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Publications

Independent work

Coming soon! 

Graduate and Postdoctoral work

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Liu, Y.; et. al., “Complete biosynthesis of QS-21 in engineered yeast” Nature, 2024629, 937–944.

(Highlighted on Nature, ScienceDaily,  LBNL news, Berkeley news).

Crowe, S. A.; Zhao, X.; Gan, F.; Chen, X.; Hudson, G. A.; Astolfi, M. C. T.; Scheller, H. V.; Liu, Y.*; Keasling, J. D.* “Engineered Saccharomyces cerevisiae as a biosynthetic platform of nucleotide sugars” ACS Syn. Biol., 2024, 13, 1215–1224.

 

Crowe, S. A.; Liu, Y.; Zhao, X.; Scheller, H. V.; Keasling, J. D. “Advances in engineering nucleotide sugar metabolism for complex glycosylation in Saccharomyces cerevisiaeACS Syn. Biol., doi: 10.1021/acssynbio.3c00737.

Martin, L. B. B.; Kikuchi, S.; Rejzek, M.; Owen, C.; Reed, J.; Orme, A.; Misra, R. C.; Demerdash, A. E-.; Hill, L.; Hodgson, H.; Liu, Y.; Keasling, J. D.; Field, R. A.; Truman, A. W.; Osbourn, A.* "Complete biosynthesis of the potent vaccine adjuvant QS-21" Nat. Chem. Biol., 2024, 20, 493–502. 

Luckie, B. A.; Kashyap, M.; Pearson, A. N.; Chen, Y.; Liu, Y.; Valencia, L. E.; Romero, A. C.; Hudson, G. A.; Tao, X. B.; Wu, B.; Petzold, C. J.; Keasling, J. D.* “Development of Corynebacterium glutamicum as a monoterpene production platform” Metab. Eng., 2024, 81, 110–122.

Chen, X.; Hudson, G.; Mineo, C.; Amer, B.; Baidoo, E. K. K.; Crowe, S. A.; Liu, Y.; Keasling, J. D.; Scheller, H. V.* “Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria Nat Comm., 2023, 14, 7101.

Eng, T.; Banerjee, D.; Menasalvas, J.; Chen, Y.; Gin, J. W.; Choudhary, H.; Baidoo, E. K. K.; Chen, J. H.; Ekman, A.; Kakumanu, R.; Liu, Y.; Codik, A.; Larabell, C.; Gladden, J. M.; Simmons, B. A.; Keasling, J. D.; Petzold, C. J.; Mukhopadhyay, A.* “Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering” Cell Rep., 2023, 42, 113087.

Zhan, C.; Lee, N.; Lan, G.; Dan, Q.; Cowan, A.; Wang, Z.; Baidoo, E. E. K.; Kakumanu, R.; Luckie, B.; Kuo, R. C.; McCauley, J.; Liu, Y.; Valencia, L.; Haushalter, R. W.; Keasling, J. D.* "Leveraging propionate-induced growth inhibition in Corynebacterium glutamicum to evolve improved methylmalonyl-CoA-dependent polyketide production" Nat. Metab. 2023, 5, 1127–1140. 

Englund, E.; Schmidt, M.; Nava, A. A.; Lechner, A.; Deng, K.; Jocic, R.; Lin, Y.; Roberts, J. B.; Benites, V. T.; Kakumanu, R.; Gin, J. W.; Chen, Y.; Liu, Y.; Petzold, C. J.; Baidoo, E. E. K.; Northen, T. R.; Adams, P. D.; Katz, L.; Yuzawa, S.; Keasling, J. D.* "Expanding extender substrate selection for unnatural polyketide biosynthesis by acyltransferase domain exchange within a modular polyketide synthase", J. Am. Chem. Soc., 2023, 145, 8822–8832.

Carruthers, D. N.; Kim, J.; Mendez-Perez, D.; Monroe, E.; Myllenbeck, N.; Liu, Y.; Davis, R.; Sundstrom, E.; Lee, T. S.* “Microbial production of high octane and high sensitivity olefinic ester biofuels” Biotechnol. Biofuels Bioprod.2023, 16, 60.

