Bioinformatics Group

Institute of Molecular Biology NAS RA

Publications

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Selected publications

  1. Garikipati V. N. S., Arakelyan A., Blakely E. A., Chang P. Y., Truongcao M. M., Cimini M., … & Goukassian D. Long-Term Effects of Very Low Dose Particle Radiation on Gene Expression in the Heart: Degenerative Disease Risks. Genes 2020. 11(7), 817. PubMed Full text
  2. Nikoghosyan, M., Schmidt, M., Margaryan, K., Loeffler-Wirth, H., Arakelyan, A., & Binder, H. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes 2020. 11(7), 817. PubMed Full text
  3. Arakelyan A, Nersisyan L, Nikoghosyan M, Hakobyan S, Simonyan A, Hopp L, Loeffler-Wirth H, Binder H. Transcriptome-Guided Drug Repositioning. Pharmaceutics 2019. 11(12):E677. PubMed Full text
  4. Nersisyan L, Nikoghosyan M, Arakelyan A. WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene. Sci Rep. 2019. 9(1):18758. PubMed Full text
  5. Nikoghosyan M, Hakobyan S, Hovhannisyan A, Loeffler-Wirth H, Binder H, Arakelyan A. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach Front. Genet. 2019. 10:394.  PubMed  Full text
  6. 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. PubMed  Full text
  7. 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. PubMed   Full text
  8. 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.   PubMed Full text
  9. Nersisyan L, Arakelyan A. Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 2015, 10(4):e0125201. PubMed Full text
  10. Arakelyan A, Nersisyan L. KEGGParser: parsing and editing KEGG pathway maps in Matlab. Bioinformatics 2013 Feb 15;29(4):518-9. PubMed   Full text

The full list

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.   Full text
  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. PDF
  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. Full text

