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Zuo, Q., Park, N. H., Lee, J. K., Santaliz-Casiano, A., & Madak-Erdogan, Z. (2024). Navigating nonalcoholic fatty liver disease (NAFLD): Exploring the roles of estrogens, pharmacological and medical interventions, and life style. Steroids, 203, Article 109330. https://doi.org/10.1016/j.steroids.2023.109330
Zhu, H., Wu, J., Zhao, J., Yu, L., Liyarita, B. R., Xu, X., Xiao, Y., Hu, X., Shao, S., Liu, J., Wang, X., & Shao, F. (2024). Dual-functional DNA nanogels for anticancer drug delivery. Acta Biomaterialia, 175, 240-249. https://doi.org/10.1016/j.actbio.2023.12.013
Zhou, S., Lizarazo, S., Mouli, L., Chorghade, S., Cheng, R., Rajendra, K. C., Kalsotra, A., & Van Bortle, K. (2024). Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations. (bioRxiv : the preprint server for biology). https://doi.org/10.1101/2024.07.02.601767
Zhou, L., Xiong, Y., Dwivedy, A., Zheng, M., Cooper, L., Shepherd, S., Song, T., Hong, W., Le, L. T. P., Chen, X., Umrao, S., Rong, L., Wang, T., Cunningham, B. T., & Wang, X. (2024). Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition. Science Robotics, 9(96), Article eadi2084. https://doi.org/10.1126/scirobotics.adi2084
Zhao, H. (2024). Synthetic Biology Continues to Grow. ACS synthetic biology, 13(1), 1-2. https://doi.org/10.1021/acssynbio.3c00765
Zhao, Y., Park, I., Rubakhin, S. S., Bashir, R., Vlasov, Y., & Sweedler, J. V. (2024). 1-Octanol-assisted ultra-small volume droplet microfluidics with nanoelectrospray ionization mass spectrometry. Analytica Chimica Acta, 1321, Article 342998. https://doi.org/10.1016/j.aca.2024.342998
Zhao, H., Cao, M., Tran, V., & Fatma, Z. (2024). Genetic Toolbox For Metabolic Engineering Of Non-conventional Yeast. (U.S. Patent No. 12116580).
Zhao, S., Gao, K., Han, H., Stenzel, M., Yin, B., Song, H., Lawanprasert, A., Nielsen, J. E., Sharma, R., Arogundade, O. H., Pimcharoen, S., Chen, Y. J., Paul, A., Tuma, J., Collins, M. G., Wyle, Y., Cranick, M. G., Burgstone, B. W., Perez, B. S., ... Murthy, N. (2024). Acid-degradable lipid nanoparticles enhance the delivery of mRNA. Nature Nanotechnology, 19(11), 1702-1711. https://doi.org/10.1038/s41565-024-01765-4
Zhang, X., Sands, M., Lin, M., Guelfo, J., & Irudayaraj, J. (2024). In vitro toxicity of Lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) on Human Renal and Hepatoma Cells. Toxicology Reports, 12, 280-288. https://doi.org/10.1016/j.toxrep.2024.02.008
Yuan, F., Yang, L., Hsiao, S. H., Herndon, N. L., Gaulke, C. A., & Fang, Y. (2024). A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis. Virology, 592, Article 109996. https://doi.org/10.1016/j.virol.2024.109996
You, J. S., Karaman, K., Reyes-Ordoñez, A., Lee, S., Kim, Y., Bashir, R., & Chen, J. (2024). Leucyl-tRNA Synthetase Contributes to Muscle Weakness through Mammalian Target of Rapamycin Complex 1 Activation and Autophagy Suppression in a Mouse Model of Duchenne Muscular Dystrophy. American Journal of Pathology, 194(8), 1571-1580. https://doi.org/10.1016/j.ajpath.2024.04.006
Xun, G., Zhu, Z., Singh, N., Lu, J., Jain, P. K., & Zhao, H. (2024). Harnessing noncanonical crRNA for highly efficient genome editing. Nature communications, 15(1), Article 3823. https://doi.org/10.1038/s41467-024-48012-x
Wang, Y., Saha, U., Rubakhin, S. S., Roy, E. J., Smith, A. M., Sweedler, J. V., & Lam, F. (2024). High-resolution 1H-MRSI at 9.4 T by integrating relaxation enhancement and subspace imaging. NMR in Biomedicine, 37(10), Article e5161. https://doi.org/10.1002/nbm.5161
Wang, Q., Zhang, Z., Li, H., Liu, X., Han, J., Zhao, H., & Ji, H. (2024). Chem-FINESE: Validating Fine-Grained Few-shot Entity Extraction through Text Reconstruction. In Y. Graham, M. Purver, & M. Purver (Eds.), EACL 2024 - 18th Conference of the European Chapter of the Association for Computational Linguistics, Findings of EACL 2024 (pp. 1-16). (EACL 2024 - 18th Conference of the European Chapter of the Association for Computational Linguistics, Findings of EACL 2024). Association for Computational Linguistics (ACL).
Wang, H., & Zhao, Y. (2024). Plasmon-enhanced chiral absorption through electric dipole–electric quadrupole interaction. Journal of Optics, 26(8), Article 085002. https://doi.org/10.1088/2040-8986/ad535e
Wang, Y., Chembazhi, U. V., Yee, D., Chen, S., Ji, J., Wang, Y., Nguyen, KL., Lin, P., Ratti, A., Hess, RA., Qiao, H., Ko, C., Yang, J., Kalsotra, A., & Mei, W. (2024). PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators. Nucleic acids research, 52(20), 12244-12261. Article gkae862. https://doi.org/10.1093/nar/gkae862
Walukiewicz, H. E., Farris, Y., Burnet, M. C., Feid, S. C., You, Y., Kim, H., Bank, T., Christensen, D., Payne, S. H., Wolfe, A. J., Rao, C. V., & Nakayasu, E. S. (2024). Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation. mBio, 15(10), Article 01773. https://doi.org/10.1128/mbio.01773-24
Umrao, S., Zheng, M., & Wang, X. (2024). Net-Shaped DNA Nanostructure-Based Lateral Flow Assays for Rapid and Sensitive SARS-CoV-2 Detection. Analytical Chemistry, 96(8), 3291-3299. https://doi.org/10.1021/acs.analchem.3c03698
Tran, V. G., Mishra, S., Bhagwat, S. S., Shafaei, S., Shen, Y., Allen, J. L., Crosly, B. A., Tan, S. I., Fatma, Z., Rabinowitz, J. D., Guest, J. S., Singh, V., & Zhao, H. (2024). Correction to: An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis (Nature Communications, (2023), 14, 1, (6152), 10.1038/s41467-023-41616-9). Nature communications, 15(1), Article 1161. https://doi.org/10.1038/s41467-024-45331-x
Tan, S. I., Ng, I. S., & Zhao, H. (in press). Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5-Aminolevulinic Acid Production. Biotechnology and bioengineering. https://doi.org/10.1002/bit.28877
Stinson, J. A., Barbosa, M. M. P., Sheen, A., Momin, N., Fink, E., Hampel, J., Selting, K. A., Kamerer, R. L., Bailey, K. L., Wittrup, K. D., & Fan, T. M. (2024). Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs. Clinical Cancer Research, 30(18), 4029-4043. https://doi.org/10.1158/1078-0432.CCR-24-0861
Song, T., Cooper, L., Galván Achi, J., Wang, X., Dwivedy, A., Rong, L., & Wang, X. (2024). Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. Journal of the American Chemical Society, 146(9), 5894-5900. https://doi.org/10.1021/jacs.3c11760
Sivaguru, M., Mori, S., Fouke, K. W., Ajijola, O. A., Shivkumar, K., Samuel, A. Z., Bhargava, R., & Fouke, B. W. (2024). Osteopontin stabilization and collagen containment slows amorphous calcium phosphate transformation during human aortic valve leaflet calcification. Scientific reports, 14(1), Article 12222. https://doi.org/10.1038/s41598-024-62962-8
Sima, J., Wu, C., Milenkovic, O., & Szpankowski, W. (2024). Online Distribution Learning with Local Privacy Constraints. Proceedings of Machine Learning Research, 238, 460-468.
Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (2024). Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials. Journal of Nutrition, 154(1), 271-283. https://doi.org/10.1016/j.tjnut.2023.11.001
Shi, C., Patel, V. A., Mitchell, D. A., & Zhao, H. (2024). Enterolyin S, a Polythiazole-containing Hemolytic Peptide from Enterococcus caccae. ChemBioChem, 25(12), Article e202400212. https://doi.org/10.1002/cbic.202400212
Shen, Y., Dinh, H. V., Cruz, E. R., Chen, Z., Bartman, C. R., Xiao, T., Call, C. M., Ryseck, R. P., Pratas, J., Weilandt, D., Baron, H., Subramanian, A., Fatma, Z., Wu, Z. Y., Dwaraknath, S., Hendry, J. I., Tran, V. G., Yang, L., Yoshikuni, Y., ... Rabinowitz, J. D. (2024). Mitochondrial ATP generation is more proteome efficient than glycolysis. Nature chemical biology, 20(9), 1123-1132. https://doi.org/10.1038/s41589-024-01571-y
Sands, M., Zhang, X., gal, A., Laws, M., Spinella, M., Erdogan, Z. M., & Irudayaraj, J. (2024). Comparative hepatotoxicity of novel lithium bis(trifluoromethanesulfonyl)imide (LiTFSI, ie. HQ-115) and legacy Perfluorooctanoic acid (PFOA) in male mice: Insights into epigenetic mechanisms and pathway-specific responses. Environment international, 185, Article 108556. https://doi.org/10.1016/j.envint.2024.108556
Sands, M., Zhang, X., Jensen, T., La Frano, M., Lin, M., & Irudayaraj, J. (2024). PFAS assessment in fish – Samples from Illinois waters. Science of the Total Environment, 927, Article 172357. https://doi.org/10.1016/j.scitotenv.2024.172357
Saba, C. F., Fan, T. M., Phillips, B. S., Wright, Z. M., & Thamm, D. H. (2024). Alternating rabacfosadine and doxorubicin for treatment of naïve canine lymphoma. Veterinary and comparative oncology, 22(2), 278-283. https://doi.org/10.1111/vco.12975
Ren, H., Huang, C., Pan, Y., Dommaraju, S. R., Cui, H., Li, M., Gadgil, M. G., Mitchell, D. A., & Zhao, H. (2024). Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides. Nature Chemistry, 16(8), 1320-1329. https://doi.org/10.1038/s41557-024-01491-3
Ren, W., Sands, M., Han, X., Tsipursky, M., & Irudayaraj, J. (2024). Hydrogel-Based Oxygen and Drug Delivery Dressing for Improved Wound Healing. ACS Omega, 9(22), 24095-24104. https://doi.org/10.1021/acsomega.4c03324
Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B., Burke, M. D., Fan, T. M., & Hergenrother, P. J. (2024). Saliva-based molecular testing for SARS-CoV-2. (U.S. Patent No. 11926877).
Rana, V., Peng, J., Pan, C., Lyu, H., Cheng, A., Kim, M., & Milenkovic, O. (2024). Interpretable online network dictionary learning for inferring long-range chromatin interactions. PLoS computational biology, 20(5 MAY), Article e1012095. https://doi.org/10.1371/journal.pcbi.1012095
Quinn, T. P., Hess, J. L., Marshe, V. S., Barnett, M. M., Hauschild, A. C., Maciukiewicz, M., Elsheikh, S. S. M., Men, X., Schwarz, E., Trakadis, Y. J., Breen, M. S., Barnett, E. J., Zhang-James, Y., Ahsen, M. E., Cao, H., Chen, J., Hou, J., Salekin, A., Lin, P. I., ... Glatt, S. J. (2024). A primer on the use of machine learning to distil knowledge from data in biological psychiatry. Molecular Psychiatry, 29(2), 387-401. https://doi.org/10.1038/s41380-023-02334-2
Peh, G. R., Tay, T., Tan, L. L., Tiong, E., Bi, J., Goh, Y. L., Ye, S., Lin, F., Tan, C. J. X., Tan, Y. Z., Wong, J., Zhao, H., Wong, F. T., Ang, E. L., & Lim, Y. H. (2024). Site-selective chlorination of pyrrolic heterocycles by flavin dependent enzyme PrnC. Communications Chemistry, 7(1), Article 7. https://doi.org/10.1038/s42004-023-01083-1
Park, I., Kim, S., Brenden, C. K., Shi, W., Iyer, H., Bashir, R., & Vlasov, Y. (2024). Highly Localized Chemical Sampling at Subsecond Temporal Resolution Enabled with a Silicon Nanodialysis Platform at Nanoliter per Minute Flows. ACS Nano, 18(9), 6963-6974. https://doi.org/10.1021/acsnano.3c09776
Oltman, C. G., Kim, T. P., Lee, J. W. Y., Lupu, J. D., Zhu, R., & Moussa, I. D. (2024). Prevalence, Management, and Comorbidities of Adults With Atrial Fibrillation in the United States, 2019 to 2023. JACC: Advances, 3(11), Article 101330. https://doi.org/10.1016/j.jacadv.2024.101330
Oh, C., Xun, G., Lane, S. T., Petrov, V. A., Zhao, H., & Nguyen, T. H. (2024). Portable, single nucleotide polymorphism-specific duplex assay for virus surveillance in wastewater. Science of the Total Environment, 912, Article 168701. https://doi.org/10.1016/j.scitotenv.2023.168701
Nik Zulkarnine, N. H., Faramarzi, V., Huang, S., Chandrasekar, N., Perala, R. S., Park, J. S., Koprowski, K., Chen, S., Zhang, Y., Darsi, S., Adoni, M., Kim, A. Y., Baek, J., Valera, E., Ryu, J., van der Zande, A. M., Kim, M. J., Park, I., Bashir, R., & Hwang, M. T. (in press). Multi-modal biosensing enabled by on-chip nano-corrugated graphene. Device, Article 100572. https://doi.org/10.1016/j.device.2024.100572
Nambiar, A., Pan, C., Rana, V., Cheraghchi, M., Ribeiro, J., Maslov, S., & Milenkovic, O. (2024). Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads. BMC bioinformatics, 25(1), Article 195. https://doi.org/10.1186/s12859-024-05798-3
Moustakides, G. V., Liu, X., & Milenkovic, O. (2024). Optimal stopping methodology for the secretary problem with random queries. Journal of Applied Probability, 61(2), 578-602. https://doi.org/10.1017/jpr.2023.61
Monaco, M. H., Coyne, S., Wang, M., Flaws, J. A., Irudayaraj, J. M., Cann, I., & Donovan, S. M. (2024). Effects of early life exposure to di(2-ethylhexyl) phthalate on jejunal morphology, sucrase activity, and colonic microbiota composition in young pigs. Journal of Environmental Exposure Assessment, 3(3), Article 18. https://doi.org/10.20517/jeea.2024.10
Mogol, A. N., Kaminsky, A. Z., Dutton, D. J., & Madak Erdogan, Z. (2024). Targeting NAD+ metabolism: Pre-clinical insights into potential cancer therapy strategies. Endocrinology, 165(5), Article bqae043. https://doi.org/10.1210/endocr/bqae043
Mishra, S., Deewan, A., Zhao, H., & Rao, C. V. (2024). Nitrogen starvation causes lipid remodeling in Rhodotorula toruloides. Microbial cell factories, 23(1), Article 141. https://doi.org/10.1186/s12934-024-02414-0
Madak-Erdogan, Z., Hammes, S. R., & Furkan Burak, M. (2024). From Fundamentals to the Clinic: Advancing Obesity Research in Endocrinology. Journal of the Endocrine Society, 8(6). https://doi.org/10.1210/jendso/bvae066
Ma, K., Xue, B., Chu, R., Zheng, Y., Sharma, S., Jiang, L., Hu, M., Xie, Y., Hu, Y., Tao, T., Zhou, Y., Liu, D., Li, Z., Yang, Q., Chen, Y., Wu, S., Tong, Y., Robinson, R. C., Yew, W. S., ... Zhang, Y. (2024). A Widespread Radical-Mediated Glycolysis Pathway. Journal of the American Chemical Society, 146(38), 26187-26197. https://doi.org/10.1021/jacs.4c07718
Lu, J., Baby, A., Asserghine, A., Rodríguez-López, J., & Zhao, H. (2024). Amino acid based ionic liquids for revitalization of sulfated lead anodes. Journal of Power Sources, 591, Article 233824. https://doi.org/10.1016/j.jpowsour.2023.233824
Liu, L., Bhaskar, S., & Cunningham, B. T. (2024). Hybrid interfacial cryosoret nano-engineering in photonic resonator interferometric scattering microscopy: Insights from nanoparticles and nano-assemblies. Applied Physics Letters, 124(23), Article 234101. https://doi.org/10.1063/5.0203701
Liu, L., Tibbs, J., Li, N., Bacon, A., Shepherd, S., Lee, H., Chauhan, N., Demirci, U., Wang, X., & Cunningham, B. T. (2024). A Photonic Resonator Interferometric Scattering Microscope for Label-free Imaging of Bio-nanoparticles in Point-of-use Environments. Paper presented at CLEO: Applications and Technology in CLEO 2024, CLEO: A and T 2024 - Part of Conference on Lasers and Electro-Optics, Charlotte, United States.
