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Antibody Engineering and the MHC Class I-Related Receptor, FcRn

Ma, G., Crowley, A.R., Heyndrickx, L., Rogiers, I., Parthoens, E., Van Santbergen, J., Ober, R.J., Bobkov, V., de Haard, H., Ulrichts, P., Hofman, E., Louagie, E., Balbino, B., Ward, E.S. Differential effects of FcRn antagonists on the subcellular trafficking of FcRn and albumin. Journal of Clinical Investigation Insight, 9(10), 2024 . Journal URL – Full Text

Ward, E.S., Gelinas, D., Dreesen, E., Van Stantbergen, J., Andersen, J.T., Silvestri, N.J., Kiss, J.E., Sleep, D., Rader, D.J., Kastelein, J.J.P., Louagie, E., Vidarsson, G., Spriet, I. Clinical significance of serum albumin and implications of FcRn inhibitor treatment in IgG-mediated autoimmune disorders. Frontiers in Immunology, 13, 2022. Journal URL – Full Text

Khare, P., Sun ,W., Ramakrishnan, S., Hao, G., Lo, S., Nham, K., Sun, X., Ober, R.J., Ward, E.S., and Swiercz, R. Selective depletion of radiolabeled HER2-specific antibody for contrast improvement during PET. mAbs, 13(1): 1976705, 2021. Journal URL – Full Text

Ward, E.S., Jones, P., Buss, T., Rada, C., Winter, G., Willson, R. In memoriam: Jefferson Foote. MAbs, 13(1), 2021 Jan. Journal URL – Pub Med

Vatansever, E.C., Kang, J., Tuley, A., Ward, E.S., and Liu, W.R. An optimal “Click” formulation strategy for antibody-drug conjugate synthesis. Bioorganic Medicinal Chemistry, 28(24), 2020. Journal URL – Pub Med

Newland, A.C., Sánchez-González, B., Rejtő, L., Egyed, M., Romanyuk, N., Godar, M., Verschueren, K., Gandini, D., Ulrichts, P., Beauchamp, J., Dreier, T., Ward, E.S., Michel, M., Liebman, H.A., de Haard, H., Leupin, N., and Kuter, D.J. Phase 2 study of efgartigimod, a novel FcRn antagonist, in adult patients with primary immune thrombocytopenia. American Journal of Hematology, 95(2): 178-187, 2020. Journal URL – Full Text – Pub Med — Supplementary Text

Challa, D.K., Wang, X., Montoyo, H.P., Velmurugan, R., Ober, R.J., and Ward, E.S. Neonatal Fc receptor expression in macrophages is indispensable for IgG homeostasis. mABs, 11(5): 848-860, 2019. Journal URL – Full Text – Pub Med — Supplementary Text

Kang, J. C., Sun, W., Khare, P., Karimi, M., Wang, X., Shen, W., Ober, R. J., and Ward, E. S. Engineering a HER2-specific antibody–drug conjugate to increase lysosomal delivery and therapeutic efficacy. Nature Biotechnology, 37: 523-526, 2019. Journal URL – Pub Med — Supplementary Text

Howard, J. F. Jr., Bril, V., Burns, T. M., Mantegazza, R., Bilinska, M., Szczudlik, A., Beydoun, S., Rodriguez De Rivera Garrido, F. J., Piehl, F., Rottoli, M., Van Damme, P., Vu, T., Evoli, A. , Freimer, M., Mozaffar, T., Ward, E. S., Dreier, T., Ulrichts, P., Verschueren, K., Guglietta, A., de Haard, H., Leupin, N., and Verschuuren, J. J. G. M. Randomized Phase 2 study of FcRn antagonist efgartigimod in generalized myasthenia gravis. Neurology, 92(23): e2661-e2673, 2019. Journal URL – Pub Med

Ward, E. S. and Ober, R. J. Targeting FcRn to generate antibody-based therapeutics. Trends in Pharmacological Sciences, 39(10): 892-904, 2018. Journal URL — Full Text — PubMed

Ulrichts, P., Guglietta, A., Dreier, T., van Bragt, T., Hanssens, V., Hofman, E., Vankerckhoven, B., Verheesen, P., Ongenae, N., Lykhopiy, V., Enriquez, F. J., Cho, J., Ober, R. J., Ward, E. S., de Haard, H., and Leupin, N. Neonatal Fc receptor antagonist efgartigimod safely and sustainably reduces IgGs in humans. The Journal of Clinical Investigation, 128(10): 4372-4386, 2018. Journal URL — Full Text — PubMed —Supplementary Text

