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Vasty Osei-Amponsa, Monika Chandravanshi, Xiuxiu Lu, Valentin Magidson, Sudipto Das, Thorkell Andresson, Marzena Dyba, Venkata R Sabbasani, Rolf E Swenson, Caroline Fromont, Biraj Shrestha, Yongmei Zhao, Michelle E Clapp, Raj Chari, Kylie J Walters.  hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50.   Mol Cell. 2024 Feb 1;84(3):522-537.


Ahn, J. I., Zhang, L., Ravishankar, H., Fan, L., Kirsch, K., Zeng, Y., Meng, L., Park, J.-E., Yun, H.-Y., Ghirlando, R., Ma, B., Ball, D., Ku, B., Nussinov, R., Schmit, J. D., Heinz, W. F., Kim, S. J., Karpova, T., Wang, Y.-X. & Lee, K. S. Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun. Biol. 6, 712 (2023).

Cheng, R. Y. S., Ridnour, L. A., Wink, A. L., Gonzalez, A. L., Femino, E. L., Rittscher, H., Somasundaram, V., Heinz, W. F., Coutinho, L., Rangel, M. C., Edmondson, E. F., Butcher, D., Kinders, R. J., Li, X., Wong, S. T. C., Mcvicar, D. W., Anderson, S. K., Pore, M. & Hewitt, S. M. Interferon-gamma is quintessential for NOS2 and COX2 expression in ER – breast tumors that lead to poor outcome. Cell Death and Disease 12 (2023).

Moissoglu, K., Lockett, S. J. & Mili, S. Cell Migration in Three Dimensions. Methods Mol. Biol. (Clifton, NJ) 2608, 263–280 (2023).

Wang, Y.-X., Degenhardt, M., Degenhardt, H., Bhandari, Y., Lee, Y.-T., Ding, J., Heinz, W., Stagno, J., Schwieters, C. & Zhang, J. Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks. Res. Sq. (2023).


Somasundaram, V., Ridnour, L. A., Cheng, R. Y., Walke, A. J., Kedei, N., Bhattacharyya, D. D., Wink, A. L., Edmondson, E. F., Butcher, D., Warner, A. C., Dorsey, T. H., Scheiblin, D. A., Heinz, W., Bryant, R. J., Kinders, R. J., Lipkowitz, S., Wong, S. T., Pore, M., Hewitt, S. M., McVicar, D.W., Anderson, S.K., Chang, J., Glynn, S. S., Ambs, S., Locket, S. J., Wink, D. A. (2022). Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density. Redox Biology, 58(November), 102529.

Fernandez-de Céspedes, M. V, Hoffman, H. K., Carter, H., Simons, L. M., Naing, L., Ablan, S. D., Scheiblin, D. A., Hultquist, J. F., van Engelenburg, S. B., & Freed, E. O. (2022). Rab11-FIP1C is Dispensable for HIV-1 Replication in Primary CD4(+) T Cells, but its Role is Cell Type Dependent in Immortalized Human T-Cell Lines. Journal of Virology, 96(23), e0087622.

Basu, S., Luke, B. T., Karim, B., Martin, N., Lockett, S., Das, S., Andresson, T., Saylor, K., Kozlov, S., Bassel, L., Esposito, D., & Johnson, P. F. (2022). CK2 signaling from TOLLIP-dependent perinuclear endosomes is an essential feature of KRAS mutant cancers. BioRxiv, 2022.04.05.487175.

Lee, H. K., Conrad, C. E., Magidson, V., Heinz, W. F., Pauly, G., Yu, P., Ramakrishnan, S., Stagno, J. R., & Wang, Y. (2022). Developing methods to study conformational changes in RNA crystals using a photocaged ligand. Frontiers in Molecular Biosciences, August, 1–13.

delas Peñas, K. E., Haeusler, R., Feng, S., Magidson, V., Dmitrieva, M., Wink, D., Lockett, S., Kinders, R., & Rittscher, J. (2022). Profiling DNA Damage in 3D Histology Samples. In Y. Huo, B. A. Millis, Y. Zhou, X. Wang, A. P. Harrison, & Z. Xu (Eds.), Medical Optical Imaging and Virtual Microscopy Image Analysis (pp. 84–93). Springer Nature Switzerland.