Liu, W., Ayupova, T., Wang, W., Shepherd, S., Wang, X., Akin, L. D., Kohli, M., Demirci, U., & Cunningham, B. T. (2024). Dynamic and large field of view photonic resonator absorption microscopy for ultrasensitive digital resolution detection of nucleic acid and protein biomarkers. Biosensors and Bioelectronics, 264, Article 116643. https://doi.org/10.1016/j.bios.2024.116643
Lim, J., Zhou, S., Baek, J., Kim, A. Y., Valera, E., Sweedler, J., & Bashir, R. (2024). A Blood Drying Process for DNA Amplification. Small, 20(11), Article 2307959. https://doi.org/10.1002/smll.202307959
Lim, J., Hwang, J., Min, H., Wester, M., Kim, C., Valera, E., Kong, H. J., & Bashir, R. (2024). Dried Blood Matrix as a New Material for the Detection of DNA Viruses. Advanced Healthcare Materials, 13(29), Article 2402506. https://doi.org/10.1002/adhm.202402506
Lim, J., Koprowski, K., Stavins, R., Xuan, N., Hoang, T. H., Baek, J., Kindratenko, V., Khaertdinova, L., Kim, A. Y., Do, M., King, W. P., Valera, E., & Bashir, R. (in press). Point-of-Care Multiplex Detection of Respiratory Viruses. ACS Sensors, 9(8), 4058-4068. https://doi.org/10.1021/acssensors.4c00992
Liao, C., Priyanka, P., Lai, Y. H., Rao, C. V., & Lu, T. (2024). How Does Escherichia coli Allocate Proteome? ACS synthetic biology, 13(9), 2718-2732. https://doi.org/10.1021/acssynbio.3c00537
Li, M., Harrison, W., Zhang, Z., Yuan, Y., & Zhao, H. (2024). Remote stereocontrol with azaarenes via enzymatic hydrogen atom transfer. Nature Chemistry, 16(2), 277-284. https://doi.org/10.1038/s41557-023-01368-x
Li, M., Yuan, Y., Harrison, W., Zhang, Z., & Zhao, H. (2024). Asymmetric photoenzymatic incorporation of fluorinated motifs into olefins. Science (New York, N.Y.), 385(6707), 416-421. https://doi.org/10.1126/science.adk8464
Lee, Y. G., Kang, N. K., Kim, C., Tran, V. G., Cao, M., Yoshikuni, Y., Zhao, H., & Jin, Y. S. (2024). Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis. Bioresource Technology, 399, Article 130641. https://doi.org/10.1016/j.biortech.2024.130641
Lee, W., & Smith, A. M. (2024). Interdiffusion-enhanced cation exchange for HgSe and HgCdSe nanocrystals with infrared bandgaps. Nature Synthesis, 3(10), 1243-1254. https://doi.org/10.1038/s44160-024-00597-3
Le, L. T. P., Nguyen, A. H. Q., Phan, L. M. T., Ngo, H. T. T., Wang, X., Cunningham, B., Valera, E., Bashir, R., Taylor-Robinson, A. W., & Do, C. D. (2024). Current smartphone-assisted point-of-care cancer detection: Towards supporting personalized cancer monitoring. TrAC - Trends in Analytical Chemistry, 174, Article 117681. https://doi.org/10.1016/j.trac.2024.117681
Law, Y. S., Muthaliff, N. A., Wei, Y., Lin, F., Zhao, H., & Ang, E. L. (2024). Biochemical Investigation and Engineering of a Tardigrade X Family DNA Polymerase for Template-Independent DNA Synthesis. ACS Catalysis, 14(16), 12318-12330. https://doi.org/10.1021/acscatal.4c00756
Kolossov, V. L., Kanakaraju, K., Sarkar, S., Arogundade, O. H., Kuo, C. W., Mara, N. R., & Smith, A. M. (2024). Quantum Dot-Fab′ Conjugates as Compact Immunolabels for Microtubule Imaging and Cell Classification. ACS Nano, 18(23), 15084-15095. https://doi.org/10.1021/acsnano.4c02215
Koh, H. G., Yook, S., Oh, H., Rao, C. V., & Jin, Y. S. (2024). Toward rapid and efficient utilization of nonconventional substrates by nonconventional yeast strains. Current Opinion in Biotechnology, 85, Article 103059. https://doi.org/10.1016/j.copbio.2023.103059
Klumbys, E., Xu, W., Koduru, L., Heng, E., Wei, Y., Wong, F. T., Zhao, H., & Ang, E. L. (2024). Discovery, characterization, and engineering of an advantageous Streptomyces host for heterologous expression of natural product biosynthetic gene clusters. Microbial cell factories, 23(1), Article 149. https://doi.org/10.1186/s12934-024-02416-y
King, W. P., Bashir, R., Aydin, M., Berger, J., & Valera Cano, E. A. (2024). Microfluidic diagnostic device with a three-dimensional (3D) flow architecture. (U.S. Patent No. 11938480).
Khemtonglang, K., Liu, W., Lee, H., Wang, W., Li, S., Li, Z. Y., Shepherd, S., Yang, Y., Diel, D. G., Fang, Y., & Cunningham, B. T. (2024). Portable, smartphone-linked, and miniaturized photonic resonator absorption microscope (PRAM Mini) for point-of-care diagnostics. Biomedical Optics Express, 15(10), 5691-5705. https://doi.org/10.1364/BOE.531388
Jiang, G., Lu, J., Zhou, M., Harrison, W., & Zhao, H. (2024). Multifunctional Glucose Dehydrogenase Enabled Synthesis of Chiral-Bridged Bicyclic Nitrogen Heterocycles. ACS Catalysis, 14(9), 7074-7079. https://doi.org/10.1021/acscatal.4c00825
Jiang, L., Yang, Y., Huang, L., Zhou, Y., An, J., Zheng, Y., Chen, Y., Liu, Y., Huang, J., Ang, E. L., Zhao, S., Zhao, H., Liao, R., Wei, Y., & Zhang, Y. (2024). Glycyl Radical Enzymes Catalyzing the Dehydration of Two Isomers of N-Methyl-4-hydroxyproline. ACS Catalysis, 14(7), 4407-4422. https://doi.org/10.1021/acscatal.4c00216
Jeong, Y., Ahmad, S., & Irudayaraj, J. (2024). Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes. ACS Biomaterials Science and Engineering, 10(3), 1461-1472. https://doi.org/10.1021/acsbiomaterials.3c01678
Jeong, Y., Han, X., Vyas, K., & Irudayaraj, J. (2024). Microbial β-Glucuronidase Hydrogel Beads Activate Chemotherapeutic Prodrug. ACS Applied Materials and Interfaces, 16(22), 28093-28103. https://doi.org/10.1021/acsami.4c02568
Jeong, Y., Hsieh, P. H., Phal, Y., Bhargava, R., & Irudayaraj, J. (2024). Label-Free Monitoring of Coculture System Dynamics: Probing Probiotic and Cancer Cell Interactions via Infrared Spectroscopic Imaging. Analytical Chemistry, 96(28), 11247-11254. https://doi.org/10.1021/acs.analchem.4c00894
Jankelow, A., Chen, C. L., Cowell, T. W., Espinosa de los Monteros, J., Bian, Z., Kindratenko, V., Koprowski, K., Darsi, S., Han, H. S., Valera, E., & Bashir, R. (in press). Multiplexed electrical detection of whole viruses from plasma in a microfluidic platform. Analyst, 149(4), 1190-1201. https://doi.org/10.1039/d3an01510f
Jain, S., Xun, G., & Zhao, H. (2024). Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing. ACS synthetic biology, 13(10), 3056-3068. https://doi.org/10.1021/acssynbio.4c00099
Ivanov, A., Mukherjee, U. K., Bose, S., Seshadri, S., Watkins, R., England, A. C., Suriano, J., Ahsen, M. E., & Souyris, S. (2024). COVID-19 test-to-stay program for K-12 schools: Opt-in versus opt-out consent model. iScience, 27(1), Article 108770. https://doi.org/10.1016/j.isci.2023.108770
Hur, S. W., Kwon, M., Manoharaan, R., Mohammadi, M. H., Samuel, A. Z., Mulligan, M. P., Hergenrother, P. J., & Bhargava, R. (2024). Capturing cell morphology dynamics with high temporal resolution using single-shot quantitative phase gradient imaging. Journal of biomedical optics, 29, S22712. https://doi.org/10.1117/1.JBO.29.S2.S22712
Huang, K.-Y., Upadhyay, G., Ahn, Y., Sakakura, M., Pagan-Diaz, G. J., Cho, Y., Weiss, A. C., Huang, C., Mitchell, J. W., Li, J., Tan, Y., Deng, Y.-H., Ellis-Mohr, A., Dou, Z., Zhang, X., Kang, S., Chen, Q., Sweedler, J. V., Im, S. G., ... Kong, H. (2024). Neuronal innervation regulates the secretion of neurotrophic myokines and exosomes from skeletal muscle. Proceedings of the National Academy of Sciences, 121(19), Article e2313590121. https://doi.org/10.1073/pnas.2313590121
Heath, H., Mogol, A. N., Santaliz Casiano, A., Zuo, Q., & Madak-Erdogan, Z. (2024). Targeting systemic and gut microbial metabolism in ER+ breast cancer. Trends in Endocrinology and Metabolism, 35(4), 321-330. https://doi.org/10.1016/j.tem.2023.12.008
Heath, H., Yoo, J. Y., Akter, S., Jain, A., Sharma, V., McGee, H., Soliman, A., Mahmoud, A. M., Matthews, A. K., Winn, R. A., Madak-Erdogan, Z., & Kim, S. J. (2024). The effect of exposure to neighborhood violence on Glucocorticoid Receptor signaling in lung tumors. Cancer Research Communications, 4(7), 1643-1654. https://doi.org/10.1158/2767-9764.CRC-24-0032
Hatano, R., Smith, A. M., Raman, R., Zamora, J. E., Bashir, R., & McCloskey, K. E. (2024). Comparing fabrication techniques for engineered cardiac tissue. Journal of Biomedical Materials Research - Part A, 112(11), 1921-1929. https://doi.org/10.1002/jbm.a.37737
Harrison, W., Jiang, G., Zhang, Z., Li, M., Chen, H., & Zhao, H. (2024). Photoenzymatic Asymmetric Hydroamination for Chiral Alkyl Amine Synthesis. Journal of the American Chemical Society, 146(15), 10716-10722. https://doi.org/10.1021/jacs.4c00620
Han, X., Ju, L., Saengow, C., Ren, W., Ewoldt, R., Fan, T., & Irudayaraj, J. (2024). Nano oxygen chamber by cascade reaction for hypoxia mitigation and reactive oxygen species scavenging in wound healing. Bioactive Materials, 35, 67-81. https://doi.org/10.1016/j.bioactmat.2024.01.010
Han, X., Saengow, C., Ju, L., Ren, W., Ewoldt, R. H., & Irudayaraj, J. (2024). Exosome-coated oxygen nanobubble-laden hydrogel augments intracellular delivery of exosomes for enhanced wound healing. Nature communications, 15(1), Article 3435. https://doi.org/10.1038/s41467-024-47696-5
Hampel, J. M., Cheuk, N., Barbosa, M. M. P., & Fan, T. M. (2024). The promise of immunotherapeutic strategies to advance cancer treatment in pet dogs. Journal of the American Veterinary Medical Association, 262(12), 1583-1593. https://doi.org/10.2460/javma.24.08.0532
Guo, X., Bai, Z., Zhao, H., & Shi, S. (2024). Development of a multigene expression system using 2A peptides in Rhodosporidium toruloides. Biotechnology and bioengineering, 121(12), 3893-3905. https://doi.org/10.1002/bit.28843
Goo, Y. H., Plakkal Ayyappan, J., Cheeran, F. D., Bangru, S., Saha, P. K., Baar, P., Schulz, S., Lydic, T. A., Spengler, B., Wagner, A. H., Kalsotra, A., Yechoor, V. K., & Paul, A. (2024). Lipid droplet-associated hydrolase mobilizes stores of liver X receptor sterol ligands and protects against atherosclerosis. Nature communications, 15(1), Article 6540. https://doi.org/10.1038/s41467-024-50949-y
Gnanasambandam, B., Prince, J., Limaye, S., Moran, E., Lee, B., Huynh, J., Irudayaraj, J., & Tsipursky, M. (2024). Addressing retinal hypoxia: pathophysiology, therapeutic innovations, and future prospects. Therapeutic Advances in Ophthalmology, 16. https://doi.org/10.1177/25158414241280187
García Martín, H., Mazurenko, S., & Zhao, H. (2024). Special Issue on Artificial Intelligence for Synthetic Biology. ACS synthetic biology, 13(2), 408-410. https://doi.org/10.1021/acssynbio.3c00760
Foo, M., Frietze, L. R., Enghiad, B., Yuan, Y., Katanski, C. D., Zhao, H., & Pan, T. (2024). Prokaryotic RNA N1-Methyladenosine Erasers Maintain tRNA m1A Modification Levels in Streptomyces venezuelae. ACS chemical biology, 19(7), 1616-1625. https://doi.org/10.1021/acschembio.4c00278
Fang, Z., Wu, Z., Wu, X., Chen, S., Wang, X., Umrao, S., & Dwivedy, A. (2024). APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions. Journal of Chemical Information and Modeling, 64(7), 2290-2301. https://doi.org/10.1021/acs.jcim.3c00713
Dong, G., Zhao, Y., Ding, W., Xu, S., Zhang, Q., Zhao, H., & Shi, S. (2024). Metabolic engineering of Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids. Metabolic Engineering, 82, 100-109. https://doi.org/10.1016/j.ymben.2024.01.009
