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claudejrogers/README.md

@claudejrogers

I'm interested in

  • Computational biology/chemistry
  • 🧬 Bioinformatics/biomarker discovery
  • πŸ’Š Drug delivery
  • Bayesian modeling
  • Data analysis/visualization
  • Python, R, and C

Publications

  • Hamade, D. F., Epperly, M. W., Fisher, R., Hou W., Shields, D., van Pijkeren, J.-P., Leibowitz, B.-J., Coffman, L. G., Wang, H., Huq M. S., Huang, Z., Rogers, C. J., Vlad, A. M., Greenberger, J. S., & Mukherjee, A. (2024). Genetically engineered probiotic Limosilactobacillus reuteri releasing IL-22 (LR-IL-22) modifies the tumor microenvironment, enabling irradiation in ovarian cancer. Cancers, 16, 3, 474. https://doi.org/10.3390/cancers16030474
  • Gao, L., Kyubwa, E.M., Starbird, M.A., Diaz de Leon, J., Nguyen, M., Rogers, C. J., & Menon, N. (2023). Circulating miRNA profiles in COVID-19 patients and meta-analysis: implications for disease progression and prognosis. Sci. Rep. 13, 21656. https://doi.org/10.1038/s41598-023-48227-w
  • Hamade, D. F., Epperly, M. W., Fisher, R., Hou, W., Shields, D., van Pijkeren, J.-P., Mukherjee, A., Yu, J., Leibowitz, B. J., Vlad, A. M., Coffman, L., Wang, H., Huq, M. S., Huang, Z., Rogers, C. J., & Greenberger, J. S. (2023). Release of interferon-Ξ² (IFN-Ξ²) from probiotic Limosilactobacillus reuteri-IFN-Ξ² (LR-IFN-Ξ²) mitigates gastrointestinal acute radiation syndrome (GI-ARS) following whole abdominal irradiation. Cancers, 15, 1670. https://doi.org/10.3390/cancers15061670
  • Brehove M., Rogers C. J., Menon R., Minor P., Allington J., Lam A., Vielmetter J., Menon N. (2023). Cell monitoring with optical coherence tomography. Cytotherapy, 25(2), 120-124. http://dx.doi.org/10.1016/j.jcyt.2022.09.008
  • Whitener, R., Henchir, J. J., Miller, T. A., Levy, E., Krysiewicz-Bell, A., Abrams, E. S. L., Carlson, S. W., Menon, N., Dixon, C. E., Whalen, M. J., & Rogers, C. J. (2022). Localization of multi-lamellar vesicle nanoparticles to injured brain tissue in a controlled cortical impact injury model of traumatic brain injury in rodents. Neurotrauma Rep., 3(1), 158–167. http://dx.doi.org/10.1089/neur.2021.0049
  • Garcia, A. N., Casanova, N. G., Kempf, C. L., Bermudez, T., Valera, D. G., Song, J. H., Sun, X., Cai, H., Moreno-Vinasco, L., Gregory, T., Oita, R. C., Hernon, V. R., Camp, S. M., Rogers, C. J., Kyubwa, E. K., Menon, N., Axtelle, J., Rappaport, J., Bime, C., Sammani, S., Cress, A. E., & Garcia, J. G. N. (2022). eNAMPT is a novel damage-associated molecular pattern protein that contributes to the severity of radiation-induced lung fibrosis. Am. J. Respir. Cell Mol. Biol., 66(5), 497–509. http://dx.doi.org/10.1165/rcmb.2021-0357OC
  • Rogers, C. J., Kyubwa, E. M., Lukaszewicz, A. I., Starbird, M. A., Nguyen, M., Copeland, B. T., Yamada-Hanff, J., & Menon, N. (2021). Observation of unique circulating miRNA signatures in non-human primates exposed to total-body vs. whole thorax lung irradiation. Radiat. Res., 196(5), 547–559. http://dx.doi.org/10.1667/RADE-21-00043.1
  • Rogers, C. J., Kyubwa, E. M., Lukaszewicz, A. I., Yamada-Hanff, J., Starbird, M. A., Miller, T. A., Phelps, A. A., Wallack, S., Mahendra, S., Thrall, K., & Menon, N. (2021). Identification of miRNA associated with reduced survival after whole-thorax lung irradiation in non-human primates. Radiat. Res., 196(5), 510–522. http://dx.doi.org/10.1667/RADE-20-00031.1
  • Rogers, C. J., Lukaszewicz, A. I., Yamada-Hanff, J., Micewicz, E. D., Ratikan, J. A., Starbird, M. A., Miller, T. A., Nguyen, C., Lee, J. T., Olafsen, T., Iwamoto, K. S., McBride, W. H., Schaue, D., & Menon, N. (2020). Identification of mirna signatures associated with radiation-induced late lung injury in mice. PloS One, 15(5), 0232411. http://dx.doi.org/10.1371/journal.pone.0232411
  • Griffith, A. R., Rogers, C. J., Miller, G. M., Abrol, R., Hsieh-Wilson, L. C., & Goddard, W. A. 3. (2017). Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth. Proc. Natl. Acad. Sci. U.S.A., 114(52), 13697–13702. http://dx.doi.org/10.1073/pnas.1715093115
  • Menon, N., Rogers, C. J., Lukaszewicz, A. I., Axtelle, J., Yadav, M., Song, F., Chakravarti, A. & Jacob, N. K. (2016). Detection of acute radiation sickness: a feasibility study in non-human primates circulating miRNAs for triage in radiological events. PloS One, 11(12), 0167333. http://dx.doi.org/10.1371/journal.pone.0167333
