Publications

2023 - Present

20

Programmable design of functional proteins from natural language

Nature, (2026)

Fengyuan Dai; Shiyang You; Yudian Zhu; Yuan Gao; Lihao Fu; Xibin Zhou; Jin Su; Chentong Wang; Yuliang Fan; Qingsong Tan; Xiaoxiao Ma; Xianjun Deng; Letong Yu; Hui Qian; Yan He; Yitao Ke; Zhe Zhang; Chenchen Han; Xing Chang; Liangzhen Zheng; Sheng Wang; Yuan Ji; Kexin Hao; Longxing Cao; Yajie Wang; Anping Zeng; Shunzhi Wang; Chunjun Zhan; Jing Zhao; Tong Si*; Jianming Liu*; Hongyuan Lu*; Fajie Yuan*

19

Decoding the Molecular Language of Proteins with Evolla

BioRxiv, (2026)

Xibin Zhou; Chenchen Han; Yingqi Zhang; Huan Du; Jiayuan Tian; Jin Su; Renju Liu; Kai Zhuang; Shiyu Jiang; Anthony Gitter; Li Liu; Huayu Li; Meiqi Wu; Shiyang You; Zichen Yuan; Feng Ju; Huilin Zhang; Wei Zheng; Fengyuan Dai; Yuyang Zhou; Yuyang Tao; Dan Wu; Zongze Shao; Yang Liu*; Hongyuan Lu*; Fajie Yuan*

18

Pathogen context reshapes antimicrobial peptide generation

BioRxiv, (2026)

Shiyang You; Chen Zhang; Yingchun Han; Qiuyun Jiang; Xuan Guo; Mingjia Li; Yongxin Su; Xiyang Dong; Menglin Yang; Hongyuan Lu*

17

A coupled fluorescence assay for high-throughput screening of polyurethane-degrading enzymes

Journal of Hazardous Materials, (2026), 504, 141400

Liujun Yang; Xianjun Deng; Renju Liu; Jianyang Li; Junyao Zhai; Xiaoxiao Ma; Shiyang You; Qinghao He; K.L. LIN Arthur; Zongze Shao; Hongyuan Lu*

16

A trimodal protein language model enables advanced protein searches

Nature Biotechnology, (2025)

Jin Su; Yan He; Shiyang You; Shiyu Jiang; Xibin Zhou; Xuting Zhang; Yuxuan Wang; Xining Su; Igor Tolstoy; Xing Chang*; Hongyuan Lu*; Fajie Yuan*

15

Theranostic Probiotic Engineered Living Materials That Dynamically Respond to Inflammation Markers

Advanced Healthcare Materials, (2025), 15, e03809

Altin-Yavuzarslan Gokce; M. Brooks Sierra; O. Park James; B. Reed Kevin; Flynn McKenna; L. Lanier Olivia; Hongyuan Lu; Hal S. Alper*; Nelson Alshakim*

14

Evaluating the effectiveness of a lysine mutation and its portability across different Poly(ethylene terephthalate)-hydrolyzing enzymes

Biochemical Engineering Journal, (2025), 214, 109573-109578

Huaimin Wang; Bergeson Amelia R.; Hongyuan Lu; Acosta Daniel J.; Silvera Ashli J.; Dittoe Ryan E.; Lam Jessica L. M.; Aspiras Larissa G. S.; Longo August K.; Lynd Nathaniel A.; Hal S. Alper*

13

Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system

Proceedings of the National Academy of Sciences, (2024), 121, e2317027121

B. Reed Kevin; Kim Wantae; Hongyuan Lu; T. Larue Clayton; Shirley Guo; R. Montez Michael; M. Wagner James; Jessie Zhang Y.; Hal S. Alper*

12

Machine learning-aided engineering of hydrolases for PET depolymerization

Nature, (2022), 604, 662-667

Hongyuan Lu; J. Diaz Daniel; J. Czarnecki Natalie; Congzhi Zhu; Kim Wantae; Shroff Raghav; J. Acosta Daniel; R. Alexander Bradley; O. Cole Hannah; Yan Zhang; A. Lynd Nathaniel; D. Ellington Andrew; Hal S. Alper*

11

A secretion‐based dual fluorescence assay for high‐throughput screening of alcohol dehydrogenases

Biotechnology and Bioengineering, (2021), 118, 1605-1616

Hongyuan Lu; Shiqin Yu; Fengyu Qin; Wenbo Ning; Xiaoqiang Ma; Kaiyuan Tian; Kang Zhou*; Zhi Li*

10

A standard for near-scarless plasmid construction using reusable DNA parts

Biotechnology and Bioengineering, (2019), 118, 1605-1616

Xiaoqiang Ma; Hong Liang; Xiaoyi Cui; Yurou Liu; Hongyuan Lu; Wenbo Ning; Yu Poon Nga; Ho Benjamin; Kang Zhou*

9

Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production

Frontiers in Microbiology, (2019), 10, 1027-1040

Kent Lim Chee; C. Villada Juan; Chalifour Annie; F. Duran Maria; Hongyuan Lu; Patrick K. H. Lee *

8

Modular Metabolic Engineering for Biobased Chemical Production

Trends in Biotechnology, (2018), 37, 152-166

Hongyuan Lu; C. Villada Juan; Patrick K. H. Lee *

7

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Biotechnology for Biofuels, (2018), 11, 117-131

Yangyang Jia; Ng Siu‐Kin; Hongyuan Lu; Mingwei Cai; Patrick K. H. Lee *

6

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammoniaand Nitrite-Oxidizing Bacteria in Freshwater Nitrification

Frontiers in Microbiology, (2018), 9, 280-292

Mingwei Cai; Ng Siu-Kin; Kent Lim Chee; Hongyuan Lu; Yangyang Jia; Patrick K. H. Lee *

5

Physiological and molecular characterizations of the interactions in two cellulose-to-methane cocultures

Biotechnology for Biofuels, (2017), 10, 37-50

Hongyuan Lu; Ng Siu‐Kin; Yangyang Jia; Mingwei Cai; Patrick K. H. Lee *

4

Transcriptomic Responses of the Interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a Cellulose-Grown Coculture for Enhanced Hydrogen Production

Applied and Environmental Microbiology, (2016), 82, 4546-4559

Hongyuan Lu; Jiahua Chen; Yangyang Jia; Mingwei Cai; Patrick K. H. Lee *

3

Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems

Frontiers in Microbiology, (2016), 7, 778-789

Mingwei Cai; Wilkins David; Jiapeng Chen; Ng Siu-Kin; Hongyuan Lu; Yangyang Jia; Patrick K. H. Lee *

2

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Applied and Environmental Microbiology, (2015), 82, 1519-1529

Yangyang Jia; Wilkins David; Hongyuan Lu; Mingwei Cai; Patrick K. H. Lee *

1

Effects of cellulose concentrations on the syntrophic interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in coculture fermentation for biohydrogen production

International Journal of Hydrogen Energy, (2015), 40, 11800-11808

Hongyuan Lu; Patrick K. H. Lee *

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