Dewald, Z., Adesanya, O., Bae, H., Gupta, A., Derham, J. M., Chembazhi, U. V., & Kalsotra, A. (2024). Altered drug metabolism and increased susceptibility to fatty liver disease in a mouse model of myotonic dystrophy. Nature communications, 15(1), Article 9062. https://doi.org/10.1038/s41467-024-53378-z
Deshavath, N. N., Woodruff, W., Eller, F., Susanto, V., Yang, C., Rao, C. V., & Singh, V. (2024). Scale-up of microbial lipid and bioethanol production from oilcane. Bioresource Technology, 399, Article 130594. https://doi.org/10.1016/j.biortech.2024.130594
Cortés-Peña, Y. R., Woodruff, W., Banerjee, S., Li, Y., Singh, V., Rao, C. V., & Guest, J. S. (2024). Integration of plant and microbial oil processing at oilcane biorefineries for more sustainable biofuel production. GCB Bioenergy, 16(11), Article e13183. https://doi.org/10.1111/gcbb.13183
Chen, J., Laverty, D. J., Talele, S., Bale, A., Carlson, B. L., Porath, K. A., Bakken, K. K., Burgenske, D. M., Decker, P. A., Vaubel, R. A., Eckel-Passow, J. E., Bhargava, R., Lou, Z., Hamerlik, P., Harley, B., Elmquist, W. F., Nagel, Z. D., Gupta, S. K., & Sarkaria, J. N. (2024). Aberrant ATM signaling and homology-directed DNA repair as a vulnerability of p53-mutant GBM to AZD1390-mediated radiosensitization. Science Translational Medicine, 16(734), Article eadj5962. https://doi.org/10.1126/scitranslmed.adj5962
Chen, C., Martins, M., Nooruzzaman, M., Yettapu, D., Diel, D. G., Reinhart, J. M., Urbasic, A., Robinson, H., Varga, C., & Fang, Y. (2024). Spatial and temporal clustering of anti-SARSCoV-2 antibodies in Illinois household cats, 2021–2023. PloS one, 19(5), 1-18. Article e0299388. https://doi.org/10.1371/journal.pone.0299388
Chen, S., Zhang, Y., King, W. P., Bashir, R., & van der Zande, A. M. (2024). Edge-Passivated Monolayer WSe2 Nanoribbon Transistors. Advanced Materials, 36(39), Article 2313694. https://doi.org/10.1002/adma.202313694
Burke, M. D., Denmark, S. E., Diao, Y., Han, J., Switzky, R., & Zhao, H. (2024). Molecule Maker Lab Institute: Accelerating, advancing, and democratizing molecular innovation. AI Magazine, 45(1), 117-123. https://doi.org/10.1002/aaai.12154
Boyd, R. I., Shokry, D., Fazal, Z., Rennels, B. C., Freemantle, S. J., La Frano, M. R., Prins, G. S., Madak Erdogan, Z., Irudayaraj, J., Singh, R., & Spinella, M. J. (2024). Perfluorooctanesulfonic Acid Alters Pro-Cancer Phenotypes and Metabolic and Transcriptional Signatures in Testicular Germ Cell Tumors. Toxics, 12(4), Article 232. https://doi.org/10.3390/toxics12040232
Boob, A. G., Chen, J., & Zhao, H. (2024). Enabling pathway design by multiplex experimentation and machine learning. Metabolic Engineering, 81, 70-87. https://doi.org/10.1016/j.ymben.2023.11.006
Boob, A. G., Zhu, Z., Intasian, P., Jain, M., Petrov, VA., Lane, S. T., Tan, S.-I., Xun, G., & Zhao, H. (2024). CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration. Nucleic acids research, 52(6), Article gkae062. https://doi.org/10.1093/nar/gkae062
Blake, A. D., Chao, J., SantaMaria, A. M., Ekaputri, S., Green, K. J., Brown, S. T., Rakowski, C. K., Choi, E. K., Aring, L., Chen, P. J., Snead, N. M., Matje, D. M., Geng, T., Octaviani, A., Bailey, K., Hollenbach, S. J., Fan, T. M., Seo, Y. A., & Burke, M. D. (2024). Minimizing higher-order aggregation maximizes iron mobilization by small molecules. Nature chemical biology, 20(10), 1282-1293. https://doi.org/10.1038/s41589-024-01596-3
Bhaskar, S., Liu, W., Tibbs, J., & Cunningham, B. T. (2024). Photonic crystal-coupled enhanced steering emission: A prism-free, objective-free, and metal-free loss-less approach for biosensing. Applied Physics Letters, 124(16), Article 161102. https://doi.org/10.1063/5.0203999
Bale, A. A., Thammineni, S., Bhargava, R., & Harley, B. (in press). Hyaluronic Acid Influences Amino Acid Metabolism via Differential L-Type Amino Acid Transporter 1 Expression in the U87-Malignant Glioma Cell Line. Advanced NanoBiomed Research. https://doi.org/10.1002/anbr.202400107
Asserghine, A., Baby, A., Gao, E., Zhao, H., & Rodríguez-López, J. (2024). Inducing and real-time monitoring of lead (de)sulfation processes using scanning electrochemical microscopy for applications in the refurbishment of lead-acid batteries. Electrochimica Acta, 475, Article 143620. https://doi.org/10.1016/j.electacta.2023.143620
Arredondo Eve, A., Tunc, E., Mehta, D., Yoo, J. Y., Yilmaz, H. E., Emren, S. V., Akçay, F. A., & Madak Erdogan, Z. (2024). PFAS and their association with the increased risk of cardiovascular disease in postmenopausal women. Toxicological Sciences, 200(2), 312-323. Article kfae065. https://doi.org/10.1093/toxsci/kfae065
Applegate, C. C., Nelappana, M. B., Cui, Y., Okoro, G., Nielsen, E. A., Dovalovsky, N. P., Smith, A. M., Dobrucki, I. T., & Dobrucki, L. W. (2024). Biodistribution of PET radiotracers in tumor-bearing TRAMP mice administered by retroorbital or jugular vein injections. Scientific reports, 14(1), Article 20241. https://doi.org/10.1038/s41598-024-71221-9
Ahsen, M. E., Vogel, R., & Stolovitzky, G. (2024). Optimal linear ensemble of binary classifiers. Bioinformatics Advances, 4(1), Article vbae093. https://doi.org/10.1093/bioadv/vbae093
Ahsen, M. E., Raghunathan, S., Ayvaci, M. U. S., & Subramanyam, R. (2024). Contests for Predictive Algorithms: Ensembling, Interdependency, and Optimal Rewards Design. In T. X. Bui (Ed.), Proceedings of the 57th Annual Hawaii International Conference on System Sciences, HICSS 2024 (pp. 6171-6180). (Proceedings of the Annual Hawaii International Conference on System Sciences). IEEE Computer Society.
Ahsen, M. E., & Moshref-Javadi, M. (2024). The Role of Technologies in Supply Chain Efficiency and Resiliency. In M. Moshref-Javadi, & S. Seshadri (Eds.), Impacts of COVID-19 on Supply Chains: Disruptions, Technologies, and Solutions (pp. 117-144). (Springer Business Cases). Springer. https://doi.org/10.1007/978-3-031-47734-8_5
Adesanya, O., Das, D., & Kalsotra, A. (2024). Emerging roles of RNA-binding proteins in fatty liver disease. Wiley interdisciplinary reviews. RNA, 15(2), Article e1840. https://doi.org/10.1002/wrna.1840
- 2023
-
Boudreau, M. W., Tonogai, E. J., Schane, C. P., Xi, M. X., Fischer, J. H., Vijayakumar, J., Ji, Y., Tarasow, T. M., Fan, T. M., Hergenrother, P. J., & Dudek, A. Z. (2023). The combination of PAC-1 and entrectinib for the treatment of metastatic uveal melanoma. Melanoma research, 33(6), 514-524. https://doi.org/10.1097/CMR.0000000000000927
Chen, S., & Bashir, R. (2023). Advances in field-effect biosensors towards point-of-use. Measurement Science and Technology, 34(49), Article 492002. https://doi.org/10.1088/1361-6528/acf3f0
Tran, V. G., Mishra, S., Bhagwat, S. S., Shafaei, S., Shen, Y., Allen, J. L., Crosly, B. A., Tan, S. I., Fatma, Z., Rabinowitz, J. D., Guest, J. S., Singh, V., & Zhao, H. (2023). An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis. Nature communications, 14(1), Article 6152. https://doi.org/10.1038/s41467-023-41616-9
Yue, Q., Meng, J., Qiu, Y., Yin, M., Zhang, L., Zhou, W., An, Z., Liu, Z., Yuan, Q., Sun, W., Li, C., Zhao, H., Molnár, I., Xu, Y., & Shi, S. (2023). A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi. Nature communications, 14(1), Article 4267. https://doi.org/10.1038/s41467-023-40027-0
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. (2023). Estimating Heterogeneous Treatment Effect on Multivariate Responses Using Random Forests. Statistics in Biosciences, 15(3), 545-561. https://doi.org/10.1007/s12561-021-09310-w
Ren, H., Dommaraju, S. R., Huang, C., Cui, H., Pan, Y., Nesic, M., Zhu, L., Sarlah, D., Mitchell, D. A., & Zhao, H. (2023). Genome mining unveils a class of ribosomal peptides with two amino termini. Nature communications, 14(1), Article 1624. https://doi.org/10.1038/s41467-023-37287-1
Zhao, S., Hartanto, J., Joseph, R., Wu, C. H., Zhao, Y., & Chen, Y. S. (2023). Hybrid photoacoustic and fast super-resolution ultrasound imaging. Nature communications, 14(1), Article 2191. https://doi.org/10.1038/s41467-023-37680-w
Santaliz-Casiano, A., Mehta, D., Danciu, O. C., Patel, H., Banks, L., Zaidi, A., Buckley, J., Rauscher, G. H., Schulte, L., Weller, L. R., Taiym, D., Liko-Hazizi, E., Pulliam, N., Friedewald, S. M., Khan, S., Kim, J. J., Gradishar, W., Hegerty, S., Frasor, J., ... Madak-Erdogan, Z. (2023). Identification of metabolic pathways contributing to ER+ breast cancer disparities using a machine-learning pipeline. Scientific reports, 13(1), Article 12136. https://doi.org/10.1038/s41598-023-39215-1
Guo, X., Bai, Z., Zhang, Y., Zhao, H., & Shi, S. (2023). Mining and application of constitutive promoters from Rhodosporidium toruloides. AMB Express, 13(1), Article 17. https://doi.org/10.1186/s13568-023-01522-1
Zhang, M., Ehmann, M. E., Matukumalli, S., Boob, A. G., Gilbert, D. M., & Zhao, H. (2023). SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. Nature communications, 14(1), Article 5616. https://doi.org/10.1038/s41467-023-41468-3
Zhang, M., Zhu, Z., Xun, G., & Zhao, H. (2023). To cut or not to cut: Next-generation genome editors for precision genome engineering. Current Opinion in Biomedical Engineering, 28, Article 100489. https://doi.org/10.1016/j.cobme.2023.100489
Maji, A., Soutar, C. P., Zhang, J., Lewandowska, A., Uno, B. E., Yan, S., Shelke, Y., Murhade, G., Nimerovsky, E., Borcik, C. G., Arango, A. S., Lange, J. D., Marin-Toledo, J. P., Lyu, Y., Bailey, K. L., Roady, P. J., Holler, J. T., Khandelwal, A., SantaMaria, A. M., ... Burke, M. D. (2023). Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. Nature, 623(7989), 1079-1085. https://doi.org/10.1038/s41586-023-06710-4
Liu, X., Milenkovic, O., & Moustakides, G. V. (2023). Query-based selection of optimal candidates under the Mallows model. Theoretical Computer Science, 979, Article 114206. https://doi.org/10.1016/j.tcs.2023.114206
Piersma, S. J., Bangru, S., Yoon, J., Liu, T. W., Yang, L., Hsieh, C. S., Plougastel-Douglas, B., Kalsotra, A., & Yokoyama, W. M. (2023). NK cell expansion requires HuR and mediates control of solid tumors and long-term virus infection. The Journal of experimental medicine, 220(11). https://doi.org/10.1084/jem.20231154
Gapinske, L., Clark, L., Caro-Rivera, L. M., & Bashir, R. (2023). Cryopreservation Alters Tissue Structure and Improves Differentiation of Engineered Skeletal Muscle. Tissue Engineering - Part A, 29(21-22), 557-568. https://doi.org/10.1089/ten.tea.2023.0075
Barya, P., Xiong, Y., Shepherd, S., Gupta, R., Akin, L. D., Tibbs, J., Lee, H., Singamaneni, S., & Cunningham, B. T. (2023). Photonic-Plasmonic Coupling Enhanced Fluorescence Enabling Digital-Resolution Ultrasensitive Protein Detection. Small, 19(44), Article 2207239. https://doi.org/10.1002/smll.202207239
Nguyen, V., Xue, P., Li, Y., Zhao, H., & Lu, T. (2023). Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metabolic Engineering, 80, 173-183. https://doi.org/10.1016/j.ymben.2023.09.013
Zhang, M., Singh, N., Ehmann, M. E., Zheng, L., & Zhao, H. (2023). Incorporation of noncanonical base Z yields modified mRNA with minimal immunogenicity and improved translational capacity in mammalian cells. iScience, 26(10), Article 107739. https://doi.org/10.1016/j.isci.2023.107739
