Lyu, M., Kong, L., Yang, Z., Wu, Y., Mcghee, C. E., & Lu, Y. (Accepted/In press). PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity. Journal of the American Chemical Society. https://doi.org/10.1021/jacs.1c03129
Pathania, A., Liu, W., Matityahu, A., Irudayaraj, J., & Onn, I. (2021). Chromosome loading of cohesin depends on conserved residues in Scc3. Current Genetics, 67(3), 447-459. https://doi.org/10.1007/s00294-020-01150-3
Barg, A., Dolecek, L., Gabrys, R., Katona, G. O. H., Korner, J., McGregor, A., Milenkovic, O., Mesnager, S., & Zemor, G. (2021). Guest Editorial Special Issue: 'From Deletion-Correction to Graph Reconstruction: In Memory of Vladimir I. Levenshtein'. IEEE Transactions on Information Theory, 67(6), 3187-3189. [9437360]. https://doi.org/10.1109/TIT.2021.3072555
Ganguli, A., Mostafa, A., Berger, J., Lim, J., Araud, E., Baek, J., Stewart de Ramirez, S. A., Baltaji, A., Roth, K., Aamir, M., Aedma, S., Mady, M., Mahajan, P., Sathe, S., Johnson, M., White, K., Kumar, J., Valera, E., & Bashir, R. (2021). Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples. Analytical Chemistry. https://doi.org/10.1021/acs.analchem.0c05170
Tian, S., Fan, R., Albert, T., Khade, R. L., Dai, H., Harnden, K. A., Hosseinzadeh, P., Liu, J., Nilges, M. J., Zhang, Y., Moënne-Loccoz, P., Guo, Y., & Lu, Y. (2021). Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins. Chemical Science, 12(19), 6569-6579. https://doi.org/10.1039/d1sc00364j
Valera, E., Jankelow, A., Lim, J., Kindratenko, V., Ganguli, A., White, K., Kumar, J., & Bashir, R. (2021). COVID-19 Point-of-Care Diagnostics: Present and Future. ACS Nano. https://doi.org/10.1021/acsnano.1c02981
Baek, A. E., Krawczynska, N., Das Gupta, A., Dvoretskiy, S. V., You, S., Park, J., Deng, Y-H., Sorrells, J. E., Smith, B. P., Ma, L., Nelson, A. T., McDowell, H. B., Sprenger, A., Henn, M. A., Madak-Erdogan, Z., Kong, H., Boppart, S. A., Boppart, M. D., & Nelson, E. R. (Accepted/In press). The cholesterol metabolite 27-hydroxycholesterol increases the secretion of extracellular vesicles which promote breast cancer progression. Endocrinology, [bqab095]. https://doi.org/10.1210/endocr/bqab095
Arredondo Eve, A., Tunc, E., Liu, Y-J., Agrawal, S., Erbak Yilmaz, H., Emren, S. V., Akyıldız Akçay, F., Mainzer, L., Žurauskienė, J., & Madak Erdogan, Z. (2021). Identification of Circulating Diagnostic Biomarkers for Coronary Microvascular Disease in Postmenopausal Women Using Machine-Learning Techniques. Metabolites, 11(6). https://doi.org/10.3390/metabo11060339
Ren, W., Ahmad, S., & Irudayaraj, J. (2021). 16S rRNA Monitoring Point-of-Care Magnetic Focus Lateral Flow Sensor. ACS Omega, 6(16), 11095-11102. https://doi.org/10.1021/acsomega.1c01307
Qian, R. C., Zhou, Z. R., Guo, W., Wu, Y., Yang, Z., & Lu, Y. (2021). Cell Surface Engineering Using DNAzymes: Metal Ion Mediated Control of Cell-Cell Interactions. Journal of the American Chemical Society, 143(15). https://doi.org/10.1021/jacs.1c00060
Ganguli, A., Mostafa, A., Saavedra, C., Kim, Y., Le, P., Faramarzi, V., Feathers, R. W., Berger, J., Ramos-Cruz, K. P., Adeniba, O., Diaz, G. J. P., Drnevich, J., Wright, C. L., Hernandez, A. G., Lin, W., Smith, A. M., Kosari, F., Vasmatzis, G., Anastasiadis, P. Z., & Bashir, R. (2021). Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging. Science Advances, 7(17), [eabc1323]. https://doi.org/10.1126/sciadv.abc1323
Xing, S., Lin, Y., Cai, L., Basa, P. N., Shigemoto, A. K., Zheng, C., Zhang, F., Burdette, S. C., & Lu, Y. (2021). Detection and Quantification of Tightly Bound Zn2+in Blood Serum Using a Photocaged Chelator and a DNAzyme Fluorescent Sensor. Analytical Chemistry, 93(14), 5856-5861. https://doi.org/10.1021/acs.analchem.1c00140
Shi, Y., Wang, M., Zhou, L., Shen, X., Wang, J., Mo, N., Zhao, G., Yang, S., Zhu, X., & Smith, A. M. (2021). Construction, release and cellular imaging application of triethylamine-responsive fluorescent quantum dots based on supramolecular self-assembly. European Polymer Journal, 148, [110353]. https://doi.org/10.1016/j.eurpolymj.2021.110353
Chembazhi, U. V., Bangru, S., Hernaez, M., & Kalsotra, A. (2021). Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver. Genome Research, 31(4), 576-591. https://doi.org/10.1101/gr.267013.120
Zhao, B., Che, C., Wang, W., Li, N., & Cunningham, B. T. (2021). Single-step, wash-free digital immunoassay for rapid quantitative analysis of serological antibody against SARS-CoV-2 by photonic resonator absorption microscopy. Talanta, 225, [122004]. https://doi.org/10.1016/j.talanta.2020.122004
Solomon, E. A., Rooney, A. M., Rodriguez, A. M., Micheva-Viteva, S., Bashir, R., Iyer, R., & Harris, J. F. (2021). Neuromuscular Junction Model Optimized for Electrical Platforms. Tissue Engineering - Part C: Methods, 27(4), 242-252. https://doi.org/10.1089/ten.tec.2020.0292