Journal articles

  1. Nersisyan L., Simonyan A., Binder H., Arakelyan A. Telomere maintenance pathway activity analysis enables tissue-and gene-level inferences. bioRxiv. 2021. PubMed Full text
  2. Binder H, Arakelyan A. Special Issue “Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level”. Genes (Basel). 2020. 11(12):1463. PubMed Full text
  3. Loeffler-Wirth H, Reikowski J, Hakobyan S, Wagner J, Binder H. oposSOM-Browser: an interactive tool to explore omics data landscapes in health science. BMC Bioinformatics 2020. 21(1):465. PubMed Full text
  4. Schmidt M, Hopp L, Arakelyan A, Kirsten H, Engel C, Wirkner K, Krohn K, Burkhardt R, Thiery J, Loeffler M, Loeffler-Wirth H, Binder H. The Human Blood Transcriptome in a Large Population Cohort and Its Relation to Aging and Health. Front. Big Data 2020. 3:548873. PubMed Full text
  5. Boyarskikh UA, Gulyaeva LF, Avdalyan AM, Kechin AA, Khrapov EA, Lazareva DG, Kushlinskii NE, Melkonyan A, Arakelyan A, Filipenko ML. Spectrum of TP53 Mutations in BRCA1/2 Associated High-Grade Serous Ovarian Cancer. Front Oncol 2020. 10:1103. PubMed Full text
  6. Nikoghosyan, M., Schmidt, M., Margaryan, K., Loeffler-Wirth, H., Arakelyan, A., & Binder, H. SOMmelier—Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes 2020. 11(7), 817. PubMed Full text
  7. Arakelyan A, Nersisyan L, Nikoghosyan M, Hakobyan S, Simonyan A, Hopp L, Loeffler-Wirth H, Binder H. Transcriptome-Guided Drug Repositioning. Pharmaceutics 2019. 11(12):E677. PubMed Full text
  8. Nersisyan L, Nikoghosyan M, Arakelyan A. WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene. Sci Rep. 2019. 9(1):18758. PubMed Full text
  9. Nersisyan L, Hopp L, Loeffler-Wirth H, Galle J, Loeffler M, Arakelyan A, Binder H. Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma. Front Oncol. 2019. 9:1172. PubMed Full text
  10. Nikoghosyan M, Hakobyan S, Hovhannisyan A, Loeffler-Wirth H, Binder H, Arakelyan A. Population Levels Assessment of the Distribution of Disease-Associated Variants With Emphasis on Armenians – A Machine Learning Approach Front. Genet. 2019. 10:394.  PubMed  Full text
  11. Khachatrian H, Nersisyan L, Hambardzumyan K, Galstyan T, Hakobyan A, Arakelyan A, Rzhetsky A, Galstyan A. BioRelEx 1.0: Biological Relation Extraction Benchmark. Proceedings of the BioNLP 2019 workshop 2019. pages 176-190. Full text
  12. Loeffler-Wirth H, Kreuz M, Hopp L, Arakelyan A, et al. A modular transcriptome map of mature B cell lymphomas. Genome Med. 2019. 10:394.  PubMed  Full text
  13. Hodorová V, Lichancová H, Zubenko S, Sienkiewicz K, Penir SMU, Afanasyev P, Boceck D, Bonnin S, Hakobyan S, et al. Genome Sequence of the Yeast Saprochaete ingens CBS 517.90. Microbiol Resour Announc. 2019. 8(50):e01366-19. PubMed Full text
  14. Hopp L, Loeffler-Wirth H, Nersisyan L, Arakelyan A, Binder H.Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Front Immunol. 2018. 9:1620. PubMed Full text
  15. Kovalchuk A, Nersisyan L,  et al.  Growth of Malignant Non-CNS Tumors Alters Brain Metabolome. Front Genet. 2018. 20;9:41. PubMed Full text
  16. Arsen Arakelyan , Lilit Nersisyan, David Poghosyan, Lusine Khondkaryan, Anna Hakobyan, Henry Löffler-Wirth, Evie Melanitou, Hans Binder. Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PLoS One 2017. 12(11):e0187572. PubMed Full text
  17. Nersisyan L, Arakelyan A. A transcriptome and literature guided algorithm for reconstruction of pathways to assess activity of telomere maintenance mechanisms. bioRxiv 200535.  doi: https://doi.org/10.1101/200535
  18. Binder H., Hopp L., et al. Genomic and transcriptomic heterogeneity of colorectal tumors arising in Lynch Syndrome. J. Pathol. 2017. PubMed Full text
  19. Nersisyan L. Integration of Telomere Length Dynamics into Systems Biology Framework: A Review. Gene Regul Syst Bio. 2016, 10:35-42. PubMed  Full text
  20. 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. PubMed  Full text
  21. Nersisyan L, Löffler-Wirth H, Arakelyan A, Binder H. Gene Set- and Pathway- Centered Knowledge Discovery Assigns Transcriptional Activation Patterns in Brain, Blood, and Colon Cancer: A Bioinformatics Perspective. Int. J. of Knowl. Disc. in Bioinf. (IJKDB) 2016, 4(2):46-49. Full text
  22. 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. PubMed   Full text
  23. Arakelyan A. Functional gene sets in post-traumatic stress disorder. Proc. Yerevan State  Un. 2016, 1: 43-48. PDF
  24. 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. PubMed   Full text
  25. 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.   PubMed Full text
  26. Nersisyan L, Arakelyan A. Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 2015, 10(4):e0125201. PubMed Full text
  27. Arakelyan A, Nersisyan L, Gevorgyan A, Boyajyan A. Geometric Approach for Gaussian-Kernel Bolstered Error Estimation for Linear Classification in Computational Biology. Int. J. Inf. Theor. Appl. 2014, 21: 170-182. PDF
  28. Nersisyan L, Samsonyan R, Arakelyan A. CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows. Version 2. F1000Res 2014, 3:145. PubMed   Full text
  29. 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. PubMed Full text
  30. Nersisyan L, Arakelyan A. MEFV expression during macrophage activation. Nat. El. J. Nat. Sci., 2(21): 77-81, 2013. Abstract
  31. Arakelyan A, Nersisyan L. KEGGParser: parsing and editing KEGG pathway maps in Matlab. Bioinformatics 2013 Feb 15;29(4):518-9. PubMed   Full text
  32. Boyajyan A, Arakelyan A, Nersisyan L, Avetisyan N, Martirosyan G. Evidence-Based Validation of Pyrin Structural Models. Protein Science 2012, 21 Special Issue, Suppl. 1: 196-196.
  33. Nersisyan L, Arakelyan A. In silico structure characterization of Familial Mediterranean fever gene product (pyrin). IPCBEE 2012; 29: 40-44. Abstract PDF
  34. Karalyan ZA, Djaghatspanyan NG, Hakobyan LH, Zakaryan HS, Abroyan LO, Arakelyan AA, Ter-Pogossyan ZR, Semerjyan ZB, Voskanyan HE, Karalova EM. Main biological determinants of Continuous Cell Lines elucidated by a principal component analysis. Caryologia: Int. J. of Cyt., Cytosys. Cytogen. 2011; 64 (3): 309-319. Abstract  PDF
  35. Karapetyan D, Arakelyan A, Nersisyan L, Aslanyan L, Boyajyan A. GOMESH: A tool for analyzing gene ontology data. Biol. J.  Armenia 2010, Suppl. 1(62): 41-43.

