- 2024
-
Zhou, Y., Zhou, S., Lyons, S., Sun, H., Sweedler, J. V., & Lu, Y. (2024). Enhancing 2-Pyrone Synthase Efficiency by High-Throughput Mass-Spectrometric Quantification and In Vitro/In Vivo Catalytic Performance Correlation. ChemBioChem, 25(5), Article e202300849. https://doi.org/10.1002/cbic.202300849
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
Zhang, Z., Gomes Viana, J. P., Zhang, B., Walden, K. K. O., Müller Paul, H., Moose, S. P., Morris, G. P., Daum, C., Barry, K. W., Shakoor, N., & Hudson, M. (2024). Major impacts of widespread structural variation on sorghum. Genome Research, 34(2), 286-299. https://doi.org/10.1101/gr.278396.123
Xie, Y. R., Castro, D. C., Rubakhin, S. S., Trinklein, T. J., Sweedler, J. V., & Lam, F. (2024). Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry. Nature Methods, 21(3), 521-530. https://doi.org/10.1038/s41592-024-02171-3
Xie, Z., Kim, C., Miller, M. J., & Jin, Y. S. (2024). Effects of 2′-fucosyllactose on the viability of starter cultures and Bifidobacterium strains of human origin in yogurt during refrigerated storage. Journal of food science, 89(5), 2546-2556. https://doi.org/10.1111/1750-3841.16996
Werner, M. S., & Schroeder, N. (2024). Editorial: Physiological alterations of nematodes influenced by cross-phylum symbioses. Frontiers in Physiology, 15, Article 1417354. https://doi.org/10.3389/fphys.2024.1417354
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
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
Vijayakumar, S., Wang, Y., Lehretz, G., Taylor, S., Carmo-Silva, E., & Long, S. (2024). Kinetic modeling identifies targets for engineering improved photosynthetic efficiency in potato (Solanum tuberosum cv. Solara). Plant Journal, 117(2), 561-572. https://doi.org/10.1111/tpj.16512
Tan, Y., De La Toba, E., Rubakhin, S. S., Labriola, L. T., Canfield, C., Pan, D., & Sweedler, J. V. (2024). NanoLC-timsTOF-Assisted Analysis of Glycated Albumin in Diabetes-Affected Plasma and Tears. Journal of the American Society for Mass Spectrometry, 35(1), 106-113. https://doi.org/10.1021/jasms.3c00331
Subramanian, C., McNamara, K., Croslow, S. W., Tan, Y., Hess, D., Kiseljak-Vassiliades, K., Wierman, M. E., Sweedler, J. V., & Cohen, M. S. (in press). Novel repurposing of sulfasalazine for the treatment of adrenocortical carcinomas, probably through the SLC7A11/xCT-hsa-miR-92a-3p-OIP5-AS1 network pathway. Surgery (United States). https://doi.org/10.1016/j.surg.2024.07.075
Su, P., Hollas, M. A. R., Butun, F. A., Kanchustambham, V. L., Rubakhin, S., Ramani, N., Greer, J. B., Early, B. P., Fellers, R. T., Caldwell, M. A., Sweedler, J. V., Kafader, J. O., & Kelleher, N. L. (2024). Single Cell Analysis of Proteoforms. Journal of Proteome Research, 23(6), 1883-1893. https://doi.org/10.1021/acs.jproteome.4c00075
Srivastava, A., Srinivasan, V., & Long, S. P. (2024). Stomatal conductance reduction tradeoffs in maize leaves: A theoretical study. Plant Cell and Environment, 47(5), 1716-1731. https://doi.org/10.1111/pce.14821
Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L., & Sweedler, J. V. (2024). Bioinformatics for Prohormone and Neuropeptide Discovery. In Methods in Molecular Biology (pp. 151-178). (Methods in Molecular Biology; Vol. 2758). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-3646-6_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.
Siebers, M. H., Fu, P., Blakely, B. J., Long, S. P., Bernacchi, C. J., & McGrath, J. M. (2024). Fast, Nondestructive and Precise Biomass Measurements Are Possible Using Lidar-Based Convex Hull and Voxelization Algorithms. Remote Sensing, 16(12), Article 2191. https://doi.org/10.3390/rs16122191
Shin, J., Liao, S., Kuanyshev, N., Xin, Y., Kim, C., Lu, T., & Jin, Y. S. (2024). Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nature communications, 15(1), Article 781. https://doi.org/10.1038/s41467-024-45011-w
Shin, J., Kim, S. R., Xie, Z., Jin, Y.-S., & Wang, Y.-C. (2024). A CRISPR/Cas12a-Based System for Sensitive Detection of Antimicrobial-Resistant Genes in Carbapenem-Resistant Enterobacterales. Biosensors, 14(4), Article 194. https://doi.org/10.3390/bios14040194
Sharmili, N., Lee, Y. H., & Allison, J. T. (2024). Battery Thermal Management Systems Design Considering Model Fidelity Levels and Design Optimization Utility. In AIAA SciTech Forum and Exposition, 2024 (AIAA SciTech Forum and Exposition, 2024). American Institute of Aeronautics and Astronautics Inc, AIAA. https://doi.org/10.2514/6.2024-2363
Salesse-Smith, C. E., Lochocki, E. B., Doran, L., Haas, B. E., Stutz, S. S., & Long, S. P. (2024). Greater mesophyll conductance and leaf photosynthesis in the field through modified cell wall porosity and thickness via AtCGR3 expression in tobacco. Plant Biotechnology Journal, 22(9), 2504-2517. https://doi.org/10.1111/pbi.14364
Sadman Sakib, M., Todd Griffith, D., Hossain, S., Bayat, S., & Allison, J. T. (2024). Intracycle RPM control for vertical axis wind turbines. Wind Energy, 27(3), 202-224. https://doi.org/10.1002/we.2885
Rotundo, J. L., Marshall, R., McCormick, R., Truong, S. K., Styles, D., Gerde, J. A., Gonzalez-escobar, E., Carmo-silva, E., Janes-bassett, V., Logue, J., Annicchiarico, P., Visser, C. D., Dind, A., Dodd, I. C., Dye, L., Long, S. P., Lopes, M. S., Pannecoucque, J., Reckling, M., ... Rufino, M. C. (2024). European soybean to benefit people and the environment. Scientific reports, 14(1), Article 7612. https://doi.org/10.1038/s41598-024-57522-z
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
Perez-Pinera, P., & Gaj, T. (2024). Editorial overview: The next-generation of genome editing: The future is now. Current Opinion in Biomedical Engineering, 30, Article 100522. https://doi.org/10.1016/j.cobme.2024.100522
