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Bioinformatics Group, Institute of Molecular Biology NAS RA

2 Orders Completed
Yerevan, AM

About Bioinformatics Group, Institute of Molecular Biology NAS RA

We develop and provide creative solutions to high-throughput biological data analysis. Our lab members are experienced in various aspects of bioinformatics and computational biology: starting from raw data processing, ending with systems biology level analysis, as well as with bioinformatics software development. Our group is engaged in research projects aimed at...

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We develop and provide creative solutions to high-throughput biological data analysis. Our lab members are experienced in various aspects of bioinformatics and computational biology: starting from raw data processing, ending with systems biology level analysis, as well as with bioinformatics software development. Our group is engaged in research projects aimed at secondary analyses of publicly available datasets to reveal the mechanisms of the development of complex human diseases. On one hand, we develop novel algorithms, approaches, and software for efficient knowledge inference from genomics, transcriptomics, and epigenomics. On the other hand, we use existing tools to perform actual biological research.


Another research direction at focus is telomere bioinformatics: development and application of novel computational approaches for analysis of telomere length dynamics and telomere maintenance mechanisms from gene expression/DNA sequencing data. These and other interests of our group are reflected in the following publications and described at our website (http://big.sci.am/).

Selected publications:

1.       Arakelyan A, Nersisyan L, Nikoghosyan M, et al. Transcriptome-Guided Drug Repositioning. Pharmaceutics. 2019 Dec 12;11(12). pii: E677.

2.       Nersisyan L, Nikoghosyan M, Arakelyan A; Genome of the Netherlands consortium. WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene. Sci Rep. 2019 Dec 10;9(1):18758.

3.       Nersisyan L, Hopp L, Loeffler-Wirth H, et al. Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma. Front Oncol. 2019 Nov 5;9:1172.

4.       Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, et al. A modular transcriptome map of mature B cell lymphomas. Genome Med. 2019 Apr 30;11(1):27.

5.       Nikoghosyan M, Hakobyan S, Hovhannisyan A, et al. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians - A Machine Learning Approach. Front Genet. 2019 Apr 26;10:394.

6.       Hopp L, Loeffler-Wirth H, Nersisyan L, et al. Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Front Immunol. 2018 Jul 17;9:1620.

7.       Arakelyan A, Nersisyan L, Poghosyan D, et al. Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PLoS One. 2017 Nov 3;12(11):e0187572. Arakelyan A, Nersisyan L, Petrek M, et al. Cartography of pathway signal perturbations identifies distinct molecular pathomechanisms in malignant and chronic lung diseases. Front. Genet. 2016, 7:79.

8.       Hakobyan A, Nersisyan L, Arakelyan A. Quantitative trait association study for mean telomere length in the South Asian Genomes. Bioinformatics 2016, 32(11):1697-700.

9.       Nersisyan L, Johnson G, Riel-Mehan M et al. PSFC: a Pathway Signal Flow Calculator App for Cytoscape F1000Research 2015, 4:480.

10.   Nersisyan L, Arakelyan A. Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 2015, 10(4):e0125201.

11.   Nersisyan L, Samsonyan R, Arakelyan A. CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows. Version 2. F1000Res 2014, 3:145.

12.   Arakelyan A, Nersisyan L. KEGGParser: parsing and editing KEGG pathway maps in Matlab. Bioinformatics 2013 Feb 15;29(4):518-9.

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Our Services (23)


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Bioinformatics

Starting at $30.00 per hour

We provide a wide range of bioinformatics data analysis pipelines. For details, see the available specialized services. If none are relevant, you may contact us through this service.

We provide a wide range of bioinformatics data analysis pipelines. For details, see the available specialized services. If none are relevant, you may contact us through this service.

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Bioinformatics Bioinformatics pipelines Computational Biology Biological data analysis Knowledge inference Biodata mining Show 6 more tags Show less

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Computational Systems Biology

Starting at $50.00 per hour

We have considerable experience in systems biology analysis of high-throughput data, including enrichment/overreperesntation analysis for pathways and functional gene sets, as well as advanced pathway analysis, machine learning approaches and others. If none of the more specialized services correspond to the type of systems biology analyses you'd like to undertake, contact us through this one.

We have considerable experience in systems biology analysis of high-throughput data, including enrichment/overreperesntation analysis for pathways and functional gene sets, as well as advanced pathway analysis, machine learning approaches and others. If none of the more specialized services correspond to the type of systems biology analyses you'd like to undertake, contact us through this one.