Conference proceedings

  1. Nersisyan L, Hakobyan A, Arakelyan A. Telomere-associated gene network in lung adenocarcinoma. European Respiratory Journal Sep 2015, 46 (suppl 59) doi: 10.1183/13993003.congress-2015.OA3493.
  2. Nersisyan L, Hakobyan A, Löffler-Wirth H, Binder Hans, Arakelyan A. Association of mean telomere length with biomolecular pathway deregulations in lung adenocarcinoma. F1000Research 2015, 4(ISCB Comm J):608 (poster) (doi: 10.7490/f1000research.1110351.1).
  3. Hakobyan A, Nersisyan L and Arakelyan A. Quantitative trait association study for mean telomere length in the South Asian Genomes. F1000Research 2015, 4(ISCB Comm J):605 (poster) (doi: 10.7490/f1000research.1110349.1).
  4. Nersisyan L, Lusine K, Hakobyan A et al. A systems view on mining common pathway deregulation profiles in autoimmunity, autoinflammation and inflammation. F1000Research 2015, 4(ISCB Comm J):604 (poster) (doi: 10.7490/f1000research.1110348.1).
  5. Nersisyan L, Wirth H, Gevorgyan A, Binder H, Arakelyan A. Methylation associated pathway activity deregulation in lung adenocarcinoma. Eur Respir J 2014; 44: Suppl. 58, 403. abstract
  6. Arakelyan A, Nersisyan L, Wirth H, Binder H. Mining common pathway deregulation profiles in lung diseases. Eur Respir J 2014; 44: Suppl. 58, 2021. abstract
  7. Arakelyan A., Aslanyan L., Boyajyan A. Gene expression data analytics. Proceedings of the IX International Conference “Computer Science and Information Technologies”, Yerevan, September 23-27, 2013, p.174-176.
  8. Arakelyan A., Aslanyan L, Boyajyan A. On knowledge-based gene expression data analysis. Extended papers of Proceedings of Computer Science and Information Technologies (CSIT), 2013; 1-6. abstract
  9. Nersisyan L, Arakelyan A. 3D structure prediction of pyrin-d2 isoform. 2nd International Conference “Postgenomic methods of analyses in biology, laboratory and clinical medicine: genomics, proteomics, bioinformatics” 2011 (p. 112), Novosibirsk, Russia.
  10. Arakelyan A, Boyajian A, Aslanyan L, Nersisyan L, Sahakyan H. Growing Support Sets For Pathway Specific Microarray Gene Expression Analysis. “8th International Conference on Computer Science and Information Technologies” 2011 (p.207-210), Yerevan, Armenia.

IMB Bioinformatics Group 2019