Ward, E. S. and Ober, R. J. Hepatic function of FcRn revealed: implications for overcoming drug-mediated hepatotoxicity. Hepatology, 66(6): 2083-2085, 2017. Journal URL— Full Text – PubMed

Devanaboyina, S. C., Khare, P., Challa, D. K., Ober, R. J., and Ward, E. S. Engineered clearing agents for the selective depletion of antigen-specific antibodies. Nature Communications, 8, 15314, 2017. Journal URL — Full Text — PubMed —Supplementary Text

Swiercz, R., Mo, M., Khare, P., Schneider, Z., Ober, R. J., and Ward, E. S. Loss of expression of the recycling receptor, FcRn, promotes tumor cell growth by increasing albumin consumption. Oncotarget, 8(2): 3528-3541, 2017. Journal URL — Full Text — PubMed — Supplementary Text

Taha, M., Ward, E.S., and Nam, H.-J. The x-Ray crystallographic structure of the human neonatal Fc receptor at acidic pH gives insights into pH-dependent conformational changes. Protein and Peptide Letters, 23(6): 525-529, 2016. Journal URL — Full Text – PubMed

Velmurugan, R., Challa, D. K., Ram, S., Ober, R. J., and Ward, E. S. Macrophage-mediated trogocytosis leads to death of antibody-opsonized tumor cells. Molecular Cancer Therapeutics, 15(8): 1879-1889, 2016. Journal URL — Full text – PubMed — Supplementary Text

Ward, E. S. and Ober, R. J. Commentary: “There’s been a flaw in our thinking”. Frontiers in Immunology, 6: 351, 2015. Journal URL — Full Text — PubMed

Ward, E. S., Devanaboyina, S. C., and Ober, R. J. Targeting FcRn for the modulation of antibody dynamics. Molecular Immunology, 67(2): 131–141, 2015. Journal URL — PubMed

Challa, D. K., Velmurugan, R., Ober, R. J., and Ward, E. S. FcRn: From molecular interactions to regulation of IgG pharmacokinetics and functions. Fc Receptors, Current Topics in Microbiology and Immunology, 382: 249-272, 2014. Journal URL — PubMed

Ram, S., Kim, D., Ober, R. J., and Ward, E. S. The level of HER2 expression is a predictor of antibody-HER2 trafficking behavior in cancer cells. mAbs, 6(5): 1211-1219, 2014. Journal URL — Full Text — PubMed — Supplementary Text