Pelech, E. A., Stutz, S. S., Wang, Y., Lochocki, E. B., & Long, S. P. (in press). Have We Selected for Higher Mesophyll Conductance in Domesticating Soybean? Plant Cell and Environment. https://doi.org/10.1111/pce.15206
Parmar, D., Rosado-Rosa, J. M., Shrout, J. D., & Sweedler, J. V. (2024). Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods, 224, 21-34. https://doi.org/10.1016/j.ymeth.2024.01.014
Park, J., Park, S., Evelina, G., Kim, S., Jin, Y.-S., Chi, W.-J., Kim, I. J., & Kim, S. R. (2024). Metabolic Engineering of Komagataella phaffii for Xylose Utilization from Cellulosic Biomass. Molecules, 29(23), Article 5695. https://doi.org/10.3390/molecules29235695
Okyem, S., Romanova, E. V., Tai, H. C., Checco, J. W., & Sweedler, J. V. (2024). Nontargeted Identification of d-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS. In Methods in Molecular Biology (pp. 227-240). (Methods in Molecular Biology; Vol. 2758). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-3646-6_12
Nie, Y., Wang, H., Zhang, G., Ding, H., Han, B., Liu, L., Shi, J., Du, J., Li, X., Li, X., Zhao, Y., Zhang, X., Liu, C., Weng, J., Li, X., Zhang, X., Zhao, X., Pan, G., Jackson, D., ... Zhang, Z. (2024). The maize PLASTID TERMINAL OXIDASE (PTOX) locus controls the carotenoid content of kernels. Plant Journal, 118(2), 457-468. https://doi.org/10.1111/tpj.16618
Nguyen, V., Li, Y., & Lu, T. (2024). Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae. ACS synthetic biology, 13(5), 1442-1453. https://doi.org/10.1021/acssynbio.3c00542
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
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
Meacham-Hensold, K., Cavanagh, A. P., Sorensen, P., South, P. F., Fowler, J., Boyd, R., Jeong, J., Burgess, S., Stutz, S., Dilger, R. N., Lee, M., Ferrari, N., Larkin, J., & Ort, D. R. (2024). Shortcutting Photorespiration Protects Potato Photosynthesis and Tuber Yield Against Heatwave Stress. Global change biology, 30(12), Article e17595. https://doi.org/10.1111/gcb.17595
Mao, R. T., Guo, S. Q., Zhang, G., Li, Y. D., Xu, J. P., Wang, H. Y., Fu, P., Liu, C. P., Wu, S. Q., Chen, P., Mei, Y. S., Jin, Q. C., Liu, C. Y., Zhang, Y. C. F., Ding, X. Y., Liu, W. J., Romanova, E. V., Zhou, H. B., Cropper, E. C., ... Jing, J. (2024). Two C-terminal isoforms of Aplysia tachykinin–related peptide receptors exhibit phosphorylation-dependent and phosphorylation-independent desensitization mechanisms. Journal of Biological Chemistry, 300(8), Article 107556. https://doi.org/10.1016/j.jbc.2024.107556
Maitra, S., Cheng, M. H., Liu, H., Cao, V. D., Kannan, B., Long, S. P., Shanklin, J., Altpeter, F., & Singh, V. (2024). Sustainable co-production of plant lipids and cellulosic sugars from transgenic energycane at an industrially relevant scale: A proof of concept for alternative feedstocks. Chemical Engineering Journal, 487, Article 150450. https://doi.org/10.1016/j.cej.2024.150450
Long, S. P., Glowacka, K., Kromdijk, J., Niyogi, K. K., & Leonelli, L. (2024). Plants With Increased Water Use Efficiency. (U.S. Patent No. 12054727).
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
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
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
Kumar, P., Gholamalamdari, O., Zhang, Y., Zhang, L., Vertii, A., van Schaik, T., Peric-Hupkes, D., Sasaki, T., Gilbert, D. M., van Steensel, B., Ma, J., Kaufman, P. D., & Belmont, A. S. (2024). Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types. Communications biology, 7(1), Article 1135. https://doi.org/10.1038/s42003-024-06838-7
Kong, W., Collins, J. J., & Lu, T. (2024). Addendum: Designing microbial consortia with defined social interactions. Nature chemical biology, 20(6), 789-790. https://doi.org/10.1038/s41589-024-01560-1
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
Jin, Y.-S., Liu, J., Yu, S., Yun, E. J., Kwak, S., Kim, K. H., & Lee, J. W. (2024). Engineered Microorganisms For Production Of 2'focusyllactose And L-fucose. (U.S. Patent No. 12077792).
Ji, N., Liang, D., Studer, A. J., Moose, S. P., & Kent, A. D. (2024). Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum. GCB Bioenergy, 16(6), Article e13148. https://doi.org/10.1111/gcbb.13148
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
Hilgendorf, K., Wang, Y., Miller, M. J., & Jin, Y. S. (2024). Precision fermentation for improving the quality, flavor, safety, and sustainability of foods. Current Opinion in Biotechnology, 86, Article 103084. https://doi.org/10.1016/j.copbio.2024.103084
He, Y., Jaiswal, D., Long, S. P., Liang, X. Z., & Matthews, M. L. (2024). Biomass yield potential on U.S. marginal land and its contribution to reach net-zero emission. GCB Bioenergy, 16(2), Article e13128. https://doi.org/10.1111/gcbb.13128
Han, J., Ficca, A., Kleczewski, N., & Schroeder, N. (2024). Effect of Fluopyram on Pratylenchus penetrans on Corn in the Field and In Vitro. Plant disease, 108(2), 342-347. https://doi.org/10.1094/PDIS-04-23-0725-RE
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
Dai, D., & Jin, Y. S. (2024). Rare sugar bioproduction: advantages as sweeteners, enzymatic innovation, and fermentative frontiers. Current Opinion in Food Science, 56, Article 101137. https://doi.org/10.1016/j.cofs.2024.101137
Croslow, S. W., Trinklein, T. J., & Sweedler, J. V. (2024). Advances in multimodal mass spectrometry for single-cell analysis and imaging enhancement. FEBS Letters, 598(6), 591-601. https://doi.org/10.1002/1873-3468.14798
Croce, R., Carmo-Silva, E., Cho, Y. B., Ermakova, M., Harbinson, J., Lawson, T., McCormick, A. J., Niyogi, K. K., Ort, D. R., Patel-Tupper, D., Pesaresi, P., Raines, C., Weber, A. P. M., & Zhu, X. G. (2024). Perspectives on improving photosynthesis to increase crop yield. Plant Cell, 36(10), 3944-3973. https://doi.org/10.1093/plcell/koae132
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