Asserghine, A., Baby, A., Putnam, S. T., Qian, P., Gao, E., Zhao, H., & Rodríguez-López, J. (2023). In situ detection of reactive oxygen species spontaneously generated on lead acid battery anodes: a pathway for degradation and self-discharge at open circuit. Chemical Science, 14(43), 12292-12298. https://doi.org/10.1039/D3SC04736A
Orr, J. S., Zen, E., Wang, X., & Rao, C. V. (2023). Emulsion-based evolution of Escherichia coli for higher growth yield on D-xylose identifies central role of cyclic AMP. Systems Microbiology and Biomanufacturing, 3(4), 730-738. https://doi.org/10.1007/s43393-022-00136-1
Lee, W., & Smith, A. M. (2023). Magic reactions transform nanoclusters. Nature Synthesis, 2(10), 904-905. https://doi.org/10.1038/s44160-023-00346-y
Martínez–Sánchez, C., Bassegoda, O., Deng, H., Almodóvar, X., Ibarzabal, A., de Hollanda, A., Martínez García de la Torre, RA. A., Blaya, D., Ariño, S., Jiménez-Esquivel, N., Aguilar-Bravo, B., Vallverdú, J., Montironi, C., Osorio-Conles, O., Fundora, Y., Sánchez Moreno, F. J., Gómez-Valadés, A. G., Aguilar-Corominas, L., Soria, A., ... Coll, M. (2023). Therapeutic targeting of adipose tissue macrophages ameliorates liver fibrosis in non-alcoholic fatty liver disease. JHEP Reports, 5(10), Article 100830. https://doi.org/10.1016/j.jhepr.2023.100830
Ouyang, L., Wang, N., Irudayaraj, J., & Majima, T. (2023). Virus on surfaces: Chemical mechanism, influence factors, disinfection strategies, and implications for virus repelling surface design. Advances in Colloid and Interface Science, 320, Article 103006. https://doi.org/10.1016/j.cis.2023.103006
Rodriguez, A., Gandavadi, D., Mathivanan, J., Song, T., Madhanagopal, B. R., Talbot, H., Sheng, J., Wang, X., & Chandrasekaran, A. R. (2023). Self-Assembly of DNA Nanostructures in Different Cations. Small, 19(39), Article 2300040. https://doi.org/10.1002/smll.202300040
Chauhan, N., Xiong, Y., Ren, S., Dwivedy, A., Magazine, N., Zhou, L., Jin, X., Zhang, T., Cunningham, B. T., Yao, S., Huang, W., & Wang, X. (2023). Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus. Journal of the American Chemical Society, 145(37), 20214-20228. https://doi.org/10.1021/jacs.2c04835
Yuan, Y., Shi, C., & Zhao, H. (2023). Machine Learning-Enabled Genome Mining and Bioactivity Prediction of Natural Products. ACS synthetic biology, 12(9), 2650-2662. https://doi.org/10.1021/acssynbio.3c00234
Gapinske, M., Winter, J., Swami, D., Gapinske, L., Woods, W. S., Shirguppe, S., Miskalis, A., Busza, A., Joulani, D., Kao, C. J., Kostan, K., Bigot, A., Bashir, R., & Perez-Pinera, P. (2023). Targeting Duchenne muscular dystrophy by skipping DMD exon 45 with base editors. Molecular Therapy - Nucleic Acids, 33, 572-586. https://doi.org/10.1016/j.omtn.2023.07.029
Lee, G., Jeong, W. H., Kim, B., Jeon, S., Smith, A. M., Seo, J., Suzuki, K., Kim, J. Y., Lee, H., Choi, H., Chung, D. S., Choi, J., Choi, H., & Lim, S. J. (2023). Design and Synthesis of CdHgSe/HgS/CdZnS Core/Multi-Shell Quantum Dots Exhibiting High-Quantum-Yield Tissue-Penetrating Shortwave Infrared Luminescence. Small, 19(36), Article 2301161. https://doi.org/10.1002/smll.202301161
Sarker, K., Zhu, R., Holscher, H. D., & Zhai, C. X. (2023). Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake. In ACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics Article 4 (ACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery. https://doi.org/10.1145/3584371.3612958
Gordon, D. L., Foreman, J. H., Connolly, S. L., Schnelle, A. N., Fan, T. M., & Barger, A. M. (2023). Acute phase protein concentrations following serial procaine penicillin G injections in horses. Equine veterinary journal, 55(5), 916-922. https://doi.org/10.1111/evj.13886
Yu, T., Boob, A. G., Singh, N., Su, Y., & Zhao, H. (2023). In vitro continuous protein evolution empowered by machine learning and automation. Cell Systems, 14(8), 633-644. https://doi.org/10.1016/j.cels.2023.04.006
Jeong, Y., Vyas, K., & Irudayaraj, J. (2023). Toxicity of per- and polyfluoroalkyl substances to microorganisms in confined hydrogel structures. Journal of Hazardous Materials, 456, Article 131672. https://doi.org/10.1016/j.jhazmat.2023.131672
Pattabiraman, S., Gabrys, R., & Milenkovic, O. (2023). Coding for Polymer-Based Data Storage. IEEE Transactions on Information Theory, 69(8), 4812-4836. https://doi.org/10.1109/TIT.2023.3267620
Zhang, Z., Feng, J., Yang, C., Cui, H., Harrison, W., Zhong, D., Wang, B., & Zhao, H. (2023). Photoenzymatic enantioselective intermolecular radical hydroamination. Nature Catalysis, 6(8), 687-694. https://doi.org/10.1038/s41929-023-00994-5
You, J. S., Kim, Y., Lee, S., Bashir, R., & Chen, J. (2023). RhoA/ROCK signalling activated by ARHGEF3 promotes muscle weakness via autophagy in dystrophic mdx mice. Journal of Cachexia, Sarcopenia and Muscle, 14(4), 1880-1893. https://doi.org/10.1002/jcsm.13278
Ren, W., Messerschmidt, V., Tsipursky, M., & Irudayaraj, J. (2023). Oxygen Nanobubbles-Embedded Hydrogel as Wound Dressing to Accelerate Healing. ACS Applied Nano Materials, 6(14), 13116-13126. https://doi.org/10.1021/acsanm.3c01812
Han, X., Ju, L. S., & Irudayaraj, J. (2023). Oxygenated Wound Dressings for Hypoxia Mitigation and Enhanced Wound Healing. Molecular pharmaceutics, 20(7), 3338-3355. https://doi.org/10.1021/acs.molpharmaceut.3c00352
Fatma, Z., Tan, S. I., Boob, A. G., & Zhao, H. (2023). A landing pad system for multicopy gene integration in Issatchenkia orientalis. Metabolic Engineering, 78, 200-208. https://doi.org/10.1016/j.ymben.2023.06.010
Peh, G., Gunawan, G. A., Tay, T., Tiong, E., Tan, L. L., Jiang, S., Goh, Y. L., Ye, S., Wong, J., Brown, C. J., Zhao, H., Ang, E. L., Wong, F. T., & Lim, Y. H. (2023). Further Characterization of Fungal Halogenase RadH and Its Homologs. Biomolecules, 13(7), Article 1081. https://doi.org/10.3390/biom13071081
Bashir, R., Ganguli, A., Kosari, F., & Wampfler, E. (2023). Spatial Molecular Analysis Of Tissue. (U.S. Patent No. 11667970).
Stinson, J. A., Sheen, A., Momin, N., Hampel, J., Bernstein, R., Kamerer, R., Fadl-Alla, B., Samuelson, J., Fink, E., Fan, T. M., & Wittrup, K. D. (2023). Collagen-Anchored Interleukin-2 and Interleukin-12 Safely Reprogram the Tumor Microenvironment in Canine Soft-Tissue Sarcomas. Clinical Cancer Research, 29(11), 2110-2122. https://doi.org/10.1158/1078-0432.CCR-23-0006
Lee, H., Wang, W., Chauhan, N., Xiong, Y., Magazine, N., Valdescruz, O., Kim, D. Y., Qiu, T., Huang, W., Wang, X., & Cunningham, B. T. (2023). Rapid detection of intact SARS-CoV-2 using designer DNA Nets and a pocket-size smartphone-linked fluorimeter. Biosensors and Bioelectronics, 229, Article 115228. https://doi.org/10.1016/j.bios.2023.115228
Valera, E., Kindratenko, V., Jankelow, A. M., Heredia, J., Kim, A. Y., Cowell, T. W., Chen, C. L., White, K., Han, H. S., & Bashir, R. (2023). Electrochemical point-of-care devices for the diagnosis of sepsis. Current Opinion in Electrochemistry, 39, Article 101300. https://doi.org/10.1016/j.coelec.2023.101300
Derham, J. M., & Kalsotra, A. (2023). The discovery, function, and regulation of epithelial splicing regulatory proteins (ESRP) 1 and 2. Biochemical Society transactions, 51(3), 1097-1109. https://doi.org/10.1042/BST20221124
Ranoa, D. R. E., Sharma, P., Schane, C. P., Lewis, A. N., Valdez, E., Marada, V. V. V. R., Hager, M. V., Montgomery, W., Wolf, S. P., Schreiber, K., Schreiber, H., Bailey, K., Fan, T. M., Hergenrother, P. J., Roy, E. J., & Kranz, D. M. (2023). Single CAR-T cell treatment controls disseminated ovarian cancer in a syngeneic mouse model. Journal for ImmunoTherapy of Cancer, 11(5), Article e006509. https://doi.org/10.1136/jitc-2022-006509
Cunningham, B. T., Bashir, R., Ganguli, A., Damhorst, G. L., Brooks, I., Yu, H., Chen, W., Sun, F., Ornob, A., Nash, D., & Hirschberg, D. L. (2023). System For Rapid, Portable, And Multiplexed Detection And Identification Of Pathogen Specific Nucleic Acid Sequences. (U.S. Patent No. 11654429).
Jiang, G., Huang, C., Harrison, W., Li, H., Zhou, M., & Zhao, H. (2023). Ene Reductase Enabled Intramolecular β-C−H Functionalization of Substituted Cyclohexanones for Efficient Synthesis of Bridged Bicyclic Nitrogen Scaffolds. Angewandte Chemie - International Edition, 62(22), Article e202302125. https://doi.org/10.1002/anie.202302125
Meng, J., Qiu, Y., Zhang, Y., Zhao, H., & Shi, S. (2023). CMI: CRISPR/Cas9 Based Efficient Multiplexed Integration in Saccharomyces cerevisiae. ACS synthetic biology, 12(5), 1408-1414. https://doi.org/10.1021/acssynbio.2c00591
Xiong, X., Tasan, I., Yang, C., Zhang, M., Hernandez Gonzalez, G. A., Liu, S., Chaturvedi, P., Belmont, A. S., & Zhao, H. (2023). Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. ACS synthetic biology, 12(5), 1424-1436. https://doi.org/10.1021/acssynbio.2c00433
Liu, L., Tibbs, J., Li, N., Bacon, A., Shepherd, S., Lee, H., Chauhan, N., Demirci, U., Wang, X., & Cunningham, B. T. (2023). A photonic resonator interferometric scattering microscope for label-free detection of nanometer-scale objects with digital precision in point-of-use environments. Biosensors and Bioelectronics, 228, Article 115197. https://doi.org/10.1016/j.bios.2023.115197
Mogol, A. N., Zuo, Q., Yoo, J. Y., Kaminsky, A. Z., Imir, O. B., Landesman, Y., Walker, C. J., & Madak erdogan, Z. (2023). NAD + Metabolism Generates a Metabolic Vulnerability in Endocrine-Resistant Metastatic Breast Tumors in Females. Endocrinology, Article bqad073. Advance online publication. https://doi.org/10.1210/endocr/bqad073
Volk, M. J., Tran, V. G., Tan, S. I., Mishra, S., Fatma, Z., Boob, A., Li, H., Xue, P., Martin, T. A., & Zhao, H. (2023). Metabolic Engineering: Methodologies and Applications. Chemical reviews, 123(9), 5521-5570. https://doi.org/10.1021/acs.chemrev.2c00403
Calderón-Olvera, R. M., Arroyo, E., Jankelow, A. M., Bashir, R., Valera, E., Ocaña, M., & Becerro, A. I. (2023). Persistent Luminescence Zn2GeO4:Mn2+ Nanoparticles Functionalized with Polyacrylic Acid: One-Pot Synthesis and Biosensing Applications. ACS Applied Materials and Interfaces, 15(17), 20613-20624. https://doi.org/10.1021/acsami.2c21735
Kuo, C. W., & Smith, A. M. (2023). Digital and Absolute Assays for Low Abundance Molecular Biomarkers. Accounts of chemical research, 56(9), 1031-1042. https://doi.org/10.1021/acs.accounts.3c00030
Pan, C., Chien, E., & Milenkovic, O. (2023). Unlearning Graph Classifiers with Limited Data Resources. In ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023 (pp. 716-726). (ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023). Association for Computing Machinery. https://doi.org/10.1145/3543507.3583547
Wang, X., Shepherd, S., Li, N., Che, C., Song, T., Xiong, Y., Palm, I. R., Zhao, B., Kohli, M., Demirci, U., Lu, Y., & Cunningham, B. T. (2023). A Target Recycling Amplification Process for the Digital Detection of Exosomal MicroRNAs through Photonic Resonator Absorption Microscopy. Angewandte Chemie - International Edition, 62(16), Article e202217932. https://doi.org/10.1002/anie.202217932
Smith, L., & Smith, A. M. (2023). Ultrasensitive Micro Rna Quantification. (U.S. Patent No. 11618919).
