Skills

R

Statistics

Genomics

Experience

 
 
 
 
 

Doctoral Research

The Ohio State University - College of Pharmacy

June 2016 – Present Ohio, USA

Conducting genome-wide association studies (GWAS) to determine the independent and joint effects of recipient and donor genetic variation associated with survival after HLA-matched unrelated donor Hematopoietic Stem Cell Transplantation (HSCT) in leukemia patients.

Responsibilities include:

  • Constructing Cox proportional hazard and competing risk models to test associations with clinical events.
  • Determining interactions between genetic variants and agents used during treatment.
  • Further evaluation of specific risk groups by stratification of clinical variables.
 
 
 
 
 

Master Thesis Research

Roswell Park Cancer Institute

June 2014 – September 2015 NY, USA

Understanding the transcriptomic control of Retinoic Acid Receptors and LSD1 in prostate cancer to explore their potential as drug targets for prostate cancer treatment

Responsibilities include:

  • Differential gene expression analyses on publicly available prostate cancer datasets (TCGA) and on RNA-sequencing datasets obtained from human prostate cell line LNCaP-C42 under different gene knock-down conditions and drug treatments.
  • Dose response experiments with commercially available prostate cancer cell lines while targeting RAR-gamma, LSD1 or both.
 
 
 
 
 

Student Assistant

Luxembourg Centre for Systems Biomedicine

April 2014 – August 2014 Esch-sur-Alzette, Luxembourg
Worked at the Metabolomics Department in Dr. Karsten Hiller’s lab as a student technician for various projects

Certificates

Computational Genomics Winter Institute

Advanced Gene Mapping Course

Analysis of NGS Data for Complex Traits Course

Advanced Graduate Certificate in Applied Biostatistics

Publications

  1. Tang H, Hahn TE, Karaesmen E, Rizvi AA, Wang J, Paczesny S, Wang T, Preus L, Zhu Q, Haiman CA, Stram D, Pooler L, Sheng X, Van Den Berg D, Brock G, Webb A, Pasquini MC, McCarthy PL, Spellman SR, Sucheston-Campbell LE. Validation of genetic associations with acute GVHD and non-relapse mortality in DISCOVeRY-BMT. Blood Adv. - Accepted

  2. Karaesmen E, Hahn TE, Dile A, Rizvi AA, Wang J, Wang T, Haagenson M, Preus L, Zhu Q, Liu Q, Yan L, Liu S, Haiman CA, Stram D, Pooler L, Sheng X, Van Den Berg D, Brock G, Webb A, McCarthy PL, Pasquini MC, Spellman SR, Lee SJ, Paczesny S, Sucheston-Campbell LE Multiple functional variants in IL1RL1 region are pre-transplant markers for risk of GVHD and infection deaths. Blood Adv. - Accepted

  3. Rizvi AA, Karaesmen E, Morgan M, Preus L, Wang J, Sovic M, Hahn T, Sucheston-Campbell LE. gwasurvivr: an R package for genome-wide survival analysis. Bioinformatics. 2018 Nov 5. PMID: 30395168. doi:10.1093/bioinformatics/bty920

  4. Karaesmen E, Rizvi AA, Preus L, McCarthy PL, Pasquini MC, Onel K, Zhu X, Spellman S, Haiman CA, Stram DO, Pooler L, Sheng X, Zhu Q, Yan L, Liu Q, Hu Q, Webb A, Brock G, Clay-Gilmour AI, Battaglia S, Tritchler D, Liu S, Hahn TE, Sucheston-Campbell LE. Replication and validation of genetic polymorphisms associated with survival after allogeneic blood or marrow transplant. Blood 2017 Sep 28;130(13):1585-1596. PMID: 28811306. doi:10.1182/blood-2017-05-784637

  5. Clay-Gilmour AI, Hahn T, Preus LM, Onel K, Skol A, Hungate E, Zhu Q, Haiman CA, Stram DO, Pooler L, Sheng X, Yan L, Liu Q, Hu Q, Liu S, Battaglia S, Zhu X, Block AW, Sait SN, Karaesmen E, Rizvi AA, Weisdorf DJ, Ambrosone CB, Tritchler D, Ellinghaus E, Ellinghaus D, Stanulla M, Clavel J, Orsi L, Spellman S, Pasquini, MC, McCarthy PL, Sucheston-Campbell LE. Genetic association with B-cell acute lymphoblastic leukemia in allogeneic transplant patients differs by age and sex. Blood Adv. 2017 Sep 8;1(20):1717-1728. PMID: 28811306. doi:10.1182/bloodadvances.2017006023

