About Me

Investigating functional genetic variation
in diverse human populations.

I am a Ph.D. candidate in the Cell, Molecular, Developmental Biology and Biophysics (CMDB) program at Johns Hopkins University, advised by Dr. Rajiv McCoy. My research focuses on generating large, globally diverse human transcriptomics datasets, and developing computational and statistical methods that use these datasets to investigate genetic variation underlying gene expression and splicing differences between individuals. Through functional annotation of this variation, we can uncover the molecular mechansims by which genetic variation drives human traits and disease.

I obtained my B.S. in Biology from the University of Maryland, College Park. There, I worked with Dr. Mihai Pop to develop computational tools for high-resolution metagenomic profiling assays.

Publications

Research Articles and Preprints

Aganezov, S., Yan, S. M., Soto, D. C. , ..., Taylor, D. J. (7/33), ..., & Schatz, M. C. (2021) A complete reference genome improves analysis of human genetic variation. Science, in press.

Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife.

Beisel, N. S., Callaham, J. B., Sng, N. J., Taylor, D. J., Paul, A. L., & Ferl, R. J. (2018). Utilization of single‐image normalized difference vegetation index (SI‐NDVI) for early plant stress detection. Applications in Plant Sciences.

Conference Papers

Sakowski, E., Uritskiy, G., Cooper, R., ..., Taylor, D. J. (28/30), …, & Preheim, S. P. (2019). Current state of and future opportunities for prediction in microbiome research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January, 2019. Msystems.

Honors and Awards

NSF Graduate Research Fellowship Program - Honorable Mention (2021)

The National Science Foundation (NSF) Graduate Research Fellowship Program provides Fellowships to individuals selected early in their graduate careers based on their demonstrated potential for significant achievements in science and engineering. The NSF accords Honorable Mention to meritorious applicants who do not receive Fellowship awards. This is considered a significant national academic achievement and provides access to cyberinfrastructure resources through the Extreme Science and Engineering Discovery Environment (XSEDE).
Adapted from nsf.gov

Johns Hopkins University Center for Education Resources Technology Fellowship Grant Recipient (2021)

The Technology Fellowship Program is a mini-grant initiative that enables faculty to partner with technology savvy students to develop resources that enhance pedagogy, increase or facilitate access to course content, encourage active learning, promote critical thinking, or support student collaboration. Each faculty member receives $1,000 for project leadership and oversight; student fellows receive $4,000 for resource development and implementation.
Adapted from cer.jhu.edu

Johns Hopkins University Department of Biology Victor G. Corces Teaching Award (2021)

The Victor G. Corces Teaching Award recognizes a graduate Teaching Assistant in the Department of Biology for their outstanding efforts, enduring devotion to their students, and excellence in education in the biological sciences. This is a funded award.

Student Speaker for Univeristy of Maryland CMNS Commencement (2018)

I was selected as the Student Commencement Speaker for the University of Maryland College of Computer, Mathematical, and Natural Sciences (CMNS) Winter 2018 graduation ceremony.

Other Awards

  • American Society for Microbiology Sigma Alpha Omicron Honors Society for excellence in Microbiology (2018)
  • University of Maryland Integrated Life Sciences Honors College Citation (2016)
  • Gold Medal and Nomination for Best-in-Track at iGEM 2015
  • University of Maryland Dean’s Scholarship (2014)

Teaching

Quantitative Biology

The past two years, I served as a teaching assistant for the CMDB program's one-week Quantitative Biology Bootcamp. The course is taken by all first-year Ph.D. students in the CMDB program and is designed to introduce biology students with little to no computational experience to the basics of computational biology. Students learn basic Python and Bash, and apply these languages to carry out simple analyses on biological data.

These concepts are built on in a year-long Quantitative Biology Lab course, for which I also served as a teaching assistant this year. Using the skills they learned in the bootcamp, students develop their own implementations of widely-used computational biology tools. These projects range from genome assembly, to sequence alignment and GWAS.

In addition to serving as a teaching assistant for the Quantitative Biology lab course, I also led a lecture for the course this year. My lecture covered local and global sequence alignment, introduced students to tools in use in the field today, and led students in developing their own implementation of the Needleman-Wunsch dynamic programming algorithm for global sequence alignment. My lecture was listed as one of the student's favorite lectures in anonymous reviews at the end of the semester.

Developmental Genetics

During the 2020-2021 school year, I served as a teaching assistant for the undergraduate Developmental Genetics Lab course. This course covers the basics of C. elegans development and introduces them to CRISPR modification. As part of the lab, students use CRISPR to add a fluorescent tag to a protein of interest, allowing them to track this protein over the course of C. elegans development. A large portion of this course focuses on properly designing the genetic constructs necessary to carry out their specific CRISPR modification.

Designing CRISPR reagents requires analysis of DNA sequences and extraction of specific strings of bases, and therefore lends itself to teaching students basic string manipulation skills. Sara Carioscia (a fellow TA) and I were recently awarded a Technology Fellowship by the Johns Hopkins University Center for Educational Resources to design a module for the Developmental Genetics course that guides students through building a tool in Python that will design CRISPR reagents for some given gene and modification of interest. This was implemented starting in the Fall 2021 semester as a 5-week module covering the basics of Python and string manipulation, and includes projects that reinforce these basics, and later require students to use the skills they’ve learned to build a full CRISPR reagent design tool from scratch. This module allows us to introduce computational biology to undergraduate students that may not have had previous exposure, and gives them the chance to use what they’ve learned to build a computational tool that they can use in their own research.

Academic Service

HMM Workshop with Agara Bio

This past year, I worked with Sara Carioscia to develop a computational biology workshop for Agara Bio, an undergraduate-driven community lab at JHU. We offered a two-part workshop covering Hidden Markov Models (HMMs), and led attendees in building their own gene-finding HMM in Jupyter Notebooks.

CMDB BioReps

The BioReps are student-elected representatives within the CMDB program that act as liasons between their graduate cohort, and the program directors and administration. We meet regularly with our cohorts, host monthly town halls, and are also involved in organizing the recruitment event for prospective students.

Curriculum Vitae


You can download my current CV here. If you'd like to contact me, feel free to reach out via twitter or email using the links provided at the bottom of the navigation pane.