Biodesign Center TIB

Publications

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2024

AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR Cas System
AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design for Microbial Genome Editing Based on the CRISPR/Cas System
Chunhe Yang, Yi Yang, Guangyun Chu, Ruoyu Wang, Haoran Li, Yufeng Mao, Meng Wang, Jian Zhang, Xiaoping Liao, Hongwu Ma
ACS Synthetic Biology  ·  07 Jun 2024  ·  doi:10.1021/acssynbio.4c00063
Website
Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis
Enhancing Machine-Learning Prediction of Enzyme Catalytic Temperature Optima through Amino Acid Conservation Analysis
Yinyin Cao, Boyu Qiu, Xiao Ning, Lin Fan, Yanmei Qin, Dong Yu, Chunhe Yang, Hongwu Ma, Xiaoping Liao, Chun You
International Journal of Molecular Sciences  ·  06 Jun 2024  ·  doi:10.3390/ijms25116252
REME: an integrated platform for reaction enzyme mining and evaluation
REME: an integrated platform for reaction enzyme mining and evaluation
Zhenkun Shi, Dehang Wang, Yang Li, Rui Deng, Jiawei Lin, …, Muqiang Zhao, Zhitao Mao, Qianqian Yuan, Xiaoping Liao, Hongwu Ma
Nucleic Acids Research  ·  20 May 2024  ·  doi:10.1093/nar/gkae405
Website
DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes
DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes
Rui Deng, Ke Wu, Jiawei Lin, Dehang Wang, Yuanyuan Huang, …, Zihan Zhang, Zhiwen Wang, Zhitao Mao, Xiaoping Liao, Hongwu Ma
International Journal of Molecular Sciences  ·  28 Apr 2024  ·  doi:10.3390/ijms25094803
Omics data analysis reveals the system-level constraint on cellular amino acid composition
Omics data analysis reveals the system-level constraint on cellular amino acid composition
Yuanyuan Huang, Zhitao Mao, Yue Zhang, Jianxiao Zhao, Xiaodi Luan, …, Lili Yun, Jing Yu, Zhenkun Shi, Xiaoping Liao, Hongwu Ma
Synthetic and Systems Biotechnology  ·  14 Mar 2024  ·  doi:10.1016/j.synbio.2024.03.001
Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis
Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis
Xiongying Yan, Weiwei Bao, Yalun Wu, Chenyue Zhang, Zhitao Mao, …, Hongwu Ma, Shouwen Chen, Qiang Fei, Qiaoning He, Shihui Yang
Nature Communications  ·  30 Nov 2024  ·  doi:10.1038/s41467-024-54897-5
GitHub
Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design
Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design
Fan Wei, Jingyi Cai, Yufeng Mao, Ruoyu Wang, Haoran Li, …, Aonan Li, Xiaogui Deng, Feiran Li, Qianqian Yuan, Hongwu Ma
Advanced Science  ·  16 Oct 2024  ·  doi:10.1002/advs.202404632
Website
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
Yutao Wang, Zhitao Mao, Jiacheng Dong, Peiji Zhang, Qiang Gao, Defei Liu, Chaoguang Tian, Hongwu Ma
Microbial Cell Factories  ·  15 May 2024  ·  doi:10.1186/s12934-024-02415-z
ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models
ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models
Zhitao Mao, Jinhui Niu, Jianxiao Zhao, Yuanyuan Huang, Ke Wu, …, Jirun Guan, Qianqian Yuan, Xiaoping Liao, Zhiwen Wang, Hongwu Ma
Synthetic and Systems Biotechnology  ·  15 Apr 2024  ·  doi:10.1016/j.synbio.2024.04.005
GitHub

