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Research Areas

Biosystems Design: Publications

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

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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

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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

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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

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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

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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