Employment
- 2020—Present
-
Amgen, Postdoctoral Research Fellow
Developed and executed a research plan studying the genetics of mammalian recombinant protein expression using CRISPR methods and transcriptomics.
Managers: Irwin Chen &
Rene Hubert
Keywords: High-throughput Mammalian Expression / RNAseq / Arrayed & pooled CRISPR screening / Protein Engineering / Multispecifics / Biologics Discovery / Biologics Optimization
- 2020 Spring
-
Roche/Genentech, Clinical Genomics Data Science Consultant
Evaluated variant calling from RNAseq while on a short-term consulting contract with pREDi (Pharma Research & Early Development Informatics).
Managers: Venus So &
Vitalay Fomin
Keywords: Genome Analysis toolkit (GATK) / RNAseq / Real World Data / High-performance Computing Cluster (HPC) / Bioinformatics Workflow Managers, CWL, Nextflow, Seven Bridges Genomics
- 2009—2011
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Gene Oracle, Research Assistant
Role: De-novo gene synthesis & degenerate codon library construction. Pipeline management and development.
Manager: Shannon Phan
Education
- 2011—2018
-
- 2006—2009
-
- 2004—2006
-
Software
- 2019
-
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
screenmill
can be found in
Figure 1D.
A shiny app is included to enable manual review of processed images.
- 2017
-
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.
iSTOP
can be configured to design guides to generate any desired missense
mutation using any hypothetical base editor in any genome with
annotated coding sequence coordinates.
Awards
- 2018
-
Departmental distinction for PhD dissertation defense
- 2017—2018
-
TL1 NIH training grant, clinical and translational research
- 2016—2017
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T32 NIH training grant, cancer biology
- 2013—2015
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T32 NIH training grant, biological sciences
- 2013
-
James Howard McGregor award
(student with unusual promise as a teacher of zoology)
Publications
Lead contribution
- 2019-09-26
-
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
- 2019-01-09
-
Systems genetics of DNA damage tolerance – Cisplatin, RAD5 &
CRISPR-mediated nonsense.
Bryant EE.
Columbia University.
DOI: 10.7916/d8-k1d0-kb09
- 2017-09-21
-
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
*co-first authors
Supporting contribution
- 2022-03-24
-
Temporal coordination between chromosome mobility and homologous recombination.
Joseph F, Lee SJ, Bryant EE, Reid RJD, Šunjevarić I, Rothstein R.
BioRxiv. 2022.
BioRxiv: 10.1101/2022.03.24.485580v1
–
DOI: 10.1101/2022.03.24.485580
- 2020-08-26
-
Measuring chromosome pairing during homologous recombination in yeast.
Joseph F, Lee SJ, Bryant EE, Rothstein R.
Methods in Molecular Biology. 2021;2153:253—265.
PMID: 32840785
–
DOI: 10.1007/978-1-0716-0644-5_18
- 2019-10-01
-
DNA damage triggers increased mobility of chromosomes in G1 phase cells.
Smith MJ, Bryant EE, Joseph FJ, Rothstein R.
Molecular Biology of the Cell. 2019 Oct 1;30(21):2620—2625
PMID: 31483739
–
PMCID: PMC6761769
–
DOI: 10.1091/mbc.E19-08-0469
- 2018-09-01
-
Increased chromosomal mobility after DNA damage is controlled by
interactions between the recombination machinery and the checkpoint.
Smith MJ, Bryant EE, Rothstein R.
Genes & Development. 2018 Sep 1;32(17-18):1242—1251
PMID: 30181361
–
PMCID: PMC6120718
–
DOI: 10.1101/gad.317966.118
- 2016-10-01
-
A synthetic dosage lethal genetic interaction between CKS1B and PLK1 is
conserved in yeast and human cancer cells.
Reid RJD, Du X, Šunjevarić I, Rayannavar V, Dittmar J,
Bryant EE, Maurer M, and Rothstein R.
Genetics. 2016 Oct 1;204(2):807—819
PMID: 27558135
–
PMCID: PMC5068864
–
DOI: 10.1534/genetics.116.190231
Select Acknowledgements
- 2021-02-18
-
Functional interrogation of DNA damage response variants with base editing
screens.
Cuella-Martin R, Hayward SB, Fan X, Chen Xiao, Huang JW,
Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A.
Cell. 2021 Feb 18;184(4):1081-1097.e19
PMID: 33606978
–
PMCID: PMC8018281
–
DOI: 10.1016/j.cell.2021.01.041
Acknowledged for bioinformatics support. I designed the CRISPR base
editing guide library.