BigData@CityTech

Since 2017 I am the program director of the Big Data to Biomedical Informatics (BD2BMI) at CityTech. BD2BMI offers year-long educational and research training opportunities to students enrolled in the Biomedical Informatics baccalaureate program (BIB) of CityTech CUNY, in a mission to prepare the next generation of innovators and visionaries in the field of biomedical Big Data science.

This is a NIH-funded program in collaboration with Weill Cornell Medicine.

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BIO

I am an Assistant Professor at the Biological Sciences Department in the New York City College of Technology (CityTech), of the City University of New York (CUNY). I work in the areas of computational biology and bioinformatics. I have experience in the analysis of a wide range of –omics data (genomics, epigenomics, proteomics). I design and develop software tools for the analysis of next-generation sequencing data. 

I hold a joint appointment as Adjunct Assistant Research Scientist at the David Z. Rosensweig Genomics Research Center in the Hospital for Special Surgery, where I am involved in high-throughput data analysis and biologically-driven projects related to rheumatoid arthritis (RA) and other autoimmune and inflammatory diseases.



Education

Ph.D., Computer Science - Bioinformatics, 2009
Department of Computer Science and Technology, University of Peloponnese
Biomedical Research Foundation of the Academy of Athens
Dissertation Thesis: "Integration and Visualization of Proteomics Data"
 
BSc, Computer Science, 2004
Department of Computer Science, Athens University of Economics and Business
Undergraduate Thesis: "Data mining techniques for antibiotic resistance surveillance"



Professional Appointments

Assistant Professor (2014 - current)
Biological Sciences Department
New York City College of Technology (CityTech)
City University of New York

Assistant Research Scientist (2014 - current)
David Z. Rosensweig Genomics Research Center
Hospital for Special Surgery

Assistant Computational Genomics Scientist (2013 - 2014)
Department of Physiology and Biophysics, Applied Bioinformatics Core
Weill Cornell Medicine

Postdoctoral associate (2009 - 2013)
Institute for Computational Biomedicine  (Elemento lab)
Weill Cornell Medicine

Research Associate (2005 - 2009)
Virtual Reality & Human-Computer Interaction Lab
University of Peloponnese, Greece

Research Associate (2005 - 2009)
Bioinformatics & Medical Informatics Group
Biomedical Research Foundation, Academy of Athens (BRFAA), Greece

Research Associate (2005)
Data and Web Mining Team (DB-NET)
Athens University of Economics and Business, Greece



Grants and Awards

NIH R01 (Collaborator) (2018-2022)
Project: A novel role of proteolytic pathway in osteoclastogenesis and arthritic bone resorption.

NIH R25 Big Data to Knowledge (BD2K) Enhancing Diversity in Biomedical Data (PI) (2017-2021)
Project: City Tech-WCM Big Data Training Program in Biomedical Informatics.

Professional Development Advisory Council (PDAC) Travel Award (Nov. 2017)

GRTI 19 (Graduate Research and Technology Initiative) grant, 19 (Jan. 2017)
Project: Enhancement of computational facilities of the Center for Theoretical Physics for multidisciplinary research.

PSC-CUNY Research Award - Cycle 47 (Apr. 2016)

Materials Research Society Foundation Grassroots 2016 (Mar. 2016)
Project: What materials do for our world? Increasing awareness of materials science among traditionally underrepresented minority college and school students, and school teachers at New York City.

Professional Development Advisory Council (PDAC) Travel Award (Feb. 2015)

GRTI 17 (Graduate Research and Technology Initiative) grant, 17 (Dec. 2014)
Project: Computer Cluster for Big Data Bioinformatics Analyses

Lorraine Beitler Student Endowment Fund (Oct. 2014)
Project: Biomedical Informatics student conference at City Tech (BIBCON 2015)

