Lilit Nersisyan

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About Lilit Nersisyan:

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SEEK ID: https://armlifebank.am/people/24

Location: Armenia

ORCID: https://orcid.org/0000-0001-8525-420X

Joined: 2nd Apr 2025

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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

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We investigate telomeric fragments in cell-free DNA in blood plasma in disease. We aim to develop novel diagnostic approaches to identify and monitor disease status in cancers and chronic disorders through liquid biopsies.

Programme: Genes, Environment and Chronic Diseases

Public web page: Not specified

Organisms: Human

Deciphering the Fine-Scaled Temporal Changes in Microbiome Communities Following Antibiotic Exposure

We develop bioinformatics algorithms and tools to explore the temporal dynamics of microbiome communities in response to environmental perturbations and treatments. We seek to understand the mechanisms through which the direct effects of perturbations propagate via microbial interaction networks, leading to changes in microbiome composition over time.Through application of these techniques we study antibiotic resistance in complex microbial communities, the impact of pesticides on bee gut microbiome ...

Programme: Genes, Environment and Chronic Diseases

Public web page: Not specified

Organisms: Human, Microbiome

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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

Showing 5 out of a possible 6 Publications Advanced Publications list for this Person with search and filtering

PSF toolkit: an R package for pathway curation and topology-aware analysis

Molecular characterization of cancers with long-read RNA sequencing

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Abstract (Expand)

Most high throughput genomic data analysis pipelines currently rely on over-representation or gene set enrichment analysis (ORA/GSEA) approaches for functional analysis. In contrast, topology-based … pathway analysis methods, which offer a more biologically informed perspective by incorporating interaction and topology information, have remained underutilized and inaccessible due to various limiting factors. These methods heavily rely on the quality of pathway topologies and often utilize predefined topologies from databases without assessing their correctness. To address these issues and make topology-aware pathway analysis more accessible and flexible, we introduce the PSF (Pathway Signal Flow) toolkit R package. Our toolkit integrates pathway curation and topology-based analysis, providing interactive and command-line tools that facilitate pathway importation, correction, and modification from diverse sources. This enables users to perform topology-based pathway signal flow analysis in both interactive and command-line modes. To showcase the toolkit’s usability, we curated 36 KEGG signaling pathways and conducted several use-case studies, comparing our method with ORA and the topology-based signaling pathway impact analysis (SPIA) method. The results demonstrate that the algorithm can effectively identify ORA enriched pathways while providing more detailed branch-level information. Moreover, in contrast to the SPIA method, it offers the advantage of being cut-off free and less susceptible to the variability caused by selection thresholds. By combining pathway curation and topology-based analysis, the PSF toolkit enhances the quality, flexibility, and accessibility of topology-aware pathway analysis. Researchers can now easily import pathways from various sources, correct and modify them as needed, and perform detailed topology-based pathway signal flow analysis. In summary, our PSF toolkit offers an integrated solution that addresses the limitations of current topology-based pathway analysis methods. By providing interactive and command-line tools for pathway curation and topology-based analysis, we empower researchers to conduct comprehensive pathway analyses across a wide range of applications.

Authors: Siras Hakobyan, Ani Stepanyan, Lilit Nersisyan, Hans Binder, Arsen Arakelyan

Date Published: 23rd Aug 2023

Publication Type: Journal

DOI: 10.3389/fgene.2023.1264656

Citation: Frontiers in Genetics,14

Created: 19th Aug 2025 at 08:25

Atlas of mRNA translation and decay for bacteria.

Deciphering the Fine-Scaled Temporal Changes in Microbiome Communities Following Antibiotic Exposure

Abstract (Expand)

Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA …

Authors: S. Huch, L. Nersisyan, M. Ropat, D. Barrett, M. Wu, J. Wang, V. D. Valeriano, N. Vardazaryan, J. Huerta-Cepas, W. Wei, J. Du, L. M. Steinmetz, L. Engstrand, V. Pelechano

Date Published: 5th Jun 2023

Publication Type: Journal

PubMed ID: 37217719

Citation: Nat Microbiol. 2023 Jun;8(6):1123-1136. doi: 10.1038/s41564-023-01393-z. Epub 2023 May 22.