  • Rogers, C. J., & Hsieh-Wilson, L. C. (2012). Microarray method for the rapid detection of glycosaminoglycan-protein interactions. Methods Mol. Biol., 808, 321–336. http://dx.doi.org/10.1007/978-1-61779-373-8\_22
  • Brown, J. M., Xia, J., Zhuang, B., Cho, K., Rogers, C. J., Gama, C. I., Rawat, M., Tully, S. E., Uetani, N., Mason, D. E., Tremblay, M. L., Peters, E. C., Habuchi, O., Chen, D. F., & Hsieh-Wilson, L. C. (2012). A sulfated carbohydrate epitope inhibits axon regeneration after injury. Proc. Natl. Acad. Sci. U.S.A., 109(13), 4768–4773. http://dx.doi.org/10.1073/pnas.1121318109
  • Rogers, C. J., Clark, P. M., Tully, S. E., Abrol, R., Garcia, K. C., Goddard, W. A. 3., & Hsieh-Wilson, L. C. (2011). Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches. Proc. Natl. Acad. Sci. U.S.A., 108(24), 9747–9752. http://dx.doi.org/10.1073/pnas.1102962108
  • Rexach, J. E., Rogers, C. J., Yu, S., Tao, J., Sun, Y. E., & Hsieh-Wilson, L. C. (2010). Quantification of O-glycosylation stoichiometry and dynamics using resolvable mass tags. Nat. Chem. Biol., 6(9), 645–651. http://dx.doi.org/10.1038/nchembio.412
  • Lee, S., Brown, J. M., Rogers, C. J., Matson, J. B., Krishnamurthy, C., Rawat, M., & Hsieh-Wilson, L. C. (2010). End-functionalized glycopolymers as mimetics of chondroitin sulfate proteoglycans. Chem. Sci., 1(3), 322–325. http://dx.doi.org/10.1039/C0SC00271B
  • McKenzie, K. M., Mee, J. M., Rogers, C. J., Hixon, M. S., Kaufmann, G. F., & Janda, K. D. (2007). Identification and characterization of single chain anti-cocaine catalytic antibodies. J. Mol. Biol., 365(3), 722–731. http://dx.doi.org/10.1016/j.jmb.2006.10.031
  • Zhu, X., Dickerson, T. J., Rogers, C. J., Kaufmann, G. F., Mee, J. M., McKenzie, K. M., Janda K. M., & Wilson, I. A. (2006). Complete reaction cycle of a cocaine antibody at atomic resolution. Structure, 14(2), 205-216. https://doi.org/10.1016/j.str.2005.10.014
  • Rogers, C. J., Dickerson, T. J., & Janda, K. D. (2006). Kinetic isotope and thermodynamic analysis of the nornicotine-catalyzed aqueous aldol reaction. Tetrahedron, 62(2-3), 352–356. http://dx.doi.org/10.1016/j.tet.2005.09.094
  • Rogers, C. J., Eubanks, L. M., Dickerson, T. J., & Janda, K. D. (2006). Unexpected acetylcholinesterase activity of cocaine esterases. J. Am. Chem. Soc., 128(48), 15364–15365. http://dx.doi.org/10.1021/ja066241+
  • Eubanks, L. M., Rogers, C. J., Beuscher, A. E. 4., Koob, G. F., Olson, A. J., Dickerson, T. J., & Janda, K. D. (2006). A molecular link between the active component of marijuana and Alzheimer's disease pathology. Mol. Pharm., 3(6), 773–777. http://dx.doi.org/10.1021/mp060066m
  • Rogers, C. J., Dickerson, T. J., Wentworth Jr, P., & Janda, K. D. (2005). A high-swelling reagent scaffold suitable for use in aqueous and organic solvents. Tetrahedron, 61(51), 12140–12144. http://dx.doi.org/10.1016/j.tet.2005.07.115
  • Rogers, C. J., Mee, J. M., Kaufmann, G. F., Dickerson, T. J., & Janda, K. D. (2005). Toward cocaine esterase therapeutics. J. Am. Chem. Soc., 127(28), 10016–10017. http://dx.doi.org/10.1021/ja053086a
  • Rogers, C. J., Dickerson, T. J., Brogan, A. P., & Janda, K. D. (2005). Hammett correlation of nornicotine analogues in the aqueous aldol reaction: implications for green organocatalysis. J. Org. Chem., 70(9), 3705–3708. http://dx.doi.org/10.1021/jo050161r
  • Kaufmann, G. F., Sartorio, R., Lee, S., Rogers, C. J., Meijler, M. M., Moss, J. A., Clapham, B., Brogan, A. P., Dickerson, T. J., & Janda, K. D. (2005). Revisiting quorum sensing: discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones. Proc. Natl. Acad. Sci. U.S.A., 102(2), 309–314. http://dx.doi.org/10.1073/pnas.0408639102
  • Dickerson, T. J., Beuscher, A. E. 4., Rogers, C. J., Hixon, M. S., Yamamoto, N., Xu, Y., Olson, A. J., & Janda, K. D. (2005). Discovery of acetylcholinesterase peripheral anionic site ligands through computational refinement of a directed library. Biochemistry, 44(45), 14845–14853. http://dx.doi.org/10.1021/bi051613x
  • Liu, W., Rogers, C. J., Fisher, A. J., & Toney, M. D. (2002). Aminophosphonate inhibitors of dialkylglycine decarboxylase: structural basis for slow binding inhibition. Biochemistry, 41(41), 12320–12328. http://dx.doi.org/10.1021/bi026318g

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