TEACHING

  • BIO 4050 - Biomedical Informatics Colloquium
    A seminar-based course that exposes students to current research topics in the fields of Bioinformatics and Medical Informatics. Weekly presentations by invited speakers and/or faculty introduce students to the broad diversity of research areas in both fields, and engages them in critical thinking and writing. Online lectures and reading activities will also be given periodically.
  • BIO 2000 - Introduction to Biomedical Informatics 
    An introduction to the field of Biomedical Informatics for prospective majors. The course explores the application of computation in the biomedical sciences and in healthcare and provides an overview of the two components of the field, bioinformatics and medical informatics, their respective histories, technologies and methodologies. The course also illuminates the ways these two components come together in cutting edge applications in healthcare such as precision medicine. Exposure to these two subfields should provide students with the ability to choose which track to pursue in the major.
  • BIO 3352 - Bioinformatics II 
    This course is a continuation of Bioinformatics I. Topics include gene expression, microarrays, next- generation sequencing methods, RNA-seq, large genomic projects, protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; and protein-nucleic acid interactions. The lab component includes R-based statistical data analysis on large datasets, introduction to big data analysis tools, protein visualization software, internet-based tools and high-level programming languages.
  • BIO 3354 - Computational Genomic 
    Covers selected advanced topics in computational genomics. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods.
  • PHIL 2203ID - Health Care Ethics
    Invited lecture "Ethical Perspectives on Personal Genomics"
  • BIO 3601 - Biochemistry
    Invited lab "Introduction to the UCSC Genome Browser"
  • Statistical Methods for Functional Genomics: CSHL Summer school 2014
    Working with massive parallel sequencing data (lab)
    Analyzing ChIP-seq data (lab)
  • Statistical Analysis of Genome Scale Data: CSHL Summer school 2012
    Tutorial on high-throughput sequencing (lab)
    Tutorial on ChIP-seq analysis (lab)
    Overview of ENCODE data resources (lecture)
  • Statistical Analysis of Genomic Data: CSHL Summer school 2011
    Basics of high-throughput sequencing (lab)
    ChIP-seq analysis (lab)

PUBLICATIONS


2019

Kusnadi A, Park SH, Yuan R, Pannellini T, Giannopoulou E, Oliver D, Lu T,  Park-Min K, Ivashkiv LB. TNF promotes SREBP activity and binding to inflammatory target genes to regulate macrophage polarization and tissue repair. Submitted.

Donlin LT, Park SH, Giannopoulou E, Park S, Ivovic A, Park-Min KH,  Siegel RM, Ivashkiv L. Insights into rheumatic diseases from next-generation sequencing. Nat. Rev. Rheumatol. 2019 Apr 18.

2018

Inoue K, Deng Z, Chen Y, Giannopoulou E, Xu R, Gong S, Greenblatt MB, Mangala LS, Lopez-Berestein G, Kirsch DG, Sood AK, Zhao L, Zhao B. Bone protection by inhibition of microRNA-182. Nat Commun. 2018 Oct 5;9(1):4108.

2017

Park SH, Kang K, Giannopoulou E, Qiao Y, Kang K, Kim G, Park-Min KH, Ivashkiv  LB. Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation. Nat Immunol. 2017 Oct;18(10):1104-1116.

Kang K, Park SH, Chen J, Qiao Y, Giannopoulou E, Berg K, Hanidu A, Li J, Nabozny G, Kang K, Park-Min KH, Ivashkiv LB. Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF. Immunity. 2017 Aug 15;47(2):235-250.

Murata K, Fang C, Terao C, Giannopoulou EG, Lee YJ, Lee MJ, Mun SH, Bae S, Qiao Y, Yuan R, Furu M, Ito H, Ohmura K, Matsuda S, Mimori T, Matsuda F, Park-Min KH, Ivashkiv LB. Hypoxia-Sensitive COMMD1 Integrates Signaling and Cellular Metabolism in Human Macrophages and Suppresses Osteoclastogenesis. Immunity. 2017 Jul 18;47(1):66-79.

Loupasakis K, Kuo D, Sokhi UK, Sohn C, Syracuse D, Giannopoulou EG, Park S, Kang H, Rätsch G, Ivashkiv LB, Kalliolias GD. Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes. PLoS One. 2017 Jul 14;12(7).

Giannopoulou E, Elemento O. Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets. Methods Mol Biol. 2017;1507:43-58. 

