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Bioinformatics Group, Institute of Molecular Biology NAS RA

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Yerevan, AM

About Bioinformatics Group, Institute of Molecular Biology NAS RA

We are a team of bioinformatics researchers at the Institute of Molecular Biology, that develops and provides 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... Show more »

We are a team of bioinformatics researchers at the Institute of Molecular Biology, that develops and provides 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 development of complex human diseases. On one hand, we develop novel algorithms, approaches and software for efficient knowledge inference from gene expression and sequencing datasets. On the other hand, we use existing tools to perform actual biological research. We have more than seven years of experience in pathway-based analysis of high-throughput gene expression data, particularly using the pathway signal flow algorithm developed in our group. 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:
Book chapters
1. Arakelyan A, Nersisyan L, Hakobyan A. Application of MATLAB in -Omics and Systems Biology. Applications from Engineering with MATLAB Concepts, Associate Prof. Jan Valdman (Ed.), ISBN: 978-953-51-2459-7. InTech, Croatia, 2016. DOI: 10.5772/62847.
2. Arakelyan A, Aslanyan L, Boyajyan A. High-throughput Gene Expression Analysis Concepts and Applications. Sequence and Genome Analysis II – Bacteria, Viruses and Metabolic Pathways. ISBN: 978-1-480254-14-5. iConcept Press Ltd, USA , 2013, 71-95.
3. Arakelyan A, Boyajyan A, Sahakyan H, Aslanyan L, Ivanova K, Mitov I. Growing support set systems in analysis of high-throughput gene expression data. In: New trends in classification and data mining (Editors: K. Markov, V. Ryazanov, V. Velychko, L. Aslanyan), Sofia: ITHEA, 2010, 47-53.
Journal articles
1. Arakelyan A, Nersisyan L, Petrek M, Löffler-Wirth H, Binder H. Cartography of pathway signal perturbations identifies distinct molecular pathomechanisms in malignant and chronic lung diseases. Front. Genet. 2016, 7:79.
2. 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.
3. Hopp L, Nersisyan L, Löffler-Wirth H, Arakelyan A, Binder H. Epigenetic heterogeneity of B-cell lymphoma: Chromatin modifiers. Genes 2015, 6(4):1076-1112.
4. Nersisyan L, Johnson G, Riel-Mehan M et al. PSFC: a Pathway Signal Flow Calculator App for Cytoscape [version 1; referees: 1 approved] F1000Research 2015, 4:480.
5. Nersisyan L, Arakelyan A. Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 2015, 10(4):e0125201.
6. Binder H, Wirth H, Arakelyan A, Lembcke K, Tiys ES, Ivanisenko VA, Kolchanov NA, Kononikhin A, Popov I, Nikolaev EN, Pastushkova L, Larina IM. Time-course human urine proteomics in space-flight simulation experiments. BMC Genomics 2014, 15 Suppl 12:S2.
7. Nersisyan L, Samsonyan R, Arakelyan A. CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows. Version 2. F1000Res 2014, 3:145.
8. 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 (27)


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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 pipelines Bioinformatics 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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Proteomics Bioinformatics Systems biology Computational Biology Computational systems biology Pathways Pathway analysis Gene set enrichment Overrepresentation analysis Network analysis Protein-protein interaction networks Metobolomics Transcriptomics 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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Bioinformatics pipelines Biostatistics Bioinformatics Computational Biology Biological data analysis Knowledge inference Biodata mining 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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Bioinformatics pipelines Gene expression profiling ChIP-Seq Data Visualization Whole Genome Sequencing Whole Genome whole genome bisulfite sequencing Bioinformatics RNA sequencing differential gene expression Systems biology Machine learning Data analysis Biology Genomics 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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Bioinformatics pipelines Bioinformatics Computational Biology Biological data analysis Knowledge inference Biodata mining Computational systems biology 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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PCA Biostatistics Machine learning Biological data analysis Knowledge inference Biodata mining High-throughput data analysis Differentially expressed genes Differntial gene expression Feature extraction Classification Show 11 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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Gene expression profiling RNA-Seq PCA RNA sequencing Gene set enrichment Overrepresentation analysis Transcriptomics Differntial gene expression 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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Gene expression profiling microarrays PCA Differential Expression differential gene expression Pathway analysis Overrepresentation analysis Gene expression arrays Gene set enrichment analysis 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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Proteomics metabolomics Systems biology Computational systems biology Pathways Pathway analysis Transcriptomics 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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Telomere Telomeres Telomere length Telomere maintenance mechanisms Telomere shortening Telomere lengthening Telomere elongation Alternative lengthening of telomeres Telomerase TERT TERC Biology Show 12 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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NGS Variant Calling Whole Exome Sequencing Whole Genome Sequencing Whole Genome Sequencing data analysis 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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ChIP-Seq whole genome bisulfite sequencing Epigenomics 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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Bioinformatics pipelines Java R Bash awk Pipeline automation Software development Show 7 more tags Show less

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Nucleic Acid Analysis

Price on request
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Epigenetic Studies

Price on request
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Computational Modeling

Price on request
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Omics

Price on request
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Biochemistry & Molecular Biology

Price on request
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Sequencing Data Analysis

Price on request
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Nucleic Acid Services

Price on request
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Computer Science, Software Development, and IT Services

Price on request
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DNA Services

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Equipment

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Genotyping Services

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Nucleic Acid Data Analysis

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Biology

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Arsen Arakelyan

Director, head of Bioinformatics Group
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Anna Hakobyan

Researcher, Bioinformatics Group
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Lilit Nersisyan

Researcher, Bioinformatics Group

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