Created: 14th May 2025 at 11:33

Molecular Analysis of SARS-CoV-2 Lineages in Armenia

COVID-19

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The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and …

Authors: Diana Avetyan, Siras Hakobyan, Maria Nikoghosyan, Lilit Ghukasyan, Gisane Khachatryan, Tamara Sirunyan, Nelli Muradyan, Roksana Zakharyan, Andranik Chavushyan, Varduhi Hayrapetyan, Anahit Hovhannisyan, Shah A. Mohamed Bakhash, Keith R. Jerome, Pavitra Roychoudhury, Alexander L. Greninger, Lyudmila Niazyan, Mher Davidyants, Gayane Melik-Andreasyan, Shushan Sargsyan, Lilit Nersisyan, Arsen Arakelyan

Date Published: 17th May 2022

Publication Type: Journal

DOI: 10.3390/v14051074

Citation: Viruses,14(5):1074

Created: 18th Aug 2025 at 09:38

Transcriptome Patterns of BRCA1- and BRCA2- Mutated Breast and Ovarian Cancers

Multi-Omics Molecular Diversity of Cancers

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Mutations in the BRCA1 and BRCA2 genes are known risk factors and drivers of breast and ovarian cancers. So far, few studies have been focused on understanding the differences in transcriptome and …

Authors: Arsen Arakelyan, Ani Melkonyan, Siras Hakobyan, Uljana Boyarskih, Arman Simonyan, Lilit Nersisyan, Maria Nikoghosyan, Maxim Filipenko, Hans Binder

Date Published: 28th Jan 2021

Publication Type: Journal

DOI: 10.3390/ijms22031266

Citation: International Journal of Molecular Sciences,22(3):1266

Created: 27th Aug 2025 at 11:24

WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Multi-Omics Molecular Diversity of Cancers

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Telomere length (TL) regulation is an important factor in ageing, reproduction and cancer development. Genetic, hereditary and environmental factors regulating TL are currently widely investigated, …

Authors: Lilit Nersisyan, Maria Nikoghosyan, Laurent C. Francioli, Androniki Menelaou, Sara L. Pulit, Clara C. Elbers, Wigard P. Kloosterman, Jessica van Setten, Isaäc J. Nijman, Ivo Renkens, Paul I. W. de Bakker, Freerk van Dijk, Pieter B. T. Neerincx, Patrick Deelen, Alexandros Kanterakis, Martijn Dijkstra, Heorhiy Byelas, K. Joeri van der Velde, Mathieu Platteel, Morris A. Swertz, Cisca Wijmenga, Pier Francesco Palamara, Itsik Pe’er, Kai Ye, Eric-Wubbo Lameijer, Matthijs H. Moed, Marian Beekman, Anton J. M. de Craen, H. Eka D. Suchiman, P. Eline Slagboom, Victor Guryev, Abdel Abdellaoui, Jouke Jan Hottenga, Mathijs Kattenberg, Gonneke Willemsen, Dorret I. Boomsma, Elisabeth M. van Leeuwen, Lennart C. Karssen, Najaf Amin, Fernando Rivadeneira, Aaron Isaacs, Albert Hofman, André G. Uitterlinden, Cornelia M. van Duijn, Mannis van Oven, Manfred Kayser, Martijn Vermaat, Jeroen F. J. Laros, Johan T. den Dunnen, David van Enckevort, Hailiang Mei, Mingkun Li, Mark Stoneking, Barbera D. C. van Schaik, Jan Bot, Tobias Marschall, Alexander Schönhuth, Jayne Y. Hehir-Kwa, Robert E. Handsaker, Paz Polak, Mashaal Sohail, Dana Vuzman, Karol Estrada, Steven A. McCarroll, Shamil R. Sunyaev, Fereydoun Hormozdiari, Vyacheslav Koval, Carolina Medina-Gomez, Ben Oostra, Jan H. Veldink, Leonard H. van den Berg, Steven J. Pitts, Shobha Potluri, Purnima Sundar, David R. Cox, Peter de Knijff, Qibin Li, Yingrui Li, Yuanping Du, Ruoyan Chen, Hongzhi Cao, Jun Wang, Ning Li, Sujie Cao, Jasper A. Bovenberg, Gert-Jan B. van Ommen, Arsen Arakelyan

Date Published: 10th Dec 2019

Publication Type: Journal

DOI: 10.1038/s41598-019-55109-7

Citation: Scientific Reports,9(1)

Created: 27th Aug 2025 at 15:58

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