2025
Shobade SO, Nilsen-Hamilton M and Zabotina O (2025) Plant Defense Proteins: Recent Discoveries and Applications. Plants 14(13): 2069-. DOI: 10.3390/plants14132069
Koep A, Masud N, Van't Hul J, Stanley C, Nilsen-Hamilton M, Sarkar A and. Schneider IC (2025) Design and Assembly of a Cargo-agnostic HollowTwo-lidded DNA Origami Box ACS Applied Bio Materials, 8(8):7188-7200. DOI: 10.1021/acsabm.5c00907
Rollins DK, Nilsen-Hamilton M, Kreienbrink K, Wolf S, Hurd D, and Olyer J (2025) Theoretically-based Dynamic Regression (TDR) - A New and Novel Regression Framework for Modeling Dynamic Behavior. Stats, Stats, 8(4), 89; doi: 10.3390/stats8040089
2024
Shobade SO, Zabotina OA, Nilsen-Hamilton M (2024) Plant root associated chitinases: structures and functions. Frontiers in Plant Science 15. DOI: 10.3389/fpls.2024.1344142
Anisuzzaman S, Singappuli-Arachchige D, Alimoradi N, Banerjee S, Pogorelko GV, Kaiyum YA, Johnson PE, Shrotriya P and Nilsen-Hamilton, M (2024) Pyoverdine Binding Aptamers and Label-Free Electrochemical Detection of Pseudomonads. Frontiers in Chemistry. 12, DOI: 10.3389/fchem.2024.1438710
De Penning S., Murphy MP, Kingston TA, Nilsen-Hamilton M, and Shrotriya P (2024) Influence of Crosslinker Functionality on Sensing Response and Immobilization Density of Aptamers on Non-Metallic Sensing Surfaces. Biosensors and Bioelectronics. DOI: 10.1016/j.bios.2024.116933
2023
Banerjee S, Hemmat MA, Shubham S, Gosai A, Devarakonda S, Jiang N, Geekiyanage C, Dillard JA, Maury W, Shrotriya P, Lamm MH, and Nilsen-Hamilton M (2023) Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing. Int J Mol Sci 24. DOI: 10.3390/ijms24054627
Islam MM, Hossen MM, Adjasoo J, Palo PE, Bendickson L, Kallmyer NE, Reuel NF, Nilsen-Hamilton M, Koschny T, Hillier AC (2023) Direct Measurement of Optical Resonance Modes in Gold Meta-Atoms Fabricated by Metallization of Triangle- and V-Shaped DNA Origami Templates. The Journal of Physical Chemistry C. DOI: 10.1021/acs.jpcc.3c07020
Verma KK, Alam SB, Bendickson L, Palo PE, Nilsen-Hamilton M, Prozorov T (2023) Metallization of DNA Origami Triangles Probed with HAADF-S/TEM, SEM, and AFM: a Correlative Study. Microsc Microanal 29, 2015. DOI: 10.1093/micmic/ozad067.1043
2022
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 Ligands with polyfluorophenyl moieties 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 B 126, 7114-7125. doi: 10.1021/acs.jpcb.2c04649
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 J Molecular Science 23, 10305. DOI: 10.3390/ijms231810305
2021
Ozturk M, Nilsen-Hamilton M, Ilgu M (2021) Aptamer Applications in Neuroscience. Pharmaceuticals. 14(12):1260-. DOI:10.3390/ph14121260. Aptamer Applications Google Scholar
2020
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. DOI: 10.1038/s41598-020-63393-x Lipocalin2 Gene Google Scholar
S. Yan, Peck, J., Ilgu, M., Nilsen-Hamilton, M., and Lamm, M. H., (2020) “The Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer”, ACS Omega, vol. 5, no. 32, pp. 20187–20201 doi: 10.1021/acsomega.0c01867 Sampling Performance Google Scholar
2019
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. Aptamers for diagnostics Google Scholar
S. Banerjee and Nilsen-Hamilton, M., “Aptamers for Infectious Disease Diagnosis”, in IntechOpen, 2019. Infectious Disease Diagnosis 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. DFHI Derivatives 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. aptamer-ligand interaction 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. Electron Microscopy 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. aptamer-functionalized nanoporous membrane Google Scholar
2018
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. A 2'FY-RNA 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. Aptamer-enabled uptake 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. Metamaterial building blocks Google Scholar
2017
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. IL-10R Google Scholar
2016
M. Ilgu and Nilsen-Hamilton, M., “Aptamers in Analytics”, The Analyst, vol. 141, pp. 1551-1568, 2016. Aptamers in Analytics 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. IMAGEtags 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. Magnetite Nanoparticles 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. Cocaine aptamer Google Scholar
2015
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. Confocal microscopy 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. Surface Hydrophobicity 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. FRET Aptamer 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. Morphological transformations Google Scholar
2014
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. Neomycin-B RNA aptemer 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. Alternative SELEX 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. Live-cell imaging Google Scholar
2013
J. Banerjee and Nilsen-Hamilton, M., “Aptamers: multifunctional molecules for biomedical research”, Journal of molecular medicine, vol. 91, pp. 1333-42, 2013. Aptamers: multifunctional molecules 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. Vitro selection 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. Mms6 magnetosome 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. RNA aptamers 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. Western blots Google Scholar
2012
L. Wang and Nilsen-Hamilton, M., “Biomineralization proteins: from vertebrates to bacteria”, Frontiers in Biology, vol. 8, pp. 234-246, 2012. Biomineralization proteins 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. Discrete dynamical system 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. Fluorescent compounds 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. Magnetite nanocrystals 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. Micropatterned polymer substrates 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. RNA aptamer-based microcantilever sensor 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. Plasminogen activator inhibitor typ 1 expression Google Scholar
2011
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. Aptemer functionalized microcantilever 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. ICGA-PSO-ELM 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. Lipocalin-2-loaded Amphiphilic Polyanhydride 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. Biphasic iron-binding characteristics Google Scholar
2010
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. Astrocyte-derived interleukin-6 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. Multiple-target SELEX 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. Abelson kinase 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. Expanded macrophage population Google Scholar
2009
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. Aptamer structure that controls chemical reactivity 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. Interin alpha3beta1 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. Aptamers in chemotherapy and imaging 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. Pancreatic secretory trypsin inhibitor Google Scholar
2008
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. Differential surface stress sensor 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. Fluorinated analogs of malachite green Google Scholar
2007
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. Acute endotexemia 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. Cobalt ferrite nanocrystals Google Scholar
H. A. Levine and Nilsen-Hamilton, M., “A mathematical analysis of SELEX”, Computational Biology and Chemistry, vol. 31, pp. 11-35, 2007. Mathematical analysis of SELEX 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. Protein-mediated synthesis 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. Standardized nomenclature Google Scholar