WHISE-Armenia: Chairman of the Board

Vahan Simonyan

Vahan Simonyan

Chief Scientist of Embleema

Dr. Vahan Simonyan is Chief Scientist of Embleema. He has expertise in biotechnology and biomedical informatics, previously serving at the FDA as a lead scientist of HIVE, R&D Director of Bioinformatics. Additionally, Dr. Simonyan is an adjunct professor at the George Washington University, where he teaches and develops curriculums for biomedical big data informatics and biostatistics research and development courses.

Dr Simonyan has a solid scientific background in varied academic disciplines: MS in Physical Organic Chemistry, Ph.D. in Quantum Physics and Mathematics, post-doctoral training in Nanotechnology and Quantum Statistical Thermodynamics. He is a prolific author of scientific publications in physics, chemistry, quantum chemistry, nanotechnology, biotechnology, population dynamics, and bioinformatics; and he is a recipient of multiple awards, and multimillion dollar grants for excellence in number of health informatics and biomedical informatics projects.

Dr Simonyan is a board member for several biotech companies, and advisor to national governments in digital healthcare. His accomplishments in academic and R&D technology carriers have been complemented with the success of technology leadership roles in government, academia and industry where he establishes large-scale and complex, science-heavy R&D infrastructures capable of serving worldwide communities for research and regulatory purposes.

Currently Dr. Simonyan leads large scale projects around health-IT and biomedical informatics. The subjects include but are not limited to:

  • large scale data archival, analytics in genomic, clinical, and real-world evidence domains
  • consulting in regulatory analytics in precision medicine
  • infrastructure support for registries on cancer, autoimmune diseases, rare diseases, robotics, wearable medical devices
  • standardization, harmonization and ontology development efforts for biomedical informatics and healthcare data standards
  • patient advocacy, data privacy and ownership
  • digital health policy consulting in national and international arena
  • R&D in artificial intelligence and modern bioinformatics approaches to support healthcare

Academics:

  • – Post.Doc. Nanotechnology at Chemical Engineering. University of Pittsburgh
  • – Ph.D. in Physics and Mathematics. Moscow State University. Major: Physical Chemistry
  • – MS in Chemistry. Moscow State University. Major: Physical-Organic Chemistry

Experience

  • – Founding member, President, Chief Scientific Officer of Wellness and Healthcare Information Secure Exchange (WHISE) platform Dec 2018 – present
  • -Senior Director of Bioinformatics CRISPR Therapeutics: Aug 2017 – Oct 2019
  • – Adjunct professor of bioinformatics and biostatistics at the George Washington University: Sep 2015 – present
  • -Principal investigator, director of R&D bioinformatics, HIVE lead scientists at the Food and Drug Administration/CBER: Mar 2011 – Aug 2018
  • -Scientific IT research and development, National Institutes of Health: Jan 2001 – Mar 2011
  • – Independent scientific consulting: May 2005 – Mar 2011
  • – Post-doctoral fellowship, Chemical Engineering, University of Pittsburgh: Dec 1998–Dec 2000

