Lana Karapetyan

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About Lana Karapetyan:

No description specified

SEEK ID: https://armlifebank.am/people/5

Location: Armenia

ORCID: https://orcid.org/0009-0009-7992-1366

Joined: 21st Feb 2024

Expertise: Not specified

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Showing 5 out of a possible 7 Programmes Advanced Programmes list for this Person with search and filtering

Armenian Genome Project

The Armenian Genome Project aims at unraveling our genetic background and bringing personalized and precision medicine to Armenia

Projects: Genetic History of Armenians

Web page: http://armeniangenome.am/

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

Cellular basis of diseases

Cellular dysfunction, the fundamental basis of all human diseases, underpins the pathophysiology of numerous disorders. This program presents a overview of research initiatives focused on advancing human health through the development of diagnostic, preventive, and therapeutic strategies. These projects are conducted in collaboration with multiple research institutions and are supported by diverse grant funding mechanisms.

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

Web page: Not specified

Genes, Environment and Chronic Diseases

This program is designed to encapsulate and facilitate research projects focusing on the intricate dynamics between genetic predispositions and environmental factors in the progression of chronic diseases, excluding cancer. This initiative aims to unravel the molecular mechanisms and pathways that underlie these diseases, thereby paving the way for targeted interventions and therapies.

Projects: Mental disorders and aging brain, Omics-Based Insights into Human Long-Term Exposure to Environmental Metals, Deciphering the Fine-Scaled Temporal Changes in Microbiome Communities Following Antibiotic Exposure, Telomere-related biomarkers of disease in liquid biopsies, COVID-19, Molecular epidemiology of multi-drug resistance

Web page: Not specified

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Showing 5 out of a possible 13 Projects Advanced Projects list for this Person with search and filtering

Multi-Omics Molecular Diversity of Cancers

No description specified

Programme: Cancer Omics

Public web page: Not specified

Organisms: Not specified

Molecular epidemiology of multi-drug resistance

Molecular epidemiology of multi-drug resistance focuses on investigating the genetic basis and dissemination of bacteria resistant to multiple antibiotics, with particular attention to resistance mechanisms, outbreak tracking using molecular techniques, and the evolutionary dynamics of resistant strains.

Programme: Genes, Environment and Chronic Diseases

Public web page: Not specified

Organisms: Not specified

Genetic History of Armenians

No description specified

Programme: Armenian Genome Project

Public web page: Not specified

Organisms: Human

COVID-19

Coronavirus disease 2019 (COVID-19) is a contagious disease caused by the coronavirus SARS-CoV-2. In January 2020, the disease spread worldwide, resulting in the COVID-19 pandemic.

Programme: Genes, Environment and Chronic Diseases

Public web page: Not specified

Organisms: Not specified

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

View all 13 Projects

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Institute of Molecular Biology NAS RA

Country: Armenia

City: Yerevan

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

Russian-Armenian University

Country: Armenia

City: Yerevan

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

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The Effects of Space Radiation on the Transcriptome of Heart Right Ventricle Tissue

Sex-specific differences in long-term gamma and simGCRsim-associated alterations in deferential gene expression in the heart tissue

The cited in the main text supporting Supplementary Figures and Data can be downloaded at https://doi.org/10.5281/zenodo.15624414 and the datasets can be downloaded using the following accession numbers GSE272168 for the left ventricle RNAseq dataset and GSE300189 for the right ventricle RNAseq dataset. Any additional datasets used and/or analyzed in this study are available from the corresponding authors upon request at the reasonable timeframe. Preprocessed raw gene expression count matrices ...