2023

In silico prediction of mutation sites for anthranilate synthase from Serratia marcesens to deregulate tryptophan feedback inhibition
In silico prediction of mutation sites for anthranilate synthase from Serratia marcesens to deregulate tryptophan feedback inhibition
Sadia Naz, Pi Liu, Cui Liu, Mengfei Cui, Hongwu Ma
Journal of Biomolecular Structure and Dynamics  ·  07 Sep 2023  ·  doi:10.1080/07391102.2023.2253910
Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli
Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli
Linxia Liu, Jinlong Li, Yuanming Gai, Zhizhong Tian, Yanyan Wang, …, Pi Liu, Qianqian Yuan, Hongwu Ma, Sang Yup Lee, Dawei Zhang
Nature Communications  ·  31 Aug 2023  ·  doi:10.1038/s41467-023-40928-0
Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method
Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method
Sadia Naz, Pi Liu, Umar Farooq, Hongwu Ma
Microbial Cell Factories  ·  23 Aug 2023  ·  doi:10.1186/s12934-023-02178-z
Coproduction of Bioelectricity and Acetoin by Unbalanced Fermentation of Glycerol in Shewanella oneidensis Based on a Genome-Scale Metabolic Network
Coproduction of Bioelectricity and Acetoin by Unbalanced Fermentation of Glycerol in Shewanella oneidensis Based on a Genome-Scale Metabolic Network
Shutian Kong, Juntao Zhao, Jiahao Luo, Qianqian Yuan, Tao Chen, Hongwu Ma, Zhiwen Wang
ACS Sustainable Chemistry & Engineering  ·  20 Jul 2023  ·  doi:10.1021/acssuschemeng.3c01724
Designing gene manipulation schedules for high throughput parallel construction of objective strains
Designing gene manipulation schedules for high throughput parallel construction of objective strains
Jingyi Cai, Xiaoping Liao, Yufeng Mao, Ruoyu Wang, Haoran Li, Hongwu Ma
Biotechnology Journal  ·  20 Jun 2023  ·  doi:10.1002/biot.202200578
Website
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
Zhitao Mao, Qianqian Yuan, Haoran Li, Yue Zhang, Yuanyuan Huang, …, Yongfu Yang, Yalun Wu, Shihui Yang, Xiaoping Liao, Hongwu Ma
Nucleic Acids Research  ·  09 May 2023  ·  doi:10.1093/nar/gkad360
Website
Insight into the phylogeny and metabolic divergence of Monascus species M. pilosus, M. ruber, and M. purpureus at the genome level
Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level
Zhiyu Zhang, Mengfei Cui, Panting Chen, Juxing Li, Zhitao Mao, …, Zhenjing Li, Qingbin Guo, Changlu Wang, Xiaoping Liao, Huanhuan Liu
Frontiers in Microbiology  ·  25 May 2023  ·  doi:10.3389/fmicb.2023.1199144
pUGTdb: A comprehensive database of plant UDP-dependent glycosyltransferases
pUGTdb: A comprehensive database of plant UDP-dependent glycosyltransferases
Yuqian Liu, Qian Wang, Xiaonan Liu, Jian Cheng, Lei Zhang, …, Hong Chang, Nida Ahmed, Zhonghua Wang, Xiaoping Liao, Huifeng Jiang
Molecular Plant  ·  01 Apr 2023  ·  doi:10.1016/j.molp.2023.01.003
Website
Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol
Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol
Jiaying Wang, Zhiqiang Chen, Xiaogui Deng, Qianqian Yuan, Hongwu Ma
Bioengineering  ·  26 Mar 2023  ·  doi:10.3390/bioengineering10040415
SCP4ssd: A Serverless Platform for Nucleotide Sequence Synthesis Difficulty Prediction Using an AutoML Model
SCP4ssd: A Serverless Platform for Nucleotide Sequence Synthesis Difficulty Prediction Using an AutoML Model
Jianqi Zhang, Shuai Ren, Zhenkui Shi, Ruoyu Wang, Haoran Li, Huijuan Tian, Miao Feng, Xiaoping Liao, Hongwu Ma
Genes  ·  28 Feb 2023  ·  doi:10.3390/genes14030605
Website
Complete Depolymerization of PET Wastes by an Evolved PET Hydrolase from Directed Evolution
Complete Depolymerization of PET Wastes by an Evolved PET Hydrolase from Directed Evolution
Lixia Shi, Pi Liu, Zijian Tan, Wei Zhao, Junfei Gao, Qun Gu, Hongwu Ma, Haifeng Liu, Leilei Zhu
Angewandte Chemie International Edition  ·  21 Feb 2023  ·  doi:10.1002/anie.202218390
Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors
Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors
Wei Pu, Jiuzhou Chen, Pi Liu, Jie Shen, Ningyun Cai, …, Wenjuan Zhou, Hongwu Ma, Yu Wang, Ping Zheng, Jibin Sun
Biosensors and Bioelectronics  ·  01 Feb 2023  ·  doi:10.1016/j.bios.2022.115004
Co Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction
Co‐Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction
Boyuan Xue, Yu Liu, Chen Yang, Hao Liu, Qianqian Yuan, Shaojie Wang, Haijia Su
Advanced Science  ·  13 Dec 2023  ·  doi:10.1002/advs.202306662
Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan
Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan
Peng Wu, Qianqian Yuan, Tingting Cheng, Yifan Han, Wei Zhao, …, Xiaoxia Zhang, Fuping Lu, Jingjing Wang, Hongwu Ma, Zhiyong Huang
Frontiers in Microbiology  ·  20 Nov 2023  ·  doi:10.3389/fmicb.2023.1277847
GitHub
Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production
Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production
Le Gao, Jiao Meng, Wuling Dai, Zhaokun Zhang, Haofan Dong, Qianqian Yuan, Wuyuan Zhang, Shuguang Liu, Xin Wu
Biotechnology for Biofuels and Bioproducts  ·  17 Nov 2023  ·  doi:10.1186/s13068-023-02428-7
Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis
Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis
Jing Yu, Xiaowei Wang, Qianqian Yuan, Jiaxin Shi, Jingyi Cai, Zhichao Li, Hongwu Ma
Frontiers in Plant Science  ·  03 Nov 2023  ·  doi:10.3389/fpls.2023.1281348
Model
Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501
Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501
Qianqian Yuan, Fan Wei, Xiaogui Deng, Aonan Li, Zhenkun Shi, Zhitao Mao, Feiran Li, Hongwu Ma
Synthetic and Systems Biotechnology  ·  01 Nov 2023  ·  doi:10.1016/j.synbio.2023.10.001
GitHub
Design, Evaluation, and Implementation of Synthetic Isopentyldiol Pathways in Escherichia coli
Design, Evaluation, and Implementation of Synthetic Isopentyldiol Pathways in Escherichia coli
Yongfei Liu, Lin Chen, Pi Liu, Qianqian Yuan, Chengwei Ma, Wei Wang, Chijian Zhang, Hongwu Ma, AnPing Zeng
ACS Synthetic Biology  ·  23 Oct 2023  ·  doi:10.1021/acssynbio.3c00394
Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework
Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework
Zhenkun Shi, Rui Deng, Qianqian Yuan, Zhitao Mao, Ruoyu Wang, Haoran Li, Xiaoping Liao, Hongwu Ma
Research  ·  01 Jan 2023  ·  doi:10.34133/research.0153
GitHub
Website
Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments
Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments
Xue Yang, Zhitao Mao, Jianfeng Huang, Ruoyu Wang, Huaming Dong, Yanfei Zhang, Hongwu Ma
Synthetic and Systems Biotechnology  ·  15 Sep 2023  ·  doi:10.1016/j.synbio.2023.09.002
GitHub
Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network
Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network
Jianxiao Zhao, Xi Sun, Zhitao Mao, Yangyang Zheng, Zhouxiao Geng, Yuhan Zhang, Hongwu Ma, Zhiwen Wang
Microbiological Research  ·  06 Sep 2023  ·  doi:10.1016/j.micres.2023.127485
Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories
Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories
Yalun Wu, Qianqian Yuan, Yongfu Yang, Defei Liu, Shihui Yang, Hongwu Ma
Synthetic and Systems Biotechnology  ·  18 Jul 2023  ·  doi:10.1016/j.synbio.2023.07.001
Model
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
Wu Ke, Zhitao Mao, Yufeng Mao, Jinhui Niu, Jingyi Cai, Qianqian Yuan, Lili Yun, Xiaoping Liao, Zhiwen Wang, Hongwu Ma
Microorganisms  ·  11 Jan 2023  ·  doi:10.3390/microorganisms11010178
GitHub