Zhan, C.; Li, X.; Lan,G.; Baidoo, E. E. K.; Yang, Y.; Liu, Y.; Sun, Y.; Wang, S.; Wang, Y.; Wang, G.; Nielsen, J.; Keasling, J. D.*; Chen, Y.*;  Bai, Z.* “Reprogramming methanol utilization pathways to convert Saccharomyces cerevisiae to a synthetic methylotroph” Nat. Cat., 2023, 6, 435–450.

Ma, T.; Zhou, Y.; Diercks, C. S.; Kwon, J.; Gándara,F.; Lyu, H.; Hanikel, N.; Pena-Sánchez, P.; Liu, Y.; Diercks, N. J.; Ritchie, R.; Proserpio, D.; Terasaki, O.; Yaghi, O. M.* “Infinite catenanes of polyhedra in covalent organic frameworks” Nat. Syn., 2023, 2, 286–295.

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Cruz-Morales, P.; Yin, K.; Landera, A.; Cort, J.; Young, R. P.; Kyle, J. E.; Bertrand, R.; Iavarone, A.; Acharya, S.; Cowan, A.; Gin, J. W.; Petzold, C. J.; Araujo-Barcelos, C.; Sundstorm, E.; George, A.; Liu, Y.; Klass, S.; Nava, A.; Keasling, J. D.* “Biosynthesis of polycyclopropanated high energy biofuels” Joule, 2022, 6, 1590–1605.

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Liu, Y.; Cruz-Morales, P.; Zargar, A.; Pang, B.; Belcher, M.; Englund, E. D.; Dan, Q.; Yin, K.; Keasling J. D.* “Biofuels for a sustainable future” Cell, 2021, 184, 1636–1647.

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Banerjee, D.; Eng, T.; Lau, A. K.; Sasaki, Y.; Wang, B.; Chen, Y.; Prahl, J. -P.; Singan, V. R.; Herbert, R. A.; Liu, Y.; Tanjore, D.; Petzold, C. J.; Keasling, J. D.; Mukhopadhyay A.* “Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale” Nat. Commun. 2020, 11, 5385.

Thompson, M. G.; Incha, M. R.; Pearson, A. N.; Schmidt, M.; Sharpless, W. A.; Eiben, C. B.; Cruz-Morales, P.; Blake-Hedges, J. M.; Liu, Y.; Adams, C. A.; Haushalter, R. W.; Krishna, R. N.; Lichtner, P.; Blank, L. M.; Mukhopadhyay, A.; Deutschbauer, A. M.; Shih, P. M.; Keasling, J. D.* “Fatty acid and alcohol metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing” Appl. Environ. Microbiol. 2020, 86, e01665–20.

Thompson, M. G.; Blake-Hedges, J. M.; Pereira, J. H.; Hangasky, J. A.; Belcher, M. S.; Moore, W. M.; Barajas, J. F.; Cruz-Morales, P.; Washington, L. J.; Haushalter, R. W.; Eiben, C. B.; Liu, Y.; Skyrud, W.; Benites, V. T.; Barnum, T. P.; Baidoo, E. E. K.; Scheller, H. V.; Marletta, M. A.; Shih, P. M.; Adams, P. D.; Keasling, J. D.* “An Iron (II) dependent oxygenase performs the last missing step of plant lysine Catabolism” Nat. Commun. 2020, 11, 1–10.

Zargar, A.; Lal, R.; Valencia, L.; Wang, J.; Backman, T. W. H.; Cruz-Morales, P.; Kothari, A.; Werts, M.; Wong, A. R.; Bailey, C .B.; Loubat, A.; Liu, Y.; Chen, Y.; Chang, S.; Benites, V. T.; Hernández, A. C.; Barajas, J. F.; Thompson, M. G.; Barcelos, C.; Anayah, R.; Martin, H. G.; Mukhopadhyay, A.; Petzold, C. J.; Baidoo, E. E. K.; Katz, L.; Keasling, J. D.* “Chemoinformatic-guided engineering of polyketide synthases” J. Am. Chem. Soc. 2020, 142, 9896–9901.

Incha, M. R.; Thompson, M. G.; Blake-Hedges, J. M.; Liu, Y.; Pearson, A. N.; Schmidt, M.; Gin, J. W.; Petzold, C. J.; Deutschbauer, A. M.; Keasling, J. D.* “Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida” Metab. Eng. Commun. 2020, 10, e00119.