RELEVANT PUBLICATIONS

  1. Baseline human gut microbiota profile in healthy people and standard reporting template. King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R. PLoS One. 2019, PMID: 31509535
  2. Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues. Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS. BMC Med Genet. 2019, PMID: 31409279
  3. Development of an integrated platform using multidisciplinary real-world data to facilitate biomarker discovery for medical products. Dabic S, Azarbaijani Y, Karapetyan T, Loyo-Berrios N, Simonyan V, Kitchner T, Brilliant M, Torosyan Y, Clin Transl Sci. 2019, PMID: 31386280
  4. Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm. Bosma TJ, Karagiannis K, Santana-Quintero L, Ilyushina N, Zagorodnyaya T, Petrovskaya S, Laassri M, Donnelly RP, Rubin S, Simonyan V, Sauder CJ. PLoS One. 2019, PMID: 31100083
  5. Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PVN, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA, Kimchi-Sarfaty C. J Mol Biol. 2019, PMID: 31029701
  6. Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results, Gil Alterovitz, Dennis A Dean II, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King IV, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Konstantinos Krampis, Krista Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder, BioRxiv, 2018, PMID: 30596645
  7. A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence. Lypaczewski P, Hoshizaki J, Zhang WW, McCall LI, Torcivia-Rodriguez J, Simonyan V, Kaur A, Dewar K, Matlashewski G. Sci Rep. 2018, PMID: 30409989
  8. Sequence comparison of Francisella tularensis. LVS, LVS-G and LVS-R. Kurtz SL, Voskanian-Kordi A, Simonyan V, Elkins KL, Pathog Dis. 2018, PMID: 30137434
  9. Evolution of echovirus 11 in a chronically infected immunodeficient patient., Laassri M, Zagorodnyaya T, Hassin-Baer S, Handsher R, Sofer D, Weil M, Karagiannis K, Simonyan V, Chumaakov K, Shulman L., PLoS Pathog, 2018, PMID: 29554133
  10. Separation and assembly of deep sequencing data into discrete sub-population genomes. Karagiannis K, Simonyan V, Chumakov K, Mazumder R., Nucleic Acids Res. 2017 Nov, PMID: 28977510.
  11. A new and updated resource for codon usage tables. Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C., BMC Bioinformatics. 2017 Sep, PMID: 28865429
  12. Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization”. Sreenivas Gannavaram, John Torcivia, Lusine Gasparyan, Amit Kaul1, Nevien Ismail, Vahan Simonyan*, Hira L. Nakhasi*, Nature Sci. rep., June 2017, PMID: 28680050
  13. HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls. Simonyan V*, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A. Genomics. 2017 Feb 8, PMID: 28188908
  14. Bio-compute objects – a step towards validation of bio-medical scientific computations. Vahan Simonyan*, Jeremy Goecks, Raja Mazumder. PDA J Pharm Sci Technol. 2017 Mar-Apr. PMID: 27974626
  15. Distinct Patterns of Expression of Transcription Factors in Response to Interferonβ and Interferonλ1. Novatt H, Theisen TC, Massie T, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL. J Interferon Cytokine Res. 2016 Oct; PMID: 27447339
  16. High-performance Integrated Virtual Environment (HIVE): a robust infrastructure for Next-Generation Sequence Data Analysis. Vahan Simonyan*, Konstantin Chumakov, Hayley Dingerdissen, William Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan, Alexey Pschenichnov, Alexandre Rostovtsev, Luis Santana-Quintero Krista Smith, Elaine E. Thompson, Valery Tkachenko, John Torcivia-Rodriguez, Alin Voskanian, Quan Wan, Jing Wang, Tsung-Jung Wu, Carolyn Wilson, Raja Mazumder. Database (Oxford). 2016 Mar 17; PMID: 26989153
  17. Challenges, solutions, and quality metrics of personal genome assembly in advancing precision medicine. Wenming Xiao*, Leihong Wu, Gokhan Yavas, Chunlin Xiao, Vahan Simonyan and Huixiao Hong. Pharmaceutics. 2016 Apr 22, PMID: 27110816
  18. Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Mee ET, Preston MD, Minor PD, Schepelmann S; Simonyan V as CS533 Study Participant. Vaccine. 2016 Apr 12; PMID: 26709640
  19. Pubcast and Genecast: Browsing and exploring publications and associated curated con-tent in biology through mobile devices. Goldweber S, Theodore J, John Torcivia-Rodriguez J, Simonyan V, Mazumder R. IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar 23. PMID: 27019500
  20. Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication. Christian J. Sauder1*, Vahan Simonyan2, Laurie Ngo1, Konstantinos Karagiannis, Yu Cong, Cheryl Zhang, Rong Wang,Wells W. Wu, Tahir Malik, Steven A. Rubin. Virology, Jun 2016. PMID: 27058764
  21. Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses Majid L, Zagorodnyaya T, Plant EP, Petrovskaya S, Bidzhieva B, Ye Z, Simonyan V, Chumakov K. PLoS One. 2015 Sep 25;10(9):e0138650. PMID: 26407068.
  22. Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal. Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T and Rubin SA. Virus Genes. 2015 Aug; 51(1):12-24. PMID: 25962759.
  23. Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing. Zhang W, Soika V, Meehan J, Su Z, Ge W, Ng HW, Perkins R, Simonyan V, Tong W, Hong H. Pharmacogenomics J. 2015 Aug;15(4):298-309. PMID: 25384574
