Education

  • 2021 - Post-doctoral fellow, Dana-Farber Cancer Institute/Harvard Medical School.
  • 2016 - Ph.D., Biophysics, University of Alabama at Birmingham.
    • Dissertation: Exploring bacteriophage P22 as a selective molecular scaffold and molecular sensor.
  • 2010 - B.S., Chemistry, University of Alabama at Birmingham.

Current position

Instructor in Medicine - Dana-Farber Cancer Institute/Harvard Medical School.

My current work lies at the intersection of computational and systems biology. I am broadly working to better define the genomic landscape of retroviral integration and the factors that influence it. My work pertains to disease treatment in the contexts of both retroviral infection and gene/cell therapy. Even more generally, I am particularly interested in the development and application of computational tools and statistical approaches to interesting research questions, biological or otherwise. Beyond my research efforts, I actively mentor and advise undergraduate students, graduate students, research technicians, and others in both wet and dry lab research.

Consulting - Freelance.

I have consulted companies on processing and wrangling large, asynchronous data files into smaller, harmonized, and user-friendly formats. I am open to more consulting opportunities in data wrangling, bioinformatics, and data analysis. If interested, please get in touch!

Previous positions

Post-doctoral fellow - Dana-Farber Cancer Institute/Harvard Medical School

I began my post-doctoral fellowship leveraging my knowledge of protein chemsitry and biophysics to devise a recombinant protein expression system for difficult human protein targets, enabling their characterization for the first time. Eventually, I began to more proactively pursue my long-standing interests in computational biology and bioinformatics. To this end, I was able to more granularly define the preferred gene targets of HIV-1 integration. This work ultimately formed the conceptual basis for the work that I continue to develop today.

Graduate student - University of Alabama at Birmingham.

As a graduate student, I was interested in understanding and exploiting the architecture of the bacteriophage P22. I exploited the architecture of the viral capsid to direct the synthesis of photocatalytic materials within the capsid interior, effectively solubilizing the otherwise insoluble material. I additionally worked to better define the packaging mechanism of dsDNA viruses.

Programming and statistics

Languages: Proficiency in R. Competency with Python, AWK, sed, etc. Exposure to Julia.

Computing tools and technologies: bash scripting, HPC clusters (SLURM and Grid Engine), git and GitHub, tidy data, knitr/Rmarkdown/quarto/xaringan, VS Code, LaTeX, SageMath.

Software:

  • Bioconductor: GenomicRanges, Biostrings, rtracklayer, BSgenome, SummarizedExperiment, GenomicAlignments, bamsignals, edgeR, limma, and many more.
  • Misc. bioinformatics software: FastQC, bedtools, samtools, Biopython, pysam, and more.
  • Data science software: Tidyverse, DuckDB, data.table, caret, and more.
  • Sequence aligners: BWA-MEM, bowtie, bowtie2, Rsubread, STAR.
  • Sequence searching: hh-suite, MMseqs2, PSI-BLAST.
  • Hydrodynamic modeling: hullrad, HYDROPRO.
  • Structure prediction: AlphaFold, ColabFold, ESMFold.

Statistics: nonlinear least squares, generalized linear models, regularized regression, bootstrapping, hidden Markov models, change point detection, cluster analysis, and more.

Software

  • calibrateR: An R package written to streamline common laboratory calculations. A brief description of the package and general usage can be found here.

  • nbconv: An R package that implements multiple methods for evaluating arbitrary negative binomial convolutions. See this post for more information. nbconv can be found on CRAN.

Selected Publications

Bedwell, G.J. (2023). nbconv: Evaluate Arbitrary Negative Binomial Convolutions. CRAN. https://cran.r-project.org/web/packages/nbconv/index.html. [🔓 Open Access.]

Mohammadi, A., Etemad, B., Zhang, X., Li, Y., Sharaf, R., Kittilson, A., Melberg, M., Melberg, C., Wong, C., Fajnzylber, J., Worrall, D.P., Rosenthal, A., Jordan, H., Jilg, N., Kaseke, C., Giguel, F., Lian, X., Deo, R., Gillespie, E., Chishti, R., Abrha, S., Adams, T., Siagian, A., Anderson, P.L., Deeks, S.G., Lederman, M.M., Yawetz, S., Kuritzkes, D.R., Lichterfeld, M.D., Tsibris, A., Carrington, M., Brumme, Z.L., Castillo-Mancilla, J.R., Gaiha, G.D., & Li, J.Z. (2023). Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. medRxiv. 10.1101/2023.03.30.23287124. [🔓 Open Access.]

