CV

Appointments (professional)

• Senior Bioinformatics Research Scientist Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN. April 2024 – current.
• Bioinformatics Scientist III Center for Data Driven Discovery in Biomedicine at Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA. April 2023 – March 2024.

Appointments (academic)

• Postdoctoral fellow (Dr. Iannis Aifantis and Dr. Aristotelis Tsirigos) Perlmutter Cancer Center, Department of Pathology, Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY. March 2022 – April 2023.
• Postdoctoral fellow (Dr. Sudhir Kumar) Temple University, iGEM, Philadelphia, PA. November 2018 – March 2022.

Education

• PhD Biological Sciences, University of the Aegean, Greece. Designated Emphasis in Phylogenomics and Phylogeography (Prof. Theodora Petanidou). Dissertation: Spatial patterns of genetic diversity of the genus Eumerus (Diptera: Syrphidae) in the Balkans. February 2018.
• MSc Conservation Biodiversity, University of Montpellier II, France and University of the Aegean, Greece. September 2012.
• BSc Biochemistry and Biotechnology, University of Thessaly, Greece. April 2010.

Editorial boards

• 2020 – 2022. Associate Editor-In-Chief in Postdoctoral Editors Association (PEA), Biomedical Postdoctoral Council, University of Pennsylvania. https://www.med.upenn.edu/bpc/free-editing.html.

Review boards

• 2020 – present. Member, Review committee in Genes (MDPI).
• 2019 – present. Member, Review committee in Insects (MDPI).
• 2016 - present. Peer review: Peer review: BMC Evolutionary Biology, Geobios (Elsevier); MEEGID (Infection, Genetics and Evolution); MDPI (Water, Insects, Horticulturae, Diversity, Genes); Bulletin of Entomological Research; Zoology in the Middle East. https://orcid.org/0000-0003-3655-8252
• 2020 - present. Contribution in other publications as a reviewer (as mentioned in the acknowledgements).
  • Kumar, S., Tao, Q., Weaver, S., Sanderford, M., Caraballo-Ortiz, M.A., Sharma, S., Pond, S.L. and Miura, S. (2021) An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Molecular Biology and Evolution, 38(8), 3046–3059. https://doi.org/10.1093/molbev/msab118
  • Tao, Q., Barba-Montoya, J., Huuki, L.A., Durnan, M.K., Kumar, S. (2020) Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics. Molecular Biology and Evolution, 37(6), 1819–1831. https://doi.org/10.1093/molbev/msaa049
  • Miura, S., Vu, T., Deng, J., Buturla, T., Olumide, O., Choi, J., and Kumar, S. (2020) Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data. Scientific Reports (Nature Publisher Group), 10(1). https://doi.org/10.1038/s41598-020-59006-2
• 2019 – 2022. Associate Faculty Member for F1000Prime.

Teaching experience

• January – April 2019. Coordinator, Classic Papers in Molecular Phylogenetics (spring semester). Temple University, Philadelphia, PA.
• May – September 2019. Coordinator, Lab journal (summer semester). Temple University, Philadelphia, PA.
• February 2020. Guest lecturer, BIO 3112/5112 Evolutionary Genomic Medicine. “DNA sequencing: past, present and future” lecture. Temple University, Philadelphia, PA.
• June – August 2021. Mentor of a high school student. Science Preparatory Research Opportunities for Underrepresented Teens (SPROUT) Committee. Temple University, Philadelphia, PA.