Cho, Y. B., Boyd, R. A., Ren, Y., Lee, M. S., Jones, S. I., Ruiz-Vera, U. M., McGrath, J. M., Masters, M. D., & Ort, D. R. (2024). Reducing chlorophyll levels in seed-filling stages results in higher seed nitrogen without impacting canopy carbon assimilation. Plant Cell and Environment, 47(1), 278-293. https://doi.org/10.1111/pce.14737
Chinthoju, P. K., Lee, Y. H., Das, G. K., James, K., & Allison, J. T. (2024). Optimal Design of eVTOLs for Urban Mobility using Analytical Target Cascading (ATC). In AIAA SciTech Forum and Exposition, 2024 (AIAA SciTech Forum and Exposition, 2024). American Institute of Aeronautics and Astronautics Inc, AIAA. https://doi.org/10.2514/6.2024-2235
Chen, H., Shi, Y., Huang, M., Lu, T., Zhang, H., Zhou, C., Hou, T., & Feng, Y. (2024). Recognition and acquisition of FakB2-loaded exogenous fatty acid (eFA) by a streptococcal FakA kinase. Science Bulletin, 69(21), 3355-3360. https://doi.org/10.1016/j.scib.2024.05.015
Chaturvedi, P., & Belmont, A. S. (2024). Nuclear speckle biology: At the cross-roads of discovery and functional analysis. Current Opinion in Cell Biology, 91, Article 102438. https://doi.org/10.1016/j.ceb.2024.102438
Castro, D. C., Chan-Andersen, P., Romanova, E. V., & Sweedler, J. V. (2024). Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrometry Reviews, 43(4), 888-912. https://doi.org/10.1002/mas.21841
Angello, N. H., Friday, D. M., Hwang, C., Yi, S., Cheng, A. H., Torres-Flores, T. C., Jira, E. R., Wang, W., Aspuru-Guzik, A., Burke, M. D., Schroeder, C. M., Diao, Y., & Jackson, N. E. (2024). Closed-loop transfer enables artificial intelligence to yield chemical knowledge. Nature, 633(8029), 351-358. https://doi.org/10.1038/s41586-024-07892-1
Andersen, H. M., Tai, H. C., Rubakhin, S. S., Yau, P. M., & Sweedler, J. V. (2024). A novel series of metazoan L/D peptide isomerases. Journal of Biological Chemistry, 300(7), Article 107458. https://doi.org/10.1016/j.jbc.2024.107458
- 2023
-
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
Qiu, T., Lee, C. J., Huang, C., Lee, D. K., Rubakhin, S. S., Romanova, E. V., & Sweedler, J. V. (2023). Biodistribution and racemization of gut-absorbed l/d-alanine in germ-free mice. Communications biology, 6(1), Article 851. https://doi.org/10.1038/s42003-023-05209-y
Bao, T., Qian, Y., Xin, Y., Collins, J. J., & Lu, T. (2023). Engineering microbial division of labor for plastic upcycling. Nature communications, 14(1), Article 5712. https://doi.org/10.1038/s41467-023-40777-x
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
Yun, E. J., Yu, S., Kim, D. H., Park, N. J., Liu, J. J., Jin, Y. S., & Kim, K. H. (2023). Identification of the enantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of 3,6-anhydro-l-galactose. Applied Microbiology and Biotechnology, 107(24), 7427-7438. https://doi.org/10.1007/s00253-023-12807-7
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
Zeballos C, M. A., Moore, H. J., Smith, T. J., Powell, J. E., Ahsan, N. S., Zhang, S., & Gaj, T. (2023). Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins. Nature communications, 14(1), Article 6492. https://doi.org/10.1038/s41467-023-42147-z
Hellinger, R., Sigurdsson, A., Wu, W., Romanova, E. V., Li, L., Sweedler, J. V., Süssmuth, R. D., & Gruber, C. W. (2023). Peptidomics. Nature Reviews Methods Primers, 3(1), Article 25. https://doi.org/10.1038/s43586-023-00205-2
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
Aspray, E. K., Mies, T. A., McGrath, J. A., Montes, C. M., Dalsing, B., Puthuval, K. K., Whetten, A., Herriott, J., Li, S., Bernacchi, C. J., DeLucia, E. H., Leakey, A. D. B., Long, S. P., McGrath, J. M., Miglietta, F., Ort, D. R., & Ainsworth, E. A. (2023). Two decades of fumigation data from the Soybean Free Air Concentration Enrichment facility. Scientific Data, 10(1), Article 226. https://doi.org/10.1038/s41597-023-02118-x
Wu, YF., Toba, E. A. D. L., Dvoretskiy, S., Jung, R., Kim, N., Daniels, L., Romanova, E. V., Drnevich, J., Sweedler, J. V., & Boppart, M. D. (2023). Development of a cell‐free strategy to recover aged skeletal muscle after disuse. The Journal of Physiology, 601(22), 5011-5031. https://doi.org/10.1113/JP282867
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
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
Park, S., Park, B. R., Jeong, D., Park, J., Ko, J. K., Kim, S. J., Kim, J. S., Jin, Y. S., & Kim, S. R. (2023). Functional expression of RuBisCO reduces CO2 emission during fermentation by engineered Saccharomyces cerevisiae. Process Biochemistry, 134, 286-293. https://doi.org/10.1016/j.procbio.2023.10.013
Njuguna, J. N., Clark, L. V., Lipka, A. E., Anzoua, K. G., Bagmet, L., Chebukin, P., Dwiyanti, M. S., Dzyubenko, E., Dzyubenko, N., Ghimire, B. K., Jin, X., Johnson, D. A., Nagano, H., Peng, J., Petersen, K. K., Sabitov, A., Seong, E. S., Yamada, T., Yoo, J. H., ... Sacks, E. J. (2023). Genome-wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus. GCB Bioenergy, 15(11), 1355-1372. https://doi.org/10.1111/gcbb.13097
Cavanagh, A. P., & Ort, D. R. (2023). Transgenic strategies to improve the thermotolerance of photosynthesis. Photosynthesis research, 158(2), 109-120. https://doi.org/10.1007/s11120-023-01024-y
Lei, R., Hernandez Garcia, A., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023). Erratum: Mutational fitness landscape of human influenza H3N2 neuraminidase (Cell Reports (2023) 42(1), (S2211124722018526), (10.1016/j.celrep.2022.111951)). Cell Reports, 42(10), Article 113356. https://doi.org/10.1016/j.celrep.2023.113356
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
De La Toba, E. A., Anapindi, K. D. B., & Sweedler, J. V. (2023). Assessment and Comparison of Database Search Engines for Peptidomic Applications. Journal of Proteome Research, 22(10), 3123-3134. https://doi.org/10.1021/acs.jproteome.2c00307
