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Anisuzzaman SM, Geraskin IM, Ilgu M, Bendickson L, Kraus GA, and Nilsen-Hamilton M. 'Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities'. RNA. 2022 28: 865-877. DOI: 10.1261/rna.079005.121 Google Scholar

Yan S, Ilgu M, Nilsen-Hamilton M and Lamm MH 'Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State'. The Journal of Physical Chemistry'. 2022 In press. Manuscript ID: ct-2022-00340e

Singappuli Arachchige D, Feng S, Wang L, Palo PE, Shobade SO, Thomas M and Nilsen-Hamilton M (2022) The Magnetosome Protein, Mms6 from Magnetospirillum magneticum strain AMB-1, is a Lipid-Activated Ferric Reductase. International Journal of Molecular Science'. 2022 In press. Manuscript ID: ijms-1855886


Ozturk M, Nilsen-Hamilton M, Ilgu M (2021) Aptamer Applications in Neuroscience. Pharmaceuticals. 14(12):1260-. doi:10.3390/ph14121260. Google Scholar


W. Zhao, Bendickson, L., and Nilsen-Hamilton, M., “The Lipocalin2 Gene is Regulated in Mammary Epithelial Cells by NFκB and C/EBP In Response to Mycoplasma”, Scientific Reports, vol. 10, no. 1, 2020. DOIGoogle Scholar

S. Yan, Peck, J., Ilgu, M., Nilsen-Hamilton, M., and Lamm, M. H., “The Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer”, ACS Omega, vol. 5, no. 32, pp. 20187–20201, 2020. Google Scholar


M. Ilgu, Fazlioglu, R., Ozturk, M., Ozsurekci, Y., and Nilsen-Hamilton, M., “Aptamers for diagnostics with applications for infectious diseases”, in Recent Advances in Analytical Chemistry, 2019. Google Scholar

S. Banerjee and Nilsen-Hamilton, M., “Aptamers for Infectious Disease Diagnosis”, in IntechOpen, 2019. Google Scholar

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. Google Scholar

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. Google Scholar

A. T. Londono-Calderon, Hossen, M. M., Palo, P. E., Bendickson, L., Nilsen-Hamilton, M., Hillier, A. C., and Prozorov, T., “Imaging of Unstained DNA Origami Triangles with Electron Microscopy”, Small Methods , vol. 3, no. 12, 2019. Google Scholar

A. Gosai, Yeah, B. S. Hau, Nilsen-Hamilton, M., and Shrotriya, P., “Label free thrombin detection in presence of high concentration of albumin using an aptamer-functionalized nanoporous membrane”, Biosens Bioelectron., vol. 126, pp. 88-95, 2019. Google Scholar


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. Google Scholar

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. Google Scholar

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. Google Scholar


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. Google Scholar


M. Ilgu and Nilsen-Hamilton, M., “Aptamers in Analytics”, The Analyst, vol. 141, pp. 1551-1568, 2016. Google Scholar

J. Ray, Ilgu, M., Shin, I. C., Bendickson, L., Gupta, V., Kraus, G. A., and Nilsen-Hamilton, M., “IMAGEtags; Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters”, Methods in Enzymology , vol. 572, pp. 193-213, 2016. Google Scholar

S. Nayak, Zhang, H., Liu, X., Feng, S., Palo, P., Nilsen-Hamilton, M., Akinc, M., and Mallapragada, S., “Protein Patterns Template Arrays of Magnetite Nanoparticles”, RSC Advances, vol. 6, pp. 57048-57056, 2016. Google Scholar

A. Sachan, Ilgu, M., Kempema, A. M., Kraus, G. A., and M, N. - H., “Specificity and ligand affinities of the cocaine aptamer; impact of structural features and physiological NaCl”, Analytical Chemistry , vol. 88, pp. 7715-23, 2016. Google Scholar


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. Google Scholar

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. Google Scholar

M. Ilgu, Ray, J., Bendickson, L., Wang, T., Geraskin, I. M., Kraus, G. A., and Nilsen-Hamilton, M., “Light-up and FRET Aptamer Reporters; Evaluating Their Applications for Imaging Transcription in Eukaryotic Cells”, Methods, vol. 98, pp. 26-33, 2015. Google Scholar