Pei, X.; Buergi, H. -B.; Kapustin, E.; Liu, Y.; Yaghi, O. M.* “Coordinative alignment in the pores of MOFs for the structural determination of N-, S-, and P-containing organic compounds including complex chiral molecules” J. Am. Chem. Soc. 2019, 141, 18862–18869.

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Wehrs M.; Gladden, J. M.; Liu, Y.; Platz, L.; Prahl, J. -P.; Moon, J.; Papa, G.; Sundstrom, E.; Geiselman, G. M.; Tanjore, D.; Keasling, J. D.; Pray, T. R.; Simmons, B. A.; Mukhopadhyay, A.* “Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides” Green Chem. 2019, 21, 3394–3406.

Liu, Y.; Diercks, C. S.; Ma, Y.; Lyu, H.; Zhu, C.; Yaghi, O. M.* “3D covalent organic frameworks of interlocking complex 1D threads” J. Am. Chem. Soc. 2019, 141, 677–683.

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Liu, Y.; Ma, Y.; Yang, J.; Diercks, C. S.; Tamura, N.; Jin, F.; Yaghi, O. M.* “Molecular weaving of covalent organic frameworks for adaptive guest inclusion” J. Am. Chem. Soc. 2018, 140, 16015–16019. (Highlighted on the JACS cover)

Liu, Y.; O’Keeffe, M.* “Regular figures, minimal transitivity, and reticular chemistry” Isr. J. Chem. 2018, 58, 962–970. (Invited accounts article in honor of Professor Omar M. Yaghi receiving the 2018 Wolf Prize)

Liu, Y.; O’Keeffe, M.; Treacy, M. M. J.; Yaghi, O. M.* “The geometry of periodic knots, polycatenanes and weaving from a chemical perspective: A library for reticular chemistry” Chem. Soc. Rev., 2018, 47, 4642–4664.

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Liu, Y.; Yaghi, O. M.* “Metal coordination as a template strategy to make resilient woven materials” Bull. Chem. Soc. Jpn. 2018, 71, 12–17. 

Diercks, C. S.; Liu, Y.; Cordova, K. E.; Yaghi, O. M.* “The role of reticular chemistry in the design of CO2 reduction catalysts” Nat. Mater., 2018, 17, 301–307.

Liu, Y.;§ Ma, Y.;§ Zhao, Y.;§ Sun, X.; Furukawa, H.; Gandara, F.; Liu, Z.; Zhu, H.; Zhu, C.; Suenaga, K. Oleynikov, P.; Zhang, X.; Terasaki, O.; Yaghi, O. M.* “Weaving of organic threads into a crystalline covalent organic framework” Science, 2016, 351, 365–369. (Highlighted on the Science cover, Science perspective, Nature, C&EN news, Forbes news, LBNL news, ScienceDaily, The Daily Californian, Chemistryworld)

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Savelieff, M. G.; Liu, Y.; Senthamarai, R. R. P.; Korshavn, K. J.; Lee, H. J.; Ramamoorthy, A.; Lim, M. H.* “A small molecule that displays marked reactivity toward copper–versus zinc–amyloid-β implicated in Alzheimer’s Disease” Chem. Commun. 2014, 50, 5301–5303. (Highlighted in Chem. Commun. "Contributors to the Emerging Investigators Issue 2014”)

Liu, Y.;§ Kochi, A.;§ Pithadia, A. S.; Lee, S.; Nam, Y.; Beck, M. W.; He, X.; Lee, D.; Lim, M. H.* “Tuning reactivity switching of diphenylpropynone derivatives with metal-associated amyloid-β species via structural modifications” Inorg. Chem. 2013, 52, 8121–8130.

Savelieff, M. G.; Lee, S.; Liu, Y.; Lim, M. H.* “Alzheimer’s Disease: Untangling amyloid-β, tau, and metals” ACS Chem. Biol. 2013, 8, 856–865.

Pithadia A. S.;§ Kochi, A.;§ Soper, T. S.; Beck, M. W.; Liu, Y.; Lee, S.; DeToma, A. S.; Ruotolo, B. T.; Lim, M. H.* “Reactivity of dipheylpropynone derivatives toward metal-associated amyloid-β species” Inorg. Chem. 2012, 51, 12959–12967.

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