Peddada, S. R. T., Dunfield, N. M., Zeidner, L. E., Givans, Z. R., James, K., & Allison, J. (2023). Enumeration and Identification of Unique 3D Spatial Topologies of Interconnected Engineering Systems Using Spatial Graphs. Journal of Mechanical Design, 145(10), Article 101708. https://doi.org/10.1115/1.4062978
Holland, B. L., Matthews, M. L., Bota, P., Sweetlove, L. J., Long, S. P., & diCenzo, G. C. (2023). A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation. New Phytologist, 240(2), 744-756. https://doi.org/10.1111/nph.19203
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
Cho, Y. B., Stutz, S. S., Jones, S. I., Wang, Y., Pelech, E. A., & Ort, D. R. (2023). Impact of pod and seed photosynthesis on seed filling and canopy carbon gain in soybean. Plant physiology, 193(2), 966-979. Article kiad324. https://doi.org/10.1093/plphys/kiad324
Nguyen, M. T., Kim, S. A., Cheng, Y. Y., Hong, S. H., Jin, Y. S., & Han, N. S. (2023). A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. Journal of Microbiology and Biotechnology, 33(9), 1228-1237. https://doi.org/10.4014/jmb.2305.05010
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
Long, C. C., Antevska, A., Mast, D. H., Okyem, S., Sweedler, J. V., & Do, T. D. (2023). Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. Journal of the American Society for Mass Spectrometry, 34(9), 1898-1907. https://doi.org/10.1021/jasms.3c00092
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
Kim, J., Cheong, Y. E., Yu, S., Yun, E. J., Jin, Y. S., & Kim, K. H. (2023). Biosynthesis of L-fucose and L-fuculose using engineered Saccharomyces cerevisiae. Process Biochemistry, 132, 152-156. https://doi.org/10.1016/j.procbio.2023.07.010
Głowacka, K., Kromdijk, J., Salesse-Smith, C. E., Smith, C., Driever, S. M., & Long, S. P. (2023). Is chloroplast size optimal for photosynthetic efficiency? New Phytologist, 239(6), 2197-2211. https://doi.org/10.1111/nph.19091
Wang, Y., Smith, J. A. C., Zhu, X. G., & Long, S. P. (2023). Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana. New Phytologist, 239(6), 2180-2196. https://doi.org/10.1111/nph.19128
Bayat, S., & Allison, J. T. (2023). SS-MPC: A user-friendly software based on single shooting optimization to solve Model Predictive Control problems[Formula presented]. Software Impacts, 17, Article 100566. https://doi.org/10.1016/j.simpa.2023.100566
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
Li, N., Bullock, D., Butts-Wilmsmeyer, C., Gentry, L., Goodwin, G., Han, J., Kleczweski, N., Martín, N. F., Paulausky, P., Pistorius, P., Seiter, N., Schroeder, N., & Margenot, A. J. (2023). Distinct soil health indicators are associated with variation in maize yield and tile drain nitrate losses. Soil Science Society of America Journal, 87(6), 1332-1347. Advance online publication. https://doi.org/10.1002/saj2.20586
Ros, K., Jin, M., Levine, J., & Zhai, C. X. (2023). Retrieving Webpages Using Online Discussions. In ICTIR 2023 - Proceedings of the 2023 ACM SIGIR International Conference on the Theory of Information Retrieval (pp. 159-168). (ICTIR 2023 - Proceedings of the 2023 ACM SIGIR International Conference on the Theory of Information Retrieval). Association for Computing Machinery. https://doi.org/10.1145/3578337.3605139
Ort, D. R., & Lunn, J. E. (2023). Society for Experimental Biology Centenary (1923-2023). Journal of experimental botany, 74(14), 3877-3878. https://doi.org/10.1093/jxb/erad206
Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B. J., Bruneau, B. G., Belmont, A. S., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C. M., Gilbert, D. M., Gregor, T., Hansen, A. S., Huang, B., Huangfu, D., Kalhor, R., Leslie, C. S., Li, W., Li, Y., ... Zhong, S. (2023). Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular cell, 83(15), 2624-2640. https://doi.org/10.1016/j.molcel.2023.06.018
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
Basso, T. P., Procópio, D. P., Petrin, T. H. C., Giacon, T. G., Jin, Y. S., Basso, T. O., & Basso, L. C. (2023). Engineering xylose fermentation in an industrial yeast: continuous cultivation as a tool for selecting improved strains. Letters in Applied Microbiology, 76(7). https://doi.org/10.1093/lambio/ovad077
Choe, K., Jindra, M. A., Hubbard, S. C., Pfleger, B. F., & Sweedler, J. V. (2023). MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants. Analytical Biochemistry, 672, Article 115169. https://doi.org/10.1016/j.ab.2023.115169
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
Lee, M. S., Boyd, R. A., Boateng, K. A., & Ort, D. R. (2023). Exploring 3D leaf anatomical traits for C4 photosynthesis: chloroplast and plasmodesmata pit field size in maize and sugarcane. New Phytologist, 239(2), 506-517. https://doi.org/10.1111/nph.18956
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
Nguyen, P. Q., Huang, X., Collins, D. S., Collins, J. J., & Lu, T. (2023). Harnessing synthetic biology to enhance ocean health. Trends in Biotechnology, 41(7), 860-874. https://doi.org/10.1016/j.tibtech.2022.12.015
Lai, T. M., Zhai, C. X., & Ji, H. (2023). KEBLM: Knowledge-Enhanced Biomedical Language Models. Journal of Biomedical Informatics, 143, Article 104392. https://doi.org/10.1016/j.jbi.2023.104392
Bernacchi, C. J., Ruiz-Vera, U. M., Siebers, M. H., DeLucia, N. J., & Ort, D. R. (2023). Short- and long-term warming events on photosynthetic physiology, growth, and yields of field grown crops. Biochemical Journal, 480(13), 999-1014. https://doi.org/10.1042/BCJ20220433
Liu, J., Huang, Z., Zhai, C., & Liu, Q. (2023). Learning by Applying: A General Framework for Mathematical Reasoning via Enhancing Explicit Knowledge Learning. In B. Williams, Y. Chen, & J. Neville (Eds.), AAAI-23 Technical Tracks 4 (pp. 4497-4506). (Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023; Vol. 37). American Association for Artificial Intelligence (AAAI) Press.