H. Zhang, Liu, X., Feng, S., Wang, W., Schmidt-Rohr, K., Akinc, M., Nilsen-Hamilton, M., Vaknin, D., and Mallapragada, S., “Morphological transformations in the magnetite biomineralizing protein mms6 in iron solutions: a small-angle X-ray scattering study”, Langmuir, vol. 31, no. 9, pp. 2818-25, 2015. Google Scholar


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. Google Scholar

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. Google Scholar

I. Shin, Ray, J., Gupta, V., Ilgu, M., Beasley, J., Bendickson, L., Mehanovic, S., Kraus, G. A., and Nilsen-Hamilton, M., “Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters”, Nucleic acids research, vol. 42, p. e90, 2014. Google Scholar


J. Banerjee and Nilsen-Hamilton, M., “Aptamers: multifunctional molecules for biomedical research”, Journal of molecular medicine, vol. 91, pp. 1333-42, 2013. Google Scholar

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. Google Scholar

S. Feng, Wang, L., Palo, P., Liu, X., Mallapragada, S. K., and Nilsen-Hamilton, M., “Integrated self-assembly of the Mms6 magnetosome protein to form an iron-responsive structure”, International journal of molecular sciences, vol. 14, pp. 14594-606, 2013. Google Scholar

M. Ilgu, Wang, T., Lamm, M. H., and Nilsen-Hamilton, M., “Investigating the malleability of RNA aptamers”, Methods, vol. 63, pp. 178-87, 2013. Google Scholar

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. Google Scholar


L. Wang and Nilsen-Hamilton, M., “Biomineralization proteins: from vertebrates to bacteria”, Frontiers in Biology, vol. 8, pp. 234-246, 2012. Google Scholar

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. Google Scholar

S. Nath, Spencer, V. A., Han, J., Chang, H., Zhang, K., Fontenay, G. V., Anderson, C., Hyman, J. M., Nilsen-Hamilton, M., Chang, Y. T., and Parvin, B., “Identification of fluorescent compounds with non-specific binding property via high throughput live cell microscopy”, PloS one, vol. 7, p. e28802, 2012. Google Scholar

W. Wang, Bu, W., Wang, L., Palo, P. E., Mallapragada, S., Nilsen-Hamilton, M., and Vaknin, D., “Interfacial properties and iron binding to bacterial proteins that promote the growth of magnetite nanocrystals: X-ray reflectivity and surface spectroscopy studies”, Langmuir : the ACS journal of surfaces and colloids, vol. 28, pp. 4274-82, 2012. Google Scholar

C. L. Howk, Levine, H. A., Smiley, M. W., Mallapragada, S. K., Nilsen-Hamilton, M., Oh, J., and Sakaguchi, D. S., “A mathematical model for selective differentiation of neural progenitor cells on micropatterned polymer substrates”, Mathematical biosciences, vol. 238, pp. 65-79, 2012. Google Scholar

L. Zhai, Wang, T., Kang, K., Zhao, Y., Shrotriya, P., and Nilsen-Hamilton, M., “An RNA aptamer-based microcantilever sensor to detect the inflammatory marker, mouse lipocalin-2”, Analytical chemistry, vol. 84, pp. 8763-70, 2012. Google Scholar

X. Song, Thalacker, F. W., and Nilsen-Hamilton, M., “Synergistic and multidimensional regulation of plasminogen activator inhibitor type 1 expression by transforming growth factor type beta and epidermal growth factor”, The Journal of biological chemistry, vol. 287, pp. 12520-8, 2012. Google Scholar


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. Google Scholar

S. Saraswathi, Sundaram, S., Sundararajan, N., Zimmermann, M., and Nilsen-Hamilton, M., “ICGA-PSO-ELM approach for accurate multiclass cancer classification resulting in reduced gene sets in which genes encoding secreted proteins are highly represented”, IEEE/ACM transactions on computational biology and bioinformatics, vol. 8, pp. 452-63, 2011. Google Scholar

