Publications

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Book Chapter
H. A. Levine and Nilsen-Hamilton, M., Angiogenesis - a biochemical/mathematical perspective, in Tutorials in Mathematical Biosciences III; Cell cycle, proliferation and cancer, Mathematical Biosciences subseries 1872, Berlin: Springer-Verlag, 2006, pp. 23-76.
L. Bendickson and Nilsen-Hamilton, M., Applications, in Making and Using Antibodies; A Practical Handbook, Boca Raton: CRC Press, 2006, pp. 247-72.
M. Ilgu, Fazlioglu, R., Ozturk, M., Ozsurekci, Y., and M, N. - H., Aptamers for diagnostics with applications for infectious diseases , in Recent Advances in Analytical Chemistry, 2019.
S. Banerjee and Nilsen-Hamilton, M., Aptamers for Infectious Disease Diagnosis, in IntechOpen, 2019.
M. Nilsen-Hamilton, Growth factors signalling in early mammalian development, in CRC Reviews. Growth Factors in Mammalian Development (I.Y. Rosenblum and S. Heyner, eds) , Florida: CRC Press, 1989, pp. 135-166.
T. Wang, Cong, X., and Nilsen-Hamilton, M., In vitro selection of aptamers, in In Making and Using Antibodies: A Practical Handbook, Second Edition., Boca Raton, FLA: CRC Press, 2013, pp. 173-206.
R. T. Hamilton, Nilsen-Hamilton, M., Fienup, V. R., and Jeng, M. H., Mitogen-Regulated Protein, a member of the prolactin/growth hormone family is regulated like prolactin at the transcriptional and post-translational levels, in Advances in Gene Technology: Molecular Biology of the Endocrine System, ICSU Short Reports, vol. 4, 1986.
M. Nilsen-Hamilton and Hamilton, R. T., Specific increase in the phosphorylation of a protein in mitogen-stimulated 3T3 cells compared with SV40-transformed 3T3 cells: Comparison of in vivo and in vitro assays, in Control Mechanisms in Animal Cells (Eds: R. Shields, R. Levi-Montalcini, and L. Jimenez de Asua), New York: Raven Press., 1980, pp. 97-107.
F. W. Thalacker, Crabill, L. J., Miller, S. J., and Nilsen-Hamilton, M., Type transforming growth factors, epidermal growth factor and tumor promotors selectively induce secreted proteins in mink lung epithelial cells, in Advances in Gene Technology: Molecular Biology of the Endocrine System, ICSU Short Reports, vol. 4, Cambridge University Press, 1986.
L. Bendickson and Nilsen-Hamilton, M., Western blots and other applications, in Making and Using Antibodies: A Practical Handbook, Second Edition., Boca Raton, FLA: CRC Press, 2013, pp. 275-302.
Conference Proceedings
J. Ourednik, Ourednik, V., Sakaguchi, D. S., and M, editorsNilsen- Ham, Stem Cell Biology, Annals of the New Academy of Sciences, vol. 1049. New York Academy of Sciences, 2004.
Journal Article
S. Shubham, Hoinka, J., Banerjee, S., Swanson, E., Dillard, J. A., Lennemann, N. J., Przytycka, T. M., Maury, W., and Nilsen-Hamilton, M., A 2'FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein, Sci Rep., vol. 8, no. 8, p. 12373, 2018.
V. R. Sunil, Patel, K. J., Nilsen-Hamilton, M., Heck, D. E., Laskin, J. D., and Laskin, D. L., Acute endotoxemia is associated with upregulation of lipocalin 24p3/Lcn2 in lung and liver, Experimental and Molecular Pathology, vol. 83, pp. 177-87, 2007.
M. Ilgu, Fulton, D. B., Yennamalli, R. M., Lamm, M. H., Sen, T. Z., and Nilsen-Hamilton, M., An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures, RNA, vol. 20, pp. 815-24, 2014.
X. Cong and Nilsen-Hamilton, M., Allosteric aptamers: targeted reversibly attenuated probes, Biochemistry, vol. 44, pp. 7945-54, 2005.
D. H. Burke, Ozerova, N. D., and Nilsen-Hamilton, M., Allosteric hammerhead ribozyme TRAPs, Biochemistry, vol. 41, pp. 6588-94, 2002.
K. Kang, Sachan, A., Nilsen-Hamilton, M., and Shrotriya, P., Aptamer functionalized microcantilever sensors for cocaine detection, Langmuir : the ACS journal of surfaces and colloids, vol. 27, pp. 14696-702, 2011.
A. SL, YJ., S., M, I., J, R., RR, F., S, S., L, B., HA, L., and M, N. - H., Aptamer-enabled uptake of small molecule ligands, Sci Rep. , vol. 8, no. 1.
