. 2026 Mar 1;27(2):bbag135. doi: 10.1093/bib/bbag135.

Created: 25th Jun 2026 at 05:13

Population structure of wild and cultivated grapevines in Armenia

Functional Genomics of Vine

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Abstract (Expand)

Background: The South Caucasus region, including Armenia, is recognized as a center of early viticulture, home to the oldest known winery and a rich tradition of winemaking. Armenia's topography … has contributed to the preservation of genetically diverse grapevine populations. Cultivated grapevines (Vitis vinifera ssp. vinifera or V.V. ssp. vinifera) and their wild ancestor (V. vinifera ssp. sylvestris or V.V. ssp. sylvestris) exhibit high genetic diversity, making them valuable resources for understanding domestication, adaptation, and breeding. Despite Armenia’s historical and economic importance, the genomic diversity of its wild and cultivated grapevines remains underexplored. We re-analyzed whole-genome sequencing data of 164 grapevine accessions from Armenia, including cultivated and wild individuals, taken from a previous study on worldwide collected vine accessions to characterize genomic diversity, population structure, and domestication history of this gene pool. Results: Our analysis uncovered genetic patterns partly unique to Armenia. Population structure analysis revealed a clear genetic separation between wild and cultivated groups and three distinct ancestral components within the cultivated gene pool, reflecting a west-to-east geographical gradient in Armenia. This genetic cline correlates with a shift in usage, from table to wine grapes, and a transition in berry skin color from white to black. Additionally, we identified four distinct subgroups within wild populations in Syunik, suggesting notable diversity. Evolutionary history analysis indicates that wild and cultivated lineages began to separate ~18.5k years ago, with divergence intensifying ~4k years ago under human cultivation. Comparative genomic scans for divergent selection identified genomic regions associated with domestication traits, including disease resistance and biosynthesis of anthocyanin and flavanol. Genome-wide association, including k-mer-based approach studies, uncovered candidate markers linked to agronomic traits, such as berry skin color and bunch density. These results provide genomic resources and highlight targets for grapevine improvement and conservation. Conclusions: This whole-genome study on the genetic diversity of wild and cultivated grapevines from Armenia provides a valuable resource for identifying candidate genes and domestication-related regions associated with agronomic traits. The results underscore the importance of conserving local grapevine diversity in Armenia, a historically significant and genetically rich viticultural region.

Authors: Maria Nikoghosyan, Emma Hovhannisyan, Nate Zadirako, Shengchang Duan, Armine Asatryan, Arsen Arakelyan, Kristine Margaryan, Anush Baloyan, Tomas Konecny, Hans Binder