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Systems biology Computational systems biology Pathways Pathway analysis Gene set enrichment Overrepresentation analysis Network analysis Protein-protein interaction networks Metobolomics Transcriptomics Proteomics Bioinformatics Computational Biology Show 13 more tags Show less

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Biostatistics & Bioinformatics

Starting at $30.00 per hour

We provide a wide range of biostatistics and bioinformatics data analysis pipelines. For details, see the available specialized services. If none are relevant, you may contact us through this service.

We provide a wide range of biostatistics and bioinformatics data analysis pipelines. For details, see the available specialized services. If none are relevant, you may contact us through this service.

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Biostatistics Biodata mining Bioinformatics Bioinformatics pipelines Biological data analysis Computational Biology Knowledge inference Show 7 more tags Show less

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Bioinformatics Consulting

Starting at $75.00 per hour

Brainstorming/miscellaneous requests

This service is for the cases where:

  • You have non-standard data you’d like to analyze
  • You have standard data you’d like to analyze in a non-standard manner
  • You don’t really understand what to do with the data
  • Any other cases requiring non-standard or creative approach

Brainstorming/miscellaneous requests

This service is for the cases where:

  • You have non-standard data you’d like to analyze
  • You have standard data you’d like to analyze in a non-standard manner
  • You don’t really understand what to do with the data
  • Any other cases requiring non-standard or creative approach
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Biology Genomics Bioinformatics Bioinformatics pipelines Whole Genome Whole Genome Sequencing RNA sequencing ChIP-Seq whole genome bisulfite sequencing Gene expression profiling differential gene expression Systems biology Machine learning Data analysis Data Visualization Show 15 more tags Show less

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Bioinformatics Data Analysis

Price on request
  • Pathway and network based analysis
  • NGS data analysis
  • Computational research of telomere biology
  • Integrative analysis of transcriptomic, proteomic and metabolomic data
  • Population genetics studies
  • Pathway and network based analysis
  • NGS data analysis
  • Computational research of telomere biology
  • Integrative analysis of transcriptomic, proteomic and metabolomic data
  • Population genetics studies
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Biodata mining Bioinformatics Bioinformatics pipelines Biological data analysis Computational Biology Computational systems biology Knowledge inference Telomere bioinformatics Show 8 more tags Show less

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Biostatistical Analysis

Starting at $50.00 per hour

Biostatistics/Machine-learning

  • Basic and advanced descriptive statistics and visualization
  • Hypothesis testing analysis
  • Correlation/Regression analysis
  • Application of self organizing maps algorithm for high-dimensional gene expression data processing and feature identification
  • PCA and clustering... Show more »

Biostatistics/Machine-learning

  • Basic and advanced descriptive statistics and visualization
  • Hypothesis testing analysis
  • Correlation/Regression analysis
  • Application of self organizing maps algorithm for high-dimensional gene expression data processing and feature identification
  • PCA and clustering analysis

Input: Any spreadsheet type file with data.

Output: Results are presented in graphical format with clear, comprehensive and aesthetic figures and schemes, as well as in tabular and text formats. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Biostatistics Knowledge inference Biological data analysis Machine learning High-throughput data analysis Differentially expressed genes Differntial gene expression Feature extraction Classification PCA Show 10 more tags Show less

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RNA-Seq Data Analysis

Starting at $40.00 per hour
  • RNA-seq data processing
  • sequencing data quality control
  • read alignment
  • gene- and transcript-based quantitation, TPM/RPKM/FPKM-based quantitation
  • Identification of alternatively spliced variants
  • Identification of differentially expressed genes
  • Overrepresentation and gene set enrichment analysis
  • PCA... Show more »
  • RNA-seq data processing
  • sequencing data quality control
  • read alignment
  • gene- and transcript-based quantitation, TPM/RPKM/FPKM-based quantitation
  • Identification of alternatively spliced variants
  • Identification of differentially expressed genes
  • Overrepresentation and gene set enrichment analysis
  • PCA analysis
  • Hierarchical clustering/heatmap rendering
  • Advanced pathway analysis (described in details in a separate service)

Input: Fastq or BAM raw data files or already processed RPKM/TPM/FPKM files.