Xu, W., He, W., Du, Z., Zhu, L., Huang, K., Lu, Y., & Luo, Y. (2021). Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications. Angewandte Chemie - International Edition, 60(13), 6890-6918. https://doi.org/10.1002/anie.201909927
Li, N., Canady, T. D., Huang, Q., Wang, X., Fried, G. A., & Cunningham, B. T. (2021). Photonic resonator interferometric scattering microscopy. Nature communications, 12(1), [1744]. https://doi.org/10.1038/s41467-021-21999-3
Zhang, S., Luan, Y., Xiong, M., Zhang, J., Lake, R., & Lu, Y. (2021). DNAzyme Amplified Aptasensing Platform for Ochratoxin A Detection Using a Personal Glucose Meter. ACS Applied Materials and Interfaces, 13(8), 9472-9481. https://doi.org/10.1021/acsami.0c20417
Zhou, Z., Yan, R., Jiang, W., & Irudayaraj, J. M. K. (2021). Chromatin hierarchical branching visualized at the nanoscale by electron microscopy. Nanoscale Advances, 3(4), 1019-1028. https://doi.org/10.1039/d0na00359j
Reed, C. J., Lam, Q. N., Mirts, E. N., & Lu, Y. (2021). Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chemical Society Reviews, 50(4), 2486-2539. https://doi.org/10.1039/d0cs01297a
Geng, J., Zhang, X., Prabhu, S., Shahoei, S. H., Nelson, E. R., Swanson, K. S., Anastasio, M. A., & Smith, A. M. (2021). 3D microscopy and deep learning reveal the heterogeneity of crown-like structure microenvironments in intact adipose tissue. Science Advances, 7(8), [eabe2480]. https://doi.org/10.1126/sciadv.abe2480
Chen, S., Son, J., Huang, S., Watanabe, K., Taniguchi, T., Bashir, R., Van Der Zande, A. M., & King, W. P. (2021). Tip-Based Cleaning and Smoothing Improves Performance in Monolayer MoS2Devices. ACS Omega, 6(5), 4013-4021. https://doi.org/10.1021/acsomega.0c05934
Ahsen, M. E., Garimella, A., Subramanyam, R., & Wu, A. (2021). Keeping Kids Learning: Online Crowdfunding Communities Respond to the COVID-19 Pandemic. https://doi.org/10.2139/ssrn.3779438
Petrik, I. D., Davydov, R., Kahle, M., Sandoval, B., Dwaraknath, S., Adelroth, P., Hoffman, B., & Lu, Y. (2021). An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network. Biochemistry, 60(4), 346-355. https://doi.org/10.1021/acs.biochem.0c00852
Shinn, L. M., Li, Y., Mansharamani, A., Auvil, L. S., Welge, M. E., Bushell, C. B., Khan, N. A., Charron, C. S., Novotny, J. A., Baer, D. J., Zhu, R., & Holscher, H. D. (2021). Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of nutrition, 151(2), 423-433. https://doi.org/10.1093/jn/nxaa285
Prabhu, S., Deng, H., Cross, T. W. L., Shahoei, S. H., Konopka, C. J., Gonzalez Medina, N., Applegate, C. C., Wallig, M. A., Dobrucki, W., Nelson, E. R., Smith, A. M., & Swanson, K. S. (2021). Nanocarriers targeting adipose macrophages increase glucocorticoid anti-inflammatory potency to ameliorate metabolic dysfunction. Biomaterials Science, 9(2), 506-518. https://doi.org/10.1039/d0bm01142h
Liu, X., Machado, R. A., & Milenkovic, O. (2021). Directed Intersection Representations and the Information Content of Digraphs. IEEE Transactions on Information Theory, 67(1), 347-357. [9236641]. https://doi.org/10.1109/TIT.2020.3033168
Taneja, I., Damhorst, G. L., Lopez-Espina, C., Zhao, S. D., Zhu, R., Khan, S., White, K., Kumar, J., Vincent, A., Yeh, L., Majdizadeh, S., Weir, W., Isbell, S., Skinner, J., Devanand, M., Azharuddin, S., Meenakshisundaram, R., Upadhyay, R., Syed, A., ... Bashir, R. (Accepted/In press). Diagnostic and prognostic capabilities of a biomarker and EMR-based machine learning algorithm for sepsis. Clinical and Translational Science. https://doi.org/10.1111/cts.13030
Guo, B., Holscher, H. D., Auvil, L. S., Welge, M. E., Bushell, C. B., Novotny, J. A., Baer, D. J., Burd, N. A., Khan, N. A., & Zhu, R. (Accepted/In press). Estimating Heterogeneous Treatment Effect on Multivariate Responses Using Random Forests. Statistics in Biosciences. https://doi.org/10.1007/s12561-021-09310-w
Liu, Y., Han, Z., Sarkar, S., & Smith, A. M. (2021). Fluorescence In Situ Hybridization with Quantum Dot Labels in E. coli Cells. In Methods in Molecular Biology (pp. 141-155). (Methods in Molecular Biology; Vol. 2246). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-1115-9_10
Vega-Vásquez, P., Mosier, N. S., & Irudayaraj, J. (Accepted/In press). Hormesis-Inducing Essential Oil Nanodelivery System Protects Plants against Broad Host-Range Necrotrophs. ACS Nano. https://doi.org/10.1021/acsnano.0c09759
Shi, Y., Lim, S. J., Ma, L., Duan, N., Yan, X., Tang, X., Yang, W., Yang, S., Hu, J., Smith, A. M., & Zhu, X. (Accepted/In press). Inorganic-Ligand Quantum Dots Meet Inorganic-Ligand Semiconductor Nanoplatelets: A Promising Fusion to Construct All-Inorganic Assembly. Inorganic Chemistry. https://doi.org/10.1021/acs.inorgchem.1c00880
