Research

The lab’s central interests are describing and understanding genomic regulation, its diversity, and its impact on health and disease. We address a wide range of issues such as

  • Mechanisms of cancer heterogeneity, treatment resistance, and immune therapy at the single-cell level
  • Genome atlas of vine accessions in the Caucasus
  • Evolution of Coronavirus genomes
  • Molecular mechanisms of human aging

Under a methodical perspective, we are developing and applying methods for multi-omics analytics (transcriptomics, epi-/genetics, and others), phenotypic associations, feature extraction, and clustering with a strong focus on visualization. 

  • Machine learning of genomic diversity and function prediction
  • Single-cell omics analysis: from pseudotime to cell-cell interactions
  • Pathway analysis

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. 

People

Lab Leader

Research Students

Vardan Saroyan

Vardan Saroyan

Hripsime Gasoyan

Susanna Avagyan

Uni-leipzig Mentors

Maria Schmidt

University of Leipzig
Ph.D. Student

Henry Loffler-Wirth

University of Leipzig
Ph.D. Student

Lena S. Mortensen

University of Leipzig
MSc Student

ABI Mentors

Maria Nikoghosyan

Institute of Molecular Biology NAS RA
Ph.D. Student

Siras Hakobyan

Institute of Molecular Biology NAS RA
Ph.D. Student

Publications

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

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

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

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

Covid-19 transmission trajectories–monitoring the pandemic in the worldwide context. H Loeffler-Wirth, M Schmidt & H Binder. Viruses 2020, 12(7), 777. DOI: https://doi.org/10.3390/v12070777

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

Covid‐19 trajectories – Monitoring pandemic in the worldwide context. H Loeffler-Wirth, M Schmidt & H Binder. medRxiv, 2020.06.04.20120725. DOI: https://doi.org/10.1101/2020.06.04.20120725

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

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

DNA methylation, transcriptome, and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development. H Binder, E Willscher, H Loeffler-Wirth, et al. acta neuropathol commun 7, 59 (2019). DOI: https://doi.org/10.1186/s40478-019-0704-8

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

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

Open Positions

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

Nersisyan Lab

The lab’s central interest is the development of algorithms and software solutions for genomics research.

Binder Lab

The lab’s central interests are describing and understanding genomic regulation, its diversity, and its impact on health and disease.

 

Welome to ABI Research School!

ABI Research School provides an opportunity for students to learn bioinformatics by engaging in research projects supervised by researchers at ABI or abroad. The projects may serve as an entry to a junior researcher’s position, or as a capstone for a bachelor’s or master’s thesis, and may eventually lead to a publication.

Ongoing Supervisions

As a part of ABI Research School, students find their supervisors to conduct projects.

Mentor & Mentee Program

The Mentor & Mentee program at ABI supports life science Postdoctoral fellows around the world…

Projects Offered

Find out what topics you may get engaged in as a student.

Ongoing projects

At ABI Research School, students can engage in research projects supervised by scientists from Armenia and abroad. The remote supervisions are supported through mentors at ABI.

Finding telomere-related cancer biomarkers in cell free DNA

Supervisor: Dr. Lilit Nersisyan, ABI

Student: Narek Shamamyan, BSc in Computer Science from AUA

Molecular mechanisms of aging

Supervisor: Prof. Hans Binder, Leipzig University, Germany & ABI

Student: Vardan Saroyan, Resident at YSMU

Analysis of SARS-CoV Variants

Supervisor: Prof. Hans Binder, Leipzig University, Germany & ABI

Student: Hripsime Gasoyan, BSc in Applied Math from YSU

Oncogenic pathway alterations across large scale cancer studies

Supervisor: Anna Hakobyan, PhD student at Max Perutz Labs, Austria

Student: Nelly Vardazaryan, MSc student in Molecular and Cell Biology at ISEC NAS RA

Developmental neuroscience and single cell transcriptomics

Supervisor: Dr. Araks Martirosyan, KU Leuven, Belgium

Student: Arabo Apresyan, Resident at YSMU

Tissue specificity of transcriptional programs in immune cells

Supervisor: Lilit Grigoryan, PhD student at Stanford University, USA
Mentor: Lilit Nersisyan, ABI

Student: Nerses Shahbazyan, Student at YSMU

Signaling pathways states in health and disease with integrative genomics

Supervisor: Dr. Arsen Arakelyan (ABI), Siras Hakobyan, Ph.D. Student, Institute of Molecular Biology NAS RA

Student: Mher Kurghinyan, Student at YSMU

Evaluation of genetic risk factors for complex human disorders

Supervisor: Dr. Arsen Arakelyan (ABI), Siras Hakobyan (Ph.D. student and ABI mentor), Maria Nikoghosyan (Ph.D. student at Institute of Molecular Biology NAS RA and ABI mentor)

Student: Anush Baloyan, Data Science BSc at AUA

D3.JS for a gene-editing application

Supervisors: Harutyun Minasyan (D3.js) and Lilit Nersisyan (Bioinformatics)

Backend: Tatevik Jalatyan (R & bash) 

Understanding vulnerability in ALS using multi-omics

The project focuses on investigating disease mechanisms and novel therapeutic approaches for devastating neurological disorders including Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the second most common dementia.

Mentor & Mentee Program

The Mentor & Mentee program at ABI supports life science Postdoctoral fellows around the world to get mentorship for data analysis aspects of their research at the same time mentoring an ABI student and engaging them in their research.

ABI provides a supervision to the student to gain the skills needed for the project proposed by the fellow.

The student shares her/his knowledge and skills with the postdoc, while the postdoc shares the details of their study. 

Design and analysis of AAV vectors for gene editing applications

Life Science Postdoc

Dr. Erik Aznauryan, Church Lab, Wyss Institute, Harvard University, USA

Bioinformatics Student

Tatevik Jalatyan, Data Science BSc at AUA

Computational analysis of telomere sequences in cell-free DNA

Life Science Postdoc

Jakub Wudarski, PhD, Specially Appointed Assistant Professor at National Institute for Basic Biology Japan

Bioinformatics Supervisor

Lilit Nersisyan, PhD, Director at ABI, researcher at Karolinska Institutet, Sweden

Projects Offered

M&M: Computational analysis of telomere sequences in cell-free DNA

Life Science Postdoc

Jakub Wudarski, PhD, Specially Appointed Assistant Professor at National Institute for Basic Biology Japan

Bioinformatics Supervisor

Lilit Nersisyan, PhD, Director at ABI, researcher at Karolinska Institutet, Sweden

D3.JS for a gene-editing application

Supervisors: Harutyun Minasyan (D3.js) and Lilit Nersisyan (Bioinformatics)

Backend: Tatevik Jalatyan (R & bash) 

Understanding vulnerability in ALS using multi-omics

The project focuses on investigating disease mechanisms and novel therapeutic approaches for devastating neurological disorders including Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the second most common dementia.