2022

Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum
Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum
Ye Liu, Ruoyu Wang, Jiahui Liu, Hui Lu, Haoran Li, …, Junwei Li, Yanmei Guo, Hongwu Ma, Xiaoping Liao, Meng Wang
Science Advances  ·  02 Sep 2022  ·  doi:10.1126/sciadv.abq2157
Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced by Monascus purpureus Hong Qu
Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced by Monascus purpureus (Hong Qu)
Hao Zhang, Huanhuan Liu, Lin Shu, Huimin Xu, Ying Cheng, Zhitao Mao, Bin Liu, Xiaoping Liao, Di Huang
Foods  ·  21 Jul 2022  ·  doi:10.3390/foods11142168
Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars
Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars
Chaoyu Tian, Jiangang Yang, Cui Liu, Peng Chen, Tong Zhang, Yan Men, Hongwu Ma, Yuanxia Sun, Yanhe Ma
Nature Communications  ·  23 Jun 2022  ·  doi:10.1038/s41467-022-31371-8
Artificial intelligence: a solution to involution of design build test learn cycle
Artificial intelligence: a solution to involution of design–build–test–learn cycle
Xiaoping Liao, Hongwu Ma, Yinjie J Tang
Current Opinion in Biotechnology  ·  01 Jun 2022  ·  doi:10.1016/j.copbio.2022.102712
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms
Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, …, Yu Wang, Meng Wang, Ping Zheng, Xiaoping Liao, Hongwu Ma
Nucleic Acids Research  ·  26 May 2022  ·  doi:10.1093/nar/gkac417
Website
Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis
Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis
Zhitao Mao, Ping Yang, Huanhuan Liu, Yufeng Mao, Yu Lei, Dongwei Hou, Hongwu Ma, Xiaoping Liao, Wenxia Jiang
Frontiers in Microbiology  ·  24 May 2022  ·  doi:10.3389/fmicb.2022.880946
Reconstruction and analysis of genome scale metabolic model for thermophilic fungus Myceliophthora thermophila
Reconstruction and analysis of genome‐scale metabolic model for thermophilic fungus Myceliophthora thermophila
Defei Liu, Zixiang Xu, Jingen Li, Qian Liu, Qianqian Yuan, Yanmei Guo, Hongwu Ma, Chaoguang Tian
Biotechnology and Bioengineering  ·  24 Mar 2022  ·  doi:10.1002/bit.28080
Natural 5-Aminolevulinic Acid: Sources, Biosynthesis, Detection and Applications
Natural 5-Aminolevulinic Acid: Sources, Biosynthesis, Detection and Applications
Meiru Jiang, Kunqiang Hong, Yufeng Mao, Hongwu Ma, Tao Chen, Zhiwen Wang
Frontiers in Bioengineering and Biotechnology  ·  25 Feb 2022  ·  doi:10.3389/fbioe.2022.841443
Digital cell models and their applications: a review
Digital cell models and their applications: a review
Yuan Qianqian, Mao Zhitao, Yang Xue, Liao Xiaoping, Ma Hongwu
Chinese Journal of Biotechnology  ·  25 Oct 2022  ·  doi:10.13345/j.cjb.220590
Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
Niu Jinhui, Zhitao Mao, Yufeng Mao, Ke Wu, Zhenkun Shi, Qianqian Yuan, Jingyi Cai, Hongwu Ma
Biomolecules  ·  17 Oct 2022  ·  doi:10.3390/biom12101499
GitHub
Directed Evolution of Laccase for Improved Thermal Stability Facilitated by Droplet-Based Microfluidic Screening System
Directed Evolution of Laccase for Improved Thermal Stability Facilitated by Droplet-Based Microfluidic Screening System
Xiaolan Su, Jianhua Yang, Huiling Yuan, Cui Liu, Ran Tu, Pi Liu, Qinhong Wang, Leilei Zhu
Journal of Agricultural and Food Chemistry  ·  14 Oct 2022  ·  doi:10.1021/acs.jafc.2c05048
DNA Origami Encoded Integration of Heterostructures
DNA Origami‐Encoded Integration of Heterostructures
Xinpei Dai, Xiaoliang Chen, Xinxin Jing, Yinan Zhang, Muchen Pan, Mingqiang Li, Qian Li, Pi Liu, Chunhai Fan, Xiaoguo Liu
Angewandte Chemie International Edition  ·  27 Jan 2022  ·  doi:10.1002/anie.202114190
Graph-based and constraint-based heterologous metabolic pathway design methods and application
Graph-based and constraint-based heterologous metabolic pathway design methods and application
Yu Wentong, Yuan Qianqian, Ma Hongwu, Wang Zhiwen
Chinese Journal of Biotechnology  ·  13 Jan 2022  ·  doi:10.13345/j.cjb.210828
Enhanced 3-Hydroxypropionic Acid Production From Acetate via the Malonyl-CoA Pathway in Corynebacterium glutamicum
Enhanced 3-Hydroxypropionic Acid Production From Acetate via the Malonyl-CoA Pathway in Corynebacterium glutamicum
Zhishuai Chang, Wei Dai, Yufeng Mao, Zhenzhen Cui, Zhidan Zhang, Zhiwen Wang, Hongwu Ma, Tao Chen
Frontiers in Bioengineering and Biotechnology  ·  13 Jan 2022  ·  doi:10.3389/fbioe.2021.808258
Recent progress in ergothioneine biosynthesis: a review
Recent progress in ergothioneine biosynthesis: a review
Liu Qi, Mao Yufeng, Liao Xiaoping, Luo Jiahao, Ma Hongwu, Jiang Wenxia
Chinese Journal of Biotechnology  ·  12 Jan 2022  ·  doi:10.13345/j.cjb.210797
Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems
Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems
Jiahao Luo, Qianqian Yuan, Yufeng Mao, Fan Wei, Juntao Zhao, …, Yanmei Guo, Jingyi Cai, Xiaoping Liao, Zhiwen Wang, Hongwu Ma
Frontiers in Bioengineering and Biotechnology  ·  12 May 2022  ·  doi:10.3389/fbioe.2022.913077
Model
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database
Zhitao Mao, Ruoyu Wang, Haoran Li, Yixin Huang, Qiang Zhang, Xiaoping Liao, Hongwu Ma
Nucleic Acids Research  ·  30 Apr 2022  ·  doi:10.1093/nar/gkac288
Website
ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Mao Zhitao, Xin Zhao, Xue Yang, Peiji Zhang, Jiawei Du, Qianqian Yuan, Hongwu Ma
Biomolecules  ·  02 Jan 2022  ·  doi:10.3390/biom12010065
Metabolic engineering of Zymomonas mobilis for continuous co-production of bioethanol and poly-3-hydroxybutyrate PHB
Metabolic engineering of Zymomonas mobilis for continuous co-production of bioethanol and poly-3-hydroxybutyrate (PHB)
Yang Li, Ying Wang, Ruxiang Wang, Xiongying Yan, Jiewen Wang, Xia Wang, Shouwen Chen, Fengwu Bai, Qiaoning He, Shihui Yang
Green Chemistry  ·  01 Jan 2022  ·  doi:10.1039/d1gc04522a