Bae S, Lee MJ, Mun SH, Giannopoulou EG, Yong-Gonzalez V, Cross JR, Murata K, Giguère V, van der Meulen M, Park-Min KH. MYC-dependent oxidative metabolism regulates osteoclastogenesis via nuclear receptor ERRα. J Clin Invest. 2017 May 22. 

2016

Liu Y, Giannopoulou E, Falciatori I, Allis CD, Elemento O, Seandel M, Rafii S: Epigenetic Profiles Signify Cell Fate Plasticity in Unipotent Spermatogonial Stem and Progenitor Cells. Nature Communications 2016 Apr 27;7:11275. 

Chandrasekaran U, Yi W, Gupta S, Weng C, Giannopoulou E, Chinenov Y, Jessberger R, Weaver C, Bhagat G, Pernis AB: Regulation of effector Tregs in murine lupus. Arthritis Rheumatol. 2016 Jan 27. 

Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F: Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Feb 8. 

2015

Yun J, Mullarky E, Lu C, Bosch KN, Kavalier A, Rivera K, Roper J, Chio II, Giannopoulou E, Rago C, Muley A, Asara JM, Paik J, Elemento O, Chen Z, Pappin DJ, Dow LE, Papadopoulos N, Gross SS, Cantley LC: Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH. Science. 2015 Dec 11. 

Giannopoulou EG, Elemento O, Ivashkiv L: Use of RNA-seq to evaluate rheumatic disease patients. Arthritis Res Ther. 2015 Jul 1;17:167. 
 
Su X, Yu Y, Giannopoulou EG, Hu X, Rice CM, Ivashkiv LB: IFN-γ Regulates mTORC1, Cellular Metabolism and mRNA Translation to Potentiate Inflammatory Macrophage Activation. Nature Immunology 2015. 

Subtil-Rodríguez A, Ceballos-Chávez M, Giannopoulou E, Soronellas D, Elemento O, Beato M, Reyes JC: The chromatin remodeler CHD8 is involved in activation of progesterone receptor-dependent enhancers. PLoS Genet. 2015 Apr 20;11(4). 

2014

Park-Min KH, Lim E, Lee MJ, Park SH, Giannopoulou E, Yarilina A, van der Meulen M, Zhao B, Smithers N, Witherington J, Lee K, Tak PP, Prinjha RK, Ivashkiv LB: Inhibition of Osteoclastogenesis and Inflammatory Bone Resorption by Targeting BET Proteins and Epigenetic Regulation. Nature Communications 2014.

Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM,
Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA: The Estrogen receptor alpha regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nature Communications 2014. 

Li S, Miller CH, Giannopoulou EG, Hu X, Ivashkiv LB and Zhao B: RBP-J imposes a requirement for ITAM-mediated costimulation of osteoclastogenesis. J Clin Invest. 2014. 

Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC et al: Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome Through Global and Focal Changes in H3K36 and H3K27 Methylation. Plos Genetics 2014. 

Donlin LT, Jayatilleke A, Giannopoulou EG, Kalliolias GD, Ivashkiv LB: Modulation of TNF-Induced Macrophage Polarization by Synovial Fibroblasts. The Journal of Immunology 2014. 

Walker S, Liu S, Xiang M, Nicolais M, Hatzi K, Giannopoulou EG, Elemento O, Cerchietti L, Melnick A, Frank D: The transcriptional modulator BCL6 as a molecular target for breast cancer therapy. Oncogene 2014. 

2013

Chang C-Y, Pasolli HA, Giannopoulou EG, Guasch G, Gronostajski RM, Elemento O, Fuchs E: NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche. Nature 2013. 

Giannopoulou EG, Elemento O: Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Research 2013, 23(8):1295-1306. 

Qiao Y, Giannopoulou EG, Chan CH, Park S-h, Gong S, Chen J, Hu X, Elemento O, Ivashkiv LB: Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and Toll-like receptor signaling. Immunity 2013, 39(3):454-469. 

Qiao Y, Giannopoulou EG, Elemento O, Ivashkiv L: Priming of regulatory DNA elements activates inflammatory cytokine genes synergistically with TLR signaling to increase transcription (P1230). The Journal of Immunology 2013, 190:138.113. 