Kim, J., Jin, Y. S., & Kim, K. H. (2023). L-Fucose is involved in human–gut microbiome interactions. Applied Microbiology and Biotechnology, 107(12), 3869-3875. https://doi.org/10.1007/s00253-023-12527-y
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), Article 341. https://doi.org/10.3390/md21060341
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
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
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. (2023). Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chemical Science, 14(22), 5936-5944. https://doi.org/10.1039/d3sc00678f
Castro, D. C., Smith, K. W., Norsworthy, M. D., Rubakhin, S. S., Weisbrod, C. R., Hendrickson, C. L., & Sweedler, J. V. (2023). Single-Cell and Subcellular Analysis Using Ultrahigh Resolution 21 T MALDI FTICR Mass Spectrometry. Analytical Chemistry, 95(17), 6980-6988. https://doi.org/10.1021/acs.analchem.3c00393
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
Jindra, M. A., Choe, K., Chowdhury, R., Kong, R., Ghaffari, S., Sweedler, J. V., & Pfleger, B. F. (2023). Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids. Metabolic Engineering, 77, 21-31. https://doi.org/10.1016/j.ymben.2023.02.012
Bhavya, B., Xiong, J., & Zhai, C. (2023). CAM: A Large Language Model-based Creative Analogy Mining Framework. In ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023 (pp. 3903-3914). (ACM Web Conference 2023 - Proceedings of the World Wide Web Conference, WWW 2023). Association for Computing Machinery. https://doi.org/10.1145/3543507.3587431
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
Lane, S., Turner, T. L., & Jin, Y. S. (2023). Glucose assimilation rate determines the partition of flux at pyruvate between lactic acid and ethanol in Saccharomyces cerevisiae. Biotechnology Journal, 18(4), Article 2200535. https://doi.org/10.1002/biot.202200535
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
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
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
Eberwine, J., Kim, J., Anafi, R. C., Brem, S., Bucan, M., Fisher, S. A., Grady, M. S., Herr, A. E., Issadore, D., Jeong, H., Kim, H. B., Lee, D., Rubakhin, S., Sul, J. Y., Sweedler, J. V., Wolf, J. A., Zaret, K. S., & Zou, J. (2023). Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. Nature Methods, 20(3), 331-335. https://doi.org/10.1038/s41592-023-01788-0
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
De Souza, A. P., Burgess, S. J., Doran, L., Manukyan, L., Hansen, J., Maryn, N., Leonelli, L., Niyogi, K. K., & Long, S. P. (2023). Response to Comments on “Soybean photosynthesis and crop yield is improved by accelerating recovery from photoprotection”. Science, 379(6634), Article eadf2189. https://doi.org/10.1126/science.adf2189
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).
Sweedler, J. (2023). Welcome to 2023. Analytical Chemistry, 95(5), 2589. https://doi.org/10.1021/acs.analchem.3c00132
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
Schaerer, L. G., Wu, R., Putman, L. I., Pearce, J. M., Lu, T., Shonnard, D. R., Ong, R. G., & Techtmann, S. M. (2023). Killing two birds with one stone: chemical and biological upcycling of polyethylene terephthalate plastics into food. Trends in Biotechnology, 41(2), 184-196. https://doi.org/10.1016/j.tibtech.2022.06.012
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
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), Article 1827. https://doi.org/10.3390/s23041827
Lei, R., Hernandez Garcia, A., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023). Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Reports, 42(1), Article 111951. https://doi.org/10.1016/j.celrep.2022.111951
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), Article e202212440. https://doi.org/10.1002/anie.202212440
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
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, 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
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), Article 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, Article 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), Article e435. https://doi.org/10.1002/fes3.435
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
Ren, L., Sidhu, M., Zeng, Q., Reddy, R. G., Ji, H., & Zhai, C. X. (2023). C-PMI: Conditional Pointwise Mutual Information for Turn-level Dialogue Evaluation. In S. Muresan, V. Chen, C. Kennington, D. Vandyke, N. Dethlefs, K. Inoue, E. Ekstedt, & S. Ultes (Eds.), DialDoc 2023 - Proceedings of the 3rd DialDoc Workshop on Document-Grounded Dialogue and Conversational Question Answering, Proceedings of the Workshop (pp. 80-85). (Proceedings of the Annual Meeting of the Association for Computational Linguistics). Association for Computational Linguistics (ACL).
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
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
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
Sun, C., Xu, T., Zhai, C. X., & Ji, H. (2023). Incorporating Task-Specific Concept Knowledge into Script Learning. In EACL 2023 - 17th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings of the Conference (pp. 3018-3032). (EACL 2023 - 17th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings of the Conference). Association for Computational Linguistics (ACL).
Sun, C., Li, J., Chan, H. P., Zhai, C. X., & Ji, H. (2023). Measuring the Effect of Influential Messages on Varying Personas. In Short Papers (pp. 554-562). (Proceedings of the Annual Meeting of the Association for Computational Linguistics; Vol. 2). Association for Computational Linguistics (ACL).
Vedant, Haddox, P., & Allison, J. T. (2023). Multifunctional Oscillating Structures for Slewing and Active Jitter Cancellation. In 2023 IEEE Aerospace Conference, AERO 2023 (IEEE Aerospace Conference Proceedings; Vol. 2023-March). IEEE Computer Society. https://doi.org/10.1109/AERO55745.2023.10115853
Tan, Y., De La Toba, E., Rubakhin, S. S., Labriola, L. T., Canfield, C., Pan, D., & Sweedler, J. V. (in press). NanoLC-timsTOF-Assisted Analysis of Glycated Albumin in Diabetes-Affected Plasma and Tears. Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.3c00331
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
Vedant, Haddox, P., & Allison, J. T. (2023). New Mission and Spacecraft Design Enabled Using MSAC. In 2023 IEEE Aerospace Conference, AERO 2023 (IEEE Aerospace Conference Proceedings; Vol. 2023-March). IEEE Computer Society. https://doi.org/10.1109/AERO55745.2023.10115834
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
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.
Castro, D. C., Chan-Andersen, P., Romanova, E. V., & Sweedler, J. V. (in press). Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrometry Reviews. https://doi.org/10.1002/mas.21841
Xue, X., Beuchat, G., Wang, J., Yu, Y. C., Moose, S., Chen, J., & Chen, L. Q. (2023). Sugar accumulation enhancement in sorghum stem is associated with reduced reproductive sink strength and increased phloem unloading activity. Frontiers in Plant Science, 14, Article 1233813. https://doi.org/10.3389/fpls.2023.1233813
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
Pei, K., Jindal, I., Chang, K. C. C., Zhai, C., & Li, Y. (2023). When to Use What: An In-Depth Comparative Empirical Analysis of OpenIE Systems for Downstream Applications. In Long Papers (pp. 929-949). (Proceedings of the Annual Meeting of the Association for Computational Linguistics; Vol. 1). Association for Computational Linguistics (ACL).
