2022
(2022) Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.
Nature Communications 13(1), 922.
10.1038/s41467-022-28540-0
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(2022) EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning.
Current Research in Biotechnology 4, 1-9.
10.1016/j.crbiot.2021.12.002
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(2022) Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host.
eLife 11, e70936.
10.7554/elife.70936
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(2022) pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar.
Plant Physiology 188(2), 1014-1027.
10.1093/plphys/kiab546
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(2022) Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE.
Metabolic Engineering 69, 188-197.
10.1016/j.ymben.2021.11.012
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(2022) Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters.
Metabolic Engineering 69, 262-274.
10.1016/j.ymben.2021.12.001
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(2022) A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β‑Linked GlcNAc Polysaccharides.
ACS Central Science .
10.1021/acscentsci.1c01570
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(2022) Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline.
STAR Protocols 3(1), 101184.
10.1016/j.xpro.2022.101184
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(2022) Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom.
ACS Synthetic Biology 11(2), 835-842.
10.1021/acssynbio.1c00503
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(2022) Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences.
Nucleic Acids Research 50(6), 3523-3534.
10.1093/nar/gkac142
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(2022) Metabolic engineering for valorization of macroalgae biomass.
Metabolic Engineering 71, 42-61.
10.1016/j.ymben.2022.01.005
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(2022) Structure and Function of the β‑Asp-Arg Polymerase Cyanophycin Synthetase 2.
ACS Chemical Biology 17(3), 670-679.
10.1021/acschembio.1c01007
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(2022) A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes.
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(2022) Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons.
Molecular Cell 82(6), 1210-1224.e6.
10.1016/j.molcel.2022.01.026
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2021
(2021) Three mutations repurpose a plant karrikin receptor to a strigolactone receptor.
Proceedings of the National Academy of Sciences of the United States of America 118(30).
10.1073/pnas.2103175118
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(2021) Editorial: Cell Free Biocatalysis for the Production of Bioproducts.
Frontiers in Energy Research 9, 781552.
10.3389/fenrg.2021.781552
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(2021) Sorting for secreted molecule production using a biosensor-in-microdroplet approach.
Proceedings of the National Academy of Sciences of the United States of America 118(36).
10.1073/pnas.2106818118
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(2021) An orthogonal metabolic framework for one-carbon utilization.
Nature Metabolism 3(10), 1385-1399.
10.1038/s42255-021-00453-0
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(2021) Intracellular pathways for lignin catabolism in white-rot fungi.
Proceedings of the National Academy of Sciences of the United States of America 118(9), 10.
10.1073/pnas.2017381118
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(2021) Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus.
Scientific Reports 11(1), 22849.
10.1038/s41598-021-02180-8
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(2021) Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C-4 photosynthetic efficiency.
Plant Journal 105(6), 1677-1688.
10.1111/tpj.15141
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(2021) Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation.
Annual Review of Chemical and Biomolecular Engineering 12, 439-470.
10.1146/annurev-chembioeng-120120-021122
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(2021) Transcriptional control of Clostridium autoethanogenum using CRISPRi.
Synthetic Biology 6(1).
10.1093/synbio/ysab008
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(2021) Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives.
Scientific Reports 11(1).
10.1038/s41598-021-91756-5
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(2021) Microfabrication of a chamber for high-resolution, in situ imaging of the whole root for plant–microbe interactions.
International Journal of Molecular Sciences 22(15).
10.3390/ijms22157880
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(2021) Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture.
Trends in Biotechnology 39(3), 244-261.
10.1016/j.tibtech.2020.07.008
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(2021) CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria.
Cell Chemical Biology 29.
https://doi.org/10.1016/j.chembiol.2021.08.009
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(2021) A plant host, Nicotiana benthamiana, enables the production and study of fungal lignin-degrading enzymes.
Communications Biology 4(1).
10.1038/s42003-021-02464-9
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(2021) Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high-throughput microbial screening platform.
Biotechnology and Bioengineering .
10.1002/bit.27926
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(2021) Flavin-dependent halogenases catalyze enantioselective olefin halocyclization.
Nature Communications 12(1).
10.1038/s41467-021-23503-3
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(2021) TRIMER: Transcription Regulation Integrated with Metabolic Regulation.
iScience 24(11), 103218.
10.1016/j.isci.2021.103218
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(2021) An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts.
Nature Communications 12.
10.1038/s41467-021-25233-y
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(2021) Toward sustainable, cell-free biomanufacturing.
Current Opinion in Biotechnology 69, 136-144.
10.1016/j.copbio.2020.12.012
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(2021) A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation.
Nature Catalysis 4(2), 105-115.
10.1038/s41929-020-00557-y
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(2021) Dissolved inorganic carbon accumulating complexes from autotrophic bacteria from extreme environments.
Journal of Bacteriology , JB.00377-21.
doi:10.1128/JB.00377-21
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(2021) Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis.