Swiercz, R., Chiguru, S., Tahmasbi, A., Ramezani, S. M., Hao, G., Challa, D. K., Lewis, M. A., Kulkarni, P. V., Sun, X., Ober, R. J., Mason, R. P., and Ward, E. S.(2014) Use of Fc-engineered antibodies as clearing agents to increase contrast during PET. J. Nucl. Med., 55, 1204—1207.
Kang, J. C., Poovassery, J. S., Bansal, P., You, S., Manjarres, I. M., Ober, R. J., and Ward, E. S. (2013) Engineering multivalent antibodies to target heregulin-induced HER3 signaling in breast cancer cells. mAbs, 6, 340—353.
Devanaboyina, S., Lynch, S. M., Ober, R. J., Ram, S., Kim, D., Puig-Canto, A., Breen, S., Kasturirangan, S., Fowler, S., Peng, L., Zhong, H., Jermutus, L., Wu, H., Webster, C., Ward, E. S., and Gao, C. (2013) The effect of pH dependence of antibody-antigen interactions on subcellular trafficking dynamics. mAbs, 5, 849—857.
Gan, Z., Ram, S., Ober, R. J., and Ward, E. S. (2013) Using multifocal plane microscopy to reveal novel trafficking processes on the recycling pathway. J. Cell Sci., 126, 1176—1188.
Patel, D. A., Puig-Canto, A., Challa, D. K., Montoyo H. P., Ober, R. J., and Ward, E. S. (2011) Neonatal Fc receptor blockade by Fc engineering ameliorates arthritis in a murine model, J. Immunol., 187, 1015—1022.
Montoyo, HP., Vaccaro, C., Hafner, M., Ober, R. J., Mueller, W., and Ward, E. S.(2009) Conditional deletion of the MHC class I-related receptor FcRn reveals the sites of IgG homeostasis in mice, Proc. Natl. Acad. Sci. USA, 106, 2788—2793.
Gan, Z., Ram, S., Vaccaro, C., Ober, R. J., and Ward, E. S. (2009) Analyses of the recycling receptor, FcRn, in live cells reveal novel pathways for lysosomal delivery, Traffic, 10, 600—614.
Mi, W., Wanjie, S., Lo, S. T., Gan, Z., Pickl-Herk, B., Ober, R. J., and Ward, E. S.(2008) Targeting the neonatal Fc receptor for antigen delivery using engineered Fc fragments, J. Immunol., 181, 7550—7561.
Prabhat, P., Gan, Z., Chao, J., Ram, S., Vaccaro, C., Gibbons, S., Ober, R. J. and Ward, E. S. (2007) Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,Proc. Natl. Acad. Sci. USA, 104, 5889—5894.
Vaccaro, C., Bawdon, R., Wanjie, S., Ober, R. J. and Ward, E. S. (2006)Divergent activities of an engineered antibody in murine and human systems have implications for therapeutic antibodies, Proc. Natl. Acad. Sci. USA, 103, 18709—18714.
Vaccaro, C., Zhou, J., Ober, R. J. and Ward, E. S. (2005) Engineering the Fc region of immunoglobulin G to modulate in vivo antibody levels, Nature Biotech., 23, 1283—1288.
Zhou, J., Mateos, F., Ober, R. J. and Ward, E. S. (2005) Conferring the binding properties of the mouse MHC Class I-related receptor, FcRn, onto the human ortholog by sequential rounds of site-directed mutagenesis, J. Mol. Biol., 345, 1071—1081.
Ober, R. J., Martinez, C., Lai, X., Zhou, J. and Ward, E. S. (2004) Exocytosis of IgG as mediated by the receptor, FcRn: an analysis at the single-molecule level, Proc. Natl. Acad. Sci. USA, 101, 11076—11081.
Ober, R. J., Martinez, C., Vaccaro, C., Zhou, J., and Ward, E. S. (2004) Visualizing the site and dynamics of IgG salvage by the MHC Class I-related receptor, FcRn, J. Immunol., 172, 2021—2029.
Zhuo, J., Johnson, J., Ghetie, V., Ober, R. J. and Ward, E. S. (2003) Generation of mutated variants of the human form of the MHC class I-related receptor, FcRn, with increased affinity for mouse immunoglobulin G, J. Mol. Biol., 332, 901—913.
Kim, J-K., Firan, M., Radu, C., Kim, C-H., Ghetie, V. and Ward, E. S. (1999)Mapping of the site on human IgG1 for binding of the MHC class I related receptor, FcRn, Eur. J. Immunol., 29, 2819—2825.
Ghetie, V., Popov, S., Borvak, J., Radu, C., Matesoi, D., Medesan, C., Ober, R. J. and Ward, E. S. (1997) Increasing the serum persistence of an IgG fragment by random mutagenesis, Nature Biotech., 15, 637—640.
Medesan, C., Matesoi, D., Radu, C., Ghetie, V. and Ward, E. S. (1997)Delineation of the amino acid residues involved in transcytosis and catabolism of mouse IgG, J. Immunol., 158, 2211—2217.
Ghetie, V., Hubbard, J. G., Kim, J-K., Tsen, M-F., Lee, Y. and Ward, E. S. (1996)Abnormally short serum half lives of IgGs in beta2-microglobulin deficient mice, Eur. J. Immunol., 26, 690—696.
Ward, E.S., Güssow, D., Griffiths, A., Jones, P.T. and Winter, G. (1989) Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli, Nature, 341, 544—546.

Autoimmune Disease and T Cell Biology

Zhang, P., Fleming, P., Andoniou, C.E., Waltner, O.G., Bhise, S.S., Martins, J.P., McEnroe, B.A., Voigt, V., Daly, S., Kuns, R.D., Ekwe, A.P., Henden, A,S., Saldan, A., Olver, S., Varelias, A., Smith, C., Schmidt, C.R., Ensbey, K.S., Legg, S.R., Sekiguchi, T., Minnie, S.A., Gradwell, M., Wagenaar, I., Clouston, A.D., Koyama, M., Furlan, S.N., Kennedy, G.A., Ward, E.S., Degli-Esposti, M.A., Hill, G.R., Tey, S.K. IL-6-mediated endothelial injury impairs antiviral humoral immunity after bone marrow transplantation. Journal of Clinical Investigation, 134(7), 2024. Journal URL — Full Text