2021

Cell-free chemoenzymatic starch synthesis from carbon dioxide
Cell-free chemoenzymatic starch synthesis from carbon dioxide
Tao Cai, Hongbing Sun, Jing Qiao, Leilei Zhu, Fan Zhang, …, Yin Li, Can Li, Huifeng Jiang, Qinhong Wang, Yanhe Ma
Science  ·  24 Sep 2021  ·  doi:10.1126/science.abh4049
Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro
Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro
Yufeng Mao, Qianqian Yuan, Xue Yang, Pi Liu, Ying Cheng, …, Huanhuan Liu, Yonghong Yao, Hongbing Sun, Tao Cai, Hongwu Ma
Frontiers in Microbiology  ·  02 Jun 2021  ·  doi:10.3389/fmicb.2021.677596
Advances in biotechnological production of β-alanine
Advances in biotechnological production of β-alanine
Leilei Wang, Yufeng Mao, Zhiwen Wang, Hongwu Ma, Tao Chen
World Journal of Microbiology and Biotechnology  ·  05 Apr 2021  ·  doi:10.1007/s11274-021-03042-1
Analyzing the genetic characteristics of a tryptophan-overproducing Escherichia coli
Analyzing the genetic characteristics of a tryptophan-overproducing Escherichia coli
Dongqin Ding, Danyang Bai, Jinlong Li, Zhitao Mao, Yaru Zhu, Pi Liu, Jianping Lin, Hongwu Ma, Dawei Zhang
Bioprocess and Biosystems Engineering  ·  22 Mar 2021  ·  doi:10.1007/s00449-021-02552-4
Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens
Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens
Xiao-Jie Yuan, Wen-Jing Chen, Zeng-Xin Ma, Qian-Qian Yuan, Min Zhang, …, Chong Zhang, Chang-Tai Zhang, Meng-Ying Wang, Xin-Hui Xing, Song Yang
Metabolic Engineering  ·  01 Mar 2021  ·  doi:10.1016/j.ymben.2021.01.009
Directed Evolution and Rational Design of Mechanosensitive Channel MscCG2 for Improved Glutamate Excretion Efficiency
Directed Evolution and Rational Design of Mechanosensitive Channel MscCG2 for Improved Glutamate Excretion Efficiency
Zhihua Nie, Pi Liu, Yu Wang, Xuan Guo, Zijian Tan, …, Zijing Tang, Jianping Lin, Jibin Sun, Ping Zheng, Leilei Zhu
Journal of Agricultural and Food Chemistry  ·  20 Dec 2021  ·  doi:10.1021/acs.jafc.1c07086
Molecular Mechanism of the Cytosine CRISPR Base Editing Process and the Roles of Translesion DNA Polymerases
Molecular Mechanism of the Cytosine CRISPR Base Editing Process and the Roles of Translesion DNA Polymerases
Guo Jiang, Jie Wang, Dongdong Zhao, Xuxu Chen, Shiming Pu, …, Hongwu Ma, Yanhe Ma, Zuping Zhou, Changhao Bi, Xueli Zhang
ACS Synthetic Biology  ·  01 Dec 2021  ·  doi:10.1021/acssynbio.1c00293
Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis
Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis
Yajie Gao, Qianqian Yuan, Zhitao Mao, Hao Liu, Hongwu Ma
BMC Microbiology  ·  25 Oct 2021  ·  doi:10.1186/s12866-021-02357-1
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum
Yi Yang, Yufeng Mao, Ye Liu, Ruoyu Wang, Hui Lu, Haoran Li, Jiahao Luo, Meng Wang, Xiaoping Liao, Hongwu Ma
Frontiers in Bioengineering and Biotechnology  ·  15 Oct 2021  ·  doi:10.3389/fbioe.2021.768289
Website
Development of metabolic models with multiple constraints: a review
Development of metabolic models with multiple constraints: a review
Yang Xue, Zhang Peiji, Mao Zhitao, Zhao Xin, Wang Ruoyu, Cai Jingyi, Wang Zhiwen, Ma Hongwu
Chinese Journal of Biotechnology  ·  30 Jul 2021  ·  doi:10.13345/j.cjb.210335
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
Xue Yang, Zhitao Mao, Xin Zhao, Ruoyu Wang, Peiji Zhang, Jingyi Cai, Chaoyou Xue, Hongwu Ma
Metabolic Engineering  ·  28 Jun 2021  ·  doi:10.1016/j.ymben.2021.06.005
GitHub

2020

Three new acrylic acid derivatives from Achillea mellifolium as potential thymidine phosphorylase inhibitor: molecular docking and MD simulation studies
Three new acrylic acid derivatives from Achillea mellifolium as potential thymidine phosphorylase inhibitor: molecular docking and MD simulation studies
Sadia Naz, Umar Farooq, Hongwu Ma, Rizwana Sarwar, Nadia Riaz
Journal of Biomolecular Structure and Dynamics  ·  20 Aug 2020  ·  doi:10.1080/07391102.2020.1808071
Recent progress in metabolic engineering of microbial formate assimilation
Recent progress in metabolic engineering of microbial formate assimilation
Wen Mao, Qianqian Yuan, Hongge Qi, Zhiwen Wang, Hongwu Ma, Tao Chen
Applied Microbiology and Biotechnology  ·  21 Jun 2020  ·  doi:10.1007/s00253-020-10725-6
Capturing transient antibody conformations with DNA origami epitopes
Capturing transient antibody conformations with DNA origami epitopes
Ping Zhang, Xiaoguo Liu, Pi Liu, Fei Wang, Hirotaka Ariyama, …, Jianping Lin, Lihua Wang, Jun Hu, Bin Li, Chunhai Fan
Nature Communications  ·  19 Jun 2020  ·  doi:10.1038/s41467-020-16949-4
High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 in Bacillus subtilis for the Conversion of Chitinaceous Wastes Into Chitooligosaccharides
High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 in Bacillus subtilis for the Conversion of Chitinaceous Wastes Into Chitooligosaccharides
Sijia Wang, Gang Fu, Jinlong Li, Xunfan Wei, Huan Fang, Dawei Huang, Jianping Lin, Dawei Zhang
Frontiers in Bioengineering and Biotechnology  ·  07 May 2020  ·  doi:10.3389/fbioe.2020.00432
Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum
Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum
Yu Wang, Liwen Fan, Philibert Tuyishime, Jiao Liu, Kun Zhang, …, Qianqian Yuan, Hongwu Ma, Ping Zheng, Jibin Sun, Yanhe Ma
Communications Biology  ·  07 May 2020  ·  doi:10.1038/s42003-020-0954-9
Engineering central pathways for industrial-level 3R -acetoin biosynthesis in Corynebacterium glutamicum
Engineering central pathways for industrial-level (3R)-acetoin biosynthesis in Corynebacterium glutamicum
Lingxue Lu, Yufeng Mao, Mengyun Kou, Zhenzhen Cui, Biao Jin, Zhishuai Chang, Zhiwen Wang, Hongwu Ma, Tao Chen
Microbial Cell Factories  ·  12 May 2020  ·  doi:10.1186/s12934-020-01363-8
MEMOTE for standardized genome-scale metabolic model testing
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, …, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
Nature Biotechnology  ·  01 Mar 2020  ·  doi:10.1038/s41587-020-0446-y
Engineered LPMO Significantly Boosting Cellulase-Catalyzed Depolymerization of Cellulose
Engineered LPMO Significantly Boosting Cellulase-Catalyzed Depolymerization of Cellulose
Chao Cheng, Junaid Haider, Pi Liu, Jianhua Yang, Zijian Tan, Tianchen Huang, Jianping Lin, Min Jiang, Haifeng Liu, Leilei Zhu
Journal of Agricultural and Food Chemistry  ·  08 Dec 2020  ·  doi:10.1021/acs.jafc.0c05979
Effective Glycosylation of Cucurbitacin Mediated by UDP-Glycosyltransferase UGT74AC1 and Molecular Dynamics Exploration of Its Substrate Binding Conformations
Effective Glycosylation of Cucurbitacin Mediated by UDP-Glycosyltransferase UGT74AC1 and Molecular Dynamics Exploration of Its Substrate Binding Conformations
Shicheng Mu, Jiao Li, Cui Liu, Yan Zeng, Yan Men, Yi Cai, Ning Chen, Hongwu Ma, Yuanxia Sun
Catalysts  ·  15 Dec 2020  ·  doi:10.3390/catal10121466
Inverting the Enantiopreference of Nitrilase Catalyzed Desymmetric Hydrolysis of Prochiral Dinitriles by Reshaping the Binding Pocket with a Mirror Image Strategy
Inverting the Enantiopreference of Nitrilase‐Catalyzed Desymmetric Hydrolysis of Prochiral Dinitriles by Reshaping the Binding Pocket with a Mirror‐Image Strategy
Shanshan Yu, Jinlong Li, Peiyuan Yao, Jinhui Feng, Yunfeng Cui, Jianjiong Li, Xiangtao Liu, Qiaqing Wu, Jianping Lin, Dunming Zhu
Angewandte Chemie International Edition  ·  14 Dec 2020  ·  doi:10.1002/anie.202012243
Biosensor-based monitoring of the central metabolic pathway metabolites
Biosensor-based monitoring of the central metabolic pathway metabolites
Dongqin Ding, Jinlong Li, Danyang Bai, Huan Fang, Jianping Lin, Dawei Zhang
Biosensors and Bioelectronics  ·  01 Nov 2020  ·  doi:10.1016/j.bios.2020.112456
Efficient solid-state fermentation for the production of 5-aminolevulinic acid enriched feed using recombinant Saccharomyces cerevisiae
Efficient solid-state fermentation for the production of 5-aminolevulinic acid enriched feed using recombinant Saccharomyces cerevisiae
Yufeng Mao, Zetian Chen, Lingxue Lu, Biao Jin, Hongwu Ma, Yun Pan, Tao Chen
Journal of Biotechnology  ·  01 Oct 2020  ·  doi:10.1016/j.jbiotec.2020.06.001
One-pot efficient biosynthesis of 3R -acetoin from pyruvate by a two-enzyme cascade
One-pot efficient biosynthesis of (3R)-acetoin from pyruvate by a two-enzyme cascade
Zhenzhen Cui, Yufeng Mao, Yujiao Zhao, Meiyu Zheng, Zhiwen Wang, Hongwu Ma, Tao Chen
Catalysis Science & Technology  ·  01 Jan 2020  ·  doi:10.1039/d0cy01332c