Liu, W., Zhang, X., Wen, Y., Anastasio, M. A., & Irudayaraj, J. (2023). A machine learning approach to elucidating PFOS-induced alterations of repressive epigenetic marks in kidney cancer cells with single-cell imaging. Environmental Advances, 11, Article 100344. https://doi.org/10.1016/j.envadv.2023.100344
Pan, C., Chien, E., Tabaghi, P., Peng, J., & Milenkovic, O. (2023). Provably accurate and scalable linear classifiers in hyperbolic spaces. Knowledge and Information Systems, 65(4), 1817-1850. https://doi.org/10.1007/s10115-022-01820-3
Yu, T., Cui, H., Li, J. C., Luo, Y., Jiang, G., & Zhao, H. (2023). Enzyme function prediction using contrastive learning. Science, 379(6639), 1358-1363. https://doi.org/10.1126/science.adf2465
Rashid, F., Liu, W., Wang, Q., Ji, B., Irudayaraj, J., & Wang, N. (2023). Mechanomemory in protein diffusivity of chromatin and nucleoplasm after force cessation. Proceedings of the National Academy of Sciences, 120(13), Article e2221432120. https://doi.org/10.1073/pnas.2221432120
Chakraborty, R., Xiong, M., Athreya, N., Tabatabaei, S. K., Milenkovic, O., & Leburton, J. P. (2023). Solid-State MoS2 Nanopore Membranes for Discriminating among the Lengths of RNA Tails on a Double-Stranded DNA: A New Simulation-Based Differentiating Algorithm. ACS Applied Nano Materials, 6(6), 4651-4660. https://doi.org/10.1021/acsanm.3c00129
Danciu, O. C., Holdhoff, M., Peterson, R. A., Fischer, J. H., Liu, L. C., Wang, H., Venepalli, N. K., Chowdhery, R., Nicholas, M. K., Russell, M. J., Fan, T. M., Hergenrother, P. J., Tarasow, T. M., & Dudek, A. Z. (2023). Phase I study of procaspase-activating compound-1 (PAC-1) in the treatment of advanced malignancies. British Journal of Cancer, 128(5), 783-792. https://doi.org/10.1038/s41416-022-02089-7
Chembazhi, U. V., Tung, W. S., Hwang, H., Wang, Y., Lalwani, A., Nguyen, K. L., Bangru, S., Yee, D., Chin, K., Yang, J., Kalsotra, A., & Mei, W. (2023). PTBP1 controls intestinal epithelial regeneration through post-transcriptional regulation of gene expression. Nucleic acids research, 51(5), 2397-2414. Article gkad042. https://doi.org/10.1093/nar/gkad042
Xiong, Y., Shepherd, S., Tibbs, J., Bacon, A., Liu, W., Akin, L. D., Ayupova, T., Bhaskar, S., & Cunningham, B. T. (2023). Photonic Crystal Enhanced Fluorescence: A Review on Design Strategies and Applications. Micromachines, 14(3), Article 668. https://doi.org/10.3390/mi14030668
Jeong, Y., & Irudayaraj, J. (2023). Hierarchical encapsulation of bacteria in functional hydrogel beads for inter- and intra- species communication. Acta Biomaterialia, 158, 203-215. https://doi.org/10.1016/j.actbio.2023.01.003
Hu, M., Dinh, H. V., Shen, Y., Suthers, P. F., Foster, C. J., Call, C. M., Ye, X., Pratas, J., Fatma, Z., Zhao, H., Rabinowitz, J. D., & Maranas, C. D. (2023). Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metabolic Engineering, 76, 1-17. https://doi.org/10.1016/j.ymben.2023.01.001
Rashid, F., Dubinkina, V., Ahmad, S., Maslov, S., & Irudayaraj, J. M. K. (2023). Gut Microbiome-Host Metabolome Homeostasis upon Exposure to PFOS and GenX in Male Mice. Toxics, 11(3), Article 281. https://doi.org/10.3390/toxics11030281
Zhou, S., Fatma, Z., Xue, P., Mishra, S., Cao, M., Zhao, H., & Sweedler, J. V. (2023). Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture. Analytical Chemistry, 95(8), 4067-4076. https://doi.org/10.1021/acs.analchem.2c04845
Harley, B. A. C., Lu, Y., Cunningham, B. T., Zhuo, Y., Choi, J. S., Marin, T., & Singamaneni, S. (2023). Photonic Resonator Absorption Microscopy (pram) For Digital Resolution Biomolecular Diagnostics. (U.S. Patent No. 11591640).
Bacon, A., Wang, W., Lee, H., Umrao, S., Sinawang, P. D., Akin, D., Khemtonglang, K., Tan, A., Hirshfield, S., Demirci, U., Wang, X., & Cunningham, B. T. (2023). Review of HIV Self Testing Technologies and Promising Approaches for the Next Generation. Biosensors, 13(2), Article 298. https://doi.org/10.3390/bios13020298
Arif, W., Mathur, B., Saikali, M. F., Chembazhi, U. V., Toohill, K., Song, Y. J., Hao, Q., Karimi, S., Blue, S. M., Yee, B. A., Van Nostrand, E. L., Bangru, S., Guzman, G., Yeo, G. W., Prasanth, K. V., Anakk, S., Cummins, C. L., & Kalsotra, A. (2023). Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death. Nature communications, 14(1), Article 551. https://doi.org/10.1038/s41467-023-35932-3
Kwon, J. Y., Moskwa, N., Kang, W., Fan, T. M., & Lee, C. (2023). Canine as a Comparative and Translational Model for Human Mammary Tumor. Journal of Breast Cancer, 26(1), 1-13. https://doi.org/10.4048/jbc.2023.26.e4
Messerschmidt, V., Ren, W., Tsipursky, M., & Irudayaraj, J. (2023). Characterization of Oxygen Nanobubbles and In Vitro Evaluation of Retinal Cells in Hypoxia. Translational Vision Science and Technology, 12(2), Article 16. https://doi.org/10.1167/tvst.12.2.16
Tu, Z., Irudayaraj, J., & Lee, Y. (2023). Characterizing Spray-Dried Powders through NIR Spectroscopy: Effect of Two Preparation Strategies for Calibration Samples and Comparison of Two Types of NIR Spectrometers. Foods, 12(3), Article 467. https://doi.org/10.3390/foods12030467
Yu, T., Boob, A. G., Volk, M. J., Liu, X., Cui, H., & Zhao, H. (2023). Machine learning-enabled retrobiosynthesis of molecules. Nature Catalysis, 6(2), 137-151. https://doi.org/10.1038/s41929-022-00909-w
Kim, Y., Yang, Y., Zhang, X., Li, Z., Vázquez-Guardado, A., Park, I., Wang, J., Efimov, A. I., Dou, Z., Wang, Y., Park, J., Luan, H., Ni, X., Kim, Y. S., Baek, J., Park, J. J., Xie, Z., Zhao, H., Gazzola, M., ... Bashir, R. (2023). Remote control of muscle-driven miniature robots with battery-free wireless optoelectronics. Science Robotics, 8(74), eadd1053. https://doi.org/10.1126/scirobotics.add1053
Mestre, R., Fuentes, J., Lefaix, L., Wang, J., Guix, M., Murillo, G., Bashir, R., & Sánchez, S. (2023). Improved Performance of Biohybrid Muscle-Based Bio-Bots Doped with Piezoelectric Boron Nitride Nanotubes. Advanced Materials Technologies, 8(2), Article 2200505. https://doi.org/10.1002/admt.202200505
Huang, C., Cui, H., Ren, H., & Zhao, H. (2023). Investigation of the Biosynthetic Mechanism of Bipentaromycin Featuring an Unprecedented Cyclic Head-to-Tail Dimeric Scaffold. JACS Au, 3(1), 195-203. https://doi.org/10.1021/jacsau.2c00594
Cheong, C. B., Peh, G. R., Wei, Y., Rehka, T., Ang, E. L., Zhao, H., Zhang, C., & Lim, Y. H. (2023). A Spirobicyclo[3.1.0]Terpene from the Investigation of Sesquiterpene Synthases from Lactarius deliciosus. ACS chemical biology, 18(1), 134-140. https://doi.org/10.1021/acschembio.2c00760
Zhao, S., Lee, L., Zhao, Y., Liang, N-C., & Chen, Y. S. (2023). Photoacoustic signal enhancement in dual-contrast gastrin-releasing peptide receptor-targeted nanobubbles. Frontiers in Bioengineering and Biotechnology, 11, Article 1102651. https://doi.org/10.3389/fbioe.2023.1102651
Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (2023). Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults. The Journal of nutrition, 152(12), 2956-2965. Article nxac195. https://doi.org/10.1093/jn/nxac195
Singh, R., Bhagwat, S. S., Viswanathan, M. B., Cortés‐Peña, Y. R., Eilts, K. K., Mcdonough, G., Cao, M., Guest, J. S., Zhao, H., & Singh, V. (2023). Adsorptive separation and recovery of triacetic acid lactone from fermentation broth. Biofuels, Bioproducts and Biorefining, 17(1), 109-120. https://doi.org/10.1002/bbb.2427
Gabrys, R., Pattabiraman, S., & Milenkovic, O. (2023). Reconstruction of Sets of Strings From Prefix/Suffix Compositions. IEEE Transactions on Communications, 71(1), 3-12. https://doi.org/10.1109/TCOMM.2022.3222341
Lee, J. W., Bhagwat, S. S., Kuanyshev, N., Cho, Y. B., Sun, L., Lee, Y. G., Cortés-Peña, Y. R., Li, Y., Rao, C. V., Guest, J. S., & Jin, Y. S. (2023). Rewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant production. Chemical Engineering Journal, 451, Article 138886. https://doi.org/10.1016/j.cej.2022.138886
Rana, V., Chien, E., Peng, J., & Milenkovic, O. (2023). Small-Sample Estimation of the Mutational Support and Distribution of SARS-CoV-2. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(1), 668-682. https://doi.org/10.1109/TCBB.2022.3165395
Jeong, Y., Kong, W., Lu, T., & Irudayaraj, J. (2023). Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors. Biosensors and Bioelectronics, 219, Article 114809. https://doi.org/10.1016/j.bios.2022.114809
Mishra, S., Wang, Z., Volk, M. J., & Zhao, H. (2023). Design and application of a kinetic model of lipid metabolism in Saccharomyces cerevisiae. Metabolic Engineering, 75, 12-18. https://doi.org/10.1016/j.ymben.2022.11.003
Zhang, X., Flaws, J. A., Spinella, M. J., & Irudayaraj, J. (2023). The Relationship between Typical Environmental Endocrine Disruptors and Kidney Disease. Toxics, 11(1), Article 32. https://doi.org/10.3390/toxics11010032
Lim, J., Zhou, S., Baek, J., Kim, A. Y., Valera, E., Sweedler, J., & Bashir, R. (in press). A Blood Drying Process for DNA Amplification. Small. https://doi.org/10.1002/smll.202307959
Liu, X., Milenkovic, O., & Moustakides, G. V. (2023). A Combinatorial Proof for the Dowry Problem. In 2023 IEEE Information Theory Workshop, ITW 2023 (pp. 538-543). (2023 IEEE Information Theory Workshop, ITW 2023). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ITW55543.2023.10161638
Ye, X., Wang, H., Yu, J., Chen, Y. S., & Zhao, Y. (2023). Automatically Reconfigurable Metasurface for Free-Positioning Wireless Power Transfer. In 2023 IEEE Wireless Power Technology Conference and Expo, WPTCE 2023 - Proceedings (2023 IEEE Wireless Power Technology Conference and Expo, WPTCE 2023 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/WPTCE56855.2023.10216114
Lopes, D. D., Dien, B. S., Hector, R. E., Singh, V., Thompson, S. R., Slininger, P. J., Boundy-Mills, K., Jagtap, S. S., & Rao, C. V. (2023). Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass. Journal of Industrial Microbiology and Biotechnology, 50(1), Article kuad040. https://doi.org/10.1093/jimb/kuad040
Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., & Holscher, H. D. (in press). Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials. Journal of Nutrition. https://doi.org/10.1016/j.tjnut.2023.11.001
Li, Y. H., Gabrys, R., Sima, J., Shomorony, I., & Milenkovic, O. (2023). Finding a Burst of Positives via Nonadaptive Semiquantitative Group Testing. In 2023 IEEE International Symposium on Information Theory, ISIT 2023 (pp. 1848-1853). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2023-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT54713.2023.10206886
Kim, H. W., Kim, N. K., Phillips, A. P. R., Parker, D. A., Liu, P., Whitaker, R. J., Rao, C. V., & Mackie, R. I. (2023). Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Frontiers in Microbiology, 14, Article 1232587. https://doi.org/10.3389/fmicb.2023.1232587
Wang, H., Ye, X., Yu, J., Chen, Y. S., & Zhao, Y. (2023). Magnetic Nearfield Reshaping Metasurfaces. International Conference on Metamaterials, Photonic Crystals and Plasmonics, 355-356.