  24. FDA’s Activities Supporting Regulatory Application of “Next Gen” Sequencing Technologies. Wilson CA and Simonyan V*. PDA J Pharm Sci Technol. 2014 Nov-Dec; PMID: 25475637.
  25. Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. Kumari P, Mazumder R, Simonyan V and Krampis K. [v1; ref status: published, http://f1000r.es/4yw] F1000Research 2015, 4:20 . doi: 10.12688/f1000research.6016.1.
  26. High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Vahan Simonyan* and Raja Mazumder, Genes 2014, 5(4), 957-981; PMID: 25271953
  27. Census-based rapid and accurate metagenome taxonomic profiling. Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. BMC Genomics, 2014 Oct 21;15(1):918. PMID:25336203.
  28. Human germline and pan-cancer variomes and their distinct functional profiles. Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V and Mazumder R. Nucleic Acids Research, 2014 Sep 17. PMID:25232094.
  29. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R. Genomics. 2014 June 12. PMID: 24930720.
  30. HIVE-hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis. Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R and Simonyan V*. PLOS One. 2014 June 11; 9(6). PMID: 24918764.
  31. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R. Biol Direct. 2014 June 03. PMID: 24894379.
  32. Deep sequencing approach for genetic stability evaluation of influenza A viruses. Bidzhieva B, Zagorodnyaya T, Karagiannis K, Simonyan V, Laassri M, Chumakov K. J Virol Methods. 2014 Apr;199:68-75. PMID: 24406624.
  33. Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based variation detection. Abunimer A, Smith K, Wu T-J, Lam P, Simonyan V, Mazumder R. Genes. 2014. PMID:24705329.
  34. A framework for organizing cancer related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Wu T-J, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V and Mazumder R. Database. 2014. PMID: 24667251.
  35. Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050. Dabrazhynetskaya A, Soika V, Volokhov D, Simonyan V, Chizhikov V. Genome Genome Announc. 2014 Mar 6;2(2). pii: e00127-14. PMID: 24604646.
  36. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. Cole C, Krampis K, Karagiannis K, Almeida J, Faison JW, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R. BMC Bioinformatics. 2014 Jan 27;15:28. PMID:24467687.
  37. Community annotation and the evolution of cooperation: How patience matters. Basuchoudhary A, Simonyan V, Mazumder R. Open Bioinformatics Journal. 2013 7:9-18.
  38. SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. Karagiannis K, Simonyan V, Mazumder R. Genomics Proteomics Bioinformatics. 2013 Apr;11(2):122-6. PMID:23618375.
  39. Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R. Genomics Proteomics Bioinformatics. 2013 Apr;11(2):96-104. PMID: 23459159.
  40. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins. Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R. FEBS J. 2013 Mar;280(6):1542-62. PMID: 23350563.
  41. Why Don’t Biologists Contribute to Databases? Biocuration2012, Proceedings of 5th International Biocuration Conference. Basuchoudhary Atin, Vahan Simonyan, Raja Mazumder. Washington DC. April 2-4, 2012.
  42. Community annotation and the evolution of cooperation: How patience matters Basuchoudhary A, Simonyan V, Mazumder R.. Open Bioinformatics Journal. 2013 7:9-18.
  43. Storage and biocuration of extra-large (XL) data sets from next-generation sequencing technologies. Satti Priyankeswari, Simonyan Vahan, Raja Mazumder. Biocuration2012, 5th International Biocuration Conference. Washington DC. April 2-4, 2012.
  44. N-glycans in liver-secreted and immunoglogulin-derived protein fractions. Bekesova S, Kosti O, Chandler KB, Wu J, Madej HL, Brown KC, Simonyan V, Goldman R. J Proteomics. 2012 Apr 3;75(7):2216-24. doi: 10.1016/j.jprot.2012.01.024. Epub 2012 Feb 3. PMID: 22326963
  45. High-performance Integrated virtual environment clouds (HIVE) for extra-large (XL) data analysis. Comparative sequence, genome analysis, genome assembly, & genome scale computational methods session. Vahan Simonyan and Raja Mazumder. The proceedings of 2011 International Conference on Bioinformatics and Computational Biology. Las Vegas, Nevada. July 17-21, 2011.
  46. Loss or gain of functional amino acid motifs due to nsSNPs in the human genome. Konstantinos Karagiannis, Vahan Simonyan, Radoslav Goldman, Raja Mazumder. Beyond Genome 2011. September 22, 2011.
  47. RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae. Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE. Mol Phylogenet Evol. 2012 Jan;62(1):515-28. Epub 2011 Nov 17.
  48. PubChem3D: a new resource for scientists; Evan E Bolton, Vahan Simonyan, et al.; Journal of Cheminformatics; 2011; 3: 32.
  49. CDD: a Conserved Domain Database for protein classification; Marchler-Bauer A, Simonyan V, et al.; Nucleic Acids Res. 2005 Jan 1;33:D192-6.
  50. MMDB: Entrez’s 3D-structure database. Chen J, Simonyan V, et al.; Nucleic Acids Res. 2003 Jan 1;31(1):474-7.
  51. CDD: a curated Entrez database of conserved domain alignments. Marchler-Bauer A, Simonyan V, et al.; Nucleic Acids Res. 2003 Jan 1;31(1):383-7.

BOARD

Vahan Simonyan
Vahan Simonyan

Chairman of the Board

Gagik Bazikyan

Board member

Karen Meliksetyan

Board member

Tsaghkanush Sargsyan

Board member

Davit Babikyan

Board member