2019

Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum
Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum
Yu Wang, Ye Liu, Junwei Li, Yi Yang, Xiaomeng Ni, …, Hongwu Ma, Ping Zheng, Meng Wang, Jibin Sun, Yanhe Ma
Biotechnology and Bioengineering  ·  31 Jul 2019  ·  doi:10.1002/bit.27121
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
Lu Liang, Chunfeng Ma, Tengfei Du, Yufei Zhao, Xiaoyong Zhao, Mengmeng Liu, Zhonghua Wang, Jianping Lin
Journal of Cheminformatics  ·  10 Jul 2019  ·  doi:10.1186/s13321-019-0370-7
Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria
Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria
Defei Liu, Huanjun Sun, Hongwu Ma
Frontiers in Microbiology  ·  18 Jun 2019  ·  doi:10.3389/fmicb.2019.01350
In vitro biosynthesis of optically pure scp d scp b b acetoin from meso 2,3 butanediol using 2,3 butanediol dehydrogenase and NADH oxidase
In vitro biosynthesis of optically pure d‐(−)‐acetoin from meso‐2,3‐butanediol using 2,3‐butanediol dehydrogenase and NADH oxidase
Zhenzhen Cui, Yujiao Zhao, Yufeng Mao, Ting Shi, Lingxue Lu, Hongwu Ma, Zhiwen Wang, Tao Chen
Journal of Chemical Technology & Biotechnology  ·  20 May 2019  ·  doi:10.1002/jctb.6050
Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications
Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications
Xiaoguo Liu, Yan Zhao, Pi Liu, Lihua Wang, Jianping Lin, Chunhai Fan
Angewandte Chemie International Edition  ·  04 Apr 2019  ·  doi:10.1002/anie.201807779
Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors
Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors
Lei Cao, Pi Liu, Pan Yang, Qiang Gao, Hong Li, …, Ling Zhu, Jianping Lin, Dan Su, Zihe Rao, Xiangxi Wang
PLOS Biology  ·  30 Apr 2019  ·  doi:10.1371/journal.pbio.3000229
Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design
Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design
Xiaoyun Lu, Yuwan Liu, Yiqun Yang, Shanshan Wang, Qian Wang, …, Wen Wang, Yanhe Ma, Yongjun Liu, Yin Li, Huifeng Jiang
Nature Communications  ·  26 Mar 2019  ·  doi:10.1038/s41467-019-09095-z
Systematic design and in vitro validation of novel one-carbon assimilation pathways
Systematic design and in vitro validation of novel one-carbon assimilation pathways
Xue Yang, Qianqian Yuan, Hao Luo, Feiran Li, Yufeng Mao, …, Yuwan Liu, Huifeng Jiang, Yonghong Yao, Hongwu Ma, Yanhe Ma
Metabolic Engineering  ·  01 Dec 2019  ·  doi:10.1016/j.ymben.2019.09.001
Quantitative Analysis of the Substrate Specificity of Human Rhinovirus 3C Protease and Exploration of Its Substrate Recognition Mechanisms
Quantitative Analysis of the Substrate Specificity of Human Rhinovirus 3C Protease and Exploration of Its Substrate Recognition Mechanisms
Xian Fan, Xinzhi Li, Yu Zhou, Meng Mei, Pi Liu, …, Zheng-Bing Jiang, Shihui Yang, Brent L. Iverson, Guimin Zhang, Li Yi
ACS Chemical Biology  ·  15 Oct 2019  ·  doi:10.1021/acschembio.9b00539
iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis
iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis
Zhitao Mao, Hongwu Ma
Current Genomics  ·  14 Oct 2019  ·  doi:10.2174/1389202920666190626155130
Effects of Methanol on Carotenoids as Well as Biomass and Fatty Acid Biosynthesis in Schizochytrium limacinum B4D1
Effects of Methanol on Carotenoids as Well as Biomass and Fatty Acid Biosynthesis in Schizochytrium limacinum B4D1
Huanmin Du, Xiaoping Liao, Zhengquan Gao, Yang Li, Yu Lei, …, Ke Zhang, Shulin Chen, Yanhe Ma, Chunxiao Meng, Demao Li
Applied and Environmental Microbiology  ·  01 Oct 2019  ·  doi:10.1128/aem.01243-19

