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Binder Lab

Data-driven computational LifeSciences: Mining complex omics data to understand mechanisms of genomic regulation, origin and consequences of genomic diversity and applications in biomedicine and -technology.

  • Molecular and cellular mechanisms of cancer, precision diagnostics, and treatment
  • Single-cell and spatial omics to understand development and disease
  • Molecular paths of human aging
  • Genome atlas of vine cultivation, functional vine (epi-)genomics under environmental stress

Methods

  • Machine learning of complex and multidimensional biodata for function mining
  • Single-cell and bulk omics analytics in space and time
  • Integrative multiomics and phenotype-genotype maps

In general, we aim to extract information about the functioning of life hidden in large and complex data with the help of computers to improve healthcare and to save biodiversity. 

Research Projects

  • VINE Bioinformatics – grape genomics for INNOVATIVE viticulture (FAST Advance program)

Team: Maria Nikogoshyan (Co-PI), Tomas Konecny (PhD student)
Research students: Hripsime Gasoyan, Anush Baoyan, Emma Hovhannysyan, Levon Galstyan, Kristina Magaryan (advisor)

  • Functional single cell transcriptomics of fibroblast communities in skin wounds and tumours 

Junior group: Susanna Avagyan (lead), Arpine Grigoryan, Melina Tamazyan, Maria Schmidt (mentor), Marta Torregossa (mentor), Sandra Franz (advisor)

  • Computational Precision Medicine of Cancer- towards omics-driven personalized diagnostics and treatment

Cooperation with Vivan-Lab and Agenus-Lab teams.

People

Lab Leader

Research Students

Vardan Saroyan

Hripsime Gasoyan

Anush Baloyan

Emma Hovhannisyan

Melina Tamazyan

Arpine Grigoryan

Researchers

Maria Nikoghosyan
Institute of Molecular Biology NAS RA
Ph.D. Student
Tomas Konecny

Uni-leipzig Mentors

Maria Schmidt

University of Leipzig
Ph.D. Student

Henry Loffler-Wirth

University of Leipzig
PostDoc, Group Leader

ABI Mentors

Siras Hakobyan

Institute of Molecular Biology NAS RA
Ph.D. Student

Lab Publications

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

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)

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

Loeffler-Wirth H, Rade M, Arakelyan A, Kreuz M, Loeffler M, Koehl U, et al. Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying. Front Immunol. 2022;13:5395. doi: https://doi.org/10.3389/fimmu.2022.994885

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. doi: https://doi.org/10.3390/cancers14112797

M Schmidt, M Arshad, SH Bernhart, S Hakobyan, A Arakelyan, H Loeffler-Wirth & H Binder. The Evolving Faces of the SARS-CoV-2 Genome. Viruses 2021, 13(9), 1764. doi: https://doi.org/10.3390/v13091764

H Loeffler-Wirth, J Reikowski, S Hakobyan, J Wagner & H Binder. oposSOM-Browser: an interactive tool to explore omics data landscapes in health science  BMC Bioinformatics 2021465 (2020). doi: https://doi.org/10.1186/s12859-020-03806-w

M Nikoghosyan, M Schmidt, K Margaryan, H Loeffler-Wirth, A Arakelyan & H Binder. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes 2020, 11(7), 817. doi: https://doi.org/10.3390/genes11070817

A Arakelyan, L Nersisyan, M Nikoghosyan, S Hakobyan, A Simonyan, L Hopp, H Loeffler-Wirth & H Binder. Transcriptome-guided drug repositioning. Pharmaceutics 2019, 11(12), 677. doi: https://doi.org/10.3390/pharmaceutics11120677

L Nersisyan, L Hopp, H Loeffler-Wirth … A Arakelyan & H Binder. Telomere length maintenance and its transcriptional regulation in Lynch syndrome and sporadic colorectal carcinoma. Front. Oncol., 05.11.2019. doi: https://doi.org/10.3389/fonc.2019.01172

M Nikoghosyan, S Hakobyan … H Loeffler-Wirth, H Binder & A Arakelyan. Population levels assessment of the distribution of disease-associated variants with emphasis on Armenians–a machine learning approach. Front. Genet., 26.4.2019. doi: https://doi.org/10.3389/fgene.2019.00394

Previous Publications of Hans Binder

J Wolf, E Willscher, H Loeffler-Wirth, M Schmidt … H Binder. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. Int. J. Mol. Sci. 2021, 22(5), 2551. doi: https://doi.org/10.3390/ijms22052551

M Schmidt, H Loeffler-Wirth & H Binder. Developmental scRNAseq Trajectories in Gene-and Cell-State Space—The Flatworm Example. Genes 2020, 11(10), 1214. doi: https://doi.org/10.3390/genes11101214

H Loeffler-Wirth, M Schmidt & H Binder.Covid-19 transmission trajectories–monitoring the pandemic in the worldwide context. Viruses 2020, 12(7), 777. doi: https://doi.org/10.3390/v1207077

H Loeffler-Wirth, M Schmidt & H Binder. Covid‐19 trajectories – Monitoring pandemic in the worldwide context. Viruses202012(7), 777;  doi: https://doi.org/10.1101/2020.06.04.20120725

H Loeffler-Wirth, M Kreuz, L Hopp, et al. A modular transcriptome map of mature B cell lymphomas. Genome Med 11, 27 (2019). doi: https://doi.org/10.1186/s13073-019-0637-7

H Binder, E Willscher, H Loeffler-Wirth, 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 7, 59 (2019). doi: https://doi.org/10.1186/s40478-019-0704-8

Open Positions

Open positions up to internships. For more information email the lab supervisor Hans Binder.