Smith CE, Tsai Y.C., Liang Y.H., Khago D., Mariano J., Li J., Tarasov S.G., Gergel E., Tsai B., Villaneuva M., Clapp M.E., Magidson V., Chari R., Byrd R.A., Ji X., Weissman A.M. (2021). A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation. PLoS Biol. Dec 8;19(12).

Trofka, A., Huang, B.-L., Zhu, J., Heinz, W. F., Magidson, V., Shibata, Y., Shi, Y.-B., Tarchini, B., Stadler, H. S., Kabangu, M., Al Haj Baddar, N. W., Voss, S. R., & Mackem, S. (2021). Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Current Biology, 1–12.

Ramakrishnan, S., Stagno, J. R., Heinz, W. F., Zuo, X., Yu, P., & Wang, Y.-X. (2021). The mechanism driving a solid–solid phase transition in a biomacromolecular crystal. IUCrJ, 8(4), 655–664.

Ramakrishnan, S., Stagno, J. R., Magidson, V., Heinz, W. F., & Wang, Y.-X. (2021). Dependence of phase transition uniformity on crystal sizes characterized using birefringence. Structural Dynamics, 8(3), 034301.

McGinity, C. L., Palmieri, E. M., Somasundaram, V., Bhattacharyya, D. D., Ridnour, L. A., Cheng, R. Y. S., Ryan, A. E., Glynn, S. A., Thomas, D. D., Miranda, K. M., Anderson, S. K., Lockett, S. J., McVicar, D. W., & Wink, D. A. (2021). Nitric oxide modulates metabolic processes in the tumor immune microenvironment. International Journal of Molecular Sciences, 22(13).

Ramakrishnan, S., Stagno, J. R., Magidson, V., Heinz, W. F., & Wang, Y.-X. (2021). A combined approach to characterize ligand-induced solid–solid phase transitions in biomacromolecular crystals. Journal of Applied Crystallography, 54(3), 787–796.

Sjoberg, H. T., Philippou, Y., Magnussen, A. L., Tullis, I. D. C., Bridges, E., Chatrian, A., Lefebvre, J., Tam, K. H., Murphy, E. A., Rittscher, J., Preise, D., Agemy, L., Yechezkel, T., Smart, S. C., Kinchesh, P., Gilchrist, S., Allen, D. P., Scheiblin, D. A., Lockett, S. J., Wink, D.A., Lamb, A.D., Mills, I.G., Harris, A., Muschel, R.J., Vojnovic, B., Scherz, A., Hamdy, F.C. Bryant, R. J. (2021). Tumour irradiation combined with vascular-targeted photodynamic therapy enhances antitumour effects in pre-clinical prostate cancer. British Journal of Cancer, 125(4), 534–546.

Gilmore, A. C., Flaherty, S. J., Somasundaram, V., Scheiblin, D. A., Lockett, S. J., Wink, D. A., & Heinz, W. F. (2021). An in vitro tumorigenesis model based on live-cell- generated oxygen and nutrient gradients. Communications Biology, 4(477), 1–13.

Ramakrishnan, S., Stagno, J. R., Conrad, C. E., Ding, J., Yu, P., Bhandari, Y. R., Lee, Y., Pauly, G., Yefanov, O., Wiedorn, M. O., Knoska, J., Oberthür, D., White, T. A., Barty, A., Mariani, V., Li, C., Brehm, W., Heinz, W. F., Magidson, V., Wang, Y.-X. (2021). Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nature Communications.

Rausch, J. W., Heinz, W. F., Payea, M. J., Sherpa, C., Gorospe, M., & Le Grice, S. F. J. (2021). Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Research.


Renda, F., Magidson, V., Tikhonenko, I., Fisher, R., Miles, C., Mogilner, A., & Khodjakov, A. Effects of malleable kinetochore morphology on measurements of intrakinetochore tension. Open Biology, 10(7), 200101. (2020).

Biswas, K., Lipton, G. B., Stauffer, S., Sullivan, T., Cleveland, L., Southon, E., Reid, S., Magidson, V., Iversen, E. S. J., & Sharan, S. K. A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays. NPJ Genomic Medicine, 5(1), 52. (2020).

Anderson, M. J., Magidson, V., Kageyama, R., & Lewandoski, M. Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function. ELife, 9. (2020).

Chrisafis, G., Wang, T., Moissoglu, K., Gasparski, A. N., Ng, Y., Weigert, R., Lockett, S. J., & Mili, S. Collective cancer cell invasion requires RNA accumulation at the invasive front. Proceedings of the National Academy of Sciences of the United States of America, 117(44), 27423–27434. (2020).