2018

Complex silica composite nanomaterials templated with DNA origami
Complex silica composite nanomaterials templated with DNA origami
Xiaoguo Liu, Fei Zhang, Xinxin Jing, Muchen Pan, Pi Liu, …, Jianping Lin, Yan Liu, Dongyuan Zhao, Hao Yan, Chunhai Fan
Nature  ·  01 Jul 2018  ·  doi:10.1038/s41586-018-0332-7
Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea
Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea
Feiran Li, Wei Xie, Qianqian Yuan, Hao Luo, Peishun Li, Tao Chen, Xueming Zhao, Zhiwen Wang, Hongwu Ma
AMB Express  ·  27 Jun 2018  ·  doi:10.1186/s13568-018-0635-y
Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in Bacillus subtilis
Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in Bacillus subtilis
Dingyu Liu, Zhitao Mao, Jiaxin Guo, Leyi Wei, Hongwu Ma, Yajie Tang, Tao Chen, Zhiwen Wang, Xueming Zhao
ACS Synthetic Biology  ·  26 Jun 2018  ·  doi:10.1021/acssynbio.8b00115
Model-based reconstruction of synthetic promoter library in Corynebacterium glutamicum
Model-based reconstruction of synthetic promoter library in Corynebacterium glutamicum
Shuanghong Zhang, Dingyu Liu, Zhitao Mao, Yufeng Mao, Hongwu Ma, Tao Chen, Xueming Zhao, Zhiwen Wang
Biotechnology Letters  ·  31 Mar 2018  ·  doi:10.1007/s10529-018-2539-y
Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes
Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes
Pi Liu, Yan Zhao, Xiaoguo Liu, Jixue Sun, Dede Xu, …, Qian Li, Lihua Wang, Sichun Yang, Chunhai Fan, Jianping Lin
Angewandte Chemie International Edition  ·  26 Mar 2018  ·  doi:10.1002/anie.201801498
Biocatalytic Route to Chiral 2-Substituted-1,2,3,4-Tetrahydroquinolines Using Cyclohexylamine Oxidase Muteins
Biocatalytic Route to Chiral 2-Substituted-1,2,3,4-Tetrahydroquinolines Using Cyclohexylamine Oxidase Muteins
Peiyuan Yao, Peiqian Cong, Rui Gong, Jinlong Li, Guangyue Li, …, Jinhui Feng, Jianping Lin, Peter C. K. Lau, Qiaqing Wu, Dunming Zhu
ACS Catalysis  ·  26 Jan 2018  ·  doi:10.1021/acscatal.7b03552
Engineering NOG-pathway in Escherichia coli for poly- 3-hydroxybutyrate production from low cost carbon sources
Engineering NOG-pathway in Escherichia coli for poly-(3-hydroxybutyrate) production from low cost carbon sources
Yangyang Zheng, Qianqian Yuan, Hao Luo, Xue Yang, Hongwu Ma
Bioengineered  ·  01 Jan 2018  ·  doi:10.1080/21655979.2018.1467652
GCDB: a glaucomatous chemogenomics database for in silico drug discovery
GCDB: a glaucomatous chemogenomics database for in silico drug discovery
Yu Wei, Jinlong Li, Baiqing Li, Chunfeng Ma, Xuanming Xu, …, Aqin Liu, Tengfei Du, Zhonghua Wang, Zhangyong Hong, Jianping Lin
Database  ·  01 Jan 2018  ·  doi:10.1093/database/bay117
YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery
YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery
Baiqing Li, Chunfeng Ma, Xiaoyong Zhao, Zhigang Hu, Tengfei Du, Xuanming Xu, Zhonghua Wang, Jianping Lin
Computational and Structural Biotechnology Journal  ·  01 Jan 2018  ·  doi:10.1016/j.csbj.2018.11.002

2017

Studying the adsorption of DNA nanostructures on graphene in the aqueous phase using molecular dynamic simulations
Studying the adsorption of DNA nanostructures on graphene in the aqueous phase using molecular dynamic simulations
Jixue Sun, Yang Li, Jianping Lin
Journal of Molecular Graphics and Modelling  ·  01 Jun 2017  ·  doi:10.1016/j.jmgm.2017.03.003
Study of the mechanism of protonated histidine-induced conformational changes in the Zika virus dimeric envelope protein using accelerated molecular dynamic simulations
Study of the mechanism of protonated histidine-induced conformational changes in the Zika virus dimeric envelope protein using accelerated molecular dynamic simulations
Jixue Sun, Yang Li, Pi Liu, Jianping Lin
Journal of Molecular Graphics and Modelling  ·  01 Jun 2017  ·  doi:10.1016/j.jmgm.2017.04.009
Identification of novel PAD4 inhibitors based on a pharmacophore model derived from transition state coordinates
Identification of novel PAD4 inhibitors based on a pharmacophore model derived from transition state coordinates
Yu Wei, Ruihua Liu, Cui Liu, Jin Jin, Dongmei Li, Jianping Lin
Journal of Molecular Graphics and Modelling  ·  01 Mar 2017  ·  doi:10.1016/j.jmgm.2016.11.016
Phytochemicals with NO inhibitory effects and interactions with iNOS protein from Trigonostemon howii
Phytochemicals with NO inhibitory effects and interactions with iNOS protein from Trigonostemon howii
Jun Ma, Xueyuan Yang, Peixia Wang, Bangjian Dong, Guochen Su, …, Jing Xu, Dongho Lee, Yasushi Ohizumi, Jianping Lin, Yuanqiang Guo
Bioorganic Chemistry  ·  01 Dec 2017  ·  doi:10.1016/j.bioorg.2017.08.008
Engineering Escherichia coli for poly- 3-hydroxybutyrate production guided by genome-scale metabolic network analysis
Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis
Yangyang Zheng, Qianqian Yuan, Xiaoyan Yang, Hongwu Ma
Enzyme and Microbial Technology  ·  01 Nov 2017  ·  doi:10.1016/j.enzmictec.2017.07.003
Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y1 Receptor
Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y1 Receptor
Yang Li, Can Yin, Pi Liu, Dongmei Li, Jianping Lin
Scientific Reports  ·  23 Oct 2017  ·  doi:10.1038/s41598-017-14268-1
EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
Shaozhen Ding, Xiaoping Liao, Weizhong Tu, Ling Wu, Yu Tian, Qiuping Sun, Junni Chen, Qian-Nan Hu
ACS Chemical Biology  ·  12 Oct 2017  ·  doi:10.1021/acschembio.7b00605
EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
Shaozhen Ding, Xiaoping Liao, Weizhong Tu, Ling Wu, Yu Tian, Qiuping Sun, Junni Chen, Qian-Nan Hu
ACS Chemical Biology  ·  12 Oct 2017  ·  doi:10.1021/acschembio.7b00605
Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models
Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models
Qianqian Yuan, Teng Huang, Peishun Li, Tong Hao, Feiran Li, Hongwu Ma, Zhiwen Wang, Xueming Zhao, Tao Chen, Igor Goryanin
PLOS ONE  ·  13 Jan 2017  ·  doi:10.1371/journal.pone.0169437
Correction: Simultaneous engineering of an enzyme s entrance tunnel and active site: the case of monoamine oxidase MAO-N
Correction: Simultaneous engineering of an enzyme’s entrance tunnel and active site: the case of monoamine oxidase MAO-N
Guangyue Li, Peiyuan Yao, Rui Gong, Jinlong Li, Pi Liu, Richard Lonsdale, Qiaqing Wu, Jianping Lin, Dunming Zhu, Manfred T. Reetz
Chemical Science  ·  01 Jan 2017  ·  doi:10.1039/c7sc90029e
Simultaneous engineering of an enzyme s entrance tunnel and active site: the case of monoamine oxidase MAO-N
Simultaneous engineering of an enzyme's entrance tunnel and active site: the case of monoamine oxidase MAO-N
Guangyue Li, Peiyuan Yao, Rui Gong, Jinlong Li, Pi Liu, Richard Lonsdale, Qiaqing Wu, Jianping Lin, Dunming Zhu, Manfred T. Reetz
Chemical Science  ·  01 Jan 2017  ·  doi:10.1039/c6sc05381e