Goebeler, M., Bata‐Csörgő, Z., De Simone, C,. Didona, B., Remenyik, E., Reznichenko, N., Stoevesandt, J., Ward, E.S., Parys, W., de Haard., Dupuy, P., Verheesen, P., Schmidt, E., Joly, P., and the ARGX-113-1701 Investigator Study Group. Treatment of pemphigus vulgaris and foliaceus with efgartigimod, a neonatal Fc receptor inhibitor: a phase 2 multicentre, open‐label feasibility trial. British Journal of Dermatology. 2021. Journal URL – Pub Med

Wolfe, G.I., Ward, E.S., de Haard, H., Ulrichts, P., Mozaffar, T., Pasnoor, M., and Vidarsson, G. IgG regulation through FcRn blocking: A novel mechanism for the treatment of myasthenia gravis. Journal of the Neurological Sciences, 430: 118074, 2021. Journal URL

Sun, W., Khare, P., Wang, X., Challa, D.K., Greenberg, B.M., Ober, R.J., and Ward, E.S. Selective depletion of antigen-specific antibodies for the treatment of demyelinating disease. Molecular Therapy, 29(3): 1312-1323, 2020. Journal URL – Pub Med — Full Text — Supplementary text

Deason, K., Troutman, T. D., Jain, A., Challa, D. K., Mandraju, R., Brewer, T., Ward, E. S., and Pasare, C. BCAP links IL-1R to the PI3K-mTOR pathway and regulates pathogenic Th17 differentiation. Journal of Experimental Medicine, 215(9): 2413-2428, 2018. Journal URL — Full text — PubMed —Supplementary text

Khare, P., Challa, D. K., Devanaboyina, S. C., Velmurugan, R., Hughes, S., Greenberg, B. M., Ober, R. J., and Ward, E. S. Myelin oligodendrocyte glycoprotein-specific antibodies from multiple sclerosis patients exacerbate disease in a humanized mouse model. Journal of Autoimmunity, 86: 104-115, 2018. Journal URL — Full text — PubMed — Supplementary text

Challa, D. K., Mi, W., Lo, S.-T., Ober, R. J., and Ward, E. S. Antigen dynamics govern the induction of CD4+ T cell tolerance during autoimmunity. Journal of Autoimmunity, 72: 84-94, 2016. Journal URL — Full text – PubMed — Supplementary text

Ligocki, A. J., Rivas, J. R., Rounds, W. H., Guzman, A. A., Li, M., Spadaro, M., Lahey, L., Chen, D., Henson, P. M., Graves, D., Greenberg, B. M., Frohman, E. M., Ward, E. S., Robinson, W., Meinl, E., White C. L., Stowe A. M., and Monson N. L. A distinct class of antibodies may be an indicator of gray matter autoimmunity in early and established relapsing remitting multiple sclerosis patients. ASN Neuro, 7(5): 1759091415609613, 2015. Journal URL — Full text — PubMed — Supplementary text