Output: Results are presented in graphical format, with clear, comprehensive and esthetic figures and schemes, as well as in tabular and text formats. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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RNA sequencing RNA-Seq Transcriptomics Differntial gene expression Gene expression profiling PCA Overrepresentation analysis Gene set enrichment Show 8 more tags Show less

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Microarray Data Analysis

Starting at $30.00 per hour
  • Microarray raw data processing (from CEL and TXT files to gene expression matrixes)
  • Identification of differentially expressed genes
  • Overrepresentation and gene set enrichment analysis
  • PCA analysis
  • Hierarchical clustering/heatmap rendering
  • Advanced pathway analysis (described in details in a separate service)... Show more »
  • Microarray raw data processing (from CEL and TXT files to gene expression matrixes)
  • Identification of differentially expressed genes
  • Overrepresentation and gene set enrichment analysis
  • PCA analysis
  • Hierarchical clustering/heatmap rendering
  • Advanced pathway analysis (described in details in a separate service)

Input: CEL and TXT formatted raw data files or Gene Expression Omnibus dataset file formats

Output: Results are presented in graphical format, with clear, comprehensive and aesthetic figures and schemes, as well as in tabular and text formats. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Microarray Gene expression arrays Gene expression profiling Differential Expression differential gene expression Overrepresentation analysis Gene set enrichment analysis Pathway analysis PCA Clustering Heatmaps Show 11 more tags Show less

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Gene Expression Analysis

Price on request

Advanced pathway analysis

  • RNA-seq raw data processing
  • Mircroarray raw data processing
  • Identification of differentially expressed genes
  • Overreprestation and gene set enrichment analysis
  • Pathway signal flow analysis: this is our in-house algorithm for quantitative assessment of pathway activities based on gene... Show more »

Advanced pathway analysis

  • RNA-seq raw data processing
  • Mircroarray raw data processing
  • Identification of differentially expressed genes
  • Overreprestation and gene set enrichment analysis
  • Pathway signal flow analysis: this is our in-house algorithm for quantitative assessment of pathway activities based on gene expression/metabolite abundance/proteomics data, as well as pathway topology.
  • Integrative analysis of metabolomic and transcriptomic/proteomic data.
  • Identification of dysregulated pathways in the studied condition.
  • Identification of samples with similar profiles of pathway dysregulation.
  • Construction of custom pathways and further analysis based on particular biological question.

Input: Gene expression matrix (or fold-change values) files in a wide variety of formats (.txt, .csv, .xls, .xlsx). Or no additional input is required, if this is a downstream analysis of microarray and RNA-seq data analysis services.

Output: Results are presented in graphical format, with clear, comprehensive and aesthetic figures and schemes, as well as .gif files showing pathway signal flow in certain cases. Additionally, tabular and text formats will also be delivered. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Pathways Pathway analysis metabolomics Transcriptomics Proteomics Systems biology Computational systems biology Show 7 more tags Show less

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Gene Pathway Analysis

Starting at $50.00 per hour
  • Pathway signal flow analysis: this is our in-house algorithm for quantitative assessment of pathway activities based on gene expression/metabolite abundance/proteomics data, as well as pathway topology.
  • Integrative analysis of metabolomic and transcriptomic/proteomic data.
  • Identification of dysregulated pathways in the... Show more »
  • Pathway signal flow analysis: this is our in-house algorithm for quantitative assessment of pathway activities based on gene expression/metabolite abundance/proteomics data, as well as pathway topology.
  • Integrative analysis of metabolomic and transcriptomic/proteomic data.
  • Identification of dysregulated pathways in the studied condition.
  • Identification of samples with similar profiles of pathway dysregulation.
  • Construction of custom pathways and further analysis based on particular biological question.

Input: Gene expression matrix (fold-change values) files in a wide variety of formats (.txt, .csv, .xls, .xlsx). Or no additional input is required, if this is a downstream analysis of microarray and RNA-seq data analysis services.

Output: Results are presented in graphical format, with clear, comprehensive and esthetic figures and schemes, as well as .gif files showing pathway signal flow in certain cases. Additionally, tabular and text formats will also be delivered. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Telomere Computational Analysis

Starting at $80.00 per hour

Computational analysis of telomere biology

  • Computation of mean telomere length from Illumina whole genome sequencing data
  • Correlation analysis of mean telomere length with transcriptome and epigenome features
  • Computational assessment of telomerase and ALT based telomere maintenance/lengthening mechanisms from gene... Show more »

Computational analysis of telomere biology

  • Computation of mean telomere length from Illumina whole genome sequencing data
  • Correlation analysis of mean telomere length with transcriptome and epigenome features
  • Computational assessment of telomerase and ALT based telomere maintenance/lengthening mechanisms from gene expression data

Input: Please contact us for data type and format requirements.