2016

An engineered non-oxidative glycolysis pathway for acetone production in Escherichia coli
An engineered non-oxidative glycolysis pathway for acetone production in Escherichia coli
Xiaoyan Yang, Qianqian Yuan, Yangyang Zheng, Hongwu Ma, Tao Chen, Xueming Zhao
Biotechnology Letters  ·  04 May 2016  ·  doi:10.1007/s10529-016-2115-2
Production of 5-aminolevulinic acid by cell free multi-enzyme catalysis
Production of 5-aminolevulinic acid by cell free multi-enzyme catalysis
Qinglong Meng, Yanfei Zhang, Xiaozhi Ju, Chunling Ma, Hongwu Ma, …, Jibin Sun, Jun Zhu, Yanhe Ma, Xueming Zhao, Tao Chen
Journal of Biotechnology  ·  01 May 2016  ·  doi:10.1016/j.jbiotec.2016.03.024
Production of 5-aminolevulinic acid by cell free multi-enzyme catalysis
Production of 5-aminolevulinic acid by cell free multi-enzyme catalysis
Qinglong Meng, Yanfei Zhang, Xiaozhi Ju, Chunling Ma, Hongwu Ma, …, Jibin Sun, Jun Zhu, Yanhe Ma, Xueming Zhao, Tao Chen
Journal of Biotechnology  ·  01 May 2016  ·  doi:10.1016/j.jbiotec.2016.03.024
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors
Hengkai Meng, Pi Liu, Hongbing Sun, Zhen Cai, Jie Zhou, Jianping Lin, Yin Li
Scientific Reports  ·  25 Apr 2016  ·  doi:10.1038/srep24887
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors
Hengkai Meng, Pi Liu, Hongbing Sun, Zhen Cai, Jie Zhou, Jianping Lin, Yin Li
Scientific Reports  ·  25 Apr 2016  ·  doi:10.1038/srep24887
Improving chemical similarity ensemble approach in target prediction
Improving chemical similarity ensemble approach in target prediction
Zhonghua Wang, Lu Liang, Zheng Yin, Jianping Lin
Journal of Cheminformatics  ·  23 Apr 2016  ·  doi:10.1186/s13321-016-0130-x
Improving chemical similarity ensemble approach in target prediction
Improving chemical similarity ensemble approach in target prediction
Zhonghua Wang, Lu Liang, Zheng Yin, Jianping Lin
Journal of Cheminformatics  ·  23 Apr 2016  ·  doi:10.1186/s13321-016-0130-x
Metabolic engineering of Bacillus subtilis for chiral pure meso-2,3-butanediol production
Metabolic engineering of Bacillus subtilis for chiral pure meso-2,3-butanediol production
Jing Fu, Guangxin Huo, Lili Feng, Yufeng Mao, Zhiwen Wang, Hongwu Ma, Tao Chen, Xueming Zhao
Biotechnology for Biofuels  ·  19 Apr 2016  ·  doi:10.1186/s13068-016-0502-5
Metabolic engineering of Bacillus subtilis for chiral pure meso-2,3-butanediol production
Metabolic engineering of Bacillus subtilis for chiral pure meso-2,3-butanediol production
Jing Fu, Guangxin Huo, Lili Feng, Yufeng Mao, Zhiwen Wang, Hongwu Ma, Tao Chen, Xueming Zhao
Biotechnology for Biofuels  ·  19 Apr 2016  ·  doi:10.1186/s13068-016-0502-5
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking
Yu Wei, Jinlong Li, Jie Qing, Mingjie Huang, Ming Wu, …, Dongmei Li, Zhangyong Hong, Lingbao Kong, Weiqiang Huang, Jianping Lin
PLOS ONE  ·  04 Feb 2016  ·  doi:10.1371/journal.pone.0148181
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking
Yu Wei, Jinlong Li, Jie Qing, Mingjie Huang, Ming Wu, …, Dongmei Li, Zhangyong Hong, Lingbao Kong, Weiqiang Huang, Jianping Lin
PLOS ONE  ·  04 Feb 2016  ·  doi:10.1371/journal.pone.0148181
One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes
One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes
Wei Zhou, Chun You, Hongwu Ma, Yanhe Ma, Y.-H. Percival Zhang
Journal of Agricultural and Food Chemistry  ·  17 Feb 2016  ·  doi:10.1021/acs.jafc.5b05648
One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes
One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes
Wei Zhou, Chun You, Hongwu Ma, Yanhe Ma, Y.-H. Percival Zhang
Journal of Agricultural and Food Chemistry  ·  17 Feb 2016  ·  doi:10.1021/acs.jafc.5b05648
Structure-based QSAR, molecule design and bioassays of protease-activated receptor 1 inhibitors
Structure-based QSAR, molecule design and bioassays of protease-activated receptor 1 inhibitors
Weilong Zhong, Pi Liu, Qiang Zhang, Dongmei Li, Jianping Lin
Journal of Biomolecular Structure and Dynamics  ·  03 Nov 2016  ·  doi:10.1080/07391102.2016.1234413
Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Yu Guo, Wenming Wang, Yuna Sun, Chao Ma, Xu Wang, …, Baobin Li, Jianping Lin, Fei Deng, Hualin Wang, Zhiyong Lou
Journal of Virology  ·  15 Jan 2016  ·  doi:10.1128/jvi.02523-15
Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Yu Guo, Wenming Wang, Yuna Sun, Chao Ma, Xu Wang, …, Baobin Li, Jianping Lin, Fei Deng, Hualin Wang, Zhiyong Lou
Journal of Virology  ·  15 Jan 2016  ·  doi:10.1128/jvi.02523-15
Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Qiaoyun Guo, Yu Wei, Bin Xia, Yongxin Jin, Chang Liu, …, Xinqi Liu, Zhihui Cheng, Shouguang Jin, Jianping Lin, Weihui Wu
Scientific Reports  ·  11 Jan 2016  ·  doi:10.1038/srep19141
Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Qiaoyun Guo, Yu Wei, Bin Xia, Yongxin Jin, Chang Liu, …, Xinqi Liu, Zhihui Cheng, Shouguang Jin, Jianping Lin, Weihui Wu
Scientific Reports  ·  11 Jan 2016  ·  doi:10.1038/srep19141
Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor
Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor
Yang Li, Jixue Sun, Dongmei Li, Jianping Lin
Physical Chemistry Chemical Physics  ·  01 Jan 2016  ·  doi:10.1039/c6cp00798h
Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor
Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor
Yang Li, Jixue Sun, Dongmei Li, Jianping Lin
Physical Chemistry Chemical Physics  ·  01 Jan 2016  ·  doi:10.1039/c6cp00798h