Philippou, Y., Sjoberg, H. T., Murphy, E., Alyacoubi, S., Jones, K. I., Gordon-Weeks, A. N., Phyu, S., Parkes, E. E., Gillies McKenna, W., Lamb, A. D., Gileadi, U., Cerundolo, V., Scheiblin, D. A., Lockett, S. J., Wink, D. A., Mills, I. G., Hamdy, F. C., Muschel, R. J., & Bryant, R. J. Impacts of combining anti-PD-L1 immunotherapy and radiotherapy on the tumour immune microenvironment in a murine prostate cancer model. British Journal of Cancer, 123(7), 1089–1100. (2020).

Leng, Y., Sim, S., Magidson, V., & Wolin, S. L. Noncoding Y RNAs regulate the levels, subcellular distribution and protein interactions of their Ro60 autoantigen partner. Nucleic Acids Research, 48(12), 6919–6930. (2020).

Somasundaram, V., Gilmore, A.C., Basudhar, D., Palmieri, E.M., Scheiblin, D.A., Heinz, W.F., Cheng, R.Y.S., Ridnour, L.A., Altan-Bonnet, G., Lockett, S.J., McVicar, D.W. & Wink, D.A. Inducible nitric oxide synthase-derived extracellular nitric oxide flux regulates proinflammatory responses at the single cell level. Redox Biology 28, 101354 (2020).

Zakrevsky P, Kasprzak WK, Heinz WF, Wu W, Khant H, Bindewald E, et al. Truncated Tetrahedral RNA Nanostructures Exhibit Enhanced Features for Delivery of RNAi Substrates. Nanoscale 12(4) 2555–2568 (2020).


Sun, Z., Cagliero, C., Izard, J., Chen, Y., Zhou, Y.N., Heinz, W. F., Schneider, T.D. & Jin, D.J. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli Nucleic Acids Research 47, 3970-3985 (2019).

Sahabandu, N., Kong, D., Magidson, V., Nanjundappa, R., Sullenberger, C., Mahjoub, M.R. & Loncarek, J. Expansion microscopy for the analysis of centrioles and cilia. J Microsc 276, 145-159 (2019).

Nunn, N., Prabhakar, N., Reineck, P., Magidson, V., Kamiya, E., Heinz, W.F., Torelli, M.D., Rosenholm, J., Zaitsev, A. & Shenderova, O. Brilliant blue, green, yellow, and red fluorescent diamond particles: synthesis, characterization, and multiplex imaging demonstrations. Nanoscale (2019).

Matarlo, J.S., Krumpe, L.R.H., Heinz, W.F., Oh, D., Shenoy, S.R., Thomas, C.L., Goncharova, E.I., Lockett, S.J. & O’Keefe, B.R. The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation. Cell Chemical Biology, 1-10 (2019). 

Kulkarni, R.A., Briney, C.A., Crooks, D.R., Bergholtz, S.E., Mushti, C., Lockett, S.J., Lane, A.N., Fan, T.W., Swenson, R.E., Marston Linehan, W. & Meier, J.L. Photoinducible Oncometabolite Detection. Chembiochem 20, 360-365 (2019.

Insinna, C., Lu, Q., Teixeira, I., Harned, A., Semler, E.M., Stauffer, J., Magidson, V., Tiwari, A., Kenworthy, A.K., Narayan, K. & Westlake, C.J. Investigation of F-BAR domain PACSIN proteins uncovers membrane tubulation function in cilia assembly and transport. Nat Commun 10, 428 (2019).

Fernandez, M.V., Delviks-Frankenberry, K.A., Scheiblin, D.A., Happel, C., Pathak, V.K. & Freed, E.O. Authentication Analysis of MT-4 Cells Distributed by the National Institutes of Health AIDS Reagent Program. Journal of Virology 93 (2019). 

Basudhar, D., Bharadwaj, G., Somasundaram, V., Cheng, R.Y.S., Ridnour, L.A., Fujita, M., Lockett, S.J., Anderson, S.K., McVicar, D.W. & Wink, D.A. Understanding the tumour micro-environment communication network from an NOS2/COX2 perspective. Br J Pharmacol 176, 155-176 (2019).


Singh, S.K., Singh, S., Gadomski, S., Sun, L., Pfannenstein, A., Magidson, V., Chen, X., Kozlov, S., Tessarollo, L., Klarmann, K.D. & Keller, J.R. Id1 Ablation Protects Hematopoietic Stem Cells from Stress-Induced Exhaustion and Aging. Cell Stem Cell 23, 252-265.e258 (2018).