Levitin, H. A., Foss, K. D., Li, Z., Reinhart Dungar, J. M., Hague, D. W., & Fan, T. M. (Accepted/In press). Pharmacokinetics of a cytosine arabinoside subcutaneous protocol in dogs with meningoencephalomyelitis of unknown aetiology. Journal of Veterinary Pharmacology and Therapeutics. https://doi.org/10.1111/jvp.12980
Dau, S. H., Dinh, T. X., Kiah, H. M., Luong, T. T., & Milenkovic, O. (Accepted/In press). Repairing Reed-Solomon Codes via Subspace Polynomials. IEEE Transactions on Information Theory. https://doi.org/10.1109/TIT.2021.3071878
Li, Y., Zhu, R., Qu, A., Ye, H., & Sun, Z. (Accepted/In press). Topic Modeling on Triage Notes With Semiorthogonal Nonnegative Matrix Factorization. Journal of the American Statistical Association. https://doi.org/10.1080/01621459.2020.1862667
King, W. P., Amos, J., Azer, M., Baker, D., Bashir, R., Best, C., Bethke, E., Boppart, S. A., Bralts, E., Corey, R. M., Dietkus, R., Durack, G., Elbel, S., Elliott, G., Fava, J., Goldenfeld, N., Goldstein, M. H., Hayes, C., Herndon, N., ... Wooldridge, A. R. (2020). Emergency ventilator for COVID-19. PloS one, 15(12), e0244963. [e0244963]. https://doi.org/10.1371/journal.pone.0244963
Goswami, N., He, Y. R., Deng, Y-H., Oh, C., Sobh, N., Valera, E., Bashir, R., Ismail, N., Kong, H. J., Nguyen, T. H., Best-Popescu, C., & Popescu, G. (2020). Rapid SARS-CoV-2 Detection and Classification Using Phase Imaging with Computational Specificity. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.12.14.422601
Young, T. J., Cui, Y., Pfeffer, C., Hobbs, E., Liu, W., Irudayaraj, J., & Kirchmaier, A. L. (2020). CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac, preventing ectopic silencing. PLoS genetics, 16(12), [e1009226]. https://doi.org/10.1371/journal.pgen.1009226
Wang, Y., Counihan, M. J., Lin, J. W., Rodríguez-López, J., Yang, H., & Lu, Y. (2020). Quantitative Analysis of DNA-Mediated Formation of Metal Nanocrystals. Journal of the American Chemical Society, 142(48), 20368-20379. https://doi.org/10.1021/jacs.0c08604
Yazdi, S. M. H. T., Gabrys, R., & Milenkovic, O. (2020). Author Correction: Portable and Error-Free DNA-Based Data Storage (Scientific Reports, (2017), 7, 1, (5011), 10.1038/s41598-017-05188-1). Scientific reports, 10(1), [7026]. https://doi.org/10.1038/s41598-020-60080-9
Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J. P., Soloveichik, D., Zhao, H., & Milenkovic, O. (2020). DNA punch cards for storing data on native DNA sequences via enzymatic nicking. Nature communications, 11(1), [1742]. https://doi.org/10.1038/s41467-020-15588-z
Smith, B. P., Auvil, L. S., Welge, M., Bushell, C. B., Bhargava, R., Elango, N., Johnson, K., & Madak-Erdogan, Z. (2020). Identification of early liver toxicity gene biomarkers using comparative supervised machine learning. Scientific reports, 10(1), [19128]. https://doi.org/10.1038/s41598-020-76129-8
Athreya, N., Milenkovic, O., & Leburton, J. P. (2020). Interaction dynamics and site-specific electronic recognition of DNA-nicks with 2D solid-state nanopores. npj 2D Materials and Applications, 4(1), [32]. https://doi.org/10.1038/s41699-020-00166-0
Liu, F., Mao, J., Kong, W., Hua, Q., Feng, Y., Bashir, R., & Lu, T. (2020). Interaction variability shapes succession of synthetic microbial ecosystems. Nature communications, 11(1), [309]. https://doi.org/10.1038/s41467-019-13986-6
Pagan-Diaz, G. J., Drnevich, J., Ramos-Cruz, K. P., Sam, R., Sengupta, P., & Bashir, R. (2020). Modulating electrophysiology of motor neural networks via optogenetic stimulation during neurogenesis and synaptogenesis. Scientific reports, 10(1), [12460]. https://doi.org/10.1038/s41598-020-68988-y
Adeniba, O. O., Corbin, E. A., Ganguli, A., Kim, Y., & Bashir, R. (2020). Simultaneous time-varying viscosity, elasticity, and mass measurements of single adherent cancer cells across cell cycle. Scientific reports, 10(1), [12803]. https://doi.org/10.1038/s41598-020-69638-z
Cazier, J-B., Mainzer, L. S., Ge, W., Žurauskienė, J., & Madak-Erdogan, Z. (2020). Health disparities research is enabled by data diversity but requires much tighter integration of collaborative efforts. Journal of Global Health, 10(2), 020351. https://doi.org/10.7189/jogh.10.020351
Salapa, J., Bushman, A., Lowe, K., & Irudayaraj, J. (2020). Nano drug delivery systems in upper gastrointestinal cancer therapy. Nano Convergence, 7(1), [38]. https://doi.org/10.1186/s40580-020-00247-2
Saba, C. F., Clifford, C., Burgess, K., Phillips, B., Vail, D., Wright, Z., Curran, K., Fan, T., Elmslie, R., Post, G., & Thamm, D. (2020). Rabacfosadine for naïve canine intermediate to large cell lymphoma: Efficacy and adverse event profile across three prospective clinical trials. Veterinary and comparative oncology, 18(4), 763-769. https://doi.org/10.1111/vco.12605
