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Njuguna, J. N., Clark, L. V., Anzoua, K. G., Bagmet, L., Chebukin, P., Dwiyanti, M. S., Dzyubenko, E., Dzyubenko, N., Ghimire, B. K., Jin, X., Johnson, D. A., Jørgensen, U., Kjeldsen, J. B., Nagano, H., Peng, J., Petersen, K. K., Sabitov, A., Seong, E. S., Yamada, T., ... Sacks, E. J. (2023). Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America, and Europe. GCB Bioenergy, 15(5), 642-662. https://doi.org/10.1111/gcbb.13043
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
Lee, D. K., Rubakhin, S. S., & Sweedler, J. V. (2023). Chemical Decrosslinking-Based Peptide Characterization of Formaldehyde-Fixed Rat Pancreas Using Fluorescence-Guided Single-Cell Mass Spectrometry. Analytical Chemistry, 95(16), 6732-6739. https://doi.org/10.1021/acs.analchem.3c00612
Kong, W., Qian, Y., Stewart, P. S., & Lu, T. (2023). De novo engineering of a bacterial lifestyle program. Nature chemical biology, 19(4), 488-497. https://doi.org/10.1038/s41589-022-01194-1
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
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
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
Long, S. P., Morgan, G., Kromdijk, J., Glowacka, K., Niyogi, K. K., Leonelli, L., & Gabilly, S. (2023). Transgenic Plants With Increased Photosynthesis Efficiency And Growth. (U.S. Patent No. 11572569).
Xie, Y. R., Chari, V. K., Castro, D. C., Grant, R., Rubakhin, S. S., & Sweedler, J. V. (2023). Data-Driven and Machine Learning-Based Framework for Image-Guided Single-Cell Mass Spectrometry. Journal of Proteome Research, 22(2), 491-500. https://doi.org/10.1021/acs.jproteome.2c00714
Yukawa, T., Bamba, T., Matsuda, M., Yoshida, T., Inokuma, K., Kim, J., Won Lee, J., Jin, Y. S., Kondo, A., & Hasunuma, T. (2023). Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition. Biotechnology and bioengineering, 120(2), 511-523. https://doi.org/10.1002/bit.28278
Nguyen, C., Sagan, V., Bhadra, S., & Moose, S. (2023). UAV Multisensory Data Fusion and Multi-Task Deep Learning for High-Throughput Maize Phenotyping. Sensors, 23(4), [1827]. https://doi.org/10.3390/s23041827
Zhou, Y., Mirts, E. N., Yook, S., Waugh, M., Martini, R., Jin, Y. S., & Lu, Y. (2023). Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides. Angewandte Chemie - International Edition, 62(5), [e202212440]. https://doi.org/10.1002/anie.202212440
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
Jia, J., Parmar, D., Ellis, J. F., Cao, T., Cutri, A. R., Shrout, J. D., Sweedler, J. V., & Bohn, P. W. (2023). Effect of Micro-Patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress. ACS Infectious Diseases, 9(1), 150-161. https://doi.org/10.1021/acsinfecdis.2c00519
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, [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, [114809]. https://doi.org/10.1016/j.bios.2022.114809
Deshavath, N. N., Dien, B. S., Slininger, P. J., Jin, Y-S., & Singh, V. (2023). A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach. Fermentation, 9(1), [5]. https://doi.org/10.3390/fermentation9010005
Sobańska, K., Jedryszek, P., Kern, C., Basińska-Barczak, A., Pniewski, T., & Long, S. P. (2023). An efficient indirect plant regeneration from shoot apical meristem (SAM) derived embryogenic callus of Miscanthus × giganteus. Biocatalysis and Agricultural Biotechnology, 47, [102576]. https://doi.org/10.1016/j.bcab.2022.102576
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
Ruiz-Vera, U. M., Balikian, R., Larson, T. H., & Ort, D. R. (2023). Evaluation of the effects of elevated CO2 concentrations on the growth of cassava storage roots by destructive harvests and ground penetrating radar scanning approaches. Plant, Cell & Environment, 46(1), 93-105. https://doi.org/10.1111/pce.14474
Burgess, A. J., Masclaux-Daubresse, C., Strittmatter, G., Weber, A. P. M., Taylor, S. H., Harbinson, J., Yin, X., Long, S., Paul, M. J., Westhoff, P., Loreto, F., Ceriotti, A., Saltenis, V. L. R., Pribil, M., Nacry, P., Scharff, L. B., Jensen, P. E., Muller, B., Cohan, J. P., ... Baekelandt, A. (2023). Improving crop yield potential: Underlying biological processes and future prospects. Food and Energy Security, 12(1), [e435]. https://doi.org/10.1002/fes3.435
