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Research Areas

Center for Genomic Diagnostics: Publications

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 one15(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 genetics16(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 Society142(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 reports10(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 communications11(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 reports10(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 Applications4(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 communications11(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 reports10(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 reports10(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 Health10(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 Convergence7(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 oncology18(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. Toxics8(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 Journalhttps://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 Sciencehttps://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 Communications56(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 Neurochemistryhttps://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 Cryptography88(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. RNA26(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 Alliance3(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 Disease1866(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 Theory66(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 nutritionhttps://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 Edition59(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 Sciences117(37), 22727-22735. [202014739]. https://doi.org/10.1101/2020.05.21.108381https://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 Matter16(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 Letters11(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 Journalhttps://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 Letters329, 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 Pharmacology402, [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. Cancers12(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 Advances2(9), 3921-3932. https://doi.org/10.1039/d0na00381f

Ren, W., Cabush, A., & Irudayaraj, J. (2020). Checkpoint enrichment for sensitive detection of target bacteria from large volume of food matrices. Analytica Chimica Acta1127, 114-121. https://doi.org/10.1016/j.aca.2020.06.025

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Kim, Y., Pagan-Diaz, G., Gapinske, L., Kim, Y., Suh, J., Solomon, E., Harris, J. F., Nam, S. W., & Bashir, R. (Accepted/In press). Integration of Graphene Electrodes with 3D Skeletal Muscle Tissue Models. Advanced Healthcare Materials, [1901137]. https://doi.org/10.1002/adhm.201901137

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Aydin, O., Zhang, X., Nuethong, S., Pagan-Diaz, G. J., Bashir, R., Gazzola, M., & Saif, M. T. A. (2019). Neuromuscular actuation of biohybrid motile bots. Proceedings of the National Academy of Sciences of the United States of America, 116(40), 19841-19847. https://doi.org/10.1073/pnas.1907051116

Canady, T. D., Li, N., Smith, L. D., Lu, Y., Kohli, M., Smith, A. M., & Cunningham, B. T. (2019). Digital-resolution detection of microRNA with singlebase selectivity by photonic resonator absorption microscopy. Proceedings of the National Academy of Sciences of the United States of America, 116(39), 19362-19367. https://doi.org/10.1073/pnas.1904770116

Wang, W., Yu, S., Huang, S., Bi, S., Han, H., Zhang, J. R., ... Zhu, J. J. (2019). Bioapplications of DNA nanotechnology at the solid-liquid interface. Chemical Society Reviews, 48(18), 4892-4920. https://doi.org/10.1039/c8cs00402a

Li, L., Xing, H., Zhang, J., & Lu, Y. (2019). Functional DNA Molecules Enable Selective and Stimuli-Responsive Nanoparticles for Biomedical Applications. Accounts of chemical research, 52(9), 2415-2426. https://doi.org/10.1021/acs.accounts.9b00167

Rattan, S., Beers, H. K., Kannan, A., Ramakrishnan, A., Brehm, E., Bagchi, I. C., ... Flaws, J. A. (2019). Prenatal and ancestral exposure to di(2-ethylhexyl) phthalate alters gene expression and DNA methylation in mouse ovaries. Toxicology and Applied Pharmacology, 379, [114629]. https://doi.org/10.1016/j.taap.2019.114629

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

Aguirre, M. Á., Long, K. D., & Cunningham, B. T. (2019). Spectrometric Smartphone-Based System for Ibuprofen Quantification in Commercial Dosage Tablets. Journal of Pharmaceutical Sciences, 108(8), 2593-2598. https://doi.org/10.1016/j.xphs.2019.03.010

Sample, M., Boulicault, M., Allen, C., Bashir, R., Hyun, I., Levis, M., ... Zartman, J. (2019). Multi-cellular engineered living systems: Building a community around responsible research on emergence. Biofabrication, 11(4), [043001]. https://doi.org/10.1088/1758-5090/ab268c

