Hans Binder

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About Hans Binder:

No description specified

SEEK ID: https://armlifebank.am/people/4

Location: Armenia

ORCID: https://orcid.org/0000-0002-2242-4678

Expertise: Bioinformatics, Genomics, Precision Medicine, Machine Learning, Cancer Biology

Tools: Mathematical Modelling, Single Cell analysis, Computational and theoretical biology, Genomics, Transcriptomics

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Bioinformatics Tools for Analysis of Big Genomic Data

No description specified

Projects: Biological pathway activity analysis, ML approaches for omic data analysis, Tools for Telomere Biology

Web page: Not specified

Genes, Environment and Chronic Diseases

This program under 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, Epigenetic influence of human long-term environmental exposure to metals

Web page: Not specified

Cancer Omics

This Programme offers a comprehensive summary of various projects focused on deciphering the intricate molecular mechanisms of cancer development, progression, and response to treatments, utilizing bioinformatics, computational biology, and machine learning. These are multi-laboratory efforts carried out across several research institutions, supported by various grant programs.

Projects: Molecular Profiling of Cancer Metastases

Web page: Not specified

Vine Bioinformatics

Principal Investigator: Prof. Hans Binder

University: University of Leipzig

Research Group: Kristina Margaryan, Maria Nikoghosyan, Tomas Konecny, Anush Baloyan, Hripsime Gasoyan, Emma Hovhannisyan, Levon Galstyan, Duan Shengchang

Duration: 2023-2027

Co-implementing and hosting partner: Armenian Bioinformatics Institute (ABI) and Institute of Molecular Biology

Project Importance The cultivated grape (Vitis vinifera) has become the world’s leading fruit crop. Grape is unique not only because ...

Projects: Functional Genomics of Vine

Web page: https://www.fast.foundation/en/program/847/2022/new_tab/6586/6677

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Mental disorders and aging brain

This project focuses on studies around brain disorders and ageing.

Programme: Genes, Environment and Chronic Diseases

Public web page: Not specified

Organisms: Human

Biological pathway activity analysis

No description specified

Programme: Bioinformatics Tools for Analysis of Big Genomic Data

Public web page: Not specified

Organisms: Not specified

Molecular Profiling of Cancer Metastases

Together with the scientists at Agenus, a US-based biotech company specializing in innovative forms of cancer treatment, including the discovery and development of immuno-oncology therapies, ABI has formed a team of students and researchers to study cancer metastases and identify potential biomarkers and targets for cancer immunotherapies. This collaboration is also part of our long-term vision of supporting biotech developments in Armenia. The team discovers transcriptomics heterogeneity of Liver ...

Programme: Cancer Omics

Public web page: https://abi.am/research/research-labs/agenus-lab/

Start date: 21st Feb 2024

Organisms: Human

Functional Genomics of Vine

The genomic information becomes functional after transcription and translation. Omics-data (e.g., transcriptomics, epigenetics, proteomics) are increasingly generated for vine and other cultivated plants to study functional genomics with impact for improving yield, quality, and resistance. However, many issues, related to, e.g., development, stress-response, and resistance are still understudied. This opens novel opportunities to close this gap by analyzing such datasets.

Programme: Vine Bioinformatics

Public web page: Not specified

Organisms: Grapevine

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Armenian Bioinformatics Institute

Country: Armenia

City: Yerevan

Web page: https://www.abi.am

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

Temporal changes of gene expression in health, schizophrenia, bipolar disorder, and major depressive disorder.

Mental disorders and aging brain, ML approaches for omic data analysis

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Abstract (Expand)

The molecular events underlying the development, manifestation, and course of schizophrenia, bipolar disorder, and major depressive disorder span from embryonic life to advanced age. However, little …

Authors: A. Arakelyan, S. Avagyan, A. Kurnosov, T. Mkrtchyan, G. Mkrtchyan, R. Zakharyan, K. R. Mayilyan, H. Binder

Date Published: 17th Feb 2024

Publication Type: Journal

PubMed ID: 38368435

Citation: Schizophrenia (Heidelb). 2024 Feb 17;10(1):19. doi: 10.1038/s41537-024-00443-7.

Created: 28th Apr 2024 at 14:09

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

Biological pathway activity analysis

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: S. Hakobyan, A. Stepanyan, L. Nersisyan, H. Binder, A. Arakelyan

Date Published: 8th Sep 2023

Publication Type: Journal

PubMed ID: 37680201

Citation: Front Genet. 2023 Aug 23;14:1264656. doi: 10.3389/fgene.2023.1264656. eCollection 2023.

Created: 6th Mar 2024 at 19:17

Projection of High-Dimensional Genome-Wide Expression on SOM Transcriptome Landscapes

ML approaches for omic data analysis

Abstract (Expand)

organizing maps portraying has been proven to be a powerful approach for analysis of transcriptomic, genomic, epigenetic, single-cell, and pathway-level data as well as for “multi-omic” integrative …

Authors: Maria Nikoghosyan, Henry Loeffler-Wirth, Suren Davidavyan, Hans Binder, Arsen Arakelyan

Date Published: 27th Dec 2021

Publication Type: Journal

DOI: 10.3390/biomedinformatics2010004

Citation: BioMedInformatics,2(1):62-76

Created: 7th Mar 2024 at 11:00

Telomere Maintenance Pathway Activity Analysis Enables Tissue- and Gene-Level Inferences.

Biological pathway activity analysis, Tools for Telomere Biology

Abstract (Expand)

Telomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and …

Authors: L. Nersisyan, A. Simonyan, H. Binder, A. Arakelyan

Date Published: 26th Apr 2021

Publication Type: Journal

PubMed ID: 33897770

Citation: Front Genet. 2021 Apr 7;12:662464. doi: 10.3389/fgene.2021.662464. eCollection 2021.

Created: 7th Mar 2024 at 09:09, Last updated: 7th Mar 2024 at 15:40

SOMmelier-Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks.

ML approaches for omic data analysis

Abstract (Expand)

BACKGROUND: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic …

Authors: M. Nikoghosyan, M. Schmidt, K. Margaryan, H. Loeffler-Wirth, A. Arakelyan, H. Binder

Date Published: 17th Jul 2020

Publication Type: Journal

PubMed ID: 32709105

Citation: Genes (Basel). 2020 Jul 17;11(7):817. doi: 10.3390/genes11070817.

Created: 7th Mar 2024 at 10:50

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