Metabolic Engineering 66, 179-190.
10.1016/j.ymben.2021.04.005
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(2021) Structures and function of the amino acid polymerase cyanophycin synthetase.
Nature Chemical Biology 17(10), 1101-1110.
10.1038/s41589-021-00854-y
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(2021) p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA.
Computational and Structural Biotechnology Journal 19, 3087-3096.
10.1016/j.csbj.2021.05.031
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(2021) Evaluation of inducible promoter–riboswitch constructs for heterologous protein expression in the cyanobacterial species Anabaena sp. PCC 7120.
Synthetic Biology 6(1), ysab019.
10.1093/synbio/ysab019
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(2021) Biochemistry-Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides.
Angewandte Chemie - International Edition 60(43), 23403-23411.
10.1002/anie.202110658
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(2021) Enzyme engineering and in vivo testing of a formate reduction pathway.
Synthetic Biology 6(1), ysab020.
10.1093/synbio/ysab020
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(2021) Aerobic bacterial methane synthesis.
Proceedings of the National Academy of Sciences of the United States of America 118(27).
10.1073/pnas.2019229118
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(2021) Editorial overview: Energy biotechnology.
Current Opinion in Biotechnology 67, III-V.
10.1016/j.copbio.2021.01.018
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2020
(2020) Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale.
Nature Communications 11(1).
10.1038/s41467-020-19171-4
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(2020) Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach.
Proc Natl Acad Sci U S A 117(31), 18424-18430.
10.1073/pnas.2007413117
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(2020) A genetic toolbox for metabolic engineering of Issatchenkia orientalis.
Metab Eng 59, 87-97.
10.1016/j.ymben.2020.01.005
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(2020) Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity.
Nat Plants 6(11), 1375-1388.
10.1038/s41477-020-00787-9
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(2020) Modular cell-free expression plasmids to accelerate biological design in cells.
Synth Biol (Oxf) 5(1), ysaa019.
10.1093/synbio/ysaa019
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(2020) The foxtail millet (Setaria italica) terpene synthase gene family.
Plant J .
10.1111/tpj.14771
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(2020) Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways.
Metab Eng 62, 95-105.
10.1016/j.ymben.2020.06.004
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(2020) Bacterial genome editing by coupling Cre-lox and CRISPR-Cas9 systems.
PLoS One 15(11), e0241867.
10.1371/journal.pone.0241867
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(2020) Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae.
Enzyme Microb Technol 140, 109623.
10.1016/j.enzmictec.2020.109623
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(2020) Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae.
Enzyme and Microbial Technology 140, 109623.
10.1016/j.enzmictec.2020.109623
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(2020) Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression.
Enzyme Microb Technol 141.
10.1016/j.enzmictec.2020.109645
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2019
(2019) Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides.
ACS Catalysis 9(4), 3219-3227.
10.1021/acscatal.8b05179
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(2019) Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO2-Binding Potential of Reductases.
J Am Chem Soc 141(25), 9778-9782.
10.1021/jacs.9b03431
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(2019) Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis.
Mol Microbiol 112(6), 1784-1797.
10.1111/mmi.14393
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(2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences.
Nature Plants 5(10), 1043-1056.
10.1038/s41477-019-0509-6
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(2019) Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.
ISME J .
10.1038/s41396-019-0557-y
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(2019) Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates.
Synth Biol (Oxf) 4(1), ysz003.
10.1093/synbio/ysz003
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(2019) Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4.
Front Microbiol 10, 2270.
10.3389/fmicb.2019.02270
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(2019) Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling.
ACS Cent Sci 5(11), 1844-1856.
10.1021/acscentsci.9b00835
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(2019) Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides.
J Am Chem Soc 141(2), 758-762.
10.1021/jacs.8b11521
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(2019) Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases.
J Mol Biol 431(6), 1217-1233.
10.1016/j.jmb.2019.01.024
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(2019) Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes.
ISME J .
10.1038/s41396-019-0414-z
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(2019) A Standardized Synthetic Eucalyptus Transcription Factor and Promoter Panel for Re-engineering Secondary Cell Wall Regulation in Biomass and Bioenergy Crops.
ACS Synth Biol 8(2), 463-465.
10.1021/acssynbio.8b00440
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(2019) Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity.
Front Plant Sci 10, 1166.
10.3389/fpls.2019.01166
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(2019) Multi-chassis engineering for heterologous production of microbial natural products.
Curr Opin Biotechnol 62, 88-97.
10.1016/j.copbio.2019.09.005
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(2019) New voyages to explore the natural product galaxy.
J Ind Microbiol Biotechnol 46(3-4), 273-279.
10.1007/s10295-018-02122-w
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(2019) Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass (Panicum virgatum L.).
Front Plant Sci 10, 1144.
10.3389/fpls.2019.01144
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(2019) A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products.
J Vis Exp (152).