Research experience

• Aifantis Lab (https://aifantislab.com/) and Tsirigos Lab (http://www.tsirigos.com/), Department of Pathology, Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY. March 2022 – April 2023.
  • Computational approaches to analyze leukemia transcriptomes and epigenomes at the single cell level.
• Kumar Lab (https://www.kumarlab.net/), Temple University, iGEM, Philadelphia, PA. November 2018 – March 2022.
  • Data analysis of large cohorts of simulated and clinical data of patients with metastatic cancer
  • Method and computational tools development for inferring the origin and trajectories of cancer cells between tumors in a cancer patient
  • Method development for estimating evolutionary rates (dN/dS)
  • Mentoring students (> 20)
• Petanidou Lab, Laboratory of Biogeography and Ecology, Department of Geography, University of the Aegean, Greece. June 2011 – February 2018.
  • Writing of papers and projects/ fellowships
  • Mentoring students and supervising exams
  • Fieldwork: Sampling of insect – pollinators and plants combined with electromagnetic radiation measurements
  • Participation in processing and managing of insect and plant material as well as the database
  • Taxonomic identification of insects
• Vujic and Djan Lab, Laboratory of Genetics, Department of Biology and Ecology, University of Novi Sad, Serbia. June 2013 – May 2017.
  • Laboratory (DNA sequencing) and phylogenetic analyses
• Gasperi & Malacrida Lab, University of Pavia (Faculty of Sciences MMFFNN), Department of Animal Biology, Italy. March – July 2009.
  • Laboratory analyses for Diploma thesis: «Molecular sexing in the olive fruit fly, Bactrocera oleae»

Professional experience

• Administration assistant, Project Thales (co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)), “THE POLLINATORS OF THE AEGEAN ARCHIPELAGO: DIVERSITY AND THREATS (POL-AEGIS)”. March 2012 – November 2015.
  • Liaison between a PI and the Research Unit of the University of the Aegean (Greece). During that position, I built partnerships with the university and the Hellenic Ministry of Education and Religious Affairs.
  • Contracts and vacancies announcements for collaborators (paperwork and interviews), payments of collaborators and expenses, direct labor and project’s reports and budget; organization and conduct of the annual project meetings & workshops; and research, transaction and purchase for lab supplies
  • Contact with collaborators (>50, >18 foreigners)
  • Organization and conduct of the annual project meetings & workshops
  • Research, transaction and purchase for lab supplies
  • Lab manager
• Scientific laboratory technician (internship). June – August 2006. Laboratory of Blood Tests and Biochemical Analysis, General Hospital of Mytilene «Vostaneio», Lesvos, Greece

Fellowships and awards

• March – July 2009. Erasmus+ Programme/International Credit Mobility. University of Pavia, Italy.
• September 2010 – January 2011. Erasmus+ Programme/International Credit Mobility. University of Montpellier II, France.
• June – July 2013. Project ExpeER (financed by the European community’s Seventh Framework programme (FP2007-2013) under grant agreement no. 262060 (ExpeER)), “Ecosystem Research”. Project title: “GeNetic status Of EumeruS: conservatIon implications (GNOSIS)”. University of Novi Sad, Serbia.
• June – November 2014. PhD Fellowship Research – State Scholarships Foundation (Greece), “Mobility program scholarship for training in short time (‘short terms’) to qualified scientific / research centers. University of Novi Sad, Serbia.
• February – May 2017. Erasmus+ Programme/International Credit Mobility. University of Novi Sad, Serbia.
• July 2020. Young Investigator Award (conference canceled due to COVID-19 crisis). Annual meeting of Society for Molecular Biology and Evolution (SMBE), Québec City, Canada.
• June – August 2021. Frances Velay Fellowship Program (Undergraduate Research: Maansi Suvarna). Temple University, Philadelphia, PA.

Outreach and leadership

• Advocacy & Outreach Officer and Postdoc ambassador at Temple University Postdoctoral association (TUPA). 2020 – present.
  • TUPA aims to support all postdocs at Temple on a career, social and cultural level. I am currently involved to employ inclusivity and equality for Temple’s postdocs, and to foster relationships with PIs for developing social and networking opportunities.

Memberships in scientific organizations

• (2019) Society for Molecular Biology and Evolution
• (2021) American Association for Cancer Research (AACR)
• (2021) AACR Cancer Evolution group
• (2022) American Society of Hematology (ASH)

Conferences and organized symposia

• ZJ of the First Annual Temple Postdoc Symposium (virtual), Temple University, Philadelphia, US. 2021.
• Lead organizer of the symposium “Evolutionary and Ecological Perspectives in Cancer Biology” (06/28-07/2/20) (conference canceled due to COVID-19 crisis) Annual meeting of Society for Molecular Biology and Evolution (SMBE), Québec City, Canada. 2020.