Challa, D. K., Bussmeyer, U., Khan, T., Montoyo, H. P., Bansal, P., Ober, R.J., and Ward, E. S. Autoantibody depletion ameliorates disease in murine experimental autoimmune encephalomyelitis. mAbs, 5(5): 655-659, 2013. Journal URL — Full text pdf-icon — PubMed pdf-icon
Bansal, P., Khan, T., Bussmeyer, U., Challa, D. K., Swiercz, R., Velmurugan, R., Ober, R. J., and Ward, E. S. (2013) The encephalitogenic, human myelin oligodendrocyte glycoprotein-induced antibody repertoire is directed toward multiple epitopes in C57BL/6 mice. J. Immunol., 191, 1091—1101.
Maverakis, E., Menezes, J. S., Ametani, A., Han, M., Stevens, D. B., He, Y., Wang, Y., Ono, Y., Miyamura, Y., Lam, K. S., Ward, E. S., and Sercarz, E. E.,(2010) Molecular mimics can induce a nonautoaggressive repertoire that preempts induction of autoimmunity, Proc. Natl. Acad. Sci. USA, 107, 2550—2555.
Pastor, S., Minguela, A., Mi, W., and Ward, E. S. (2009) Autoantigen immunization at different sites reveals a role for anti-inflammatory effects of IFN-gamma in regulating susceptibility to experimental autoimmune encephalomyelitis, J. Immunol., 182, 5268—5275.
Minguela, A., Pastor, S., Mi, W., Richardson, J. A., and Ward, E. S. (2007)Feedback regulation of murine autoimmunity via dominant anti-inflammatory effects of interferon gamma, J. Immunol., 178, 134—144.
Huang, J. C., Ober, R. J. and Ward, E. S. (2005) The central residues of a T cell receptor sequence motif are key determinants of autoantigen recognition in murine experimental autoimmune encephalomyelitis, Eur. J. Immunol., 35, 299—304.
Huang, J. C., Han, M., Minguela, A., Pastor, S., Qadri, A. and Ward, E.S. (2003) T cell recognition of distinct peptide: I-Au conformers in murine experimental autoimmune encephalomyelitis, J. Immunol., 171, 2467—2477.
Machius, M., Cianga, P., Deisenhofer, J., and Ward, E. S. (2001) Crystal structure of a T cell receptor Va11 (AV11S5) domain: new canonical forms for the first and second complementarity determining regions, J. Mol. Biol., 310, 689—698.
Garcia, K. C., Radu, C. G., Ho, J., Ober, R. J., and Ward, E. S. (2001) Kinetics and thermodynamics of T cell receptor-autoantigen interactions in murine experimental autoimmune encephalomyelitis, Proc. Natl. Acad. Sci. USA, 98, 6818—6823.
Qadri, A., Radu, C. G., Thatte, J., Cianga, P., Ober, B. T., Ober, R. J., and Ward, E. S. (2000) A role for the region encompassing the c” strand of a T cell receptor Va domain in T cell activation events, J. Immunol., 165, 820—829.
Thatte, J., Qadri, A., Radu, C., and Ward, E. S. (1999) Molecular requirements for T cell recognition by an MHC Class II restricted T cell receptor: the involvement of the fourth hypervariable loop of the Va domain, J. Exp. Med.,189, 509—519.
Fields, B. A., Ober, B., Malchiodi, E. L., Lebedeva, M. I., Braden, B., Ysern, X., Kim, J-K., Shao, X., Ward, E. S., and Mariuzza, R. A. (1995) Crystal structure of the Va domain of a T cell antigen receptor, Science, 270, 1821—1824.

Cancer and Tumour cell biology

Stopforth, R.J. and Ward, E.S. The role of tumour-associated macrophages in antigen presentation. Critical Reviews™ in Immunology, 40(3): 205-224, 2020. Journal URL– Pub Med

Velmurugan, R., Ramakrishnan, S., Kim, M., Ober, R. J., and Ward, E. S. Phagocytosis of antibody-opsonized tumor cells leads to the formation of a discrete vacuolar compartment in macrophages. Traffic, 19(4): 273-284, 2018. Journal URL — Full text — PubMed — Supplementary text

Li, R., Chiguru, S., Li, L., Kim, D., Velmurugan, R., Kim, D., Tian, H., Schroit, A., Mason, R., Ober, R. J., and Ward, E. S. Targeting phosphatidylserine with calcium-dependent protein-drug conjugates for the treatment of cancer. Molecular Cancer Therapeutics, 17(1): 169-182, 2018. Journal URL — Full text — PubMed — Supplementary text

Lea, J., Sharma, R., Yang, F., Zhu, H., Ward, E.S., and Schroit, A.J. Detection of phosphatidylserine-positive exosomes as a diagnostic marker for ovarian malignancies: a proof of concept study. Oncotarget, 8: 14395-14407, 2017. Journal URL — Full text —PubMed

Holt, S., Ward, E. S., Ober, R. J., and Alge, D. Shooting for the moon: Using tissue-mimetic hydrogels to gain new insight on cancer biology and screen therapeutics. MRS Communications, 7(3): 427-441, 2017. Journal URL

Poovassery, J. S., Kang J. C., Kim, D., Ober, R. J., and Ward, E. S. Antibody targeting of HER2/HER3 signaling overcomes heregulin-induced resistance to PI3K inhibition in prostate cancer. International Journal of Cancer, 137(2): 267–277, 2015. Journal URL — PubMed

Fluorescence Microscopy

Lin, D., Lin, Z., Cao, J., Velmurugan, R., Ward, E.S., and Ober, R.J. A two-stage method for automated detection of ring-link endosomes in fluorescent microscopy images. PLoS ONE, 14(6): e0218931, 2019. Journal URL – Full Text – Pub Med

Patel, L, Gustafsson, N., Lin, Y., Ober, R.J., Henriques, R., and Cohen, E.A. A hidden Markov model approach to characterizing the photo-switching behaviour of fluorophores. The Annals of Applied Statistics, 13(3): 1397-1429, 2019. Journal URL — Full Text — PubMed — Supplementary text