Choe, K., & Sweedler, J. V. (2023). Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies. Bio-protocol, 13(21), Article e4862. https://doi.org/10.21769/BioProtoc.4862
- 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
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
Trieu, A., Belaffif, M. B., Hirannaiah, P., Manjunatha, S., Wood, R., Bathula, Y., Billingsley, R. L., Arpan, A., Sacks, E. J., Clemente, T. E., Moose, S. P., Reichert, N. A., & Swaminathan, K. (2022). Transformation and gene editing in the bioenergy grass Miscanthus. Biotechnology for Biofuels and Bioproducts, 15(1), [148]. https://doi.org/10.1186/s13068-022-02241-8
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
Santu, S. K. K., Hassan, M. M., Smith, M. J., Xu, L., Zhai, C., & Veeramachaneni, K. (2022). AutoML to Date and Beyond: Challenges and Opportunities. ACM Computing Surveys, 54(8), [175]. https://doi.org/10.1145/3470918
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
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
Zhao, S., Jiang, M., Qin, B., Liu, T., Zhai, C., & Wang, F. (2022). Structural and Textual Information Fusion for Symptom and Disease Representation Learning. IEEE Transactions on Knowledge and Data Engineering, 34(9), 4468-4483. https://doi.org/10.1109/TKDE.2020.3039469
Lee, C. J., Schnieders, J. H., Rubakhin, S. S., Patel, A. V., Liu, C., Naji, A., & Sweedler, J. V. (2022). d-Amino Acids and Classical Neurotransmitters in Healthy and Type 2 Diabetes-Affected Human Pancreatic Islets of Langerhans. Metabolites, 12(9), [799]. https://doi.org/10.3390/metabo12090799
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
Deewan, A., Liu, J. J., Jagtap, S. S., Yun, E. J., Walukiewicz, H., Jin, Y. S., & Rao, C. V. (2022). System analysis of Lipomyces starkeyi during growth on various plant-based sugars. Applied Microbiology and Biotechnology, 106(17), 5629-5642. https://doi.org/10.1007/s00253-022-12084-w
Labhishetty, S., & Zhai, C. X. (2022). PRE: A Precision-Recall-Effort Optimization Framework for Query Simulation. In ICTIR 2022 - Proceedings of the 2022 ACM SIGIR International Conference on the Theory of Information Retrieval (pp. 51-60). (ICTIR 2022 - Proceedings of the 2022 ACM SIGIR International Conference on the Theory of Information Retrieval). Association for Computing Machinery. https://doi.org/10.1145/3539813.3545136
De Souza, A. P., Burgess, S. J., Doran, L., Hansen, J., Manukyan, L., Maryn, N., Gotarkar, D., Leonelli, L., Niyogi, K. K., & Long, S. P. (2022). Soybean photosynthesis and crop yield are improved by accelerating recovery from photoprotection. Science, 377(6608), 851-854. https://doi.org/10.1126/science.adc9831
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
Ruiz-Vera, U. M., Acevedo-Siaca, L. G., Brown, K. L., Afamefule, C., Gherli, H., Simkin, A. J., Long, S. P., Lawson, T., & Raines, C. A. (2022). Field-grown ictB tobacco transformants show no difference in photosynthetic efficiency for biomass relative to the wild type. Journal of experimental botany, 73(14), 4897-4907. [erac193]. https://doi.org/10.1093/jxb/erac193
Deter, H. S., & Lu, T. (2022). Engineering microbial consortia with rationally designed cellular interactions. Current Opinion in Biotechnology, 76, 102730. https://doi.org/10.1016/j.copbio.2022.102730
Acevedo-Siaca, L. G., & Long, S. P. (2022). Assessing heritability of biochemical limitations in photosynthesis can help elucidate new targets for improvement. Plant Breeding, 141(4), 546-548. https://doi.org/10.1111/pbr.13018
Huang, X., Xin, Y., & Lu, T. (2022). A systematic, complexity-reduction approach to dissect the kombucha tea microbiome. eLife, 11, [e76401]. https://doi.org/10.7554/eLife.76401
Zhu, X., Zhang, Y., Wang, Y., Tian, D., Belmont, A. S., Swedlow, J. R., & Ma, J. (2022). Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. Nature Methods, 19(8), 911-913. https://doi.org/10.1038/s41592-022-01559-3
Rymut, H. E., Rund, L. A., Southey, B. R., Johnson, R. W., Sweedler, J. V., & Rodriguez-Zas, S. L. (2022). Prefrontal Cortex Response to Prenatal Insult and Postnatal Opioid Exposure. Genes, 13(8), [1371]. https://doi.org/10.3390/genes13081371
Chan-Andersen, P. C., Romanova, E. V., Rubakhin, S. S., & Sweedler, J. V. (2022). Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveals neuronal populations with distinct neuropeptide profiles. Journal of Biological Chemistry, 298(8), [102254]. https://doi.org/10.1016/j.jbc.2022.102254
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
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
Belmont, A. S. (2022). Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harbor Perspectives in Biology, 14(7), [a041268]. https://doi.org/10.1101/cshperspect.a041268
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
Xu, Y., Yang, J., Li, W., Song, S., Shi, Y., Wu, L., Sun, J., Hou, M., Wang, J., Jia, X., Zhang, H., Huang, M., Lu, T., Gan, J., & Feng, Y. (2022). Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target. PLoS pathogens, 18(7 July), [e1010615]. https://doi.org/10.1371/journal.ppat.1010615
Satheesan, S. P., Bhavya, Davies, A., Craig, A. B., Zhang, Y., & Zhai, C. (2022). Toward a big data analysis system for historical newspaper collections research. In Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2022 [12] (Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2022). Association for Computing Machinery. https://doi.org/10.1145/3539781.3539795
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
Lee, Y. G., Kim, B. Y., Bae, J. M., Wang, Y., & Jin, Y. S. (2022). Genome-edited Saccharomyces cerevisiae strains for improving quality, safety, and flavor of fermented foods. Food Microbiology, 104, [103971]. https://doi.org/10.1016/j.fm.2021.103971
Melzer, M. E., Sweedler, J. V., & Clark, K. D. (2022). Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Genes, 13(6), [1008]. https://doi.org/10.3390/genes13061008
Feid, S. C., Walukiewicz, H. E., Wang, X., Nakayasu, E. S., Rao, C. V., & Wolfe, A. J. (2022). Regulation of Translation by Lysine Acetylation in Escherichia coli. mBio, 13(3). https://doi.org/10.1128/mbio.01224-22
Murphy, S. E., & Sweedler, J. V. (2022). Metabolomics-based mass spectrometry methods to analyze the chemical content of 3D organoid models. Analyst, 147(13), 2918-2929. https://doi.org/10.1039/d2an00599a