Talks

  1. Karaesmen E, Introduction to Data Science with R. (2019 Mar) Women in Analytics Conference, Columbus OH

  2. Karaesmen E, Hahn ET, Dile A, Rizvi AA, Wang J, Wang T, Haagenson MD, Preus L, Zhu Q, Liu Q, Yan L, Liu S, Haiman C, Stram D, Pooler L, Cheng X, Van Den Berg D, Brock G, Webb A, McCarthy PL, Spellman SR, Lee JS, Paczesny S, and Sucheston-Campbell LE. Multiple Functional Donor Polymorphisms in IL1RL1 region Associate with Death Due to GvHD or Infection after Unrelated Donor Allogeneic Hematopoietic Stem Cell Transplantation (HCT) for AML and MDS. (2018 Dec) American Society of Hematology 60th Annual Meeting, San Diego, CA.

  3. Karaesmen E, Data Cleaning and Manipulation with R. (2018 Mar) Women in Analytics Conference, Columbus OH

  4. Karaesmen E, Rizvi AA, Preus L, McCarthy PL, Pasquini M, Singh S, Singh SK, Onel K, Zhu X, Spellman S, Haiman CA, Stram DO, Pooler L, Sheng X, Zhu Q, Yan L, Liu Q, Hu Q, Webb A, Brock G, Clay-Gilmour AI, Battaglia S, Tritchler D, Liu S, Hahn T, Sucheston-Campbell LE. Genome-Wide Significant Donor Genetic Associations with Death Due to Disease in AML and MDS Patients in the First 1 Year after BMT Are Not Modified By Conditioning Intensity or TBI. (2018 Feb) 2018 BMT Tandem Meetings, Salt Lake City, UT.

  5. Karaesmen E, Personalized Medicine and Genomic Data Science. (2017 Nov) Ohio DevFest, Columbus, OH.

  6. Karaesmen E, Rizvi AA, Preus L, McCarthy PL, Pasquini MC, Onel K, Zhu X, Spellman S, Haiman CA, Stram DO, Pooler L, Sheng X, Zhu Q, Yan L, Liu Q, Hu Q, Webb A, Brock G, Clay-Gilmour AI, Battaglia S, Tritchler D, Liu S, Hahn T, Sucheston-Campbell LE. Replication of Candidate SNP Survival Analyses and Gene-Based Tests of Association with Survival Outcomes after an Unrelated Donor Blood or Marrow Transplant: Results from the DISCOVeRY-BMT Study. (2016 Dec) American Society of Hematology 58th Annual Meeting, San Diego, CA.

  7. Karaesmen E, Rizvi AA, Preus L, McCarthy PL, Pasquini MC, Onel K, Zhu X, Spellman S, Haiman CA, Stram DO, Pooler L, Sheng X, Zhu Q, Yan L, Liu Q, Hu Q, Webb A, Brock G, Clay-Gilmour AI, Battaglia S, Tritchler D, Liu S, Hahn T, Sucheston-Campbell LE. Visualizing genomic results for team science: an example from the DISCOVeRY-BMT study.(2016 Oct) Inaugural The Ohio State University Pharmaceutics Retreat, Columbus, OH.

Teaching Experience

  1. Understanding Injury Data with R, Data Science for Women Summer Camp - July 17 2019
    I conducted a workshop with students in 8-10 grades. Interactive material is available here.

  2. Teaching Assistant for Introduction to the Structure, Analyses and Interpretation of Genomic Data studies Course (PHR 8194) - Spring 2019
    Addition to assistantship, I also taught Data Vizualization Module giving a two lecture introduction to ggplot2 package in R.

  3. Introduction to R Programming Workshops - 2018 - Present

    • Every year I organize multiple R programming workshops to raise funds for Pelotonia.
    • This 16 hour workshop includes the introduction of R objects and functions, methods of data cleaning and visualization for beginners.
    • Dates of past workshops:
      • April 22 - May 6, 2019
      • Sept 4 - 13, 2018
      • July 15 - Aug 8, 2017
      • June 8 - 29, 2017
  4. Bioconductor Workshop at OSU - September 11-12 2017
    Organized a 2-day Bioconductor workshop hosted by Dr. Martin Morgan with over 100 attendees