Zuo, Q., Park, N. H., Lee, J. K., Santaliz-Casiano, A., & Madak-Erdogan, Z. (in press). Navigating nonalcoholic fatty liver disease (NAFLD): Exploring the roles of estrogens, pharmacological and medical interventions, and life style. Steroids, Article 109330. https://doi.org/10.1016/j.steroids.2023.109330
Jagtap, S. S., Liu, J-J., Walukiewicz, H. E., Pangilinan, J., Lipzen, A., Ahrendt, S., Koriabine, M., Cobaugh, K., Salamov, A., Yoshinaga, Y., Ng, V., Daum, C., Grigoriev, I. V., Slininger, P. J., Dien, B. S., Jin, Y-S., & Rao, C. V. (2023). Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates. Microbiology Resource Announcements, 12(11). https://doi.org/10.1128/MRA.00426-23
Sima, J., Li, Y. H., Shomorony, I., & Milenkovic, O. (2023). On Constant-Weight Binary B2-Sequences. In 2023 IEEE International Symposium on Information Theory, ISIT 2023 (pp. 886-891). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2023-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT54713.2023.10206632
Moustakides, G. V., Liu, X., & Milenkovic, O. (in press). Optimal stopping methodology for the secretary problem with random queries. Journal of Applied Probability. https://doi.org/10.1017/jpr.2023.61
Sima, J., Pan, C., & Milenkovic, O. (2023). Perturbation-Resilient Sets for Dynamic Service Balancing. In 2023 IEEE International Symposium on Information Theory, ISIT 2023 (pp. 2278-2283). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2023-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT54713.2023.10206839
Holdhoff, M., Nicholas, M. K., Peterson, R. A., Maraka, S., Liu, L. C., Fischer, J. H., Wefel, J. S., Fan, T. M., Vannorsdall, T., Russell, M., Iacoboni, M., Tarasow, T. M., Hergenrother, P. J., Dudek, A. Z., & Danciu, O. C. (2023). Phase I dose escalation study of procaspase-activating compound-1 (PAC-1) in combination with temozolomide in patients with recurrent high-grade astrocytomas. Neuro-Oncology Advances, 5(1), Article vdad087. https://doi.org/10.1093/noajnl/vdad087
Chien, E., Zhang, J., Hsieh, C. J., Jiang, J. Y., Chang, W. C., Milenkovic, O., & Yu, H. F. (2023). PINA: Leveraging Side Information in eXtreme Multi-label Classification via Predicted Instance Neighborhood Aggregation. Proceedings of Machine Learning Research, 202, 5616-5630.
Yu, J., Wang, H., Ye, X., Chen, Y. S., & Zhao, Y. (2023). Qi Standard Compatible Metasurface for Multi-Device Wireless Power Transfer with Tunable Power Division. In 2023 IEEE Wireless Power Technology Conference and Expo, WPTCE 2023 - Proceedings (2023 IEEE Wireless Power Technology Conference and Expo, WPTCE 2023 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/WPTCE56855.2023.10215927
Lee, H., Wang, W., Chauhan, N., Xiong, Y., Magazine, N., Valdescruz, O., Kim, D. Y., Qiu, T., Huang, W., Wang, X., & Cunningham, B. T. (2023). Rapid, sensitive detection of intact SARS-CoV-2 using DNA nets and a smartphone-linked fluorimeter. In G. L. Cote (Ed.), Optical Diagnostics and Sensing XXIII: Toward Point-of-Care Diagnostics Article 123870B (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 12387). SPIE. https://doi.org/10.1117/12.2650836
Shah, M. M., Ahmad, K., Boota, S., Jensen, T., La Frano, M. R., & Irudayaraj, J. (2023). Sensor technologies for the detection and monitoring of endocrine-disrupting chemicals. Frontiers in Bioengineering and Biotechnology, 11, Article 1141523. https://doi.org/10.3389/fbioe.2023.1141523
Wang, W., Lee, H., Jankelow, A. M., Hoang, T. H., Bacon, A., Sun, F., Chae, S., Kindratenko, V., Koprowski, K., Stavins, R. A., Ceriani, D., Engelder, Z., King, W. P., Do, M. N., Bashir, R., Valera, E., & Cunningham, B. T. (2023). Smartphone Clip-On Instrument and Microfluidic Processor for Rapid Sample-to-Answer Detection of Zika Virus in Whole Blood Using Spatial RT-LAMP. In G. L. Cote (Ed.), Optical Diagnostics and Sensing XXIII: Toward Point-of-Care Diagnostics Article 123870D (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 12387). SPIE. https://doi.org/10.1117/12.2649267
Woodruff, W., Deshavath, N. N., Susanto, V., Rao, C. V., & Singh, V. (2023). Tolerance of engineered Rhodosporidium toruloides to sorghum hydrolysates during batch and fed-batch lipid production. Biotechnology for Biofuels and Bioproducts, 16(1). https://doi.org/10.1186/s13068-023-02429-6
Cunningham, B. T. (2023). Ultrasensitive and ultra selective liquid biopsy: Nanophotonics-driven digital resolution biomolecule sensing combined with target molecule recycling. In R. R. Alfano, & A. B. Seddon (Eds.), Optical Biopsy XXI: Toward Real-Time Spectroscopic Imaging and Diagnosis Article 1237304 (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; Vol. 12373). SPIE. https://doi.org/10.1117/12.2659440
- 2022
-
Milenkovic, O., Hernandez, A. G., Zhao, H., & Tabatabaei, S. (2022). Nick-based Data Storage In Native Nucleic Acids. (U.S. Patent No. 11538554).
Cabrera, A., Edelstein, H. I., Glykofrydis, F., Love, K. S., Palacios, S., Tycko, J., Zhang, M., Lensch, S., Shields, C. E., Livingston, M., Weiss, R., Zhao, H., Haynes, K. A., Morsut, L., Chen, Y. Y., Khalil, A. S., Wong, W. W., Collins, J. J., Rosser, S. J., ... Deans, T. L. (2022). The sound of silence: Transgene silencing in mammalian cell engineering. Cell Systems, 13(12), 950-973. https://doi.org/10.1016/j.cels.2022.11.005
Liu, Y., Wei, Y., Teh, T. M., Liu, D., Zhou, Y., Zhao, S., Ang, E. L., Zhao, H., & Zhang, Y. (2022). Identification and Characterization of the Biosynthetic Pathway of the Sulfonolipid Capnine. Biochemistry, 61(24), 2861-2869. https://doi.org/10.1021/acs.biochem.2c00102
Burke, M. D., Fan, T. M., Hergenrother, P. J., Brooke, C. B., Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., & Wang, L. (2022). Saliva-based Molecular Testing For SARS-CoV-2. (U.S. Patent No. 11530457).
Shi, W., Bell, S., Iyer, H., Brenden, C. K., Zhang, Y., Kim, S., Park, I., Bashir, R., Sweedler, J., & Vlasov, Y. (2022). Integrated silicon microfluidic chip for picoliter-scale analyte segmentation and microscale printing for mass spectrometry imaging. Lab on a chip, 23(1), 72-80. https://doi.org/10.1039/d2lc00688j
Sullivan, K. M., Ko, E., Kim, E. M., Ballance, W. C., Ito, J. D., Chalifoux, M., Kim, Y. J., Bashir, R., & Kong, H. (2022). Extracellular Microenvironmental Control for Organoid Assembly. Tissue Engineering - Part B: Reviews, 28(6), 1209-1222. https://doi.org/10.1089/ten.teb.2021.0186
Ayikpoe, R. S., Shi, C., Battiste, A. J., Eslami, S. M., Ramesh, S., Simon, M. A., Bothwell, I. R., Lee, H., Rice, A. J., Ren, H., Tian, Q., Harris, L. A., Sarksian, R., Zhu, L., Frerk, A. M., Precord, T. W., van der Donk, W. A., Mitchell, D. A., & Zhao, H. (2022). A scalable platform to discover antimicrobials of ribosomal origin. Nature communications, 13(1), [6135]. https://doi.org/10.1038/s41467-022-33890-w
Peng, Q., Huang, Z., Sun, K., Liu, Y., Yoon, C. W., Harrison, R. E. S., Schmitt, D. L., Zhu, L., Wu, Y., Tasan, I., Zhao, H., Zhang, J., Zhong, S., Chien, S., & Wang, Y. (2022). Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. Nature communications, 13(1), [7933]. https://doi.org/10.1038/s41467-022-35504-x
Cable, J., Arlotta, P., Parker, K. K., Hughes, A. J., Goodwin, K., Mummery, C. L., Kamm, R. D., Engle, S. J., Tagle, D. A., Boj, S. F., Stanton, A. E., Morishita, Y., Kemp, M. L., Norfleet, D. A., May, E. E., Lu, A., Bashir, R., Feinberg, A. W., Hull, S. M., ... Mulero-Russe, A. (2022). Engineering multicellular living systems—a Keystone Symposia report. Annals of the New York Academy of Sciences, 1518(1), 183-195. https://doi.org/10.1111/nyas.14896
Berry, M. R., Fadl-Alla, B. A., Samuelson, J., Rosol, T. J., & Fan, T. M. (2022). Investigating PSMA differential expression in canine uroepithelial carcinomas to aid disease-based stratification and guide therapeutic selection. BMC Veterinary Research, 18(1), [441]. https://doi.org/10.1186/s12917-022-03544-6
Schultz, J. C., Mishra, S., Gaither, E., Mejia, A., Dinh, H., Maranas, C., & Zhao, H. (2022). Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media. Microbial cell factories, 21(1), [26]. https://doi.org/10.1186/s12934-022-01750-3
Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Fredrickson, R. L., Wang, T., Wong, G. N., Uelmen, J., Maslov, S., Weiner, Z. J., Tkachenko, A. V., Zhang, H., Liu, Z., Ibrahim, A., Patel, S. J., Paul, J. M., Vance, N. P., Gulick, J. G., ... Burke, M. D. (2022). Mitigation of SARS-CoV-2 transmission at a large public university. Nature communications, 13(1), [3207]. https://doi.org/10.1038/s41467-022-30833-3
Enghiad, B., Xue, P., Singh, N., Boob, A. G., Shi, C., Petrov, V. A., Liu, R., Peri, S. S., Lane, S. T., Gaither, E. D., & Zhao, H. (2022). PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nature communications, 13(1), [2697]. https://doi.org/10.1038/s41467-022-30355-y
Pan, C., Tabatabaei, S. K., Tabatabaei Yazdi, S. M. H., Hernandez, A. G., Schroeder, C. M., & Milenkovic, O. (2022). Rewritable two-dimensional DNA-based data storage with machine learning reconstruction. Nature communications, 13(1), [2984]. https://doi.org/10.1038/s41467-022-30140-x
Khandelwal, A., Athreya, N., Tu, M. Q., Janavicius, L. L., Yang, Z., Milenkovic, O., Leburton, J. P., Schroeder, C. M., & Li, X. (2022). Self-assembled microtubular electrodes for on-chip low-voltage electrophoretic manipulation of charged particles and macromolecules. Microsystems and Nanoengineering, 8(1), [27]. https://doi.org/10.1038/s41378-022-00354-6
Peng, J., Serrano, G., Traniello, I. M., Calleja-Cervantes, M. E., Chembazhi, U. V., Bangru, S., Ezponda, T., Rodriguez-Madoz, J. R., Kalsotra, A., Prosper, F., Ochoa, I., & Hernaez, M. (2022). SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes. Communications biology, 5(1), [351]. https://doi.org/10.1038/s42003-022-03319-7
Han, X., Jeong, Y., & Irudayaraj, J. (2022). Nanocatalase-Based Oxygen-Generating Nanocarriers for Active Oxygen Delivery to Relieve Hypoxia in Pancreatic Cancer. ACS Applied Nano Materials, 5(11), 17248-17257. https://doi.org/10.1021/acsanm.2c04241
Zhao, H. (2022). The Ever-Expanding Boundaries of Synthetic Biology. ACS synthetic biology, 11(11), 3550. https://doi.org/10.1021/acssynbio.2c00582
Wen, Y., Liu, W., David, B., Ren, W., & Irudayaraj, J. (2022). Multifunctional Oxygenated Particles for Targeted Cancer Drug Delivery and Evaluation with Darkfield Hyperspectral Imaging. ACS Omega, 7(45), 41275-41283. https://doi.org/10.1021/acsomega.2c04953
Zhao, F., Wei, Y., Wang, X., Zhou, Y., Tong, Y., Ang, E. L., Liu, S., Zhao, H., & Zhang, Y. (2022). Enzymatic Synthesis of the Unnatural Nucleotide 2’-Deoxyisoguanosine 5’-Monophosphate. ChemBioChem, 23(21), [e202200295]. https://doi.org/10.1002/cbic.202200295
Erdogan, Z. M., & Hammes, S. R. (2022). Expanding Our Scope and Our Identity. Journal of the Endocrine Society, 6(11), [bvac149]. https://doi.org/10.1210/jendso/bvac149
Hsu, W., Hippe, D. S., Nakhaei, N., Wang, P. C., Zhu, B., Siu, N., Ahsen, M. E., Lotter, W., Sorensen, A. G., Naeim, A., Buist, D. S. M., Schaffter, T., Guinney, J., Elmore, J. G., & Lee, C. I. (2022). External Validation of an Ensemble Model for Automated Mammography Interpretation by Artificial Intelligence. JAMA network open, 5(11), e2242343. https://doi.org/10.1001/jamanetworkopen.2022.42343
Nelczyk, A. T., Ma, L., Gupta, A. D., Gamage, H. E. V., McHenry, M. T., Henn, M. A., Kadiri, M., Wang, Y., Krawczynska, N., Bendre, S., He, S., Shahoei, S. H., Madak-Erdogan, Z., Hsiao, S. H., Saleh, T., Carpenter, V., Gewirtz, D. A., Spinella, M. J., & Nelson, E. R. (2022). The nuclear receptor TLX (NR2E1) inhibits growth and progression of triple- negative breast cancer. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1868(11), [166515]. https://doi.org/10.1016/j.bbadis.2022.166515
Sonam, S., Bangru, S., Perry, K. J., Chembazhi, U. V., Kalsotra, A., & Henry, J. J. (2022). Cellular and molecular profiles of larval and adult Xenopus corneal epithelia resolved at the single-cell level. Developmental Biology, 491, 13-30. https://doi.org/10.1016/j.ydbio.2022.08.007
Qiao, W., Xu, S., Liu, Z., Fu, X., Zhao, H., & Shi, S. (2022). Challenges and opportunities in C1-based biomanufacturing. Bioresource Technology, 364, [128095]. https://doi.org/10.1016/j.biortech.2022.128095
Maino Vieytes, C. A., Zhu, R., Gany, F., Burton-Obanla, A., & Arthur, A. E. (2022). Empirical Dietary Patterns Associated with Food Insecurity in U.S. Cancer Survivors: NHANES 1999–2018. International journal of environmental research and public health, 19(21), [14062]. https://doi.org/10.3390/ijerph192114062
Audu, C. O., Melvin, W. J., Joshi, A. D., Wolf, S. J., Moon, J. Y., Davis, F. M., Barrett, E. C., Mangum, K. D., Deng, H., Xing, X., Wasikowski, R., Tsoi, L. C., Sharma, S. B., Bauer, T. M., Shadiow, J., Corriere, M. A., Obi, A. T., Kunkel, S. L., Levi, B., ... Gallagher, K. A. (2022). Macrophage-specific inhibition of the histone demethylase JMJD3 decreases STING and pathologic inflammation in diabetic wound repair. Cellular and Molecular Immunology, 19(11), 1251-1262. https://doi.org/10.1038/s41423-022-00919-5
