OMICs-driven bioinformatics to better understand genomic regulation for applications in the life sciences, precision biomedicine, and plant genomics.
Our studies focus on elucidating the mechanisms underlying wound healing in the skin, unraveling the spatial microarchitecture of tumors such as melanomas, and uncovering molecular communication links within the mouse brain. We have discovered that fibroblast cells undergo identity changes during skin development and exert a profound influence on the invasiveness of cancer cells. Through this interdisciplinary collaboration, we aim to advance our understanding of health, disease, and development on a cellular level. We utilize single-cell and spatial transcriptomics and chromatin data and apply and develop bioinformatics methods for their analysis.
Related work
Binder H, Schmidt M, Mortensen LS, Kunz M. Melanoma Single-Cell Biology in Experimental and Clinical Settings. J Clin Medicine. 202;10: 506
Schmidt M, Binder H. Developmental scRNAseq Trajectories in Gene- and Cell-State Space—The Flatworm Example. Genes. 2020;11: 1214
Schmidt M, Mortensen L, Löffler-Wirth H, Kosnopfel C, Krohn K, Binder H, Kunz M. Single-cell trajectories of melanoma cell resistance to targeted treatment. Cancer Biol Med. 2022
Schmidt M, Hansmann F, Loeffler-Wirth H, Zouboulis CC, Binder H, Schneider MR. A spatial portrait of the human sebaceous gland transcriptional program. Journal of Biological Chemistry 2024:107442.
Schmidt M, Avagyan S, Reiche K, Binder H, Loeffler-Wirth H. A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Current Issues in Molecular Biology 2024, 46(5):4701-4720.
Our research focuses on unraveling the diversity of Armenian vine accessions through a comprehensive analysis of their whole genomes. To achieve this, we employ DNA sequencing and harness the power of machine learning for knowledge mining. Through these methods, we gain insights into the domestication history of grapevines and their correlations with phenotypic traits, including cultivar utilization and potential resistance against diseases and parasites. The implications of our findings extend to addressing challenges in viticulture, particularly those posed by climate change. This project, one of the nine Advanced Research Programs supported by the FAST program in Armenia, is intricately woven into international collaborations.
Related work
Konecny T, Asatryan A, Nikoghosyan M, Binder H. Unveiling Iso- and Aniso-Hydric Disparities in Grapevine—A Reanalysis by Transcriptome Portrayal Machine Learning. Plants 2024, 13(17):2501.
Konecny T, Nikoghosyan M, Binder H. Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera. Front Plant Sci. 2023;14: 1303542.
Margaryan K, Nikoghosyan M, Baloyan A, Binder H, Hovhannisyan E, Galstyan L, et al. Machine learned -based visualization of the diversity of vine genomes worldwide and in Armenia using SOMmelier. BIO Web Conf. 2023;68: 01009.
Nikoghosyan M, Schmidt M, Margaryan K, Arakelyan A, Binder H. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes. 2020;11: 817.
Nikoghosyan M, Hakobyan S, Hovhannisyan A, Loeffler-Wirth H, Binder H, Arakelyan A. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach. Front Genet. 2019;10: 394.
Liver metastases significantly exacerbate the prognosis for various cancer diseases, including colorectal cancer. Our exploration of the molecular mechanisms underlying this phenomenon utilized bioinformatics and gene expression data from hundreds of patient tumor samples. Through our analysis, we uncovered that metastasis and prior treatments can give rise to fibrotic, non-immunogenic tumor states that elude standard therapies, including new immunotherapies, by acquiring epigenetic plasticity in cancer cells.
Our studies also suggest potential strategies to overcome treatment resistance through refined precision medicine options.
Related work
Ashekyan O, Shahbazyan N, Bareghamyan Y, Kudryavzeva A, Binder H, Schmidt M, et al. Transcriptomic Maps of Colorectal Liver Metastasis: Machine Learning of Gene Activation Patterns and Epigenetic Trajectories in Support of Precision Medicine. Cancers 2023, Vol 15, Page 3835. 2023;15: 3835.
Avagyan S, Binder H. Subtyping or not subtyping—Quo vadis for precision medicine of colorectal cancer. Transl Cancer Res. 2023;12: 1067–1072.
Binder H, Willscher E, Loeffler-Wirth H, Hopp L, Hones TW, Pfister SM, et al. DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development. Acta Neuropathol Commun. 2019;7: 59.
Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, Haake A, Binder H, et al. A modular transcriptome map of mature B cell lymphomas. Genome Med. 2019;11: 27.
Konecny T, Asatryan A, Nikoghosyan M, Binder H. Unveiling Iso- and Aniso-Hydric Disparities in Grapevine—A Reanalysis by Transcriptome Portrayal Machine Learning. Plants 2024, 13(17):2501.
Schmidt M, Avagyan S, Reiche K, Binder H, Loeffler-Wirth H: A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Current Issues in Molecular Biology 2024, 46(5):4701-4720.
Ashekyan O, Shahbazyan N, Bareghamyan Y, Kudryavzeva A, Mandel D, Schmidt M, et al. Transcriptomic Maps of Colorectal Liver Metastasis: Machine Learning of Gene Activation Patterns and Epigenetic Trajectories in Support of Precision Medicine. Cancers 2023, Vol 15, Page 3835. 2023;15:3835.
Avagyan S, Binder H․ Subtyping or not subtyping—Quo vadis for precision medicine of colorectal cancer. Transl Cancer Res. 2023;12:1067–72.
Hakobyan S, Stepanyan A, Nersisyan L, Binder H, Arakelyan A․ PSF toolkit: an R package for pathway curation and topology-aware analysis. Front. Genet. 2023 14:1264656. Vol 14
Konecny T, Nikoghosyan M, Binder H. Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera. Front Plant Sci. 2023;14:1303542.
Binder H, Schmidt M, Hopp L, Davitavyan S, Arakelyan A, Loeffler-Wirth H. Integrated Multi-Omics Maps of Lower-Grade Gliomas. Cancers 2022, Vol 14, Page 2797. 2022;14:2797.
Loeffler-Wirth H, Hopp L, Schmidt M, Zakharyan R, Arakelyan A, Binder H. The Transcriptome and Methylome of the Developing and Aging Brain and Their Relations to Gliomas and Psychological Disorders. Cells 2022, Vol 11, Page 362. 2022;11:362.
Loeffler-Wirth H, Rade M, Arakelyan A, Kreuz M, Loeffler M, Koehl U, Reiche K, Binder H, Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying. Front. Immunol. 2023 13:994885.
Schmidt M, Arshad M, Bernhart SH, Hakobyan S, Arakelyan A, Loeffler-Wirth H, et al. The Evolving Faces of the SARS-CoV-2 Genome. Viruses 2021, Vol 13, Page 1764. 2021;13:1764.
Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, et al. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers 2021, Vol 13, Page 3198. 2021;13:3198.
Nikoghosyan M, Loeffler-Wirth H, Davidavyan S, Binder H, Arakelyan A. Projection of High-Dimensional Genome-Wide Expression on SOM Transcriptome Landscapes. BioMedInformatics 2022, Vol 2, Pages 62-76. 2022;2:62–76.
To inquire about roles, contact hans.binder@abi.am