Sage, D., Pham, T., Babock, H., Lukes, T., Pengo, T., Chao, J., Velmurugan, R., Herbert, A., Agrawal, A., Colabrese, S., Wheeler, A., Archetti, A., Rieger, B., Ober, R., Hagen, G.M., Sibarita, J-B., Ries, J., Henriques, R., Unser, M., and Holden, S. Super-resolution fight club: Assessment of 2D & 3D single-molecule localization microscopy software. Nature Methods, 16: 387-395, 2019. Journal URL – Pub Med

Lin, D., Lin, Z., Velmurugan, R., and Ober, R. J. Automatic endosomal structure detection and localization in fluorescence microscopic images. 2017 IEEE International Symposium on Circuits and Systems (ISCAS), Baltimore, MD, 2017, pp. 1-4. Journal URL — PubMed

Chao, J., Velmurugan, R., You, S., Kim, D., Ward, E. S., and Ober, R. J. Remote focusing multifocal plane microscopy for the imaging of 3D single molecule dynamics with cellular context. Proceedings of the SPIE International Symposium on Biomedical Optics: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV, 10070: 100700L, San Francisco, CA, 2017. Journal URL — Full text — PubMed

Velmurugan, R., Chao, J., Ram, S., Ward, E. S., and Ober, R. J. Intensity-based axial localization approaches for multifocal plane microscopy. Optics Express, 25(4): 3394-3410, 2017. Journal URL — Full text — PubMed

Vahid, M. R., Chao, J., Kim, D., Ward, E. S. and Ober, R. J. State space approach to single molecule localization in fluorescence microscopy. Biomedical Optics Express, 8(3): 1332-1355, 2017. Journal URL — Full text — PubMed

Chao, J., Ram, S., Ward, E. S., and Ober, R. J. Investigating the usage of point spread functions in point source and microsphere localization. Proceedings of the SPIE International Symposium on Biomedical Optics: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIII, 9713: 97131M, San Francisco, CA, 2016. Journal URL — Full text — PubMed

Chao, J., Lee, T., Ward, E. S., and Ober, R. J. Fluorescent microspheres as point sources: a localization study. PLoS ONE, 10(7): e0134112, 2015. Journal URL — Full text — PubMed — Supplementary text

Tahmasbi, A., Ram, S., Chao, J., Ward, E. S., and Ober, R. J. An information-theoretic approach to designing the plane spacing for multifocal plane microscopy. Proceedings of the SPIE International Symposium on Biomedical Optics: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXII, 9330: 933011, San Francisco, CA, 2015. Journal URL — Full text — PubMed

Wong, Y., Chao, J., Lin, Z., and Ober, R. J. Effect of time discretization of the imaging process on the accuracy of trajectory estimation in fluorescence microscopy. Optics Express, 22(17): 20396-20420, 2014. Journal URL — Full text — PubMed