Jabeen, M., Fayyaz, M., & Irudayaraj, J. (2020). Epigenetic Modifications, and Alterations in Cell Cycle and Apoptosis Pathway in A549 Lung Carcinoma Cell Line upon Exposure to Perfluoroalkyl Substances. Toxics, 8(4), [112]. https://doi.org/10.3390/toxics8040112
Ganguli, A., Mostafa, A., Berger, J., Stewart de Ramirez, S. A., Baltaji, A., Roth, K., Aamir, M., Aedma, S., Mady, M., Mahajan, P., Sathe, S., Johnson, M., White, K., Kumar, J., Valera, E., & Bashir, R. (2020). RT-LAMP assay for ultra-sensitive detection of SARS-CoV-2 in saliva and VTM clinical samples. (medRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.11.16.20232678
Ganguli, A., Mostafa, A., Berger, J., de Ramirez, S. A. S., Baltaji, A., Roth, K., Aamir, M., Aedma, S., Mady, M., Mahajan, P., Sathe, S., Johnson, M., White, K., Kumar, J., Valera Cano, E. A., & Bashir, R. (2020). RT-LAMP assay for ultra-sensitive detection of SARS-CoV-2 in saliva and VTM clinical samples. Unknown Journal. https://doi.org/10.1101/2020.11.16.20232678
Prabhu, S., Deng, H., Cross, T-W. L., Shahoei, S. H., Konopka, C. J., Gonzalez Medina, N., Applegate, C. C., Wallig, M. A., Dobrucki, L. W., Nelson, E. R., Smith, A. M., & Swanson, K. S. (2020). Nanocarriers targeting adipose macrophages increase glucocorticoid anti-inflammatory potency to ameliorate metabolic dysfunction. Biomaterials Science. https://doi.org/10.1039/d0bm01142h
Liu, X., & Milenkovic, O. (2020). Finding the second-best candidate under the mallows model. Unknown Journal.
Jena, S., Damayanti, N. P., Tan, J., Pratt, E. D., Irudayaraj, J. M. K., & Parker, L. L. (2020). Multiplexable fluorescence lifetime imaging (FLIM) probes for Abl and Src-family kinases. Chemical Communications, 56(87), 13409-13412. https://doi.org/10.1039/D0CC05030J
Gabrys, R., Pattabiraman, S., Rana, V., Ribeiro, J., Cheraghchi, M., Guruswami, V., & Milenkovic, O. (2020). AC-DC: Amplification Curve Diagnostics for Covid-19 Group Testing. (arXiv:2011.05223).
Eagleman, D. E., Zhu, J., Liu, D. C., Seimetz, J., Kalsotra, A., & Tsai, N. P. (2020). Unbiased Proteomic Screening Identifies a Novel Role for the E3 Ubiquitin Ligase Nedd4-2 in Translational Suppression During ER Stress. Journal of Neurochemistry. https://doi.org/10.1111/jnc.15219
Chee, Y. M., Colbourn, C. J., Dau, H., Gabrys, R., Ling, A. C. H., Lusi, D., & Milenkovic, O. (2020). Access balancing in storage systems by labeling partial Steiner systems. Designs, Codes, and Cryptography, 88(11), 2361-2376. https://doi.org/10.1007/s10623-020-00786-z
SUN, QINYU., HAO, QINYU., LIN, YO. CHUEN., SONG, YOU. JIN., BANGRU, SUSHANT., ARIF, WAQAR., TRIPATHI, VIDISHA., ZHANG, YANG., CHO, JUNG. HYUN., FREIER, SUSAN. M., JENKINS, LISA. M., MA, JIAN., YOON, JE. HYUN., KALSOTRA, AUINASH., LAL, ASHISH., PRASANTH, SUPRIYA. G., & PRASANTH, KANNANGANATTU. V. (2020). Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-MIRHG for efficient cell cycle reentry. RNA, 26(11), 1603-1620. https://doi.org/10.1261/rna.075309.120
DREAM SCTC Consortium, Tanevski, J., Nguyen, T., Truong, B., Karaiskos, N., Ahsen, M. E., Zhang, X., Shu, C., Xu, K., Liang, X., Hu, Y., Pham, H. V., Xiaomei, L., Le, T. D., Tarca, A. L., Bhatti, G., Romero, R., Karathanasis, N., Loher, P., ... Meyer, P. (2020). Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Science Alliance, 3(11), [e202000867]. https://doi.org/10.26508/lsa.202000867
Aloysius Dhivya, M., Aberami, S., Nikhalashree, S., Biswas, J., Liu, W., Irudayaraj, J., Sulochana, K. N., Coral, K., & Bharathi Devi, S. R. (2020). Copper mediates mitochondrial biogenesis in retinal pigment epithelial cells. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1866(10), [165843]. https://doi.org/10.1016/j.bbadis.2020.165843
Cheraghchi, M., Gabrys, R., Milenkovic, O., & Ribeiro, J. (2020). Coded Trace Reconstruction. IEEE Transactions on Information Theory, 66(10), 6084-6103. [9097932]. https://doi.org/10.1109/TIT.2020.2996377
Shinn, L. M., Li, Y., Mansharamani, A., Auvil, L. S., Welge, M. E., Bushell, C., Khan, N. A., Charron, C. S., Novotny, J. A., Baer, D. J., Zhu, R., & Holscher, H. D. (2020). Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults. The Journal of nutrition. https://doi.org/10.1093/jn/nxaa285
Xue, C., Zhang, S., Yu, X., Hu, S., Lu, Y., & Wu, Z. S. (2020). Periodically Ordered, Nuclease-Resistant DNA Nanowires Decorated with Cell-Specific Aptamers as Selective Theranostic Agents. Angewandte Chemie - International Edition, 59(40), 17540-17547. https://doi.org/10.1002/anie.202004805
Ganguli, A., Mostafa, A., Berger, J., Aydin, M. Y., Sun, F., Stewart de Ramirez, S. A., Valera, E., Cunningham, B. T., King, W. P., & Bashir, R. (2020). Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2. Proceedings of the National Academy of Sciences, 117(37), 22727-22735. [202014739]. https://doi.org/10.1101/2020.05.21.108381, https://doi.org/10.1073/pnas.2014739117