Pattabiraman, S., Gabrys, R., & Milenkovic, O. (Accepted/In press). Coding for Polymer-Based Data Storage. IEEE Transactions on Information Theory, 1. https://doi.org/10.1109/TIT.2023.3267620
Lim, C. K. W., Miskalis, A. J., Perez-Pinera, P., & Gaj, T. (2023). Delivering Base Editors In Vivo by Adeno-Associated Virus Vectors. In Methods in Molecular Biology (pp. 135-158). (Methods in Molecular Biology; Vol. 2606). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2879-9_11
Long, C. C., Antevska, A., Mast, D. H., Okyem, S., Sweedler, J. V., & Do, T. D. (Accepted/In press). Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.3c00092
Castro, D. C., Chan-Andersen, P., Romanova, E. V., & Sweedler, J. V. (Accepted/In press). Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrometry Reviews. https://doi.org/10.1002/mas.21841
Lee, S. H., Yun, E. J., Han, N. R., Jung, I., Pelton, J. G., Lee, J-E., Kang, N. J., Jin, Y-S., & Kim, K. H. (2023). Production of Ethyl-agarobioside, a Novel Skin Moisturizer, by Mimicking the Alcoholysis from the Japanese Sake-Brewing Process. Marine Drugs, 21(6). https://doi.org/10.3390/md21060341
Li, G., Jeon, C. K., Ma, M., Jia, Y., Zheng, Z., Delafield, D. G., Lu, G., Romanova, E. V., Sweedler, J. V., Ruotolo, B. T., & Li, L. (Accepted/In press). Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chemical Science. https://doi.org/10.1039/d3sc00678f
Cavanagh, A. P., & Ort, D. R. (Accepted/In press). Transgenic strategies to improve the thermotolerance of photosynthesis. Photosynthesis research. https://doi.org/10.1007/s11120-023-01024-y
Milenkovic, O., Hernandez, A. G., Zhao, H., & Tabatabaei, S. (2022). Nick-based Data Storage In Native Nucleic Acids. (U.S. Patent No. 11538554).
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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
Cheong, Y. E., Kim, J., Jin, Y. S., & Kim, K. H. (2022). Elucidation of the fucose metabolism of probiotic Lactobacillus rhamnosus GG by metabolomic and flux balance analyses. Journal of Biotechnology, 360, 110-116. https://doi.org/10.1016/j.jbiotec.2022.11.002
Lim, C. K. W., McCallister, T. X., Saporito-Magriña, C., McPheron, G. D., Krishnan, R., Zeballos C, M. A., Powell, J. E., Clark, L. V., Perez-Pinera, P., & Gaj, T. (2022). CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes. Molecular Therapy, 30(12), 3619-3631. https://doi.org/10.1016/j.ymthe.2022.08.008
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
Peddada, S. R. T., Zeidner, L. E., Ilies, H. T., James, K. A., & Allison, J. T. (2022). Toward Holistic Design of Spatial Packaging of Interconnected Systems with Physical Interactions (SPI2). Journal of Mechanical Design, Transactions of the ASME, 144(12), [120801]. https://doi.org/10.1115/1.4055055
Lee, Y. G., Ju, Y., Sun, L., Park, S., Jin, Y. S., & Kim, S. R. (2022). Acetate-rich Cellulosic Hydrolysates and Their Bioconversion Using Yeasts. Biotechnology and Bioprocess Engineering, 27(6), 890-899. https://doi.org/10.1007/s12257-022-0217-3
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
Wang, Y., Stutz, S. S., Bernacchi, C. J., Boyd, R. A., Ort, D. R., & Long, S. P. (2022). Increased bundle sheath leakiness of CO2 during photosynthetic induction shows a lack of coordination between the C4 and C3 cycles. New Phytologist, 236(5), 1661-1675. https://doi.org/10.1111/nph.18485
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
Ort, D. R., Chinnusamy, V., & Pareek, A. (2022). Photosynthesis: diving deep into the process in the era of climate change. Plant Physiology Reports, 27(4), 539-542. https://doi.org/10.1007/s40502-022-00703-7
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
Cao, S., Wang, L., Han, T., Ye, W., Liu, Y., Sun, Y., Moose, S. P., Song, Q., & Chen, Z. J. (2022). Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize. Genome biology, 23(1), [53]. https://doi.org/10.1186/s13059-022-02614-0