Creator: Siras Hakobyan

Submitter: Lana Karapetyan

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

External Link

Created: 18th Aug 2025 at 09:10

Assigning transcriptomic subtypes to CLL samples using nanopore RNA-sequencing and self-organizing maps - dataset

Molecular Profiling of Cancer Metastases, Molecular characterization of cancers with long-read RNA sequencing

The dataset contains raw and intermediated files, and scripts required to reproduce the results associated with the manuscript "Assigning transcriptomic subtypes to CLL samples using nanopore RNA-sequencing and self-organizing maps". Here, we demonstrate that integrating publicly available short-read data with in-house generated ONT data, along with the application of machine learning approaches, enables the characterization of the CLL transcriptome landscape, the identification of clinically ...

Creator: Arsen Arakelyan

Submitter: Lana Karapetyan

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

External Link

Created: 10th Jul 2025 at 10:37

Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets

ML approaches for omic data analysis, Molecular characterization of cancers with long-read RNA sequencing

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This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes".

The archive contains three folders:

"Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data.
"IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets.
"BC" - folder ...

Creators: Maria Nikoghosyan, Suren Davitavyan, Hans Binder, Arsen Arakelyan

Submitter: Lana Karapetyan

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

External Link

Created: 10th Jul 2025 at 10:26

Showing 5 out of a possible 68 Publications Advanced Publications list for this Person with search and filtering

Topology-aware pathway analysis of spatial transcriptomics

ML approaches for omic data analysis, Molecular characterization of cancers with long-read RNA sequencing

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Abstract (Expand)

Spatial transcriptomics (ST) has transformed genomics by mapping gene expression onto intact tissue architecture, uncovering intricate cellular interactions that bulk and single-cell RNA sequencing … often overlook. Traditional ST workflows typically involve clustering spots, performing differential expression analyses, and annotating results via gene-set methods such as overrepresentation analysis (ORA) or gene set enrichment analysis (GSEA). More recent spatially-aware techniques extend these approaches by incorporating tissue organization into gene-set scoring. However, because they operate primarily at the level of individual genes, they may overlook the connectivity and topology of biological pathways, limiting their capacity to trace the propagation of signaling events within tissue regions. In this study, we address that gap by translating gene expression into pathway-level activity using the Pathway Signal Flow (PSF) algorithm. PSF integrates expression data with curated interaction networks to compute numeric activity scores for each branch of a biological pathway, producing a functionally annotated feature space that captures downstream signaling effects as branch-specific activity values. We applied PSF to two public 10x Genomics Visium datasets (human melanoma and mouse brain) and compared clustering based on PSF-derived pathway activities from 40 curated Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways and gene expression with standard Seurat Louvain clustering and spatially aware methods (Vesalius, spatialGE). We observed good correspondence between PSF-based and expression-based clustering when spatially aware clustering methods were used. This suggests that branch-level pathway activities can themselves drive clustering and pinpoint spatially deregulated processes. To assess cluster-specific functional annotation, we compared PSF results to conventional ORA (based on marker genes) and GSDensity (based on cluster-specific gene sets). PSF identified a broader set of significant pathways with substantial overlap with both ORA and GSDensity, providing increased sensitivity due to its branch-level resolution. We further demonstrated that PSF-derived activity values can be used to detect spatially deregulated pathway branches, yielding results comparable to those obtained with spatially aware gene set analysis approaches such as GSDensity and spatialGE. The availability of pathway topology and branch-specific information also enabled the identification of potential intercellular communication via ligand-receptor interactions between deregulated pathways in adjacent tumor regions. To support interactive exploration of results, we developed the PSF Spatial Browser, an R Shiny application for visualizing pathway activities, gene expression patterns, and deregulated pathway networks.