L. K. Petersen, Determan, A. S., Westgate, C., Bendickson, L., Nilsen-Hamilton, M., and Narasimhan, B., “Lipocalin-2-loaded Amphiphilic Polyanhydride Microparticles Accelerate Cell Migration”, Journal of biomaterials science: Polymer edition, 2011. Google Scholar

L. Wang, Prozorov, T., Palo, P. E., Liu, X., Vaknin, D., Prozorov, R., Mallapragada, S., and Nilsen-Hamilton, M., “Self-assembly and biphasic iron-binding characteristics of Mms6, a bacterial protein that promotes the formation of superparamagnetic magnetite nanoparticles of uniform size and shape”, Biomacromolecules, vol. 13, pp. 98-105, 2011. Google Scholar


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. Google Scholar

Y. J. Seo, Chen, S., Nilsen-Hamilton, M., and Levine, H. A., “A mathematical analysis of multiple-target SELEX”, Bulletin of Mathematical Biology, vol. 72, pp. 1623-65, 2010. Google Scholar

G. A. Kraus, Gupta, V., Mokhtarian, M., Mehanovic, S., and Nilsen-Hamilton, M., “New effective inhibitors of the Abelson kinase”, Bioorganic & Medicinal Chemistry, vol. 18, pp. 6316-21, 2010. Google Scholar

W. Zhao, Grubbs, C. J., Myers, R. K., and Nilsen-Hamilton, M., “Parity is associated with an expanded macrophage population in the mammary gland”, International Journal of Oncology, vol. 37, pp. 1195-202, 2010. Google Scholar


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. Google Scholar

K. Mitchell, Szekeres, C., Milano, V., Svenson, K. B., Nilsen-Hamilton, M., Kreidberg, J. A., and DiPersio, C. M., “Integrin alpha3beta1 in epidermis promotes wound angiogenesis and keratinocyte-to-endothelial-cell crosstalk through the induction of MRP3”, Journal of Cell Science, vol. 122, pp. 1778-87, 2009. Google Scholar

K. Boushaba, Levine, H. A., and Nilsen-Hamilton, M., “A mathematical feasibility argument for the use of aptamers in chemotherapy and imaging”, Mathematical Biosciences, vol. 220, pp. 131-42, 2009. Google Scholar

T. Marchbank, Weaver, G., Nilsen-Hamilton, M., and Playford, R. J., “Pancreatic secretory trypsin inhibitor is a major motogenic and protective factor in human breast milk”, American Journal of Physiology, Gastrointestinal and Liver Physiology, vol. 296, pp. G697-703, 2009. Google Scholar


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. Google Scholar

G. A. Kraus, Jeon, I., Nilsen-Hamilton, M., Awad, A. M., Banerjee, J., and Parvin, B., “Fluorinated analogs of malachite green: synthesis and toxicity”, Molecules, vol. 13, pp. 986-94, 2008. Google Scholar


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. Google Scholar

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. Google Scholar

H. A. Levine and Nilsen-Hamilton, M., “A mathematical analysis of SELEX”, Computational Biology and Chemistry, vol. 31, pp. 11-35, 2007. Google Scholar

T. Prozorov, Mallapragada, S. K., Narasimhan, B., Wang, L., Palo, P., Nilsen-Hamilton, M., Williams, T. J., Bazylinski, D. A., Prozorov, R., and Canfield, P. C., “Protein-mediated synthesis of uniform superparamagnetic magnetite nanocrystals”, Advanced Functional Materials, vol. 17, pp. 951–957, 2007. Google Scholar

M. J. Soares, Alam, S. M., Duckworth, M. L., Horseman, N. D., Konno, T., Linzer, D. I., Maltais, L. J., Nilsen-Hamilton, M., Shiota, K., Smith, J. R., and Wallis, M., “A standardized nomenclature for the mouse and rat prolactin superfamilies”, Mammalian Genome : Official Journal of the International Mammalian Genome Society, vol. 18, pp. 154-6, 2007. Google Scholar