Zhou, H., Zhu, R., Ung, A., & Schatz, B. (2022). Population analysis of mortality risk: Predictive models from passive monitors using motion sensors for 100,000 UK Biobank participants. PLOS Digital Health, 1(10), [e0000045]. https://doi.org/10.1371/journal.pdig.0000045
Zhang, Z., & Zhao, H. (2022). Tunnel engineering enables multifaceted improvements in halogenase. Chem Catalysis, 2(10), 2432-2434. https://doi.org/10.1016/j.checat.2022.09.010
Gordon, D. L., Foreman, J. H., Connolly, S. L., Schnelle, A. N., Fan, T. M., & Barger, A. M. (2022). Acute phase protein concentrations following serial procaine penicillin G injections in horses. Equine veterinary journal. https://doi.org/10.1111/evj.13886
Ganguli, A., Lim, J., Mostafa, A., Saavedra, C., Rayabharam, A., Aluru, N. R., Wester, M., White, K. C., Kumar, J., McGuffin, R., Frederick, A., Valera, E., & Bashir, R. (2022). A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proceedings of the National Academy of Sciences of the United States of America, 119(40), e2209607119. [e2209607119]. https://doi.org/10.1073/pnas.2209607119
LeBlanc, A. K., Mazcko, C. N., Fan, T. M., Vail, D. M., Flesner, B. K., Bryan, J. N., Li, S., Wang, F., Harris, S., Vargas, J. D., Govindharajulu, J. P., Jaganathan, S., Tomaino, F., Srivastava, A. K., Chou, T. F., Stott, G. M., Covey, J. M., Mroczkowski, B., & Doroshow, J. H. (2022). Comparative Oncology Assessment of a Novel Inhibitor of Valosin-Containing Protein in Tumor-Bearing Dogs. Molecular Cancer Therapeutics, 21(10), 1510-1523. https://doi.org/10.1158/1535-7163.MCT-22-0167
Fan, T. M., Garrett, L. D., Selting, K. A., & Constable, P. D. (2022). Novel immunotherapy offers promising weapon against canine melanoma. American journal of veterinary research, 83(10). https://doi.org/10.2460/ajvr.22.08.0133
Lee, Y. G., Kim, C., Kuanyshev, N., Kang, N. K., Fatma, Z., Wu, Z. Y., Cheng, M. H., Singh, V., Yoshikuni, Y., Zhao, H., & Jin, Y. S. (2022). Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. Journal of Agricultural and Food Chemistry, 70(38), 12085-12094. https://doi.org/10.1021/acs.jafc.2c04251
Zheng, L., Wen, Y., Ren, W., Duan, H., Lin, J., & Irudayaraj, J. (2022). Hyperspectral dark-field microscopy for pathogen detection based on spectral angle mapping. Sensors and Actuators B: Chemical, 367, [132042]. https://doi.org/10.1016/j.snb.2022.132042
Liu, X., & Milenkovic, O. (2022). Finding the second-best candidate under the Mallows model. Theoretical Computer Science, 929, 39-68. https://doi.org/10.1016/j.tcs.2022.06.029
Wang, J., Wang, Y., Kim, Y., Yu, T., & Bashir, R. (2022). Multi-actuator light-controlled biological robots. APL Bioengineering, 6(3), [036103]. https://doi.org/10.1063/5.0091507
Cao, M., Tran, V. G., Qin, J., Olson, A., Mishra, S., Schultz, JC., Huang, C., Xie, D., & Zhao, H. (2022). Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnology and bioengineering, 119(9), 2529-2540. https://doi.org/10.1002/bit.28159
Ren, W., & Irudayaraj, J. (2022). Magnetic Control-Enhanced Lateral Flow Technique for Ultrasensitive Nucleic Acid Target Detection. ACS Omega, 7(33), 29204-29210. https://doi.org/10.1021/acsomega.2c03276
Yeo, K. I., Park, I., Lee, S. H., Lee, S. Y., Chang, W. J., Bashir, R., Choi, S., & Lee, S. W. (2022). Ultra-sensitive dielectrophoretic surface charge multiplex detection inside a micro-dielectrophoretic device. Biosensors and Bioelectronics, 210, [114235]. https://doi.org/10.1016/j.bios.2022.114235
Chien, E., Tabaghi, P., & Milenkovic, O. (2022). HyperAid: Denoising in Hyperbolic Spaces for Tree-fitting and Hierarchical Clustering. In KDD 2022 - Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 201-211). (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining). Association for Computing Machinery. https://doi.org/10.1145/3534678.3539378
Wang, X. (2022). Photonic crystal enhanced fluorescence emission and blinking suppression for single quantum dot digital resolution biosensing. Nature communications. https://doi.org/10.1038/s41467-022-32387-w
Ko, E., Aydin, O., Li, Z., Gapinske, L., Huang, K. Y., Saif, T., Bashir, R., & Kong, H. (2022). Empowering engineered muscle in biohybrid pump by extending connexin 43 duration with reduced graphene oxides. Biomaterials, 287, [121643]. https://doi.org/10.1016/j.biomaterials.2022.121643
Yan, X., Shang, P., Yim-im, W., Sun, Y., Zhang, J., Firth, A. E., Lowe, J. F., & Fang, Y. (2022). Molecular characterization of emerging variants of PRRSV in the United States: new features of the -2/-1 programmed ribosomal frameshifting signal in the nsp2 region. Virology, 573, 39-49. https://doi.org/10.1016/j.virol.2022.06.004
Lee, C. J., Qiu, T. A., Hong, Z., Zhang, Z., Min, Y., Zhang, L., Dai, L., Zhao, H., Si, T., & Sweedler, J. V. (2022). Profiling of d-alanine production by the microbial isolates of rat gut microbiota. FASEB Journal, 36(8), [e22446]. https://doi.org/10.1096/fj.202101595R
Liu, W., Padhi, A., Zhang, X., Narendran, J., Anastasio, M. A., Nain, A. S., & Irudayaraj, J. (2022). Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers. ACS Nano, 16(7), 10754-10767. https://doi.org/10.1021/acsnano.2c02660
Chauhan, N., Xiong, Y., Ren, S., Dwivedy, A., Magazine, N., Zhou, L., Jin, X., Zhang, T., Cunningham, B. T., Yao, S., Huang, W., & Wang, X. (2022). Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus. Journal of the American Chemical Society. https://doi.org/10.1021/jacs.2c04835
Zhao, H. (2022). Synthetic Biology 2.0: The Dawn of a New Era. ACS synthetic biology, 11(7), 2221. https://doi.org/10.1021/acssynbio.2c00332
Kelly, A. M., Berry, M. R., Tasker, S. Z., McKee, S. A., Fan, T. M., & Hergenrother, P. J. (2022). Target-Agnostic P-Glycoprotein Assessment Yields Strategies to Evade Efflux, Leading to a BRAF Inhibitor with Intracranial Efficacy. Journal of the American Chemical Society, 144(27), 12367-12380. https://doi.org/10.1021/jacs.2c03944
Jeong, Y., & Irudayaraj, J. (2022). Multi-layered alginate hydrogel structures and bacteria encapsulation. Chemical Communications, 58(61), 8584-8587. https://doi.org/10.1039/d2cc01187e
Jeong, Y., Tin, A., & Irudayaraj, J. (2022). Flipped Well-Plate Hanging-Drop Technique for Growing Three-Dimensional Tumors. Frontiers in Bioengineering and Biotechnology, 10, [898699]. https://doi.org/10.3389/fbioe.2022.898699
Bailey, R. L., Dog, T. L., Smith-Ryan, A. E., Das, S. K., Baker, F. C., Madak-Erdogan, Z., Hammond, B. R., Sesso, H. D., Eapen, A., Mitmesser, S. H., Wong, A., & Nguyen, H. (2022). Sex Differences Across the Life Course: A Focus On Unique Nutritional and Health Considerations among Women. Journal of Nutrition, 152(7), 1597-1610. https://doi.org/10.1093/jn/nxac059
Mou, Q., Xue, X., Ma, Y., Banik, M., Garcia, V., Guo, W., Wang, J., Song, T., Chen, L. Q., & Lu, Y. (2022). Efficient delivery of a DNA aptamer-based biosensor into plant cells for glucose sensing through thiol-mediated uptake. Science Advances, 8(26), [eabo0902]. https://doi.org/10.1126/sciadv.abo0902
Huang, X., Feng, J., Cui, J., Jiang, G., Harrison, W., Zang, X., Zhou, J., Wang, B., & Zhao, H. (2022). Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition. Nature Catalysis, 5(7), 586-593. https://doi.org/10.1038/s41929-022-00777-4
Jankelow, A. M., Lee, H., Wang, W., Hoang, T. H., Bacon, A., Sun, F., Chae, S., Kindratenko, V., Koprowski, K., Stavins, R. A., Ceriani, D. D., Engelder, Z. W., King, W. P., Do, M. N., Bashir, R., Valera, E., & Cunningham, B. T. (2022). Smartphone clip-on instrument and microfluidic processor for rapid sample-to-answer detection of Zika virus in whole blood using spatial RT-LAMP. Analyst, 147(17), 3838-3853. https://doi.org/10.1039/d2an00438k
Duan, Y., Wei, Y., Xing, M., Liu, J., Jiang, L., Lu, Q., Liu, X., Liu, Y., Ang, E. L., Liao, R. Z., Yuchi, Z., Zhao, H., & Zhang, Y. (2022). Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme. Journal of the American Chemical Society, 144(22), 9715-9722. https://doi.org/10.1021/jacs.2c01673
Smith, L. D., Nalla, S., Kuo, C. W., Kohli, M., & Smith, A. M. (2022). Rapid quantification of microRNA-375 through one-pot primer-generating rolling circle amplification. Analyst, 147(13), 2936-2941. https://doi.org/10.1039/d2an00263a
Boyd, R. I., Ahmad, S., Singh, R., Fazal, Z., Prins, G. S., Erdogan, Z. M., Irudayaraj, J., & Spinella, M. J. (2022). Toward a Mechanistic Understanding of Poly-and Perfluoroalkylated Substances and Cancer. Cancers, 14(12), [2919]. https://doi.org/10.3390/cancers14122919
Zuo, Q., Park, N. H., Lee, J. K., & Madak Erdogan, Z. (2022). Liver Metastatic Breast Cancer: Epidemiology, Dietary Interventions, and Related Metabolism. Nutrients, 14(12). https://doi.org/10.3390/nu14122376
Zuo, Q., Mogol, A. N., Liu, Y. J., Casiano, A. S., Chien, C., Drnevich, J., Imir, O. B., Kulkoyluoglu-Cotul, E., Park, N. H., Shapiro, D. J., Park, B. H., Ziegler, Y., Katzenellenbogen, B. S., Aranda, E., O’Neill, J. D., Raghavendra, A. S., Tripathy, D., & Erdogan, Z. M. (2022). Targeting Metabolic Adaptations in the Breast Cancer–Liver Metastatic Niche Using Dietary Approaches to Improve Endocrine Therapy Efficacy. Molecular Cancer Research, 20(6), 923-937. https://doi.org/10.1158/1541-7786.MCR-21-0781
Wang, X. (2022, May 5). Net-shaped DNA nanostructure designed for rapid/sensitive detection and potential inhibition of SARS-CoV-2 virus. https://doi.org/10.1101/2022.05.04.490692
Zhao, B., Wang, W., Li, N., Garcia-Lezana, T., Che, C., Wang, X., Losic, B., Villanueva, A., & Cunningham, B. T. (2022). Digital-resolution and highly sensitive detection of multiple exosomal small RNAs by DNA toehold probe-based photonic resonator absorption microscopy. Talanta, 241, [123256]. https://doi.org/10.1016/j.talanta.2022.123256
Santaliz Casiano, A., Lee, A., Teteh, D., Madak Erdogan, Z., & Treviño, L. (2022). Endocrine-Disrupting Chemicals and Breast Cancer: Disparities in Exposure and Importance of Research Inclusivity. Endocrinology (United States), 163(5), [bqac034]. https://doi.org/10.1210/endocr/bqac034
Yuan, F., Sharma, J., Nanjappa, S. G., Gaulke, C. A., & Fang, Y. (2022). Effect of Killed PRRSV Vaccine on Gut Microbiota Diversity in Pigs. Viruses, 14(5), [1081]. https://doi.org/10.3390/v14051081
Barger, A., Baker, K., Driskell, E., Sander, W., Roady, P., Berry, M., Schnelle, A., & Fan, T. M. (2022). The use of alkaline phosphatase and runx2 to distinguish osteosarcoma from other common malignant primary bone tumors in dogs. Veterinary pathology, 59(3), 427-432. https://doi.org/10.1177/03009858221083035
Maino Vieytes, C. A., Rodriguez-Zas, S. L., Madak-Erdogan, Z., Smith, R. L., Zarins, K. R., Wolf, G. T., Rozek, L. S., Mondul, A. M., & Arthur , A. E. (2022). Adherence to a priori-Defined Diet Quality Indices Throughout the Early Disease Course Is Associated With Survival in Head and Neck Cancer Survivors: An Application Involving Marginal Structural Models. Frontiers in Nutrition, 9, [791141]. https://doi.org/10.3389/fnut.2022.791141
Harrison, W., Huang, X., & Zhao, H. (2022). Photobiocatalysis for Abiological Transformations. Accounts of chemical research, 55(8), 1087-1096. https://doi.org/10.1021/acs.accounts.1c00719
Chakraborty, B., Das, S., Gupta, A., Xiong, Y., T-V, V., Kizer, M. E., Duan, J., Chandrasekaran, A. R., & Wang, X. (2022). Aptamers for Viral Detection and Inhibition. ACS Infectious Diseases, 8(4), 667-692. https://doi.org/10.1021/acsinfecdis.1c00546
Lowerison, M., Zhang, W., Chen, X., Fan, T., & Song, P. (2022). Characterization of Anti-Angiogenic Chemo-Sensitization via Longitudinal Ultrasound Localization Microscopy in Colorectal Carcinoma Tumor Xenografts. IEEE Transactions on Biomedical Engineering, 69(4), 1449 - 1460. https://doi.org/10.1109/TBME.2021.3119280
Boudreau, M. W., Mulligan, M. P., Shapiro, D. J., Fan, T. M., & Hergenrother, P. J. (2022). Activators of the Anticipatory Unfolded Protein Response with Enhanced Selectivity for Estrogen Receptor Positive Breast Cancer. Journal of Medicinal Chemistry, 65(5), 3894-3912. https://doi.org/10.1021/acs.jmedchem.1c01730
Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M., & Milenkovic, O. (2022). Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing. Nano letters, 22(5), 1905-1914. https://doi.org/10.1021/acs.nanolett.1c04203
Wang, X. (2022). Resolving the sequence of DNA and RNA strands by tip-enhanced Raman spectroscopy. In Smart Photonic and Optoelectronic Integrated Circuits 2022 https://doi.org/10.1117/12.2610375
Tran, V. G., & Zhao, H. (2022). Engineering robust microorganisms for organic acid production. Journal of Industrial Microbiology and Biotechnology, 49(2), [kuab067]. https://doi.org/10.1093/jimb/kuab067
Aydin, O., Passaro, A. P., Raman, R., Spellicy, S. E., Weinberg, R. P., Kamm, R. D., Sample, M., Truskey, G. A., Zartman, J., Dar, R. D., Palacios, S., Wang, J., Tordoff, J., Montserrat, N., Bashir, R., Saif, M. T. A., & Weiss, R. (2022). Principles for the design of multicellular engineered living systems. APL Bioengineering, 6(1), [010903]. https://doi.org/10.1063/5.0076635
Zhao, H., & Enghiad, B. (2022). Programmable DNA-guided artificial restriction enzymes. (U.S. Patent No. 11261483).
