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 working to better define the genomic landscape of retroviral integration and the factors that influence that landscape. I have performed bioinformatic analyses for numerous collaborative projects across Harvard Medical School, the National Institutes of Health, and other scientific insitutions across the world. I am additionally working to develop tools and strategies that will enable scientists to more robustly characterize patterns of integration in their system-of-interest. These efforts include software/pipeline development and improvement, leveraging publically available datasets to better define genomic regions pertinent to integration, and developing methods to improve the resolution of integration site analysis. Beyond my research efforts, I actively mentor and advise undergraduate students, graduate students, research technicians, and others in the lab in both wet and dry lab research.

Consulting - Freelance.

I have consulted companies on processing and wrangling large data files into smaller, more 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. These proteins often exhibit low sequence complexity, strong compositional biases, and a large degree of disorder. The expression system I devised has been successfully applied to several protein targets, enabling their biochemical and biophysical characterization for the first time. Over time, I began to pursue my long-standing interests in computational biology and bioinformatics with increasing seriousness. In pursuing these interests, I was able to devise a new strategy for better defining the preferred gene targets of HIV-1 integration. This project 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 devised a system to selectively mineralize photocatalytic titanium dioxide within the pseudo-icosahedral shell of P22 procapsid-like particles. Confining highly insoluble titanium dioxide within the capsid shell works to effectively solubilize the material, making it more tractable for use in aqueous environments. In addition, I sought to understand the mechanism of so-called “headful” packaging, a packaging strategy utilized by many dsDNA viruses. I was able to show that the P22 portal acts as a biological pressure sensor that responds to the increasing internal pressure within the viral procapsid during genome packaging.

Programming and statistics

Languages: Proficiency in R. Competency with Python, AWK, 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, LaTeX, SageMath.

Bioinformatic tools:

  • Bioconductor: GenomicRanges, Biostrings, rtracklayer, BSgenome, SummarizedExperiment, and many more.
  • Miscellaneous bioinformatics software: FastQC, bedtools, samtools, MACS2, and more.
  • Sequence aligners: BWA-MEM, Bowtie2, Rsubread, STAR.
  • Multiple sequence alignment: hh-suite, Clustal Omega, MUSCLE.
  • Hydrodynamic modeling: hullrad, HYDROPRO.
  • Structure prediction: AlphaFold, ESMFold.
  • Molecular dynamics: CALVADOS.

Statistics: nonlinear least squares, generalized linear models, bootstrapping, hidden Markov models, changepoint detection, hull hypothesis significance testing, etc.

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 three distinct methods for evaluating the sum of 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.