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Illinois IGB

Research Areas

Biosystems Design: Publications

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), [25].

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), [226].

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, [115169].

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.

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, [kiad324].

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Long, S. P., Morgan, G., Kromdijk, J., Glowacka, K., Niyogi, K. K., Leonelli, L., & Gabilly, S. (2023). Transgenic Plants With Increased Photosynthesis Efficiency And Growth. (U.S. Patent No. 11572569).

Xie, Y. R., Chari, V. K., Castro, D. C., Grant, R., Rubakhin, S. S., & Sweedler, J. V. (2023). Data-Driven and Machine Learning-Based Framework for Image-Guided Single-Cell Mass Spectrometry. Journal of Proteome Research, 22(2), 491-500.

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.

Nguyen, C., Sagan, V., Bhadra, S., & Moose, S. (2023). UAV Multisensory Data Fusion and Multi-Task Deep Learning for High-Throughput Maize Phenotyping. Sensors, 23(4), [1827].

Zhou, Y., Mirts, E. N., Yook, S., Waugh, M., Martini, R., Jin, Y. S., & Lu, Y. (2023). Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides. Angewandte Chemie - International Edition, 62(5), [e202212440].

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.

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.

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.

Gabrys, R., Pattabiraman, S., & Milenkovic, O. (2023). Reconstruction of Sets of Strings From Prefix/Suffix Compositions. IEEE Transactions on Communications, 71(1), 3-12.

Lee, J. W., Bhagwat, S. S., Kuanyshev, N., Cho, Y. B., Sun, L., Lee, Y. G., Cortés-Peña, Y. R., Li, Y., Rao, C. V., Guest, J. S., & Jin, Y. S. (2023). Rewiring yeast metabolism for producing 2,3-butanediol and two downstream applications: Techno-economic analysis and life cycle assessment of methyl ethyl ketone (MEK) and agricultural biostimulant production. Chemical Engineering Journal, 451, [138886].

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.

Jeong, Y., Kong, W., Lu, T., & Irudayaraj, J. (2023). Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors. Biosensors and Bioelectronics, 219, [114809].

Deshavath, N. N., Dien, B. S., Slininger, P. J., Jin, Y-S., & Singh, V. (2023). A Chemical-Free Pretreatment for Biosynthesis of Bioethanol and Lipids from Lignocellulosic Biomass: An Industrially Relevant 2G Biorefinery Approach. Fermentation, 9(1), [5].

Sobańska, K., Jedryszek, P., Kern, C., Basińska-Barczak, A., Pniewski, T., & Long, S. P. (2023). An efficient indirect plant regeneration from shoot apical meristem (SAM) derived embryogenic callus of Miscanthus × giganteus. Biocatalysis and Agricultural Biotechnology, 47, [102576].

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.

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.

Burgess, A. J., Masclaux-Daubresse, C., Strittmatter, G., Weber, A. P. M., Taylor, S. H., Harbinson, J., Yin, X., Long, S., Paul, M. J., Westhoff, P., Loreto, F., Ceriotti, A., Saltenis, V. L. R., Pribil, M., Nacry, P., Scharff, L. B., Jensen, P. E., Muller, B., Cohan, J. P., ... Baekelandt, A. (2023). Improving crop yield potential: Underlying biological processes and future prospects. Food and Energy Security, 12(1), [e435].

Pattabiraman, S., Gabrys, R., & Milenkovic, O. (Accepted/In press). Coding for Polymer-Based Data Storage. IEEE Transactions on Information Theory, 1.

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..

Long, C. C., Antevska, A., Mast, D. H., Okyem, S., Sweedler, J. V., & Do, T. D. (Accepted/In press). Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. Journal of the American Society for Mass Spectrometry.

Castro, D. C., Chan-Andersen, P., Romanova, E. V., & Sweedler, J. V. (Accepted/In press). Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrometry Reviews.

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).

Li, G., Jeon, C. K., Ma, M., Jia, Y., Zheng, Z., Delafield, D. G., Lu, G., Romanova, E. V., Sweedler, J. V., Ruotolo, B. T., & Li, L. (Accepted/In press). Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chemical Science.

Cavanagh, A. P., & Ort, D. R. (Accepted/In press). Transgenic strategies to improve the thermotolerance of photosynthesis. Photosynthesis research.

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.

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.

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.

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.

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.

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].

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.

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].

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].

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.

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].

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.

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].

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].

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].

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].

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].

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.

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).

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].

Nagarajan, K., Ni, C., & Lu, T. (2022). Agent-Based Modeling of Microbial Communities. ACS synthetic biology, 11(11), 3564-3574.

Ni, C., & Lu, T. (2022). Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations. ACS synthetic biology, 11(11), 3714-3723.

Zhao, H. (2022). The Ever-Expanding Boundaries of Synthetic Biology. ACS synthetic biology, 11(11), 3550.

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].

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].

Qiao, W., Xu, S., Liu, Z., Fu, X., Zhao, H., & Shi, S. (2022). Challenges and opportunities in C1-based biomanufacturing. Bioresource Technology, 364, [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.

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.

Zhang, Z., & Zhao, H. (2022). Tunnel engineering enables multifaceted improvements in halogenase. Chem Catalysis, 2(10), 2432-2434.

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.

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].

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.

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].

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.

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.

Liu, X., & Milenkovic, O. (2022). Finding the second-best candidate under the Mallows model. Theoretical Computer Science, 929, 39-68.

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.

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].

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.

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.

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.

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.

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.

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].

Deter, H. S., & Lu, T. (2022). Engineering microbial consortia with rationally designed cellular interactions. Current Opinion in Biotechnology, 76, 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.

Huang, X., Xin, Y., & Lu, T. (2022). A systematic, complexity-reduction approach to dissect the kombucha tea microbiome. eLife, 11, [e76401].

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.

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].

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].

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].

Zhao, H. (2022). Synthetic Biology 2.0: The Dawn of a New Era. ACS synthetic biology, 11(7), 2221.

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].

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.

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].

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.

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.

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].

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].

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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.

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.

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).

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.

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.

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].

Harrison, W., Huang, X., & Zhao, H. (2022). Photobiocatalysis for Abiological Transformations. Accounts of chemical research, 55(8), 1087-1096.

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.

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].

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.

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).

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].

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.

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.

Tran, V. G., & Zhao, H. (2022). Engineering robust microorganisms for organic acid production. Journal of Industrial Microbiology and Biotechnology, 49(2), [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].

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].

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].

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.

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.

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].

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.

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].

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.

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].

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.

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].

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.

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.

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.

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.

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.

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].

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.

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].

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.

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.

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.

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..

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].

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.

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.

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].

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..

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.

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.

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.

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.

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..

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.

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.

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].

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..

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.