Authors: Siras Hakobyan, Maria Schmidt, H. Binder, A. Arakelyan

Date Published: 14th Aug 2025

Publication Type: Journal

DOI: 10.7717/peerj.19729

Citation:

Created: 18th Aug 2025 at 10:05

The effects of space radiation on the transcriptome of heart right ventricle tissue

Sex-specific differences in long-term gamma and simGCRsim-associated alterations in deferential gene expression in the heart tissue

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Abstract (Expand)

Deep space represents a challenging environment for human exploration and can be accompanied by harmful health-related risks. We aimed to assess the effect of simplified galactic cosmic ray simulated …

Authors: Roksana Zakharyan, Siras Hakobyan, Agnieszka Brojakowska, Malik Bisserier, Shihong Zhang, Mary K. Khlgatian, Amit Kumar Rai, Suren Davitavyan, Ani Stepanyan, Tamara Sirunyan, Gisane Khachatryan, Susmita Sahoo, Venkata Naga Srikanth Garikipati, Arsen Arakelyan, David A. Goukassian

Date Published: 21st Jul 2025

Publication Type: Journal

DOI: 10.1038/s41526-025-00506-8

Citation: npj Microgravity,11(1)

Created: 18th Aug 2025 at 09:04

Telomere Maintenance Pathways in Lower-Grade Gliomas: Insights from Genetic Subtypes and Telomere Length Dynamics

Molecular characterization of cancers with long-read RNA sequencing

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Abstract (Expand)

Telomere maintenance mechanisms (TMMs) play a critical role in cancer biology, particularly in lower-grade gliomas (LGGs), where telomere dynamics and pathway activity remain poorly understood. In this …

Authors: Meline Hakobyan, Hans Binder, Arsen Arakelyan

Date Published: 28th Apr 2025

Publication Type: Journal

DOI: 10.3390/ijms26094175

Citation: International Journal of Molecular Sciences,26(9):4175

Created: 5th Jul 2025 at 10:47

Long-lasting sex-specific alteration in left ventricular cardiac transcriptome following gamma and simGCRsim radiation

Sex-specific differences in long-term gamma and simGCRsim-associated alterations in deferential gene expression in the heart tissue

(Show All)

Abstract (Expand)

Space irradiation (IR) is an important health risk for deep-space missions. We reported heart failure with preserved ejection fraction like cardiac phenotype 660-days following exposure to a single-dose …

Authors: Roksana Zakharyan, Siras Hakobyan, Agnieszka Brojakowska, Suren Davitavyan, Ani Stepanyan, Tamara Sirunyan, Gisane Khachatryan, Mary K. Khlgatian, Malik Bisserier, Shihong Zhang, Susmita Sahoo, Lahouaria Hadri, Venkata Naga Srikanth Garikipati, Arsen Arakelyan, David A. Goukassian

Date Published: 18th Feb 2025

Publication Type: Journal

DOI: 10.1038/s41598-025-89815-2

Citation: Scientific Reports,15(1)

Created: 4th Jul 2025 at 11:14

Molecular Epidemiology and In-Depth Characterization of Klebsiella pneumoniae Clinical Isolates from Armenia

Molecular epidemiology of multi-drug resistance

Abstract (Expand)

The global dissemination of Klebsiella pneumoniae pathotypes with multidrug-resistant (MDR) and hypervirulent traits poses a threat to public health. The situation in Armenia is unclear, and we performed …

Authors: Anahit Sedrakyan, Zaruhi Gevorgyan, Magdalina Zakharyan, Karine Arakelova, Shoghik Hakobyan, Alvard Hovhannisyan, Rustam Aminov

Date Published: 9th Jan 2025

Publication Type: Journal

DOI: 10.3390/ijms26020504

Citation: International Journal of Molecular Sciences,26(2):504

Created: 22nd Aug 2025 at 08:07

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Patient-specific induced pluripotent stem cells (iPSCs)

Study of the molecular mechanisms of familial Mediterranean fever using genetic engineering and functional genomics

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Patient-specific induced pluripotent stem cells (iPSCs) are reprogrammed somatic cells derived from individual patients through the expression of key transcription factors (e.g., OCT4, SOX2, KLF4, and c-MYC). These cells exhibit pluripotency, allowing them to differentiate into various cell types and serve as in vitro models for studying disease mechanisms, drug screening, and regenerative medicine.

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Created: 5th Feb 2025 at 06:34

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