Lin P-C, Giannopoulou EG, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA, Elemento O: Epigenomic alterations in localized and advanced prostate cancer. Neoplasia 2013, 15(4):373-IN375. 

Lin P-C, Chiu Y-L, Banerjee S, Park K, Mosquera JM, Giannopoulou EG, Alves P, Tewari AK, Gerstein MB, Beltran H: Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. Cancer research 2013, 73(3):1232-1244. 

Hatzi K, Jiang Y, Huang C, Garrett-Bakelman F, Gearhart MD, Giannopoulou EG, Zumbo P, Kirouac K, Bhaskara S, Polo JM: A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell reports 2013, 4(3):578-588. 

Delehouzé C, Godl K, Loaëc N, Bruyère C, Desban N, Oumata N, Galons H, Roumeliotis T, Giannopoulou EG, Grenet J: CDK/CK1 inhibitors roscovitine and CR8 downregulate amplified MYCN in neuroblastoma cells. Oncogene 2013. 

Roumeliotis TI, Halabalaki M, Alexi X, Ankrett D, Giannopoulou EG, Skaltsounis A-L, Sayan BS, Alexis MN, Townsend PA, Garbis SD: Pharmacoproteomic study of the natural product Ebenfuran III in DU-145 prostate cancer cells: The quantitative and temporal interrogation of chemically induced cell death at the protein level. Journal of proteome research 2013, 12(4):1591-1603. 

2007-2012

Giannopoulou EG, Lepouras G, Manolakos ES: Visualizing Meta-Features in Proteomic Maps. BMC Bioinformatics 2011, 12(1):308.

Giannopoulou EG, Elemento O: An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics2011, 12(1):277. 

Giannopoulou EG, Garbis SD, Vlahou A, Kossida S, Lepouras G, Manolakos ES: Proteomic feature maps: a new visualization approach in proteomics analysis. Journal of biomedical informatics 2009, 42(4):644-653.

Ventoura S, Giannopoulou EG, Manolakos ES: ProtCV: A Tool for Extracting, Visualizing and Validating Protein Clusters Using Mass Spectra Peak-Lists. In: Computer-Based Medical Systems, 2008 CBMS'08 21st IEEE International Symposium on: 2008: IEEE; 2008: 221-223.

Halabalaki M, Roumeliotis I, Giannopoulou E, Alexi X, Meijer L, Alexis M, Skaltsounis A, Garbis D: Pharmacoproteomic and toxicoproteomic study of the natural product Ebenfuran III in DU-145 prostate cancer cells using iTRAQ with 2D LC and tandem mass spectrometry. Planta Medica 2008, 74(09):SL40.

Golemati M, Katifori A, Giannopoulou EG, Daradimos I, Vassilakis C, Lepouras G, Halatsis C: An Interview-Based User Study on the use of Visualizations for Folder Browsing. In: Information Visualisation, 2008 IV'08 12th International Conference: 2008: IEEE; 2008: 106-112.

Giannopoulou EG, Lepouras G, Manolakos ES: VIP: Visualization of integrated proteomics data. In: BioInformatics and BioEngineering, 2008 BIBE 2008 8th IEEE International Conference on: 2008: IEEE; 2008: 1-8.

Giannopoulou EG, Kossida S: Data Mining Applications in the Post-Genomic Era: Data Mining in Medical and Biological Research; 2008. Book chapter.

Garbis SD, Tyritzis SI, Roumeliotis T, Zerefos P, Giannopoulou EG, Vlahou A, Kossida S, Diaz J, Vourekas S, Tamvakopoulos C: Search for potential markers for prostate cancer diagnosis, prognosis and treatment in clinical tissue specimens using amine-specific isobaric tagging (iTRAQ) with two-dimensional liquid chromatography and tandem mass spectrometry. The Journal of Proteome Research 2008, 7(8):3146-3158.

Katifori A, Halatsis C, Lepouras G, Vassilakis C, Giannopoulou E: Ontology visualization methods—a survey. ACM Computing Surveys (CSUR) 2007, 39(4):10. 