Dilmurat, K., Sagan, V., & Moose, S. (2022). Ai-driven maize yield forecasting using unmanned aerial vehicle-based hyperspectral and lidar data fusion. ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences, 5(3), 193-199. https://doi.org/10.5194/isprs-Annals-V-3-2022-193-2022
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. (2022). Near-Complete Genome Sequence of Zygosaccharomyces rouxii NRRL Y-64007, a Yeast Capable of Growing on Lignocellulosic Hydrolysates. Microbiology Resource Announcements, 11(5). https://doi.org/10.1128/mra.00050-22
He, Y., Jaiswal, D., Liang, X. Z., Sun, C., & Long, S. P. (2022). Perennial biomass crops on marginal land improve both regional climate and agricultural productivity. GCB Bioenergy, 14(5), 558-571. https://doi.org/10.1111/gcbb.12937
Sharma, B. P., Zhang, N., Lee, D. K., Heaton, E., Delucia, E. H., Sacks, E. J., Kantola, I. B., Boersma, N. N., Long, S. P., Voigt, T. B., & Khanna, M. (2022). Responsiveness of miscanthus and switchgrass yields to stand age and nitrogen fertilization: A meta-regression analysis. GCB Bioenergy, 14(5), 539-557. https://doi.org/10.1111/gcbb.12929
Maitra, S., Long, S. P., & Singh, V. (2022). Optimizing Chemical-Free Pretreatment for Maximizing Oil/Lipid Recovery From Transgenic Bioenergy Crops and Its Rapid Analysis Using Time Domain-NMR. Frontiers in Energy Research, 10, [840418]. https://doi.org/10.3389/fenrg.2022.840418
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
Xie, Y. R., Castro, D. C., Rubakhin, S. S., Sweedler, J. V., & Lam, F. (2022). Enhancing the Throughput of FT Mass Spectrometry Imaging Using Joint Compressed Sensing and Subspace Modeling. Analytical Chemistry, 94(13), 5335-5343. https://doi.org/10.1021/acs.analchem.1c05279
Kang, N. K., Kim, M., Baek, K., Chang, Y. K., Ort, D. R., & Jin, Y. S. (2022). Photoautotrophic organic acid production: Glycolic acid production by microalgal cultivation. Chemical Engineering Journal, 433, [133636]. https://doi.org/10.1016/j.cej.2021.133636
Cavanagh, A. P., South, P. F., Bernacchi, C. J., & Ort, D. R. (2022). Alternative pathway to photorespiration protects growth and productivity at elevated temperatures in a model crop. Plant Biotechnology Journal, 20(4), 711-721. https://doi.org/10.1111/pbi.13750
Bodhankar, G. A., Tohidifar, P., Foust, Z. L., Ordal, G. W., & Rao, C. V. (2022). Characterization of Opposing Responses to Phenol by Bacillus subtilis Chemoreceptors. Journal of bacteriology, 204(4). https://doi.org/10.1128/jb.00441-21
Clark, K. D., Rubakhin, S. S., & Sweedler, J. V. (2022). Characterizing RNA Modifications in Single Neurons using Mass Spectrometry. Journal of Visualized Experiments, 2022(182), [e63940]. https://doi.org/10.3791/63940
Wu, YF., Toba, E. A. D. L., Dvoretskiy, S., Jung, R., Kim, N., Daniels, L., Romanova, E. V., Drnevich, J., Sweedler, J. V., & Boppart, M. D. (Accepted/In press). Development of a cell‐free strategy to recover aged skeletal muscle after disuse. The Journal of Physiology. https://doi.org/10.1113/JP282867
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
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
Zhao, H., & Enghiad, B. (2022). Programmable DNA-guided artificial restriction enzymes. (U.S. Patent No. 11261483).
Kwak, S., Robinson, S. J., Lee, J. W., Lim, H., Wallace, C. L., & Jin, Y. S. (2022). Dissection and enhancement of prebiotic properties of yeast cell wall oligosaccharides through metabolic engineering. Biomaterials, 282, [121379]. https://doi.org/10.1016/j.biomaterials.2022.121379
Kang, N. K., Lee, J. W., Ort, D. R., & Jin, Y. S. (2022). L-malic Acid Production from Xylose by Engineered Saccharomyces Cerevisiae. Biotechnology Journal, 17(3), [2000431]. https://doi.org/10.1002/biot.202000431
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
Seo, S. O., & Jin, Y. S. (2022). Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annual Review of Food Science and Technology, 13, 463-488. https://doi.org/10.1146/annurev-food-052720-012228
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
Procópio, D. P., Kendrick, E., Goldbeck, R., Damasio, A. R. D. L., Franco, T. T., Leak, D. J., Jin, Y. S., & Basso, T. O. (2022). Xylo-Oligosaccharide Utilization by Engineered Saccharomyces cerevisiae to Produce Ethanol. Frontiers in Bioengineering and Biotechnology, 10, [825981]. https://doi.org/10.3389/fbioe.2022.825981
Labhishetty, S., Zhai, C. X., Xie, M., Gong, L., Sharnagat, R., & Chembolu, S. (2022). Differential query semantic analysis: Discovery of explicit interpretable knowledge from e-com search logs. In WSDM 2022 - Proceedings of the 15th ACM International Conference on Web Search and Data Mining (pp. 535-543). (WSDM 2022 - Proceedings of the 15th ACM International Conference on Web Search and Data Mining). Association for Computing Machinery. https://doi.org/10.1145/3488560.3498503
Fu, P., Jaiswal, D., McGrath, J. M., Wang, S., Long, S. P., & Bernacchi, C. J. (2022). Drought imprints on crops can reduce yield loss: Nature's insights for food security. Food and Energy Security, 11(1), [e332]. https://doi.org/10.1002/fes3.332
Taylor, S. H., Gonzalez-Escobar, E., Page, R., Parry, M. A. J., Long, S. P., & Carmo-Silva, E. (2022). Faster than expected Rubisco deactivation in shade reduces cowpea photosynthetic potential in variable light conditions. Nature plants, 8(2), 118-124. https://doi.org/10.1038/s41477-021-01068-9
Kang, N. K., Baek, K., Koh, H. G., Atkinson, C. A., Ort, D. R., & Jin, Y. S. (2022). Microalgal metabolic engineering strategies for the production of fuels and chemicals. Bioresource Technology, 345, [126529]. https://doi.org/10.1016/j.biortech.2021.126529
Lee, Y. G., Kim, C., Sun, L., Lee, T. H., & Jin, Y. S. (2022). Selective production of retinol by engineered Saccharomyces cerevisiae through the expression of retinol dehydrogenase. Biotechnology and bioengineering, 119(2), 399-410. https://doi.org/10.1002/bit.28004
Allison, J. T., Cardin, M. A., McComb, C., Ren, M. Y., Selva, D., Tucker, C., Witherell, P., & Zhao, Y. F. (2022). Special Issue: Artificial Intelligence and Engineering Design. Journal of Mechanical Design, Transactions of the ASME, 144(2), [020301].
