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 focused on using and developing computational approaches to better understand genomic integration, intrinsically disordered proteins, and nuclear compartmentalization. This work is applicable to basic and clinical virology, gene therapy, cell therapy, protein design, and cell biology. I have developed novel tools for the improved mapping and analysis of genomic integration sites; applied machine learning algorithms and wet-bench experiments to better understand the conformational ensembles, solution behavior, and sequence determinants of specific properties of intrinsically disordered proteins; and identified conserved chromatin states related to nuclear compartmentalization. Through this interdisciplinary work, I hope to advance our understanding of complex biological problems and contribute to the development of novel therapeutic strategies.

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

During my post-doctoral fellowship, I developed a novel computational approach to better define the preferred gene targets of HIV-1 integration. This work resulted in the identification of previously un/under-appreciated target genes with implications for viral persistence. I additionally developed and optimized protein expression and purification protocols for challening protein targets – namely intrinsically disordered proteins with a propensity to undergo phase separation in solution. This work has resulted in the biochemical and structural characterization of some of these proteins for the first time.

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 utilized the 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, Python, and Bash.

Computing: Git, SLURM, Grid Engine, VS Code, Quarto, conda, etc.

Bioinformatics: GenomicRanges, bedtools, samtools, cutadapt, Bowtie(2), BWA, STAR, MACS2, epigraHMM, edgeR, limma, AlphaFold, MMseqs2, ESM(-fold), bio-embeddings, etc.

Data Science: Tidyverse, NumPy, DuckDB, tidymodels, k-NN, FAISS, DBSCAN, PCA, t-SNE, union-find, HMMs, ggplot2, etc.

Statistics: GLMs, nonlinear regression, regularization, change point detection, null hypothesis testing, expectation-maximization, etc.

Software

  • intmap: An end-to-end pipeline for mapping positions of genomic integration 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.

  • 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.