Ballance, W. C., Karthikeyan, V., Oh, I., Qin, E. C., Seo, Y., Spearman-White, T., Bashir, R., Hu, Y., Phillips, H., & Kong, H. (2020). Preoperative vascular surgery model using a single polymer tough hydrogel with controllable elastic moduli. Soft Matter, 16(34), 8057-8068. https://doi.org/10.1039/d0sm00981d
Park, I., Lim, J. W., Kim, S. H., Choi, S., Ko, K. H., Son, M. G., Chang, W. J., Yoon, Y. R., Yang, S., Key, J., Kim, Y. S., Eom, K., Bashir, R., Lee, S. Y., & Lee, S. W. (2020). Variable Membrane Dielectric Polarization Characteristic in Individual Live Cells. Journal of Physical Chemistry Letters, 11(17), 7197-7203. https://doi.org/10.1021/acs.jpclett.0c01427
Wang, J., Park, J., Zhang, X., Park, I., Kilicarslan, E., Kim, Y., Bashir, R., & Gazzola, M. (2020). Computationally assisted design and selection of maneuverable biological walking machines. Unknown Journal. https://doi.org/10.1101/2020.09.01.278622
Wen, Y., Chen, J., Li, J., Arif, W., Kalsotra, A., & Irudayaraj, J. (2020). Effect of PFOA on DNA Methylation and Alternative Splicing in Mouse Liver. Toxicology Letters, 329, 38-46. https://doi.org/10.1016/j.toxlet.2020.04.012
Wen, Y., Rattan, S., Flaws, J. A., & Irudayaraj, J. (2020). Multi and transgenerational epigenetic effects of di-(2-ethylhexyl) phthalate (DEHP) in liver. Toxicology and Applied Pharmacology, 402, [115123]. https://doi.org/10.1016/j.taap.2020.115123
Cotul, E. K., Zuo, Q., Santaliz-Casiano, A., Imir, O. B., Mogol, A. N., Tunc, E., Duong, K., Lee, J. K., Ramesh, R., Odukoya, E., Kesavadas, M. P., Ziogaite, M., Smith, B. P., Mao, C., Shapiro, D. J., Park, B. H., Katzenellenbogen, B. S., Daly, D., Aranda, E., ... Madak-Erdogan, Z. (2020). Combined Targeting of Estrogen Receptor Alpha and Exportin 1 in Metastatic Breast Cancers. Cancers, 12(9), 1-22. [2397]. https://doi.org/10.3390/cancers12092397
Lim, J. Y. C., Yu, Y., Jin, G., Li, K., Lu, Y., Xie, J., & Tan, Y. N. (2020). Establishing empirical design rules of nucleic acid templates for the synthesis of silver nanoclusters with tunable photoluminescence and functionalities towards targeted bioimaging applications. Nanoscale Advances, 2(9), 3921-3932. https://doi.org/10.1039/d0na00381f
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Huang, Q., & Cunningham, B. T. (2019). Microcavity-Mediated Spectrally Tunable Amplification of Absorption in Plasmonic Nanoantennas. Nano letters, 19(8), 5297-5303. https://doi.org/10.1021/acs.nanolett.9b01764
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Ghonge, T., Ceylan Koydemir, H., Valera, E., Berger, J., Garcia, C., Nawar, N., ... Bashir, R. (2019). Smartphone-imaged microfluidic biochip for measuring CD64 expression from whole blood. Analyst, 144(13), 3925-3935. https://doi.org/10.1039/c9an00532c
Grant, L., Raman, R., Cvetkovic, C., Ferrall-Fairbanks, M. C., Pagan-Diaz, G. J., Hadley, P., ... Bashir, R. (2019). Long-Term Cryopreservation and Revival of Tissue-Engineered Skeletal Muscle. Tissue Engineering - Part A, 25(13-14), 1023-1036. https://doi.org/10.1089/ten.tea.2018.0202
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Lee, J. Y., Bai, Y., Chembazhi, U. V., Peng, S., Yum, K., Luu, L. M., ... Zimmerman, S. C. (2019). Intrinsically cell-penetrating multivalent and multitargeting ligands for myotonic dystrophy type 1. Proceedings of the National Academy of Sciences of the United States of America, 116(18), 8709-8714. https://doi.org/10.1073/pnas.1820827116
Satyavolu, N. S. R., Peinetti, A. S., Wang, Y., Ali, A. S., Lin, J. W., & Lu, Y. (2019). Silver-Assisted Synthesis of High-Indexed Palladium Tetrahexahedral Nanoparticles and Their Morphological Variants. Chemistry of Materials, 31(8), 2923-2929. https://doi.org/10.1021/acs.chemmater.9b00275
Mirts, E. N., Bhagi-Damodaran, A., & Lu, Y. (2019). Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors. Accounts of chemical research, 52(4), 935-944. https://doi.org/10.1021/acs.accounts.9b00011
Xu, J., Qiao, X., Zhang, J., Cheng, N., Sheng, Q., Zheng, J., ... Lu, Y. (2019). Point-of-care monitoring of intracellular glutathione and serum triglyceride levels using a versatile personal glucose meter. Analytical Methods, 11(14), 1849-1856. https://doi.org/10.1039/c8ay02709a
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Dikanov, S. A., Berry, S. M., & Lu, Y. (2019). HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered Cu A Site in Azurin and Its His120Gly Variant Inorganic Chemistry, 58(7), 4437-4445. https://doi.org/10.1021/acs.inorgchem.8b03604
Zhang, J. J., & Lu, Y. (2019). Advancing point-of-care diagnostics of metabolites through engineering semisynthetic proteins. Clinical Chemistry, 65(4), 507-509. https://doi.org/10.1373/clinchem.2018.298836