S. L. Auwardt, Seo, Y. J., Ilgu, M., Ray, J., Feldges, R. R., Shubham, S., Bendickson, L., Levine, H. A., and Nilsen-Hamilton, M., Aptamer-enabled uptake of small molecule ligands, Sci Rep. , vol. 8, no. 1, p. 15712, 2018.
M. Ilgu and Nilsen-Hamilton, M., Aptamers in Analytics, The Analyst, vol. 141, pp. 1551-1568, 2016.
J. Banerjee and Nilsen-Hamilton, M., Aptamers: multifunctional molecules for biomedical research, Journal of molecular medicine, vol. 91, pp. 1333-42, 2013.
J. Oh, McCloskey, M. A., Blong, C. C., Bendickson, L., Nilsen-Hamilton, M., and Sakaguchi, D. S., An astrocyte-derived interleukin-6 promotes specific neuronal differentiation of neural progenitor cells from adult hippocampus, Journal of Neuroscience Research, vol. 88, pp. 2798-809, 2010.
T. R. Davis, Tabatabai, L., Bruns, K., Hamilton, R. T., and Nilsen-Hamilton, M., Basic fibroblast growth factor induces 3T3 fibroblasts to synthesize and secrete a cyclophilin-like protein and beta 2-microglobulin, Biochimica et Biophysica Acta, vol. 1095, pp. 145-52, 1991.
L. Wang and Nilsen-Hamilton, M., Biomineralization proteins: from vertebrates to bacteria, Frontiers in Biology, vol. 8, pp. 234-246, 2012.
M. [ Nilsen-]Hamilton and Edelstein, S. J., Cat hemoglobin: pH dependence of cooperativity of ligand binding, Journal of Biologocal Chemistry, vol. 249, pp. 1323-1329, 1974.
M. [ Nilsen-]Hamilton and Edelstein., S. J., Cat hemoglobin: pH dependent cooperativity of oxygen binding, Science, vol. 8, pp. 1104-1106, 1972.
C. L. Parfett, Hamilton, R. T., Howell, B. W., Edwards, D. R., Nilsen-Hamilton, M., and Denhardt, D. T., Characterization of a cDNA clone encoding murine mitogen-regulated protein: regulation of mRNA levels in mortal and immortal cell lines, Molecular and cellular biology, vol. 5, pp. 3289-92, 1985.
J. T. Nelson, Rosenzweig, N., and Nilsen-Hamilton, M., Characterization of the mitogen-regulated protein (proliferin) receptor, Endocrinology, vol. 136, pp. 283-8, 1995.
K. Santra, Geraskin, I. M., Nilsen-Hamilton, M., Kraus, G. A., and Petrich, J. \W., Characterization of the Photophysical Behavior of DFHBI Derivatives: Fluorogenic Molecules that Illuminate the Spinach RNA Aptamer, The Journal of Physical Chemistry B , vol. 123, no. 11, pp. 2536-2545, 2019.
T. H. Chuang, Hamilton, R. T., and Nilsen-Hamilton, M., Cloning of the mink plasminogen activator inhibitor type-1 messenger RNA: an mRNA with a short half life, Gene, vol. 162, pp. 303-8, 1995.
D. T. Denhardt, Hamilton, R. T., Parfett, C. L., Edwards, D. R., St Pierre, R., Waterhouse, P., and Nilsen-Hamilton, M., Close relationship of the major excreted protein of transformed murine fibroblasts to thiol-dependent cathepsins, Cancer research, vol. 46, pp. 4590-3, 1986.
T. Prozorov, Palo, P., Wang, L., Nilsen-Hamilton, M., Jones, D., Orr, D., Mallapragada, S. K., Narasimhan, B., Canfield, P. C., and Prozorov, R., Cobalt ferrite nanocrystals: out-performing magnetotactic bacteria, ACSNano, vol. 1, pp. 228-33, 2007.
M. Ilgu, Yan, S., Khounlo, R., Lamm, M. H., and Nilsen-Hamilton, M., Common secondary and tertiary structural features of aptamer-ligand interaction shared by RNA aptamers with different primary sequences, Molecules, vol. 24, no. 24, p. 4535, 2019.
T. Wang, Hoy, J. A., Lamm, M. H., and Nilsen-Hamilton, M., Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity, Journal of the American Chemical Society, vol. 131, pp. 14747-55, 2009.
Y. J. Seo, Nilsen-Hamilton, M., and Levine, H. A., A computational study of alternate SELEX, Bulletin of mathematical biology, vol. 76, pp. 1455-521, 2014.