Kim, J., Cheong, Y. E., Yu, S., Jin, Y. S., & Kim, K. H. (2022). Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component. Microbial cell factories, 21(1), [204]. https://doi.org/10.1186/s12934-022-01926-x
Pei, S., Liu, P., Parker, D. A., Mackie, R. I., & Rao, C. V. (2022). Systems analysis of the effect of hydrogen sulfide on the growth of Methylococcus capsulatus Bath. Applied Microbiology and Biotechnology, 106(23), 7879-7890. https://doi.org/10.1007/s00253-022-12236-y
Gupta, V. K., Bakshi, U., Chang, D., Lee, A. R., Davis, J. M., Chandrasekaran, S., Jin, Y. S., Freeman, M. F., & Sung, J. (2022). TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes. mSystems, 7(6). https://doi.org/10.1128/msystems.00925-22
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Nagarajan, K., Ni, C., & Lu, T. (2022). Agent-Based Modeling of Microbial Communities. ACS synthetic biology, 11(11), 3564-3574. https://doi.org/10.1021/acssynbio.2c00411
Ni, C., & Lu, T. (2022). Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations. ACS synthetic biology, 11(11), 3714-3723. https://doi.org/10.1021/acssynbio.2c00322
Zhao, H. (2022). The Ever-Expanding Boundaries of Synthetic Biology. ACS synthetic biology, 11(11), 3550. https://doi.org/10.1021/acssynbio.2c00582
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
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Han, N. R., Yu, S., Yun, E. J., Jin, Y. S., & Kim, K. H. (2022). Production of colanic acid hydrolysate and its use in the production of fucosylated oligosaccharides by engineered Saccharomyces cerevisiae. Process Biochemistry, 122, 332-340. https://doi.org/10.1016/j.procbio.2022.10.025
Harvey, C. M., Cavanagh, A. P., Kim, S. Y., Wright, D. A., Edquilang, R. G., Shreeves, K. S., Perdomo, J. A., Spalding, M. H., Ort, D. R., Bernacchi, C. J., & Huber, S. C. (2022). Removal of redox-sensitive Rubisco Activase does not alter Rubisco regulation in soybean. Photosynthesis research, 154(2), 169-182. https://doi.org/10.1007/s11120-022-00962-3
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
Zhang, Y., Li, K., Zhao, Y., Shi, W., Iyer, H., Kim, S., Brenden, C., Sweedler, J. V., & Vlasov, Y. (2022). Attomole-Level Multiplexed Detection of Neurochemicals in Picoliter Droplets by On-Chip Nanoelectrospray Ionization Coupled to Mass Spectrometry. Analytical Chemistry, 94(40), 13804-13809. https://doi.org/10.1021/acs.analchem.2c02323
Dilmurat, K., Sagan, V., Maimaitijiang, M., Moose, S., & Fritschi, F. B. (2022). Estimating Crop Seed Composition Using Machine Learning from Multisensory UAV Data. Remote Sensing, 14(19), [4786]. https://doi.org/10.3390/rs14194786
Bhavya, B., Chen, S., Zhang, Z., Li, W., Zhai, C., Angrave, L., & Huang, Y. (2022). Exploring collaborative caption editing to augment video-based learning. Educational Technology Research and Development, 70(5), 1755-1779. https://doi.org/10.1007/s11423-022-10137-5
Ali, A., Davidson, S., Fraenkel, E., Gilmore, I., Hankemeier, T., Kirwan, J. A., Lane, A. N., Lanekoff, I., Larion, M., McCall, L. I., Murphy, M., Sweedler, J. V., & Zhu, C. (2022). Single cell metabolism: current and future trends. Metabolomics, 18(10), [77]. https://doi.org/10.1007/s11306-022-01934-3
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
Acevedo-Siaca, L. G., Głowacka, K., Driever, S. M., Salesse-Smith, C. E., Lugassi, N., Granot, D., Long, S. P., & Kromdijk, J. (2022). Guard-cell-targeted overexpression of Arabidopsis Hexokinase 1 can improve water use efficiency in field-grown tobacco plants. Journal of experimental botany, 73(16), 5745-5757. https://doi.org/10.1093/jxb/erac218
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
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De La Toba, E. A., Anapindi, K. D. B., & Sweedler, J. V. (Accepted/In press). Assessment and Comparison of Database Search Engines for Peptidomic Applications. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00307
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