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 research is broadly focused on genomic integration. This work has direct applications to many areas of science, including basic virology, clinical virology, gene/cell therapy, and more. Even more generally, I am very interested in the development and application of computational methods/tools to biological questions. I have developed end-to-end pipelines and packages for the analysis of integration site data, utilized state-of-the-art protein language models and sequence databases to aid in hypothesis generation and data interpretation, used machine learning techniques to better define conserved chromatin states relative to nuclear compartments, and much more. 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 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. This work has enabled the biochemical characterization of some of these proteins 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. My post-doctoral work ultimately formed the basis of the research that I continue to perform 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 architectural features 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: R (primary), Python, and Bash.

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

Software:

  • Bioconductor: GenomicRanges, Biostrings, rtracklayer, BSgenome, SummarizedExperiment, GenomicAlignments, bamsignals, edgeR, limma, and many more.
  • Misc. bioinformatics software: FastQC, bedtools, samtools, Biopython, pysam, BWA, Bowtie2, MMSeqs2, FoldSeek, and more.
  • Data science and machine learning: Tidyverse, tidymodels, DuckDB, data.table, caret, FAISS, similarity search algorithms (LSH, MinHash, k-NN, etc.), cluster analysis (k-means clustering, hierarchical clustering, DBSCAN, etc.), graph algorithms (DFS, BFS), hidden Markov models, and more.
  • Hydrodynamic modeling: hullrad, HYDROPRO.
  • Structure prediction: AlphaFold/ColabFold, ESMFold, Boltz-1, AlphaFold-Metainference

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

Software

  • intmap: An end-to-end pipeline for mapping genomic integration site positions from NGS data.

  • xInt: An R/Bioconductor package to analyze integration site data post-mapping. Incoporates a wide variety of functionalities intended to provide users with a comprehensive toolkit for rigorously assessing integration site targeting trends/biases.

  • 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 and GitHub.

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.