Liu, J., Kline, B.A., Kenny, T.A., Smith, D.R., Soloveva, V., Beitzel, B., Pang, S., Lockett, S., Hess, H.F., Palacios, G., Kuhn, J.H., Sun, M.G. & Zeng, X.K. A novel sheet-like virus particle array is a hallmark of Zika virus infection. Emerging Microbes & Infections 7 (2018).

Kunduri, G., Turner-Evans, D., Konya, Y., Izumi, Y., Nagashima, K., Lockett, S., Holthuis, J., Bamba, T., Acharya, U. & Acharya, J.K. Defective cortex glia plasma membrane structure underlies light-induced epilepsy in cpes mutants. Proceedings of the National Academy of Sciences of the United States of America 115, E8919-E8928 (2018).

Michie, M.S., Gotz, R., Franke, C., Bowler, M., Kumari, N., Magidson, V., Levitus, M., Loncarek, J., Sauer, M. & Schnermann, M.J. Cyanine Conformational Restraint in the Far-Red Range. Journal of the American Chemical Society 139, 12406-12409 (2017).

Yiran Li, Stephen J. Lockett, Robert J. Kinders, Wojciech Czaja: Detection of epithelial versus mesenchymal regions in 2D images of tumor biopsies using shearlets.


Insinna-Kettenhofen, C., Lu, Q., Teixeira, I., Harned, A.S., Semler, E., Stauffer, J., Magidson, V., Narayan, K. & Westlake, C. Exploring PACSIN membrane tubulation regulation during intracellular ciliogenesis using 3D electron microscopy.

Chua, J., Senft, J.L., Lockett, S.J., Brett, P.J., Burtnick, M.N., DeShazer, D. & Friedlander, A.M. pH Alkalinization by Chloroquine Suppresses Pathogenic Burkholderia Type 6 Secretion System 1 and Multinucleated Giant Cells. Infection and Immunity 85 (2017).  Basudhar, D., Glynn, S.A., Greer, M., Somasundaram, V., No, J.H., Scheiblin, D.A., Garrido, P., Heinz, W.F., Ryan, A.E., Weiss, J.M., Cheng, R.Y.S., Ridnour, L.A., Lockett, S.J., McVicar, D.W., Ambs, S. & Wink, D.A. Coexpression of NOS2 and COX2 accelerates tumor growth and reduces survival in estrogen receptor-negative breast cancer. Proceedings of the National Academy of Sciences 114, 13030-13035 (2017).


Thirthagiri, E., Klarmann, K.D., Shukla, A.K., Southon, E., Biswas, K., Martin, B.K., North, S.L., Magidson, V., Burkett, S., Haines, D.C., Noer, K., Matthai, R., Tessarollo, L., Loncarek, J., Keller, J.R. & Sharan, S.K. BRCA2 minor transcript lacking exons 4-7 supports viability in mice and may account for survival of humans with a pathogenic biallelic mutation. Human Molecular Genetics 25, 1934-1945 (2016). 

Nandy, K., Chellappa, R., Kumar, A. & Lockett, S.J. Segmentation of Nuclei from 3D Microscopy Images of Tissue via Graphcut Optimization. IEEE Journal on Selected Topics in Signal Processing 10, 140-150 (2016). Kuhns, D.B., Fink, D.L., Choi, U., Sweeney, C., Lau, K., Priel, D.L., Riva, D., Mendez, L., Uzel, G., Freeman, A.F., Olivier, K.N., Anderson, V.L., Currens, R., Mackley, V., Kang, A., Al-Adeli, M., Mace, E., Orange, J.S., Kang, E., Lockett, S.J., Chen, D., Steinbach, P.J., Hsu, A.P., Zarember, K.A., Malech, H.L., Gallin, J.I. & Holland, S.M. Cytoskeletal abnormalities and neutrophil dysfunction in WDR1 deficiency. Blood 128, 2135-2143 (2016).  Jiang, H., Promchan, K., Lin, B.R., Lockett, S., Chen, D., Marshall, H., Badralmaa, Y. & Natarajan, V. LZTFL1 Upregulated by All-Trans Retinoic Acid during CD4(+) T Cell Activation Enhances IL-5 Production. Journal of Immunology 196, 1081-1090 (2016).