2015

Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters
Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters
Larisa Kiseleva, Sofya K. Garushyants, Hongwu Ma, David J.W. Simpson, Viatcheslav Fedorovich, Michael F. Cohen, Igor Goryanin
Journal of Integrative Bioinformatics  ·  01 Sep 2015  ·  doi:10.1515/jib-2015-273
Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli
Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli
Li Han, Pi Liu, Jixue Sun, Yuanqing Wu, Yuanyuan Zhang, Wujiu Chen, Jianping Lin, Qinhong Wang, Yanhe Ma
Scientific Reports  ·  26 Aug 2015  ·  doi:10.1038/srep13435
The Mechanism by which 146-N-Glycan Affects the Active Site of Neuraminidase
The Mechanism by which 146-N-Glycan Affects the Active Site of Neuraminidase
Pi Liu, Zhonghua Wang, Lijie Zhang, Dongmei Li, Jianping Lin
PLOS ONE  ·  12 Aug 2015  ·  doi:10.1371/journal.pone.0135487
Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods
Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods
Yu Wei, Jinlong Li, Zeming Chen, Fengwei Wang, Weiqiang Huang, Zhangyong Hong, Jianping Lin
European Journal of Medicinal Chemistry  ·  01 Aug 2015  ·  doi:10.1016/j.ejmech.2015.06.054
Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods
Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods
Yu Wei, Jinlong Li, Zeming Chen, Fengwei Wang, Weiqiang Huang, Zhangyong Hong, Jianping Lin
European Journal of Medicinal Chemistry  ·  01 Aug 2015  ·  doi:10.1016/j.ejmech.2015.06.054
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha COPA Gene
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene
Ben Dorshorst, Corneliu Henegar, Xiaoping Liao, Markus Sällman Almén, Carl-Johan Rubin, …, Paul Stothard, Brian Van Doormaal, Graham Plastow, Gregory S. Barsh, Leif Andersson
PLOS ONE  ·  04 Jun 2015  ·  doi:10.1371/journal.pone.0128969
Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis
Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis
Yanfei Zhang, Qinglong Meng, Hongwu Ma, Yongfei Liu, Guoqiang Cao, …, Ping Zheng, Jibin Sun, Dawei Zhang, Wenxia Jiang, Yanhe Ma
Microbial Cell Factories  ·  13 Jun 2015  ·  doi:10.1186/s12934-015-0275-8
Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis
Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis
Yanfei Zhang, Qinglong Meng, Hongwu Ma, Yongfei Liu, Guoqiang Cao, …, Ping Zheng, Jibin Sun, Dawei Zhang, Wenxia Jiang, Yanhe Ma
Microbial Cell Factories  ·  13 Jun 2015  ·  doi:10.1186/s12934-015-0275-8
Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep Ovis canadensis
Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)
Joshua M Miller, Stephen S Moore, Paul Stothard, Xiaoping Liao, David W Coltman
BMC Genomics  ·  20 May 2015  ·  doi:10.1186/s12864-015-1618-x
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs
Tong Huo, Wei Liu, Yu Guo, Cheng Yang, Jianping Lin, Zihe Rao
BMC Bioinformatics  ·  26 Mar 2015  ·  doi:10.1186/s12859-015-0535-y
A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline
A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline
Xin Chen, Shanshan Qin, Shuai Chen, Jinlong Li, Lixin Li, Zhongling Wang, Quan Wang, Jianping Lin, Cheng Yang, Wenqing Shui
Scientific Reports  ·  10 Feb 2015  ·  doi:10.1038/srep08361
Theoretical study of the mechanism of protein arginine deiminase 4 PAD4 inhibition by F-amidine
Theoretical study of the mechanism of protein arginine deiminase 4 (PAD4) inhibition by F-amidine
Dongmei Li, Cui Liu, Jianping Lin
Journal of Molecular Graphics and Modelling  ·  01 Feb 2015  ·  doi:10.1016/j.jmgm.2014.10.014
Metabolic engineering of Escherichia coli for poly 3-hydroxybutyrate production via threonine bypass
Metabolic engineering of Escherichia coli for poly(3-hydroxybutyrate) production via threonine bypass
Zhenquan Lin, Yan Zhang, Qianqian Yuan, Qiaojie Liu, Yifan Li, Zhiwen Wang, Hongwu Ma, Tao Chen, Xueming Zhao
Microbial Cell Factories  ·  20 Nov 2015  ·  doi:10.1186/s12934-015-0369-3
A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project
A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project
Paul Stothard, Xiaoping Liao, Adriano S. Arantes, Mary De Pauw, Colin Coros, …, John J. Crowley, John A. Basarab, Flavio Schenkel, Stephen Moore, Stephen P. Miller
Gigascience  ·  26 Oct 2015  ·  doi:10.1186/s13742-015-0090-5
An insight into antagonist binding and induced conformational dynamics of class B GPCR corticotropin-releasing factor receptor 1
An insight into antagonist binding and induced conformational dynamics of class B GPCR corticotropin-releasing factor receptor 1
Junli Xu, Zhonghua Wang, Pi Liu, Dongmei Li, Jianping Lin
Molecular BioSystems  ·  01 Jan 2015  ·  doi:10.1039/c5mb00159e

2014

Engineering the biosynthesis of novel rhamnolipids in Escherichia coli for enhanced oil recovery
Engineering the biosynthesis of novel rhamnolipids in Escherichia coli for enhanced oil recovery
L. Han, P. Liu, Y. Peng, J. Lin, Q. Wang, Y. Ma
Journal of Applied Microbiology  ·  25 Apr 2014  ·  doi:10.1111/jam.12515
Engineering of Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex to improve poly 3-hydroxybutyrate production in Escherichia coli
Engineering of Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex to improve poly(3-hydroxybutyrate) production in Escherichia coli
Yan Zhang, Zhenquan Lin, Qiaojie Liu, Yifan Li, Zhiwen Wang, Hongwu Ma, Tao Chen, Xueming Zhao
Microbial Cell Factories  ·  01 Dec 2014  ·  doi:10.1186/s12934-014-0172-6
Exploring skyline for both scp MS scp sup E sup based label free proteomics and scp HRMS scp quantitation of small molecules
Exploring skyline for both MSE‐based label‐free proteomics and HRMS quantitation of small molecules
Shanshan Liu, Xin Chen, Zhihui Yan, Shanshan Qin, Jinhua Xu, Jianping Lin, Cheng Yang, Wenqing Shui
PROTEOMICS  ·  06 Jan 2014  ·  doi:10.1002/pmic.201300352
Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking
Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking
Zhihui Yan, Lijie Zhang, Haiyang Fu, Zhonghua Wang, Jianping Lin
Bioorganic & Medicinal Chemistry Letters  ·  01 Jan 2014  ·  doi:10.1016/j.bmcl.2013.12.026