Skills

R

Statistics

Genomics

Experience

 
 
 
 
 

Senior Data Scientist

Tempus Labs, Inc

September 2020 – Present Chicago, IL, USA

Senior data scientist on the Outsights Data Science team. I lead a team of analysts that provides scientific and analytic support to Tempus’ pharma partners.

Responsibilities include:

  • Conduct clinical and molecular data analysis on Tempus data model
  • Prepare data delivery for pharma partner data licensing
  • Project manage and supervise two direct report analysts
  • Develop internal R packages and tools to enhance reproducibility and production.
 
 
 
 
 

AI Engineer/Data Scientist

Covail

June 2018 – September 2020 Columbus, OH, USA

Designed, built, and deployed artificial intelligence (AI) and machine learning (ML) projects to optimize business processes.

Responsibilities include:

  • Engage clients directly and collaboratively build data science projects
  • Establish return on investment metrics and how to measure success
  • Lead dozens of engagements across several industries (healthcare, insurance, supply chain, social work, libraries, biotechnology, and cybersecurity).
  • Built custom models for data science projects from end to end (retreival to deployment).
  • Deployed models using technologies such as cloud web services, Docker, web APIs.
 
 
 
 
 

Doctoral Research

The Ohio State University - College of Pharmacy

June 2016 – May 2019 Columbus, OH, USA

Our lab conducted a genome wide association study (GWAS) on leukemia patients who were treated with a bone marrow transplant. With bone marrow transplants, there are recipients and donors. We were interested in the independent and joint effects of recipient and donor genetic variation and how/if they were statistically associated with survival outcomes (death, relapse, etc.).

Responsibilities include:

  • Constructing Cox proportional hazard and competing risk models to test associations with clinical events.
  • Designing and build software (gwasurvivr) to conduct in an automated, large scale manner.
  • Discovered associated markers with acute lymphoblastic leukemia.
  • Published first author papers in Bioinformatics and Blood.
 
 
 
 
 

Data Scientist Intern

TROVE Predictive Data Science

August 2015 – November 2015 Buffalo, NY, USA

Conducted a small data science project focusing electrical grid outages.

Responsibilities include:

  • Clean and summarize large datasets
  • Created basic linear models to predict where outages occur
  • Learned about accuracy metrics and intepretation
 
 
 
 
 

Master Thesis Research

Roswell Park Cancer Institute

June 2014 – September 2015 NY, USA

Understanding the transcriptomic control of Androgen Receptor (AR) and LSD1 in prostate cancer to explore their potential as drug targets for a metastatic prostate cancer treatment.

Responsibilities include:

  • Conducted 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 wet lab experiments with commercially available prostate cancer cell lines while targeting AR, LSD1 or both.
 
 
 
 
 

Research Assistant

SUNY Fredonia, Biology Department

September 2011 – May 2012 Fredonia, NY, USA

Skeletal muscle fibers in mice are affected by diet. We were interested to see if fiber types would change by the diet

  • Extract mouse muscle tissue (tibealis anterior and soleus)
  • Quantified protein amount via Western blot
  • Conducted and reported statistics for experiments
  • Published in Physiological Reports

Certificates

Certified Tidyverse Instructor

RStudio Sep 2020

Computational Genomics Winter Institute

UCLA Feb 2018 – Mar 2018

Advanced Gene Mapping Course

The Rockefeller University Jan 2017 – Jan 2017

Analysis of NGS Data for Complex Traits Course

Max Delbrück Center for Molecular Medicine Jul 2016 – Jul 2016

Advanced Graduate Certificate in Applied Biostatistics

SUNY at Buffalo Aug 2015 – Sep 2016

Publications

  1. Wang J, Clay-Gilmour AI, Karaesmen E, Rizvi AA, Zhu Q, Yan L, Preus L, Liu S, Wang Y, Griffiths E, Stram DO, Pooler L, Sheng X, Haiman C, Van Den Berg D, Webb A, Brock G, Spellman S, Pasquini M, McCarthy P, Allan J, Stölzel F, Onel K, Hahn TE, Sucheston-Campbell LE. Genome-wide association analyses identify variants in IRF4 associated with Acute Myeloid Leukemia and Myelodysplastic Syndrome susceptibility. bioRxiv 773952 (2019). doi:10.1101/773952

  2. 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 Advances doi: 10.1182/bloodadvances.2019000052.

  3. 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 Advances doi: 10.1182/bloodadvances.2019000075

  4. 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

  5. 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

  6. Sucheston-Campbell LE, Clay-Gilmour AI, Barlow WE, Budd GT, Stram DO, Haiman CA, Sheng X, Yan L, Zirpoli G, Yao S, Jiang C, Owzar K, Hershman D, Albain KS, Hayes DF, Moore HC, Hobday TJ, Stewart JA, Rizvi AA, Isaacs C, Salim M, Gralow JR, Hortobagyi GN, Livingston RB, Kroetz DL, Ambrosone CB (2017) Genome-Wide Meta-Analyses Identifies Novel Taxane-Induced Peripheral Neuropathy Associated Loci. Pharmacogenetics and Genomics. pgen-2017

  7. 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 Advances. 2017 Sep 8;1(20):1717-1728. PMID: 28811306. doi:10.1182/bloodadvances.2017006023

  8. DeNies MS, Johnson J, Maliphol AB, Bruno M, Rizvi AA, Rustici K, Medler S. Diet-induced obesity alters skeletal muscle fiber types of male but not female mice. (2014) Physiological Reports.

Talks

  1. Rizvi AA, Artificial Intelligence Projects in Industry, 2020. Columbus State University, Columbus, OH, USA.

  2. Rizvi AA, Building a career in data science.. 2020. Columbus State University, Columbus, OH, USA.

  3. Rizvi AA, Gordon P, Nikitin S, Sasso K. photon: electron meets shiny. useR!2019. Lightning Talk. Toulouse, France.

  4. Rizvi AA, Gordon P, Nikitin S, Sasso K. photon: electron meets shiny. Bioconductor Conference 2019. Lightning Talk. New York, New York, USA.

  5. Rizvi AA, Karaesmen E, Morgan M, Preus L, Wang J, Sovic M, Hahn T, Sucheston-Campbell Lara. gwasurvivr: an R package for genome wide survival data. Bioconductor Conference 2018. Toronto, ON, Canada.

  6. Rizvi AA, Karaesmen E 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. Genetic Associations with Day +100 Transplant Related Mortality after HLA-matched Unrelated Donor Blood and Marrow Transplantation. (2018 Feb) BMT Tandem Meetings, Salt Lake City, UT.

  7. Rizvi AA, Karaesmen E, 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. Pending RStudio Tidyverse Instructor Certification - Course taken in July 2020

  2. C2ER Council of Economic R Training - June 2020
    Six introductory R courses organized with Ezgi Karaesmen and Katie Sasso Schafer.

  3. Introduction to R Programming Workshops - 2018 - Present

  • I was a teacher assisant for Ezgi Karaesmen’s workshops Pelotonia.
  • These were 16 hour workshops 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
  1. Bioconductor Workshop at OSU - September 11-12 2017
    Organized a 2-day Bioconductor workshop hosted by Dr. Martin Morgan with over 100 attendees