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

Kostochka, A. V., Liu, X., Machado, R., & Milenkovic, O. (2019). Directed Intersection Representations and the Information Content of Digraphs. In 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings (pp. 1477-1481). [8849253] (IEEE International Symposium on Information Theory - Proceedings; Vol. 2019-July). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2019.8849253

Gabrys, R., Dau, H., Colbourn, C. J., & Milenkovic, O. (2019). Set-Codes with Small Intersections and Small Discrepancies. In 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings (pp. 2359-2363). [8849651] (IEEE International Symposium on Information Theory - Proceedings; Vol. 2019-July). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2019.8849651

Satyavolu, N. S. R., Loh, K. Y., Tan, L. H., & Lu, Y. (2019). Discovery of and Insights into DNA “Codes” for Tunable Morphologies of Metal Nanoparticles. Small, 15(26), [1900975]. https://doi.org/10.1002/smll.201900975

Zhao, J., Chu, H., Zhao, Y., Lu, Y., & Li, L. (2019). A NIR Light Gated DNA Nanodevice for Spatiotemporally Controlled Imaging of MicroRNA in Cells and Animals. Journal of the American Chemical Society, 141(17), 7056-7062. https://doi.org/10.1021/jacs.9b01931

Walters, K. A., Zhu, R., Welge, M., Scherler, K., Park, J. K., Rahil, Z., ... Kash, J. C. (2019). Differential effects of influenza virus NA, HA head, and HA stalk antibodies on peripheral blood leukocyte gene expression during human infection. mBio, 10(3), [e00760-19]. https://doi.org/10.1128/mBio.00760-19

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

Hu, Y., Xuan, Y., Wang, X., Deng, B., Saei, M., Jin, S., ... Cheng, G. J. (2019). Correction to: Superplastic Formation of Metal Nanostructure Arrays with Ultrafine Gaps (Advanced Materials, (2016), 28, 41, (9152-9162), 10.1002/adma.201602497). Advanced Materials, 31(14), [1900190]. https://doi.org/10.1002/adma.201900190

Kulkoyluoglu-Cotul, E., Smith, B. P., Wrobel, K., Zhao, Y. C., Chen, K. L. A., Hieronymi, K., ... Madak-Erdogan, Z. (2019). Combined Targeting of Estrogen Receptor Alpha and XPO1 Prevent Akt Activation, Remodel Metabolic Pathways and Induce Autophagy to Overcome Tamoxifen Resistance. Cancers, 11(4), [479]. https://doi.org/10.3390/cancers11040479

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

Che, C., Li, N., Long, K. D., Aguirre, M. Á., Canady, T. D., Huang, Q., ... Cunningham, B. T. (2019). Activate capture and digital counting (AC + DC) assay for protein biomarker detection integrated with a self-powered microfluidic cartridge. Lab on a chip, 19(23), 3943-3953. https://doi.org/10.1039/c9lc00728h

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

Sabri, L., Huang, Q., Liu, J. N., & Cunningham, B. T. (2019). Design of anapole mode electromagnetic field enhancement structures for biosensing applications. Optics Express, 27(5), 7196-7212. https://doi.org/10.1364/OE.27.007196

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

Gabrys, R., & Milenkovic, O. (2018). Unique Reconstruction of Coded Sequences from Multiset Substring Spectra. In 2018 IEEE International Symposium on Information Theory, ISIT 2018 (Vol. 2018-June, pp. 2540-2544). [8437909] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2018.8437909

Bibak, K., & Milenkovic, O. (2018). Weight Enumerators of Some Classes of Deletion Correcting Codes. In 2018 IEEE International Symposium on Information Theory, ISIT 2018 (Vol. 2018-June, pp. 431-435). [8437121] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT.2018.8437121

Sheung, J. Y., Ge, P., Lim, S. J., Lee, S. H., Smith, A. M., & Selvin, P. R. (2018). Structural Contributions to Hydrodynamic Diameter for Quantum Dots Optimized for Live-Cell Single-Molecule Tracking. Journal of Physical Chemistry C, 122(30), 17406-17412. https://doi.org/10.1021/acs.jpcc.8b02516

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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