Output: Depending on the input data type, computation of mean telomere length (whole genome) or telomere maintenance mechanisms (gene expression data), or association analysis with -omics data from different sources (epigenomics) is possible. Results are presented in graphical format, with clear, comprehensive and aesthetic figures and schemes, as well as .gif files showing telomere maintenance mechanisms’ activity. Additionally, tabular and text formats will also be delivered. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Biology Telomere Telomeres Telomere length Telomere maintenance mechanisms Telomere shortening Telomere lengthening Telomere elongation Telomerase TERT TERC Show 11 more tags Show less

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Whole Genome Sequencing Data Analysis

Starting at $30.00 per hour
  • Sequencing data quality control
  • Read alignment
  • Variant calling
  • Genome wide association studies

Input: fastq or BAM files and phenotype data (optional).

Output: Results are presented in graphical format with clear, comprehensive and aesthetic figures and schemes, as well as in tabular and text formats. All the... Show more »

  • Sequencing data quality control
  • Read alignment
  • Variant calling
  • Genome wide association studies

Input: fastq or BAM files and phenotype data (optional).

Output: Results are presented in graphical format with clear, comprehensive and aesthetic figures and schemes, as well as in tabular and text formats. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Whole Exome Sequencing Whole Genome Whole Genome Sequencing Variant Calling Sequencing data analysis NGS Show 6 more tags Show less

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Epigenomic Data Analysis

Starting at $40.00 per hour
  • Chip-seq data processing
  • ChIP-seq quality control
  • Read mapping
  • Peak calling
  • Genomic region annotation
  • Bisulfite-seq data processing
  • Bisulfite-seq quality control
  • Bisulfite mapping
  • Methylation state identification
  • Genomic region annotation

Input: fastq or BAM files.

Output: For ChIP-seq... Show more »

  • Chip-seq data processing
  • ChIP-seq quality control
  • Read mapping
  • Peak calling
  • Genomic region annotation
  • Bisulfite-seq data processing
  • Bisulfite-seq quality control
  • Bisulfite mapping
  • Methylation state identification
  • Genomic region annotation

Input: fastq or BAM files.

Output: For ChIP-seq datasets, the output is details of detected peaks, including genomic position and width of the peak, the summit and the peak score. For BS-seq, the output is positions of all sequenced cytosines (in CpG, CHG and CHH contexts) along with the methylation score. All the results are explained in detail, with the option of further discussions and post-feedback modifications.

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Epigenomics ChIP-Seq whole genome bisulfite sequencing Bisulfite-seq DNA methylation Methylation Histone modification Epigenetics Peak calling Sequencing data analysis Show 10 more tags Show less

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Software Development

Price on request
  • Java based desktop apps
  • Cytoscape apps
  • Bash scripts and R Pipelines for NGS data analysis and visualization
  • R pipelines for transcriptomic, proteomic and metabolomic data analysis
  • Java based desktop apps
  • Cytoscape apps
  • Bash scripts and R Pipelines for NGS data analysis and visualization
  • R pipelines for transcriptomic, proteomic and metabolomic data analysis
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Java R Bash awk Bioinformatics pipelines Pipeline automation Software development Show 7 more tags Show less

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Nucleic Acid Data Analysis

Price on request
Request a quote for more information about this service.

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Computer Science, Software Development, and IT Services

Price on request
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Sequencing Data Analysis and Management

Price on request
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Computational Modeling

Price on request
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Epigenetic Studies

Price on request
Request a quote for more information about this service.

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DNA Database Searching

Price on request
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Gene Set Enrichment Analysis

Price on request
Request a quote for more information about this service.

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NGS Data Analysis

Next generation sequencing data analysis
Price on request
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Algorithm Development

Price on request
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AA

Arsen Arakelyan

Director, head of Bioinformatics Group
LN

Lilit Nersisyan

Researcher, Bioinformatics Group
  • Positive review for Bioinformatics Data Analysis:

    February 2019

    "The team at the Institute of Molecular Biology NAS RA provided excellent bioinformatics analysis for us. They recommended an approach that was unique to us among the service providers that we engaged with previously inside and outside the Science Exchange, and ultimately their methods delivered novel insights and leads on biological mechanism. The team was responsive, professional, timely, and thorough in the delivery of the work."

Bioinformatics Group, Institute of Molecular Biology NAS RA has not received any endorsements.