Tahmasbi, A., Ram, S., Chao, J., Abraham, A. V., Tang, F. W., Ward, E. S., and Ober, R. J. (2014) Designing the focal plane spacing for multifocal plane microscopy. Opt. Express, 22, 16706—16721.
Chao, J., Ram, S., Ward, E. S., and Ober, R. J. (2013) Ultrahigh accuracy imaging modality for super-localization microscopy. Nat. Methods, 10, 335—338.
Gan, Z., Ram, S., Ober, R. J., and Ward, E. S. (2013) Using multifocal plane microscopy to reveal novel trafficking processes on the recycling pathway. J. Cell Sci., 126, 1176—1188.
Ram, S., Kim, D., Ward, E. S., and Ober, R. J. (2012) 3D single molecule tracking with multifocal plane microscopy reveals rapid intercellular transferrin transport at epithelial cell barriers. Biophys. J., 103(7), 1594-1603.
Ram, S., Prabhat, P., Chao, J., Ward, E. S., and Ober, R. J. (2010) Three-dimensional Single molecule tracking of quantum-dot labeled antibody molecules, Proc. SPIE., 7575, 75750J.
Abraham, A. V., Ram, S., Chao, J., Ward, E. S., and Ober, R. J. (2009)Quantitative study of single molecule location estimation techniques, Opt. Express, 17, 23352—23373.
Ram, S., Prabhat, P., Ward, E. S., and Ober, R. J. (2009) Improved single particle localization accuracy with dual objective multifocal plane microscopy,Opt. Express, 17, 6881—6898.
Chao, J., Ram, S., Abraham, A. V., Ward, E. S., and Ober, R. J. (2009) A resolution measure for three-dimensional microscopy, Optics Com., 282, 1751—1761.
Ram, S., Prabhat, P., Chao, J., Ward, E. S., and Ober, R. J. (2008) High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells, Biophys. J ., 95, 6025—6043.
Prabhat, P., Gan, Z., Chao, J., Ram, S., Vaccaro, C., Gibbons, S., Ober, R. J., and Ward, E. S. (2007) Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy,,Proc. Natl. Acad. Sci. USA, 104, 5889—5894.
Prabhat, P., Ram, S., Ward, E. S., and Ober, R. J. (2006) Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D, Proc. SPIE., 6090, 115—121.
Ram, S., Ward, E. S., and Ober, R. J. (2006) Beyond Rayleigh’s criterion: A resolution measure with application to single-molecule microscopy, Proc. Natl. Acad. Sci. USA, 103, 4457—4462.
Lai, X., Lin Z., Ward, E. S., and Ober R. J. (2005) Noise suppression of point spread functions and its influence on deconvolution of three dimensional fluorescence microscopy image sets, J. Microscopy, 217, 93—108.
Ober, R. J., Martinez, C., Lai, X., Zhou, J., and Ward, E. S. (2004) Exocytosis of IgG as mediated by the receptor, FcRn: An analysis at the single-molecule level, Proc. Natl. Acad. Sci. USA, 101, 11076—11081.
Prabhat, P., Ram, S., Ward, E. S., and Ober, R. J. (2004) Simultaneous imaging of different focal planes in fluorescence microscopy for the study of cellular dynamics in three dimensions., IEEE Trans. Nanobio., 3, 237—242.
Ober, R. J., Ram, S., and Ward, E. S. (2004) Localization accuracy in single-molecule microscopy, Biophys. J., 86, 1185—1200. Please see MIATool for more information.

Signal Processing

Marie d’Avigneau, A., Singh, S.S., Ober, R.J. Limits of accuracy for parameter estimation and localization in single-molecule microscopy via sequential Monte Carlo methods. SIAM Journal on Imaging Sciences, 15(1): 139–171, 2022. Journal URL
You, S., Chao, J., Cohen, E.A., Ward, E.S., Ober, R.J. A microscope calibration protocol for single-molecule microscopy. Optics Express, 29(1): 182-207, 2021. Journal URL – Pub Med — Full Text

Vahid, M.R., Hanzon, B., and Ober, R.J. Effect of pixelation on the parameter estimation of single molecule trajectories. IEEE Transactions on Computational Imaging, 7: 98-113, 2021. Journal URL — Full Text pdf-icon

Vahid, M.R., Hanzon, B., and Ober, R.J. Fisher information matrix for single molecules with stochastic trajectories. SIAM Journal on Imaging Sciences, 13(1): 234-264, 2020. Journal URL — Full Text — Supplementary text

Cohen, E. A. K., Abraham, A. V., Ramakrishnan, S., and Ober, R. J. Resolution limit of image analysis algorithms. Nature Communications, 10: 793, 2019. Journal URL — Full text — PubMed — Supplementary text

Vahid, M. R., Chao, J., Ward, E. S., and Ober, R. J. A state space based approach to localizing single molecules from multi-emitter images. Proceedings of the SPIE International Symposium on Biomedical Optics: Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV, 10070: 100700J, San Francisco, CA, 2017. Journal URL — Full text — PubMed

Chao, J., Ward, E. S., and Ober, R. J. Fisher information theory for parameter estimation in single molecule microscopy: tutorial. Journal of the Optical Society of America A, 33(7): B36-B57, 2016. Journal URL — Full text — PubMed

Tahmasbi, A., Ward, E. S., and Ober, R. J. New results on the single molecule localization problem in two and three dimensions. Proceedings of the SPIE, Nanoimaging and Nanospectroscopy III, 9554: 955402, San Diego, CA. 2015. Journal URL — Full text — PubMed

Chao, J., Ram, S., Lee, T., Ward, E. S., and Ober, R. J. Investigation of the numerics of point spread function integration in single molecule localization. Optics Express, 23(13): 16866-16883, 2015. Journal URL — Full text — PubMed