Young, T. J., Cui, Y., Irudayaraj, J., & Kirchmaier, A. L. (2019). Modulation of gene silencing by Cdc7p via H4 K16 acetylation and phosphorylation of chromatin assembly factor CAF-1 in saccharomyces cerevisiae. Genetics, 211(4), 1219-1237. https://doi.org/10.1534/genetics.118.301858
Damayanti, N. P., Buno, K., Voytik Harbin, S. L., & Irudayaraj, J. M. K. (2019). Epigenetic Process Monitoring in Live Cultures with Peptide Biosensors. ACS Sensors, 4(3), 562-565. https://doi.org/10.1021/acssensors.8b01134
Zhang, J. J., Lan, T., & Lu, Y. (2019). Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications. Advanced Healthcare Materials, 8(6), [1801158]. https://doi.org/10.1002/adhm.201801158
Ko, E., Yu, S. J., Pagan-Diaz, G. J., Mahmassani, Z., Boppart, M. D., Im, S. G., ... Kong, H. (2019). Matrix Topography Regulates Synaptic Transmission at the Neuromuscular Junction. Advanced Science, 6(6), [1801521]. https://doi.org/10.1002/advs.201801521
Chen, S., Kim, S., Chen, W., Yuan, J., Bashir, R., Lou, J., ... King, W. P. (2019). Monolayer MoS 2 Nanoribbon Transistors Fabricated by Scanning Probe Lithography Nano letters, 19(3), 2092-2098. https://doi.org/10.1021/acs.nanolett.9b00271
Sun, Q., Zhu, R., Wang, T., & Zeng, D. (2019). Counting process-based dimension reduction methods for censored outcomes. Biometrika, 106(1), 181-186. https://doi.org/10.1093/biomet/asy064
Bibak, K., & Milenkovic, O. (2019). Explicit formulas for the weight enumerators of some classes of deletion correcting codes. IEEE Transactions on Communications, 67(3), 1809-1816. [8573841]. https://doi.org/10.1109/TCOMM.2018.2886354
Ren, W., Mohammed, S. I., Wereley, S., & Irudayaraj, J. M. K. (2019). Magnetic Focus Lateral Flow Sensor for Detection of Cervical Cancer Biomarkers. Analytical chemistry, 91(4), 2876-2884. https://doi.org/10.1021/acs.analchem.8b04848
Seimetz, J., Arif, W., Bangru, S., Hernaez, M., & Kalsotra, A. (2019). Cell-type specific polysome profiling from mammalian tissues. Methods, 155, 131-139. https://doi.org/10.1016/j.ymeth.2018.11.015
Ren, W., Ballou, D. R., FitzGerald, R., & Irudayaraj, J. M. K. (2019). Plasmonic enhancement in lateral flow sensors for improved sensing of E. coli O157:H7. Biosensors and Bioelectronics, 126, 324-331. https://doi.org/10.1016/j.bios.2018.10.066
Liu, W., Cui, Y., Ren, W., & Irudayaraj, J. (2019). Epigenetic biomarker screening by FLIM-FRET for combination therapy in ER+ breast cancer. Clinical epigenetics, 11(1), [16]. https://doi.org/10.1186/s13148-019-0620-6
Aguirre, M. Á., Long, K. D., Canals, A., & Cunningham, B. T. (2019). Point-of-use detection of ascorbic acid using a spectrometric smartphone-based system. Food chemistry, 272, 141-147. https://doi.org/10.1016/j.foodchem.2018.08.002
Woodburn, E. V., Long, K. D., & Cunningham, B. T. (2019). Analysis of Paper-Based Colorimetric Assays with a Smartphone Spectrometer. IEEE Sensors Journal, 19(2), 508-514. [8494768]. https://doi.org/10.1109/JSEN.2018.2876631
Kumar, P., Liu, J., Motlag, M., Tong, L., Hu, Y., Huang, X., ... Cheng, G. J. (2019). Laser Shock Tuning Dynamic Interlayer Coupling in Graphene-Boron Nitride Moiré Superlattices. Nano letters, 19(1), 283-291. https://doi.org/10.1021/acs.nanolett.8b03895
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Mi, X., Zou, F., & Zhu, R. (2019). Bagging and deep learning in optimal individualized treatment rules. Biometrics, 75(2), 674-684. https://doi.org/10.1111/biom.12990
Cui, C., Reed, J. H., Mirts, E. N., & Lu, Y. (2019). CHAPTER 2: Design and Engineering of Heme Enzymes with O 2 -dependent Catalytic Activity. In M. Ikeda-Saito, & E. Raven (Eds.), Dioxygen-dependent Heme Enzymes (13 ed., pp. 37-62). (RSC Metallobiology; Vol. 2019-January, No. 13). Royal Society of Chemistry. https://doi.org/10.1039/9781788012911-00037
Tunc, E., Eve, A. A., & Madak-Erdogan, Z. (Accepted/In press). Coronary Microvascular Dysfunction and Estrogen Receptor Signaling. Trends in Endocrinology and Metabolism. https://doi.org/10.1016/j.tem.2019.11.001
Liu, C., Yu, Y., Chen, D., Zhao, J., Yu, Y., Li, L., & Lu, Y. (2019). Cupredoxin engineered upconversion nanoparticles for ratiometric luminescence sensing of Cu2+. Nanoscale Advances, 1(7), 2580-2585. https://doi.org/10.1039/c9na00168a
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Lake, R. J., Yang, Z., Zhang, J. J., & Lu, Y. (Accepted/In press). DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions. Accounts of chemical research. https://doi.org/10.1021/acs.accounts.9b00419
Madak-Erdogan, Z., Band, S., Zhao, Y. C., Smith, B. P., Kulkoyluoglu-Cotul, E., Zuo, Q., ... Flaws, J. A. (2019). Free fatty acids rewire cancer metabolism in obesity-associated breast cancer via estrogen receptor and mTOR signaling. Cancer Research, 79(10), 2494-2510. https://doi.org/10.1158/0008-5472.CAN-18-2849
Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S., & Das, A. (2019). Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells. Journal of Lipid Research, 60(2), 375-387. https://doi.org/10.1194/jlr.M088559
Schlein, L. J., Fadl-Alla, B., Pondenis, H. C., Lezmi, S., Eberhart, C. G., LeBlanc, A. K., ... Fan, T. M. (2019). Immunohistochemical characterization of procaspase-3 overexpression as a druggable target with PAC-1, a procaspase-3 activator, in canine and human brain cancers. Frontiers in Oncology, 9(FEB), [96]. https://doi.org/10.3389/fonc.2019.00096
Feng, Z., Lin, L., Zhu, R., & Zhu, L. (2019). Nonparametric variable selection and its application to additive models. Annals of the Institute of Statistical Mathematics. https://doi.org/10.1007/s10463-019-00711-9
Dau, H., Milenkovic, O., & Puleo, G. J. (Accepted/In press). On the triangle clique cover and Kt clique cover problems. Discrete Mathematics, [111627]. https://doi.org/10.1016/j.disc.2019.111627
Xue, C., Zhang, S., Li, C., Yu, X., Ouyang, C., Lu, Y., & Wu, Z. S. (Accepted/In press). Y-Shaped Backbone-Rigidified Triangular DNA Scaffold-Directed Stepwise Movement of a DNAzyme Walker for Sensitive MicroRNA Imaging within Living Cells. Analytical chemistry. https://doi.org/10.1021/acs.analchem.9b03784
Kulkoyluoglu-Cotul, E., Arca, A., & Madak-Erdogan, Z. (2019). Crosstalk between Estrogen Signaling and Breast Cancer Metabolism. Trends in Endocrinology and Metabolism, 30(1), 25-38. https://doi.org/10.1016/j.tem.2018.10.006
Watson, M. K., Mitchell, M. A., Stern, A. W., Labelle, A. L., Joslyn, S., Fan, T. M., ... Marshall, K. (2019). EVALUATING THE CLINICAL AND PHYSIOLOGICAL EFFECTS OF LONG-TERM ULTRAVIOLET B RADIATION ON RABBITS (ORYCTOLAGUS CUNICULUS). Journal of Exotic Pet Medicine, 28, 43-55. https://doi.org/10.1053/j.jepm.2018.04.016
Dowling, M., Samuelson, J., Fadl-Alla, B., Pondenis, H. C., Byrum, M., Barger, A. M., & Fan, T. M. (2019). Overexpression of prostate specific membrane antigen by canine hemangiosarcoma cells provides opportunity for the molecular detection of disease burdens within hemorrhagic body cavity effusions. PloS one, 14(1), [e0210297]. https://doi.org/10.1371/journal.pone.0210297
Overgaard, N. H., Fan, T. M., Schachtschneider, K. M., Principe, D. R., Schook, L. B., & Jungersen, G. (2018). Of Mice, Dogs, Pigs, and Men: Choosing the Appropriate Model for Immuno-Oncology Research. ILAR Journal, 59(3), 247-262. https://doi.org/10.1093/ilar/ily014
Sabuncu, S., Reed, J. H., Lu, Y., & Moënne-Loccoz, P. (2018). Nitric Oxide Reductase Activity in Heme-Nonheme Binuclear Engineered Myoglobins through a One-Electron Reduction Cycle. Journal of the American Chemical Society, 140(50), 17389-17393. https://doi.org/10.1021/jacs.8b11037
Yang, Z., Loh, K. Y., Chu, Y. T., Feng, R., Satyavolu, N. S. R., Xiong, M., ... Lu, Y. (2018). Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles. Journal of the American Chemical Society, 140(50), 17656-17665. https://doi.org/10.1021/jacs.8b09867
Ravanmehr, V., Puleo, G. J., Bolouki, S., & Milenkovic, O. (2018). Paired threshold graphs. Discrete Applied Mathematics, 250, 291-308. https://doi.org/10.1016/j.dam.2018.05.008
Liu, Y., Le, P., Lim, S. J., Ma, L., Sarkar, S., Han, Z., ... Smith, A. M. (2018). Enhanced mRNA FISH with compact quantum dots. Nature communications, 9(1), [4461]. https://doi.org/10.1038/s41467-018-06740-x
Chen, K. L. A., Liu, X., Zhao, Y. C., Hieronymi, K., Rossi, G., Auvil, L. S., ... Madak-Erdogan, Z. (2018). Long-Term Administration of Conjugated Estrogen and Bazedoxifene Decreased Murine Fecal β-Glucuronidase Activity Without Impacting Overall Microbiome Community. Scientific reports, 8(1), [8166]. https://doi.org/10.1038/s41598-018-26506-1
Burton, J. H., Mazcko, C., LeBlanc, A., Covey, J. M., Ji, J., Kinders, R. J., ... Pommier, Y. (2018). NCI comparative oncology program testing of non-camptothecin indenoisoquinoline topoisomerase I inhibitors in naturally occurring canine lymphoma. Clinical Cancer Research, 24(23), 5830-5840. https://doi.org/10.1158/1078-0432.CCR-18-1498
Ganguli, A., Ornob, A., Spegazzini, N., Liu, Y., Damhorst, G., Ghonge, T., ... Bashir, R. (2018). Pixelated spatial gene expression analysis from tissue. Nature communications, 9(1), [202]. https://doi.org/10.1038/s41467-017-02623-9
Zhuo, Y., Choi, J. S., Marin, T., Yu, H., Harley, B. A., & Cunningham, B. T. (2018). Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM). Light: Science and Applications, 7(1), [7538]. https://doi.org/10.1038/s41377-018-0001-5
Zahid, M. U., Ma, L., Lim, S. J., & Smith, A. M. (2018). Single quantum dot tracking reveals the impact of nanoparticle surface on intracellular state. Nature communications, 9(1), [1830]. https://doi.org/10.1038/s41467-018-04185-w
