Z6ios2dqiyqlkiqyzszg big fb logo

Bioinformatics Group, Institute of Molecular Biology NAS RA

Yerevan

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... 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.

« Show less

Bioinformatics Group, Institute of Molecular Biology NAS RA has not listed any services.

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.

« Show less
Bioinformatics pipelines
Bioinformatics
Computational Biology
Biological data analysis
Knowledge inference
Biodata mining
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... Show more »

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.

« Show less
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
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.

« Show less
Bioinformatics pipelines
Biostatistics
Bioinformatics
Computational Biology
Biological data analysis
Knowledge inference
Biodata mining
Bioinformatics Analyses
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.

« Show less
Bioinformatics pipelines
Bioinformatics
Computational Biology
Biological data analysis
Knowledge inference
Biodata mining
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
« Show less
Biology
Bioinformatics pipelines
Gene expression profiling
ChIP-Seq
Genomics
Data Visualization
Whole Genome Sequencing
Whole Genome
whole genome bisulfite sequencing
Bioinformatics
RNA sequencing
differential gene expression
Systems biology
Machine learning
Data analysis
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
« Show less
Bioinformatics pipelines
Bioinformatics
Computational Biology
Biological data analysis
Knowledge inference
Biodata mining
Computational systems biology
Telomere bioinformatics
Biostatistics
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.

« Show less
PCA
Biostatistics
Machine learning
Biological data analysis
Knowledge inference
Biodata mining
High-throughput data analysis
Differentially expressed genes
Differntial gene expression
Feature extraction
Classification
RNA-Seq Data Analysis
Price on request
  • 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.

« Show less
Gene expression profiling
RNA-Seq
PCA
RNAseq
RNA seq
RNA sequencing
Gene set enrichment
Overrepresentation analysis
Transcriptomics
Differntial gene expression
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.

« Show less
Gene expression profiling
microarrays
PCA
Differential Expression
differential gene expression
Pathway analysis
Overrepresentation analysis
Gene expression arrays
Gene set enrichment analysis
Clustering
Heatmaps
Gene Expression Profiling
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.

« Show less
Proteomics
metabolomics
Systems biology
Computational systems biology
Pathways
Pathway analysis
Transcriptomics
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.

« Show less
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.

« Show less
Biology
Telomere
Telomeres
Telomere length
Telomere maintenance mechanisms
Telomere shortening
Telomere lengthening
Telomere elongation
Alternative lengthening of telomeres
Telomerase
TERT
TERC
Whole Genome/Exome Sequencing Data Analysis
Price on request
  • 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.

« Show less
NGS
Variant Calling
Whole Exome Sequencing
Whole Genome Sequencing
Whole Genome
Sequencing data analysis
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.

« Show less
ChIP-Seq
whole genome bisulfite sequencing
Epigenomics
Bisulfite-seq
DNA methylation
Methylation
Histone modification
Epigenetics
Peak calling
Sequencing data analysis
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
« Show less
Bioinformatics pipelines
Java
R
Bash
awk
Pipeline automation
Software development
Ask A Question Find what you're looking for? If not, you can ask this lab a question:

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

Be the first to endorse Bioinformatics Group, Institute of Molecular Biology NAS RA

Endorse this lab