Lin, Z., Wong, Y., and Ober, R. J. Limit of the accuracy of parameter estimation for two molecules moving in close proximity. IEEE International Symposium on Circuits and Systems, 441- 444, May 2015, Lisbon, Portugal. Journal URL — Full text — PubMed

Cohen, E. A. K., Kim, D., and Ober, R. J. Cramer-Rao lower bound for point based image registration with heteroscedastic error model for application in single molecule microscopy. IEEE Transactions on Medical Imaging, 34(12): 2632 – 2644, 2015. Journal URL— Full text — PubMed

Tahmasbi, A., Ward, E. S., and Ober, R. J. Determination of localization accuracy based on experimentally acquired image sets: applications to single molecule microscopy. Optics Express, 23(6): 7630-7652, 2015. Journal URL — Full text — PubMed

Ober, R. J., Tahmasbi, A., Lin, Z., and Ward, E. S. Quantitative aspects of single-molecule microscopy: Information-theoretic analysis of single-molecule data. IEEE Signal Processing Magazine, 32(1): 58-69, 2015. Journal URL — Full text — PubMed

Cohen, E. A. K. and Ober, R. J. (2013) Analysis of point based image registration errors with applications in single molecule microscopy, IEEE Trans. Signal Process., 61, 6291—6306.
Ram, S., Ward, E. S., and Ober, R. J. (2013) A stochastic analysis of distance estimation approaches in single molecule microscopy – quantifying the resolution limits of photon-limited imaging systems, Multidim. Sys. Sig. Proc.,24, 503—542.
Chao, J., Ward, E. S., and Ober, R. J. (2012) Fisher information matrix for branching processes with application to electron-multiplying charge-coupled devices, Multidim. Sys. Sig. Proc., 23, 349—379.
Wong, Y., Lin, Z., and Ober, R. J. (2011) Limit of the accuracy of parameter estimation for moving single molecules imaged by fluorescence microscopy,IEEE Trans. Sig. Proc., 59, 895—911.
Chao, J., Ward, E. S., and Ober, R. J. (2010) A software framework for the analysis of complex microscopy image data, IEEE Trans. Info. Tech. Biomed.,14, 1075—1087.
Abraham, A. V., Ram, S., Chao, J., Ward, E. S., and Ober, R. J. (2010)Comparison of estimation algorithms in single-molecule localization, Proc. SPIE., 7570, 757004.
Zou, Q., Lin, Z., and Ober, R. J. (2006) The Cramer Rao lower bound for bilinear systems, IEEE Trans. Sig. Proc., 54, 1666—1680.
Ram, S., Ward, E. S., and Ober, R. J. (2006) A stochastic analysis of performance limits for optical microscopes, Multidim. Sys. Sig. Proc., 15, 27—57.
Lin, Z., Zou, Q., Ward, E. S. and Ober, R. J. (2005) The Cramer Rao lower bound for parameter estimation in nonlinear systems, IEEE Sig. Proc. Letts.,12, 855—858.
Ober, R. J., Lai, X., Lin, Z. and Ward, E. S. (2005) State space realization of a three-dimensional image set with application to noise reduction in fluorescent microscopy images of cells, Multidim. Sys. Sig. Proc., 16, 7—48.
Hunt, L. R., Ward, E. S., and Ober, R. J. (2004) Approximation of trajectories of nonlinear systems by iterates of systems with linear state dynamics, Sys. Cont. Letts., 51, 377—381.
Ober, R. J., Lin, Z., and Zou, Q. (2003) Calculations of the Fisher information matrix for multidimensional data sets, IEEE Trans. on Sig. Proc., 51(10), 2679—2691.
Ober, R. J., Lin, Z., Ye, H., and Ward, E. S. (2002) Achievable accuracy of parameter estimation for multidimensional NMR experiments, J. Mag. Reson., 157, 1—16.
Ober, R. J. (2002) The Fisher information matrix for linear systems, Sys. Contr. Letts., 47, 221—226.

Surface Plasmon Resonance (SPR)

Ober, R. J., Caves, J., and Ward, E. S. (2003) Analysis of exponential data using a non-iterative technique: application to surface plasmon experiments, Anal. Biochem., 312, 57—65.
Ober, R. J. and Ward, E. S. (2002) Compensation for loss of ligand activity in surface plasmon resonance experiments, Anal. Biochem., 306, 228—236.
Ober, R. J. and Ward, E. S. (1999) The influence of signal noise on the accuracy of kinetic constants measured by surface plasmon resonance experiments., Anal. Biochem., 271, 70—80. Please see SPRTool for more information.