Rin Kim, S., Kim, S. J., Kim, S. K., Seo, S. O., Park, S., Shin, J., Kim, J. S., Park, B. R., Jin, Y. S., Chang, P. S., & Park, Y. C. (2022). Yeast metabolic engineering for carbon dioxide fixation and its application. Bioresource Technology, 346, [126349]. https://doi.org/10.1016/j.biortech.2021.126349
Choi, H. J., Jin, Y. S., & Lee, W. H. (2022). Effects of Engineered Saccharomyces cerevisiae Fermenting Cellobiose through Low-Energy-Consuming Phosphorolytic Pathway in Simultaneous Saccharification and Fermentation. Journal of Microbiology and Biotechnology, 32(1), 117-125. https://doi.org/10.4014/jmb.2111.11047
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
Lim, C. K. W., & Gaj, T. (2022). Genome Editing and CRISPR Technology. In Encyclopedia of Cell Biology: Volume 1-6, Second Edition (Vol. 1, pp. 650-656). Elsevier. https://doi.org/10.1016/B978-0-12-821618-7.00104-8
Shameer, S., Wang, Y., Bota, P., Ratcliffe, R. G., Long, S. P., & Sweetlove, L. J. (2022). A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments. Plant Journal, 109(1), 295-313. https://doi.org/10.1111/tpj.15551
Smith, P., Beaumont, L., Bernacchi, C. J., Byrne, M., Cheung, W., Conant, R. T., Cotrufo, F., Feng, X., Janssens, I., Jones, H., Kirschbaum, M. U. F., Kobayashi, K., LaRoche, J., Luo, Y., McKechnie, A., Penuelas, J., Piao, S., Robinson, S., Sage, R. F., ... Long, S. P. (2022). Essential outcomes for COP26. Global change biology, 28(1), 1-3. https://doi.org/10.1111/gcb.15926
Kim, H. W., Kim, N. K., Phillips, A. P. R., Parker, D. A., Liu, P., Whitaker, R. J., Rao, C. V., & Mackie, R. I. (2022). Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms, 10(1), [142]. https://doi.org/10.3390/microorganisms10010142
Liu, J. M., Solem, C., Lu, T., & Jensen, P. R. (2022). Harnessing lactic acid bacteria in synthetic microbial consortia. Trends in Biotechnology, 40(1), 8-11. https://doi.org/10.1016/j.tibtech.2021.09.002
Powell, J. E., Lim, C. K. W., Krishnan, R., McCallister, T. X., Saporito-Magriña, C., Zeballos, M. A., McPheron, G. D., & Gaj, T. (2022). Targeted gene silencing in the nervous system with CRISPR-Cas13. Science Advances, 8(3), [eabk2485]. https://doi.org/10.1126/sciadv.abk2485
Lee, M. S., Boyd, R. A., & Ort, D. R. (2022). The photosynthetic response of C3 and C4 bioenergy grass species to fluctuating light. GCB Bioenergy, 14(1), 37-53. https://doi.org/10.1111/gcbb.12899
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
Taylor, S. H., Gonzalez-Escobar, E., Page, R., Parry, M. A. J., Long, S. P., & Carmo-Silva, E. (Accepted/In press). Author Correction: Faster than expected Rubisco deactivation in shade reduces cowpea photosynthetic potential in variable light conditions (Nature Plants, (2022), 8, 2, (118-124), 10.1038/s41477-021-01068-9). Nature plants. https://doi.org/10.1038/s41477-022-01243-6
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
Lochocki, E. B., Rohde, S., Jaiswal, D., Matthews, M. L., Miguez, F., Long, S. P., & McGrath, J. M. (2022). BioCro II: A software package for modular crop growth simulations. In Silico Plants, 4(1), [diac003]. https://doi.org/10.1093/insilicoplants/diac003
Orr, J. S., Zen, E., Wang, X., & Rao, C. V. (Accepted/In press). Emulsion-based evolution of Escherichia coli for higher growth yield on D-xylose identifies central role of cyclic AMP. Systems Microbiology and Biomanufacturing. https://doi.org/10.1007/s43393-022-00136-1
Dey, P., & Zhai, C. X. (2022). Fine Grained Categorization of Drug Usage Tweets. In G. Meiselwitz (Ed.), Social Computing and Social Media: Design, User Experience and Impact - 14th International Conference, SCSM 2022, Held as Part of the 24th HCI International Conference, HCII 2022, Proceedings (pp. 267-280). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13315 LNCS). Springer. https://doi.org/10.1007/978-3-031-05061-9_19
Tan, L. R., Liu, J. J., Deewan, A., Lee, J. W., Xia, P. F., Rao, C. V., Jin, Y. S., & Wang, S. G. (2022). Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide. FEMS yeast research, 22(1), [foac032]. https://doi.org/10.1093/femsyr/foac032
Rubakhin, S. S., Romanova, E. V., & Sweedler, J. V. (2022). High-Throughput Image-Guided Microprobe Mass Spectrometric Analysis of Single Cells. In Neuromethods (pp. 115-163). (Neuromethods; Vol. 184). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2525-5_6
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
Long, S. P., Taylor, S. H., Burgess, S. J., Carmo-Silva, E., Lawson, T., De Souza, A. P., Leonelli, L., & Wang, Y. (2022). Into the Shadows and Back into Sunlight: Photosynthesis in Fluctuating Light. Annual Review of Plant Biology, 73, 617-648. https://doi.org/10.1146/annurev-arplant-070221-024745
Anapindi, K. D. B., Romanova, E. V., Checco, J. W., & Sweedler, J. V. (2022). Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics. Pharmacological Reviews, 74(3), 662-679. https://doi.org/10.1124/pharmrev.121.000423
De La Toba, E. A., Bell, S. E., Romanova, E. V., & Sweedler, J. V. (2022). Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. Annual Review of Analytical Chemistry, 15, 83-106. https://doi.org/10.1146/annurev-anchem-061020-022048
Zhang, L., Chen, Y., & Belmont, A. S. (2022). Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq. In Methods in Molecular Biology (pp. 145-186). (Methods in Molecular Biology; Vol. 2532). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2497-5_8
Sweedler, J. V., Eberwine, J., & Fraser, S. E. (2022). Preface. Neuromethods, 184, vii-ix.
Labhishetty, S., & Zhai, C. X. (2022). RATE: A Reliability-Aware Tester-Based Evaluation Framework of User Simulators. In M. Hagen, S. Verberne, C. Macdonald, C. Seifert, K. Balog, K. Nørvåg, & V. Setty (Eds.), Advances in Information Retrieval - 44th European Conference on IR Research, ECIR 2022, Proceedings (pp. 336-350). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13185 LNCS). Springer. https://doi.org/10.1007/978-3-030-99736-6_23
Bhattacharyya, A., Peddada, S. R. T., Bello, W. B., Zeidner, L. E., Allison, J. T., & James, K. A. (2022). Simultaneous 3D Component Packing and Routing Optimization Using Geometric Projection. In AIAA SciTech Forum 2022 [AIAA 2022-2096] (AIAA Science and Technology Forum and Exposition, AIAA SciTech Forum 2022). American Institute of Aeronautics and Astronautics Inc, AIAA. https://doi.org/10.2514/6.2022-2096
Matthews, M. L., Marshall-Colón, A., McGrath, J. M., Lochocki, E. B., & Long, S. P. (2022). Soybean-BioCro: A semi-mechanistic model of soybean growth. In Silico Plants, 4(1), [diab032]. https://doi.org/10.1093/insilicoplants/diab032
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
Bello, W. B., Peddada, S. R. T., Bhattacharyya, A., Jennings, M., Katragadda, S., James, K., & Allison, J. T. (2022). Underhood Spatial Packing and Routing of an Automotive Fuel Cell System (AFCS) Using 2D Geometric Projection. In AIAA SciTech Forum 2022 [AIAA 2022-0804] (AIAA Science and Technology Forum and Exposition, AIAA SciTech Forum 2022). American Institute of Aeronautics and Astronautics Inc, AIAA. https://doi.org/10.2514/6.2022-0804