R. T. Hamilton and Nilsen-Hamilton, M., Conversion of monensin from an ionophore to an inhibitor of Na+ uptake by SV3t3 membrane vesicles as a function of Na+ concentration, Biochemical and biophysical research communications, vol. 95, pp. 140-7, 1980.
M. M. Hossen, Bendickson, L., Palo, P. E., Yao, Z., Nilsen-Hamilton, M., and Hillier, A. C., Creating metamaterial building blocks with directed photochemical metallization of silver onto DNA origami templates, NanotechnologyNanotechnology, vol. 29, p. 355603, 2018.
V. Singh, Yeoh, B. S., Nilsen-Hamilton, M., Berger, T., Mak, T. W., and Vijay-Kumar, M., Data on IL-10R neutralization-induced chronic colitis in Lipocalin 2 deficient mice on BALB/c background, Data in Brief, vol. 11, pp. 588-592, 2017.
D. Mitra, Bouthcko, R., Ray, J., and Nilsen-Hamilton, M., Detecting cells in time varying intensity images in confocal microscopy for gene expression studies in living cells, SPIE-2015 proceedings, 2015.
M. Nilsen-Hamilton and Hamilton, R. T., Detection of proteins induced by growth regulators, Methods in enzymology, vol. 147, pp. 427-44, 1987.
M. Nilsen-Hamilton, Matrisian, L. M., and Hamilton, R. T., Developing in a family way. Transforming Growth Factor Type beta and Related Proteins in Development: the Sixth Molecular, Cellular and Developmental Biology/Iowa State University Symposium, Ames, IA, USA September 20-23, 1991, The New biologist, vol. 4, pp. 127-31, 1992.
R. T. Hamilton, Bruns, K. A., Delgado, M. A., Shim, J. K., Fang, Y., Denhardt, D. T., and Nilsen-Hamilton, M., Developmental expression of cathepsin L and c-rasHa in the mouse placenta, Molecular reproduction and development, vol. 30, pp. 285-92, 1991.
K. Kang, Nilsen-Hamilton, M., and Shrotriya, P., Differential surface stress sensor for detection of chemical and biological species, Applied Physics Letters, vol. 93, p. 142107, 2008.
H. Levine, Seo, Y., and Nilsen-Hamilton, M., A discrete dynamical system arising in molecular biology, Discrete and Continuous Dynamical Systems, Series B (DCDS-B) , vol. 17, pp. 2091-2151, 2012.
X. Liu, Zhang, H., Nayak, S., Parada, G., Anderegg, J., Feng, S., Nilsen-Hamilton, M., Akinc, M., and Mallapragada, S. K., Effect of Surface Hydrophobicity on the Function of the Immobilized Biomineralization Protein Mms6, Industrial & Engineering Chemistry Research , vol. 54, pp. 10284-10292, 2015.
C. Vizzardelli, Pavelka, N., Luchini, A., Zanoni, I., Bendickson, L., Pelizzola, M., Beretta, O., Foti, M., Granucci, F., Nilsen-Hamilton, M., and Ricciardi-Castagnoli, P., Effects of dexamethazone on LPS-induced activationand migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis, European Journal of Immunology, vol. 36, pp. 1504-15, 2006.
R. J. Playford, Belo, A., Poulsom, R., Fitzgerald, A. J., Harris, K., Pawluczyk, I., Ryon, J., Darby, T., Nilsen-Hamilton, M., Ghosh, S., and Marchbank, T., Effects of mouse and human lipocalin homologues 24p3/lcn2 and neutrophil gelatinase-associated lipocalin on gastrointestinal mucosal integrity and repair, Gastroenterology, vol. 131, pp. 809-17, 2006.
A. S. Determan, Trewyn, B. G., Lin, V. S., Nilsen-Hamilton, M., and Narasimhan, B., Encapsulation, stabilization, and release of BSA-FITC from polyanhydride microspheres, Journal of Controlled Release : official journal of the Controlled Release Society, vol. 100, pp. 97-109, 2004.
A. O. Elkhalil, Nilsen-Hamilton, M., Yoshizawa, F., and Sugita, S., Expression of SIP24 in the peripartum and postpartum rat uterus and its relation with postpartum neutrophils, Connective Tissue Research, vol. 46, pp. 235-41, 2005.
A. Trabandt, Aicher, W. K., Gay, R. E., Sukhatme, V. P., Nilsen-Hamilton, M., Hamilton, R. T., McGhee, J. R., Fassbender, H. G., and Gay, S., Expression of the collagenolytic and ras-induced cysteine protease cathepsin L and proliferation-associated oncogenes in synovial cells of MRL/1 mice and patients with rheumatoid arthritis, Matrix, vol. 10, pp. 349-361, 1990.

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