2024
Hakobyan A., Meyenberg M., Vardazaryan N., Vulliard l., Loizou I. J., Hancock j., Menche J. (2024). Pan-cancer analysis of the interplay between mutational signatures and cellular signaling. iScience of The Cell. doi.org/10.1016/j.isci.2024.109873
Hakobyan M., Binder H., Arakelyan A., (2024). Pan-cancer analysis of telomere maintenance mechanisms. Journal of Biological Chemistry. doi.org/10.1016/j.jbc.2024.107392
Schmidt M․, Avagyan S․, Reiche K., Binder B., Loeffler-Wirth H. (2024). A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Current Issues in Molecular Biology. doi.org/10.3390/cimb46050284
Arakelyan A․, Avagyan S., Kurnosov A., Mkrtchyan T., Mkrtchyan G., Zakharyan R., R. Mayilyan K., Binder H. (2024). Temporal changes of gene expression in health, schizophrenia, bipolar disorder, and major depressive disorder. Nature: Schizofrenia. doi.org/10.1038/s41537-024-00443-7
Martirosyan A., Ansari R., Pestana F., Hebestreit K., Gasparyan H., Aleksanyan R., Hnatova S., Poovathingal S., Marneffe C., Dietmar R. Thal, Kottick A., Hanson-Smith V. J., Guelfi S., Plumbly W., T. Grant Belgard, Metzakopian E. & Holt M.G. (2024). Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution. Molecular Neurodegenerationt. doi.org/10.5281/zenodo.10451502.
2023
Konecny, T., Nikoghosyan, M., Binder, H., (2023). Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera. Frontiers in Plant Science. doi:10.3389/fpls.2023.1303542
Everest-Dass A., Nersisyan S., Maar H., Novosad V., Schröder-Schwarz J., Freytag V., L. Stuke J., C. Beine M., Schiecke A., Haider M., Kriegs M., Elakad O., Bohnenberger H., Conradi L., Raygorodskaya M., Krause L., Mark von Itzstein, Tonevitsky A., Schumacher U., Maltseva D., Wicklein D., Lange T. (2023). Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria-related pathways in colorectal cancer. Molecular Oncology. doi.org/10.1002/1878-0261.13535
Margaryan K., Nikoghosyan M., Baloyan A., Gasoyan H., Hovhannisyan E., Galstyan L., Konecny T., Arakelyan A., Binder H., (2023). Machine learned -based visualization of the diversity of vine genomes worldwide and in Armenia using SOMmelier. 44th World Congress of Vine and Wine 2023 (OIV 2023)
Hakobyan S., Stepanyan A., Nersisyan L., Binder H., Arakelyan A. (2023). PSF toolkit: an R package for pathway curation and topology-aware analysis. Frontiers in Genomics. doi.org/10.3389/fgene.2023.1264656
Ashekyan O., Shahbazyan N., Bareghamyan Y., Kudryavzeva A., Mandel D., Schmidt M., Loeffler-Wirth H., Uduman M., Chand D., Underwood D., Armen G., Arakelyan A., Nersisyan L., Binder H. (2023). Transcriptomic Maps of Colorectal Liver Metastasis: Machine Learning of Gene Activation Patterns and Epigenetic Trajectories in Support of Precision Medicine. Cancers. doi.org/10.3390/cancers15153835
Avagyan S., Binder H., (2023). Subtyping or not subtyping—Quo vadis for precision medicine of colorectal cancer. Translational Cancer Research. 10.21037/tcr-23-133
Huch S., Nersisyan L., Ropat M., Barrett D., Wu M., Wang J., D. Valeriano V., Vardazaryan N., Huerta-Cepas J., Wei W., Du J., M. Steinmetz L., Engstrand L., Pelechano V. (2023). Atlas of mRNA translation and decay for bacteria. Nature Microbiology. 10.1038/s41564-023-01393-z
Zhiyanov, A., Engibaryan, N., Nersisyan, S., Shkurnikov, M., and Tonevitsky, A. (2023). Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer. Bioinformatics. 10.1093/BIOINFORMATICS/BTAD051.