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(2019) ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.
BMC Genomics 20(Suppl 12), 1003.
10.1186/s12864-019-6329-2
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(2019) A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides.
Microb Cell Fact 18(1), 117.
10.1186/s12934-019-1167-0
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(2019) Diterpene Synthase-Catalyzed Biosynthesis of Distinct Clerodane Stereoisomers.
Chembiochem 20(1), 111-117.
10.1002/cbic.201800580
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(2019) Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica.
Metab Eng 55, 102-110.
10.1016/j.ymben.2019.06.007
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(2019) Engineered root bacteria release plant-available phosphate from phytate.
Appl Environ Microbiol .
10.1128/AEM.01210-19
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(2019) Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases.
Proc Natl Acad Sci U S A .
10.1073/pnas.1901471116
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(2019) Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality.
Proc Natl Acad Sci U S A 116(16), 8070-8079.
10.1073/pnas.1818259116
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(2019) Rational Reprogramming of O-Methylation Regioselectivity for Combinatorial Biosynthetic Tailoring of Benzenediol Lactone Scaffolds.
J Am Chem Soc 141(10), 4355-4364.
10.1021/jacs.8b12967
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2018
(2018) The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite.
Nat Chem Biol 14(12), 1127-1132.
10.1038/s41589-018-0153-x
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(2018) An integrated workflow for phenazine-modifying enzyme characterization.
J Ind Microbiol Biotechnol .
10.1007/s10295-018-2025-5
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(2018) Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP.
ACS Chem Biol .
10.1021/acschembio.7b01019
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(2018) Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.
J Vis Exp (134).
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(2018) Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast.
Genetics 210(1), 219-234.
10.1534/genetics.118.301161
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(2018) Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution.
Mol Biol Evol .
10.1093/molbev/msy102
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(2018) Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification.
BMC Biotechnol 18(1), 54.
10.1186/s12896-018-0464-8
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(2018) Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize.
Plant Physiol 176(4), 2677-2690.
10.1104/pp.17.01351
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(2018) Functional Characterization of Two Class II Diterpene Synthases Indicates Additional Specialized Diterpenoid Pathways in Maize (Zea mays).
Front Plant Sci 9, 1542.
10.3389/fpls.2018.01542
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(2018) Functional Diversity of Diterpene Synthases in the Biofuel Crop Switchgrass.
Plant Physiol 178(1), 54-71.
10.1104/pp.18.00590
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(2018) Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis.
Cell Chem Biol 25(7), 833-839 e4.
10.1016/j.chembiol.2018.04.009
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(2018) Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis.
Proc Natl Acad Sci U S A 115(22), E4980-E4989.
10.1073/pnas.1716046115
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2017
(2017) Glycosyl Cations versus Allylic Cations in Spontaneous and Enzymatic Hydrolysis.
Journal of the American Chemical Society 139(31), 10629-10632.
10.1021/jacs.7b05628
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(2017) Selinene Volatiles Are Essential Precursors for Maize Defense Promoting Fungal Pathogen Resistance.
Plant Physiol 175(3), 1455-1468.
10.1104/pp.17.00879
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(2017) A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.
Yeast .
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(2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Nat Biotechnol .
10.1038/nbt.3886
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(2017) Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.
ACS Synth Biol .
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2016
(2016) Analysis of Amino Acid Substitutions in AraC Variants that Respond to Triacetic Acid Lactone.
Protein Sci .
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(2016) A Droplet Microfluidic Platform for Automating Genetic Engineering.
ACS Synth Biol .
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(2016) Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs.
ACS Synth Biol 5(6), 449-51.
10.1021/acssynbio.6b00146
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(2016) Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli.
PLoS One 11(3), e0151087.
10.1371/journal.pone.0151087
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(2016) A synthetic pathway for the fixation of carbon dioxide in vitro.
Science 354(6314), 900-904.
10.1126/science.aah5237
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(2016) SAR11 bacteria linked to ocean anoxia and nitrogen loss.
Nature 536(7615), 179-83.
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2015
(2015) Active site and laminarin binding in glycoside hydrolase family 55.
J Biol Chem 290(19), 11819-32.
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(2015) Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis.
ACS Synth Biol 4(8), 927-34.
10.1021/acssynbio.5b00087
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(2015) Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS.
Front Bioeng Biotechnol 3, 153.
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(2015) Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.
Nat Commun 6, 10005.
10.1038/ncomms10005
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(2015) Computational protein design enables a novel one-carbon assimilation pathway.
Proc Natl Acad Sci U S A 112(12), 3704-9.
10.1073/pnas.1500545112
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2014
(2014) Phylogenomically Guided Identification of Industrially Relevant GH1 beta-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry.
Acs Chemical Biology 9(9), 2082-2091.
10.1021/Cb500244v
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Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis.
Plant Molecular Biology , 1-15.
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Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.
Nature Biotechnology 40(3), 335-344.
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