Bedwell, G.J., Jang, S., Li, W., Singh, P.K., & Engelman, A.N. (2021). rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. Nucleic Acids Research, 49, 7330–7346. 10.1093/nar/gkab514. [🔓 Open Access.]

Bedwell, G.J., & Engelman, A.N. (2021). Factors that mold the nuclear landscape of HIV-1 integration. Nucleic Acids Research, 49, 621–635. 10.1093/nar/gkaa1207. [🔓 Open Access.]

Li, W., Singh, P.K., Sowd, G.A., Bedwell, G.J., Jang, S., Achuthan, V., Oleru, A.V., Wong, D., Fadel, H.J., Lee, K., KewalRamani, V.N., Poeschla, E.M., Herschhorn, A., & Engelman, A.N. (2020). CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration. mBio, 11, e02254-20. 10.1128/mBio.02254-20. [🔓 Open Access. ]

Zhang, D.-W., Luo, R.-H., Xu, L., Yang, L.-M., Xu, X.-S., Bedwell, G.J., Engelman, A.N., Zheng, Y.-T., & Chang, S. (2019). A HTRF based competitive binding assay for screening specific inhibitors of HIV-1 capsid assembly targeting the C-Terminal domain of capsid. Antiviral Research, 169, 104544. 10.1016/j.antiviral.2019.104544.

Jang, S., Cook, N.J., Pye, V.E., Bedwell, G.J., Dudek, A.M., Singh, P.K., Cherepanov, P., & Engelman, A.N. (2019). Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Nucleic Acids Research, 47, 4663–4683. 10.1093/nar/gkz206. [🔓 Open Access.]

Zhou, Z., Bedwell, G.J., Li, R., Palchoudhury, S., Prevelige, P.E. Jr., & Gupta, A. (2017). Pathways for Gold Nucleation and Growth over Protein Cages. Langmuir, 33, 5925–5931. 10.1021/acs.langmuir.7b01298.

Bedwell, G.J., & Prevelige, P.E. Jr. (2017). Targeted mutagenesis of the P22 portal protein reveals the mechanism of signal transmission during DNA packaging. Virology, 505, 127–138. 10.1016/j.virol.2017.02.019. [🔓 Open Access.]

Cherwa, J.E. Jr., Tyson, J., Bedwell, G.J., Brooke, D., Edwards, A.G., Dokland, T., Prevelige, P.E. Jr., & Fane, B.F. (2017). ϕX174 Procapsid Assembly: Effects of an Inhibitory External Scaffolding Protein and Resistant Coat Proteins In Vitro. Journal of Virology, 91, e01878-16. 10.1128/JVI.01878-16. [🔓 Open Access.]

Bedwell, G.J., Zhou, Z., Uchida, M., Dokland, T., Gupta, A., & Prevelige, P.E. Jr. (2015). Selective biotemplated synthesis of TiO2 inside a protein cage. Biomacromolecules, 16, 214–218. 10.1021/bm501443e.

Bush, D.L., Monroe, E.B., Bedwell, G.J., Prevelige, P.E. Jr., Phillips, J.M., & Vogt, V.M. (2014). Higher-order structure of the Rous sarcoma virus SP assembly domain. Journal of Virology, 88, 5617–5629. 10.1128/JVI.02659-13. [🔓 Open Access. ]

Lucon, J., Qazi, S., Uchida, M., Bedwell, G.J., LaFrance, B., Prevelige, P.E. Jr., & Dokland, T. (2012). Use of the interior cavity of the P22 capsid for site-specific initiation of atom-transfer radical polymerization with high-density cargo loading. Nature Chemistry, 4, 781–788. 10.1038/nchem.1442. [Cover story.]


A complete list of my peer-reviewed publications, can be found here.