Shkurnikov, M., Nersisyan, S., Averinskaya, D., Chekova, M., Polyakov, F., Titov, A., Doroshenko, D., Vechorko, V., and Tonevitsky, A. (2023). HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire. PeerJ 11, e14707. 10.7717/PEERJ.14707.
2022
Loeffler-Wirth, H., Rade, M., Arakelyan, A., Kreuz, M., Loeffler, M., Koehl, U., Reiche, K., and Binder, H. (2022). Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying. Front Immunol 13, 5395. 10.3389/FIMMU.2022.994885/BIBTEX.
Nersisyan, S., Gorbonos, A., Makhonin, A., Zhiyanov, A., Shkurnikov, M., and Tonevitsky, A. (2022). isomiRTar: a comprehensive portal of pan-cancer 50-isomiR targeting. PeerJ 10, e14205. 10.7717/PEERJ.14205/SUPP-3.
Binder, H., Schmidt, M., Hopp, L., Davitavyan, S., Arakelyan, A., and Loeffler-Wirth, H. (2022). Integrated Multi-Omics Maps of Lower-Grade Gliomas. Cancers 2022, Vol. 14, Page 2797 14, 2797. 10.3390/CANCERS14112797.
Goukassian, D., Arakelyan, A., Brojakowska, A., Bisserier, M., Hakobyan, S., Hadri, L., Rai, A.K., Evans, A., Sebastian, A., Truongcao, M., et al. (2022). Space flight associated changes in astronauts’ plasma-derived small extracellular vesicle microRNA: Biomarker identification. Clin Transl Med 12, e845. 10.1002/CTM2.845.
Nersisyan, S., Zhiyanov, A., Zakharova, M., Ishina, I., Kurbatskaia, I., Mamedov, A., Galatenko, A., Shkurnikov, M., Gabibov, A., and Tonevitsky, A. (2022). Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 10, e13354. 10.7717/PEERJ.13354.
Nikoghosyan, M., Loeffler-Wirth, H., Davidavyan, S., Binder, H., and Arakelyan, A. (2022). Projection of High-Dimensional Genome-Wide Expression on SOM Transcriptome Landscapes. BioMedInformatics 2022, Vol. 2, Pages 62-76 2, 62–76. 10.3390/BIOMEDINFORMATICS2010004.
Loeffler-Wirth, H., Hopp, L., Schmidt, M., Zakharyan, R., Arakelyan, A., and Binder, H. (2022). The Transcriptome and Methylome of the Developing and Aging Brain and Their Relations to Gliomas and Psychological Disorders. Cells 2022, Vol. 11, Page 362 11, 362. 10.3390/CELLS11030362.
2021
Schmidt, M., Arshad, M., Bernhart, S.H., Hakobyan, S., Arakelyan, A., Loeffler-Wirth, H., and Binder, H. (2021). The Evolving Faces of the SARS-CoV-2 Genome. Viruses 2021, Vol. 13, Page 1764 13, 1764. 10.3390/V13091764.
Willscher, E., Hopp, L., Kreuz, M., Schmidt, M., Hakobyan, S., Arakelyan, A., Hentschel, B., Jones, D.T.W., Pfister, S.M., Loeffler, M., et al. (2021). High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers 2021, Vol. 13, Page 3198 13, 3198. 10.3390/CANCERS13133198.
Al-Sanea, M.M., Chilingaryan, G., Abelyan, N., Sargsyan, A., Hovhannisyan, S., Gasparyan, H., Gevorgyan, S., Albogami, S., Ghoneim, M.M., Farag, A.K., et al. (2021). Identification of Novel Potential VEGFR-2 Inhibitors Using a Combination of Computational Methods for Drug Discovery. Life 2021, Vol. 11, Page 1070 11, 1070. 10.3390/LIFE11101070.