Golemati M, Katifori A, Giannopoulou EG, Daradimos I, Vassilakis C: Evaluating the Significance of the Windows Explorer Visualization in Personal Information Management Browsing tasks. In: IV: 2007; 2007: 93-100.

Giannopoulou EG, Kemerlis VP, Polemis M, Papaparaskevas J, Vatopoulos AC, Vazirgiannis M: A Large Scale Data Mining Approach to Antibiotic Resistance Surveillance. In: Computer-Based Medical Systems, 2007 CBMS'07 Twentieth IEEE International Symposium on: 2007: IEEE; 2007: 439-444.



TEAM

2017-2019 

2019
(Students mentored and sponsored through the BigData grant)
Mark Urbina - Project TBD
Kanta Haque - Project TBD
Brittany Taylor - Project TBD
Penina Gavrilova - Project TBD
Eric Park - Project TBD
Shaina Raklyar - Project TBD
Mohammed Rahaman - Project TBD
Rosemary Pichardo - Project TBD
2018
(Students mentored and sponsored through the BigData grant)
Ashleigh Leger - Clinical Text Processing (PI: Stephen Johnson)
John Michael Meddar - NYC-CDRN Social Determinants Research Project (PI: Jyotishman Pathak)
Princesca Dorsaint - Enhancing tumor board sessions with artificial inteligence  (PI: Olivier Elemento)
Shazeda Omar - Comparing protocols in DNA methylation analysis (PI: Doron Betel)
Tameshwar Tirlokhi - Social determinants of health in NYC (PI: Jessica Ancker)
Yonaka Harris  - A survey of clinicians' perception towards Antidepressant Pharmacogenomics testing (PI: Yiye Zhang)
Larisa Slizewski - Comparing Standard Terminologies in Clinical Research Data (PI: Jyotishman Pathak)
Ameni Alsaydi - An evaluation of QC processors FASTQC, FASTP, FASTX-Toolkit and Development of software pipeline for QC processing (PI: Doron Betel)
2017
Jazmin Castillo - Student intern, "R-shiny platform for genomics data analysis and visualization" (Summer 2017)
Dhavin Singh - Student intern/Emerging scholar CityTech, "Study of bioinformatics tools for the analysis of DNA methylation data" (Spring 2017)
Dulce Morataya - Noyce student intern Teaching Assistant, Bioinformatics (Fall 2015-Spring 2017)
Wylie Chen - Student intern, "Extension of RNA-Seq pipeline by adding gene sets analysis" (Spring 2017)

2016
Victor O. Adedara and Kabir D. Omolaja - Noyce student interns, "Effective Ways of Teaching Bioinformatics to Undergraduates" (Fall 2016)
Varuni Persaud - Student intern, "Exploring ATAC-seq peak calling options using HOMER" (Fall 2016)
Sajaad Abedian - Student intern, "Integrated platform for pathways analysis and gene networks visualization (Fall 2016) 
Hyelim Kang - Student intern, "Automatic generation of UCSC Genome Browser track hubs" (Summer-Fall 2016)
Taheefa Stephen - LSAMP Program, Undergraduate student (Biomedical Informatics) "Cancer Genomics" (Fall 2015-Spring 2016)
2015
Binita Giri - Undergraduate student (CUNY BA, Bioinformatics) "Bioinformatics for Personal Genomics" (Fall 2015)
Anwar Uddin - Emerging scholar CityTech, "Visualization Methods of Personal Genomics" (Spring 2015)
Janatul Mawa - Emerging scholar CityTech, "Building a repository of epigenomic signatures for autoimmune rheumatic diseases" (Spring 2015)
Abzal Bacchus - Undergraduate student (Biomedical Informatics), "Building a repository of epigenomic signatures for autoimmune rheumatic diseases" (Spring 2015)
2014
Faizan Malik - Emerging scholar CityTech, "Building a repository of epigenomic signatures for autoimmune rheumatic diseases", (Fall 2014)
Manhin Lam - Undergraduate student (Biomedical Informatics), "Microarray data analysis in R" (Spring 2014)

CONTACT



A502B - Academic Complex

285 Jay st, Brooklyn, NY, 11201