Bhandari, P., Novikova, G., Goergen, C. J., & Irudayaraj, J. (2018). Ultrasound beam steering of oxygen nanobubbles for enhanced bladder cancer therapy. Scientific reports, 8(1), [3112]. https://doi.org/10.1038/s41598-018-20363-8
Peters, J. W., Beratan, D. N., Bothner, B., Dyer, R. B., Harwood, C. S., Heiden, Z. M., ... Adams, M. WW. (2018). A new era for electron bifurcation. Current Opinion in Chemical Biology, 47, 32-38. https://doi.org/10.1016/j.cbpa.2018.07.026
Yi, M., Zhu, R., & Stephens, R. M. (2018). GradientScanSurv—An exhaustive association test method for gene expression data with censored survival outcome. PloS one, 13(12), [e0207590]. https://doi.org/10.1371/journal.pone.0207590
Svec, R. L., Furiassi, L., Skibinski, C. G., Fan, T. M., Riggins, G. J., & Hergenrother, P. J. (2018). Tunable Stability of Imidazotetrazines Leads to a Potent Compound for Glioblastoma. ACS chemical biology, 13(11), 3206-3216. https://doi.org/10.1021/acschembio.8b00864
Wang, Y., Reddy Satyavolu, N. S., & Lu, Y. (2018). Sequence-specific control of inorganic nanomaterials morphologies by biomolecules. Current Opinion in Colloid and Interface Science, 38, 158-169. https://doi.org/10.1016/j.cocis.2018.10.009
Smith, L., Kohli, M., & Smith, A. M. (2018). Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration. Journal of the American Chemical Society, 140(42), 13904-13912. https://doi.org/10.1021/jacs.8b08879
Yu, Z., Zhou, W., Ma, G., Li, Y., Fan, L., Li, X., & Lu, Y. (2018). Insights into the Competition between K+ and Pb2+ Binding to a G-Quadruplex and Discovery of a Novel K+-Pb2+-Quadruplex Intermediate. Journal of Physical Chemistry B, 122(40), 9382-9388. https://doi.org/10.1021/acs.jpcb.8b08161
Bangru, S., Arif, W., Seimetz, J., Bhate, A., Chen, J., Rashan, E. H., ... Kalsotra, A. (2018). Alternative splicing rewires Hippo signaling pathway in hepatocytes to promote liver regeneration. Nature Structural and Molecular Biology, 25(10), 928-939. https://doi.org/10.1038/s41594-018-0129-2
Dau, H., Duursma, I. M., Kiah, H. M., & Milenkovic, O. (2018). Repairing Reed-Solomon Codes With Multiple Erasures. IEEE Transactions on Information Theory, 64(10), 6567-6582. [8340062]. https://doi.org/10.1109/TIT.2018.2827942
Mirts, E. N., Petrik, I. D., Hosseinzadeh, P., Nilges, M. J., & Lu, Y. (2018). A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme. Science, 361(6407), 1098-1101. https://doi.org/10.1126/science.aat8474
Mukherjee, S., Mukherjee, M., Mukherjee, A., Bhagi-Damodaran, A., Lu, Y., & Dey, A. (2018). O 2 Reduction by Biosynthetic Models of Cytochrome c Oxidase: Insights into Role of Proton Transfer Residues from Perturbed Active Sites Models of CcO. ACS Catalysis, 8(9), 8915-8924. https://doi.org/10.1021/acscatal.8b02240
Ganguli, A., Pagan-Diaz, G. J., Grant, L., Cvetkovic, C., Bramlet, M., Vozenilek, J. A., ... Bashir, R. (2018). 3D printing for preoperative planning and surgical training: a review. Biomedical microdevices, 20(3), [65]. https://doi.org/10.1007/s10544-018-0301-9
Satyavolu, N. S. R., Pishevaresfahani, N., Tan, L. H., & Lu, Y. (2018). DNA-encoded morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a high-indexed core. Nano Research, 11(9), 4549-4561. https://doi.org/10.1007/s12274-018-2035-7
Reddy, B., Hassan, U., Seymour, C., Angus, D. C., Isbell, T. S., White, K., ... Bashir, R. (2018). Point-of-care sensors for the management of sepsis. Nature biomedical engineering, 2(9), 640-648. https://doi.org/10.1038/s41551-018-0288-9
Tabatabaei Yazdi, S. M. H., Kiah, H. M., Gabrys, R., & Milenkovic, O. (2018). Mutually uncorrelated primers for DNA-based data storage. IEEE Transactions on Information Theory, 64(9), 6283-6296. [8255669]. https://doi.org/10.1109/TIT.2018.2792488
Anorma, C., Hedhli, J., Bearrood, T. E., Pino, N. W., Gardner, S. H., Inaba, H., ... Chan, J. K. F. (2018). Surveillance of Cancer Stem Cell Plasticity Using an Isoform-Selective Fluorescent Probe for Aldehyde Dehydrogenase 1A1. ACS Central Science, 4(8), 1045-1055. https://doi.org/10.1021/acscentsci.8b00313
Pagan-Diaz, G. J., Zhang, X., Grant, L., Kim, Y., Aydin, O., Cvetkovic, C., ... Bashir, R. (2018). Correction to: Simulation and Fabrication of Stronger, Larger, and Faster Walking Biohybrid Machines (Advanced Functional Materials, (2018), 28, 23, (1801145), 10.1002/adfm.201801145). Advanced Functional Materials, 28(33), [1804580]. https://doi.org/10.1002/adfm.201804580
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Zhang, J., & Lu, Y. (2018). Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets. Angewandte Chemie - International Edition, 57(31), 9702-9706. https://doi.org/10.1002/anie.201804292
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