Zhang, L., Dutta, S., Xiong, S., Chan, M., Chan, K. K., Fan, T. M., Bailey, K. L., Lindeblad, M., Cooper, L. M., Rong, L., Gugliuzza, A. F., Shukla, D., Procko, E., Rehman, J., & Malik, A. B. (2022). Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variants. Nature chemical biology, 18(3), 342-351. https://doi.org/10.1038/s41589-021-00965-6
Ding, W., Meng, Q., Dong, G., Qi, N., Zhao, H., & Shi, S. (2022). Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions. Biotechnology Journal, 17(3), [2100579]. https://doi.org/10.1002/biot.202100579
Hu, W. Y., Lu, R., Hu, D. P., Imir, O. B., Zuo, Q., Moline, D., Afradiasbagharani, P., Liu, L., Lowe, S., Birch, L., Griend, D. J. V., Madak-Erdogan, Z., & Prins, G. S. (2022). Per- and polyfluoroalkyl substances target and alter human prostate stem-progenitor cells. Biochemical Pharmacology, 197, [114902]. https://doi.org/10.1016/j.bcp.2021.114902
Lim, J., Stavins, R., Kindratenko, V., Baek, J., Wang, L., White, K., Kumar, J., Valera, E., King, W. P., & Bashir, R. (2022). Microfluidic point-of-care device for detection of early strains and B.1.1.7 variant of SARS-CoV-2 virus. Lab on a chip, 22(7), 1297-1309. https://doi.org/10.1039/d2lc00021k
Che, C., Xue, R., Li, N., Gupta, P., Wang, X., Zhao, B., Singamaneni, S., Nie, S., & Cunningham, B. T. (2022). Accelerated Digital Biodetection Using Magneto-plasmonic Nanoparticle-Coupled Photonic Resonator Absorption Microscopy. ACS Nano, 16(2), 2345–2354. https://doi.org/10.1021/acsnano.1c08569
Deng, H., Konopka, C. J., Prabhu, S., Sarkar, S., Medina, N. G., Fayyaz, M., Arogundade, O. H., Vidana Gamage, H. E., Shahoei, S. H., Nall, D., Youn, Y., Dobrucka, I. T., Audu, C. O., Joshi, A., Melvin, W. J., Gallagher, K. A., Selvin, P. R., Nelson, E. R., Dobrucki, L. W., ... Smith, A. M. (2022). Dextran-Mimetic Quantum Dots for Multimodal Macrophage Imaging In Vivo, Ex Vivo, and In Situ. ACS Nano, 16(2), 1999-2012. https://doi.org/10.1021/acsnano.1c07010
Liang, J., Zhang, H., Tan, Y. L., Zhao, H., & Ang, E. L. (2022). Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity. ACS synthetic biology, 11(2), 634-643. https://doi.org/10.1021/acssynbio.1c00319
Svec, R. L., Mckee, S. A., Berry, M. R., Kelly, A. M., Fan, T. M., & Hergenrother, P. J. (2022). Novel Imidazotetrazine Evades Known Resistance Mechanisms and Is Effective against Temozolomide-Resistant Brain Cancer in Cell Culture. ACS chemical biology, 17(2), 299–313. https://doi.org/10.1021/acschembio.2c00022
Zimmerman, S. C., Bai, Y., & Kalsotra, A. (2022). Multivalent ligand for myotonic dystrophy. (U.S. Patent No. 11242326).
Li, N., Wang, X., Tibbs, J., Che, C., Peinetti, A. S., Zhao, B., Liu, L., Barya, P., Cooper, L., Rong, L., Wang, X., Lu, Y., & Cunningham, B. T. (2022). Label-Free Digital Detection of Intact Virions by Enhanced Scattering Microscopy. Journal of the American Chemical Society, 144(4), 1498-1502. https://doi.org/10.1021/jacs.1c09579
Xiong, Y., Li, N., Che, C., Wang, W., Barya, P., Liu, W., Liu, L., Wang, X., Wu, S., Hu, H., & Cunningham, B. T. (2022). Microscopies Enabled by Photonic Metamaterials. Sensors, 22(3), [1086]. https://doi.org/10.3390/s22031086
Ren, S., Fraser, K., Kuo, L., Chauhan, N., Adrian, A. T., Zhang, F., Linhardt, R. J., Kwon, P. S., & Wang, X. (2022). Designer DNA nanostructures for viral inhibition. Nature Protocols, 17(2), 282-326. https://doi.org/10.1038/s41596-021-00641-y
Li, N., Zhao, B., Stavins, R., Peinetti, A. S., Chauhan, N., Bashir, R., Cunningham, B. T., King, W. P., Lu, Y., Wang, X., & Valera, E. (2022). Overcoming the limitations of COVID-19 diagnostics with nanostructures, nucleic acid engineering, and additive manufacturing. Current Opinion in Solid State and Materials Science, 26(1), [100966]. https://doi.org/10.1016/j.cossms.2021.100966
Ma, L., Smith, A. M., & Tu, C. (2022). Compact and homogeneous quantum dots and methods of making the same. (U.S. Patent No. 11226336).
Zhang, Y., Kim, S., Shi, W., Zhao, Y., Park, I., Brenden, C., Iyer, H., Jha, P., Bashir, R., Sweedler, J. V., & Vlasov, Y. (2022). Droplet-assisted electrospray phase separation using an integrated silicon microfluidic platform. Lab on a chip, 22(1), 40-46. https://doi.org/10.1039/d1lc00758k
Shoaib, Z., Fan, T. M., & Irudayaraj, J. M. K. (2022). Osteosarcoma mechanobiology and therapeutic targets. British Journal of Pharmacology, 179(2), 201-217. https://doi.org/10.1111/bph.15713
Ahmed, R., Augustine, R., Valera, E., Ganguli, A., Mesaeli, N., Ahmad, I. S., Bashir, R., & Hasan, A. (2022). Spatial mapping of cancer tissues by OMICS technologies. Biochimica et Biophysica Acta - Reviews on Cancer, 1877(1), 188663. [188663]. https://doi.org/10.1016/j.bbcan.2021.188663
Chen, S., Hwang, M. T., Wang, J., Ganguli, A., Park, I., Kim, Y., Valera, E., Nam, S. W., Aluru, N. R., Van Der Zande, A. M., & Bashir, R. (2022). Advances in Electronic Nano-biosensors and New Frontiers in Bioengineering. In 2022 International Electron Devices Meeting, IEDM 2022 (pp. 1711-1714). (Technical Digest - International Electron Devices Meeting, IEDM; Vol. 2022-December). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IEDM45625.2022.10019512
Pan, C., Gabrys, R., Liu, X., Colbourn, C., & Milenkovic, O. (2022). Balanced and Swap-Robust Trades for Dynamical Distributed Storage. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 2385-2390). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT50566.2022.9834794
Li, Y., Zhu, R., Yeh, M., & Qu, A. (2022). Dermoscopic Image Classification with Neural Style Transfer. Journal of Computational and Graphical Statistics, 31(4), 1318-1331. https://doi.org/10.1080/10618600.2022.2061496
Wu, A., Garimella, A., Subramanyam, R., & Ahsen, M. (2022). Disaster Management Through Digital Platforms: Online Crowdfunding Communities Respond to the COVID-19 Pandemic. In T. X. Bui (Ed.), Proceedings of the 55th Annual Hawaii International Conference on System Sciences, HICSS 2022 (pp. 4402-4411). (Proceedings of the Annual Hawaii International Conference on System Sciences; Vol. 2022-January). IEEE Computer Society.
Lu, T., Qi, F., Ner, J., Feng, T., Cunningham, B., & Peng, L. (2022). GeauxTrace: A Scalable Privacy-Protecting Contact Tracing App Design Using Blockchain. In Proceedings - 2022 IEEE/ACM 9th International Conference on Big Data Computing, Applications and Technologies, BDCAT 2022 (pp. 100-109). (Proceedings - 2022 IEEE/ACM 9th International Conference on Big Data Computing, Applications and Technologies, BDCAT 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BDCAT56447.2022.00020
Xiong, X., Tasan, I., Yang, C., Zhang, M., Hernandez Gonzalez, G. A., Liu, S., Chaturvedi, P., Belmont, A. S., & Zhao, H. (Accepted/In press). Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. ACS synthetic biology. https://doi.org/10.1021/acssynbio.2c00433
Applegate, C. C., Deng, H., Kleszynski, B. L., Cross, T. W. L., Konopka, C. J., Dobrucki, L. W., Nelson, E. R., Wallig, M. A., Smith, A. M., & Swanson, K. S. (2022). Impact of administration route on nanocarrier biodistribution in a murine colitis model. Journal of Experimental Nanoscience, 17(1), 599-616. https://doi.org/10.1080/17458080.2022.2134563
Wen, Y., Rashid, F., Fazal, Z., Singh, R., Spinella, M. J., & Irudayaraj, J. (2022). Nephrotoxicity of perfluorooctane sulfonate (PFOS) - effect on transcription and epigenetic factors. Environmental Epigenetics, 8(1), [dvac010]. https://doi.org/10.1093/eep/dvac010
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Wang, X., Zhou, L., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Emission and Blinking Suppression for Single Quantum Dot Digital Resolution Biosensing of Cancer-associated miRNA Biomarkers. In CLEO: Science and Innovations, S and I 2022 [JTh6A.2] (Optics InfoBase Conference Papers). Optica Publishing Group (formerly OSA).
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Wang, X., Zhou, L., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Emission and Blinking Suppression for Single Quantum Dot Digital Resolution Biosensing of Cancer-associated miRNA Biomarkers. In 2022 Conference on Lasers and Electro-Optics, CLEO 2022 - Proceedings [JTh6A.2] (2022 Conference on Lasers and Electro-Optics, CLEO 2022 - Proceedings). Institute of Electrical and Electronics Engineers Inc..
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Che, C., Wang, X., Zhou, L., Igarashi, A., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Quantum Dot Biosensor for Cancer-associated miRNA Detection. In 2022 IEEE Sensors, SENSORS 2022 - Conference Proceedings (Proceedings of IEEE Sensors; Vol. 2022-October). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SENSORS52175.2022.9967032
Li, N., Wang, X., Tibbs, J., Canady, T. D., Huang, Q., Fried, G. A., Wang, X., Cooper, L., Rong, L., Lu, Y., & Cunningham, B. T. (2022). Photonic resonator interferometric scattering microscopy. In S. M. Garcia-Blanco, & P. Cheben (Eds.), Integrated Optics: Devices, Materials, and Technologies XXVI [120040K] (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 12004). SPIE. https://doi.org/10.1117/12.2606436
Mitra, C., Yoo, J. Y., Madak-Erdogan, Z., & Soliman, A. S. (2022). Spatial Analysis of Tumor Heterogeneity Using Machine Learning Techniques. In Proceedings - 2022 IEEE 19th International Conference on Mobile Ad Hoc and Smart Systems, MASS 2022 (pp. 781-786). (Proceedings - 2022 IEEE 19th International Conference on Mobile Ad Hoc and Smart Systems, MASS 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/MASS56207.2022.00123
Han, Z., Vaidya, R. M., Arogundade, O. H., Ma, L., Zahid, M. U., Sarkar, S., Kuo, C. W., Selvin, P. R., & Smith, A. M. (Accepted/In press). Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging. Chemistry of Materials. https://doi.org/10.1021/acs.chemmater.2c00498
Golm, R., Nahvi, M., Gabrys, R., & Milenkovic, O. (2022). The Gapped k-Deck Problem. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 49-54). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ISIT50566.2022.9834537
Han, W., Wang, X., Ahsen, M. E., & Wattal, S. (2022). The Societal Impact of Sharing Economy Platform Self-Regulations-An Empirical Investigation. Information Systems Research, 33(4), 1303-1323. https://doi.org/10.1287/isre.2021.1044
Cavalcanti, J. V. J., Selting, K. A., Ngo, M. T., Hoang, C. K. T., Schaeffer, D. J., Fan, T. M., Harley, B. A. C., & Phillips, H. (2022). Three-dimensional hydrogel culture systems support growth and determination of chemosensitivity of feline sarcoma and carcinoma cell lines. American journal of veterinary research, 83(6). https://doi.org/10.2460/ajvr.21.10.0157
Chauhan, N., Wang, W., Lee, H. K., Xiong, Y., Zhang, T., Magazine, N., Peng, L., Zhou, L., Huang, W., Wang, X., & Cunningham, B. T. (2022). V-Pods: Rapid, Sensitive Detection of Intact SARS-CoV-2 using DNA Nets and a Smartphone-Linked Fluorimeter. In B. M. Cullum, D. Kiehl, & E. S. McLamore (Eds.), Smart Biomedical and Physiological Sensor Technology XIX [1212306] (Proceedings of SPIE - The International Society for Optical Engineering; Vol. 12123). SPIE. https://doi.org/10.1117/12.2617550