Please contact me if you are looking for someone with an interest and expertise in any of the following areas:
- Genetic screening approaches, CRISPR systems & base editing
- R statistical programming, including package and shiny app development
- NGS methods, applications and computational workflows
- Systems genetics, interaction networks, synthetic lethality & epistasis
- DNA replication, recombination & repair
- Cancer genetics
- Yeast genetics
- Mammalian cell culture
- Industrial mammalian expression
- Biologics discovery and optimization
After the PhD
I am currently a postdoctoral research fellow at Amgen in Therapeutic Discovery, where I am applying CIRSPR methods and transcriptomics to study the genetics of complex molecule expression in mammalian cells. In this role I have gained valuable hands-on experience in pooled and arrayed CRISPR screening laboratory techniques, and computational methods, as well as extensive exposure to the general pharmaceutical drug development pipeline.
Prior to my role at Amgen, I enjoyed a short-term contract with Roche as a clinical genomics data science consultant, where I evaluated the sensitivity of variant calling from RNA sequencing data. Here I gained valuable experience with NGS workflows and high performance computing environments in an industry setting.
My PhD was completed in 2018 at Columbia University under the mentorship of Professor Rodney Rothstein and co-mentorship by Professor Alberto Ciccia. To read some of my PhD thesis work, check out the following publications:
Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability.
Bryant EE, Šunjevarić I, Berchowitz L, Rothstein R, Reid RJD.
Nucleic Acids Research. 2019 Sep 26;47(17):9144—9159
PMID: 31350889 – PMCID: PMC6753471 – DOI: 10.1093/nar/gkz631
CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons.
Billon P*, Bryant EE*, Joseph SA, Nambiar TS, Hayward SB, Rothstein R, and Ciccia A.
Molecular Cell. 2017 Sep 21;67(6):1068—1079.e4
PMID: 28890334 – PMCID: PMC5610906 – DOI: 10.1016/j.molcel.2017.08.008
Want to know more about my PhD work? Then check out my post on the systems genetics of DNA damage tolerance, which includes, informal introductions to the topics covered in my dissertation, and discussion of key insights from my PhD. A complete list of my publications is also available here.
For examples of my research software, check out the following:
screenmill R package: capture, annotate, quantify, review and analyze time-series colony growth. This package was used for colony quantification and interaction analysis in Bryant et al., NAR 2019. A nice example analysis using
screenmillcan be found in Figure 1D. A shiny app is included to enable manual review of processed images.
iSTOP R package: design guides to introduce stop codons with CRISPR-mediated base editors. This package was written to facilitate guide design for Billon et al., Mol Cell 2017.
iSTOPcan be configured to design guides to generate any desired missense mutation using any hypothetical base editor in any genome with annotated coding sequence coordinates.
These packages were written largely for personal use to enable analyses for the publications during my PhD that I highlight above. They were never submitted to CRAN, or Bioconductor repositories as they lack appropriate test coverage, and were part of my R package development learning journey. That said, I am proud to say that my previous collaborators still use these tools for ongoing work, including to design the CRISPR base editing guide library in Cuella-Martin et al., Cell 2021. Pretty neat to enable such exciting work and to get an acknowledgement in Cell!