OOIR: Observatory of International Research

Papers

(The TQCC of Metabolic Engineering is 23. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)

Article	Citations
Towards bio-upcycling of polyethylene terephthalate	158
CRISPR/Cas9 directed editing of lycopene epsilon-cyclase modulates metabolic flux for β-carotene biosynthesis in banana fruit	147
Machine learning for metabolic engineering: A review	140
Dynamic control in metabolic engineering: Theories, tools, and applications	97
Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator	97
In vitro prototyping of limonene biosynthesis using cell-free protein synthesis	82
Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production	81
Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440	78
Enhancing isoprenoid synthesis in Yarrowia lipolytica by expressing the isopentenol utilization pathway and modulating intracellular hydrophobicity	78
Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440	77
Engineering chimeric diterpene synthases and isoprenoid biosynthetic pathways enables high-level production of miltiradiene in yeast	74
Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield	72
A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications	71
Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica	70
Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid	67
Development of a growth coupled and multi-layered dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin biosynthesis in Escherichia coli	65
Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives	63
An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli	62
Engineering yeast subcellular compartments for increased production of the lipophilic natural products ginsenosides	61
Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator	60
Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin	60
Metabolic compartmentalization in yeast mitochondria: Burden and solution for squalene overproduction	58
Stress-driven dynamic regulation of multiple tolerance genes improves robustness and productive capacity of Saccharomyces cerevisiae in industrial lignocellulose fermentation	58
Elucidation of the complete biosynthetic pathway of the main triterpene glycosylation products of Panax notoginseng using a synthetic biology platform	58
The metabolic potential of plastics as biotechnological carbon sources – Review and targets for the future	58

Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica	57
A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids	54
Direct production of commodity chemicals from lignocellulose using Myceliophthora thermophila	53
Enzyme capacity-based genome scale modelling of CHO cells	51
Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool	51
High-yield production of L-valine in engineered Escherichia coli by a novel two-stage fermentation	51
Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis	50
Rebalancing microbial carbon distribution for L-threonine maximization using a thermal switch system	49
Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers	49
What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines	48
Green production of silybin and isosilybin by merging metabolic engineering approaches and enzymatic catalysis	47
Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide	47
Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid	47
Efficient production of saffron crocins and picrocrocin in Nicotiana benthamiana using a virus-driven system	47
Biosynthesis of functional polyhydroxyalkanoates by engineered Halomonas bluephagenesis	46
Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol	44
Synergistic improvement of N-acetylglucosamine production by engineering transcription factors and balancing redox cofactors	44
Direct biosynthesis of adipic acid from lignin-derived aromatics using engineered Pseudomonas putida KT2440	44
Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy	43
Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags	43
Cell-free styrene biosynthesis at high titers	42
Metabolic engineering of Cupriavidus necator H16 for improved chemoautotrophic growth and PHB production under oxygen-limiting conditions	42
Tailoring cyanobacteria as a new platform for highly efficient synthesis of astaxanthin	42
Simultaneous secretion of seven lignocellulolytic enzymes by an industrial second-generation yeast strain enables efficient ethanol production from multiple polymeric substrates	42
Automated engineering of synthetic metabolic pathways for efficient biomanufacturing	41
Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida	41
Tailored biosynthesis of gibberellin plant hormones in yeast	41
Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol	39
Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods	39
Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry	39
Production of moth sex pheromones for pest control by yeast fermentation	39
High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica	38
Engineering of Corynebacterium glutamicum for high-level γ-aminobutyric acid production from glycerol by dynamic metabolic control	38
Engineering of the 2,3-butanediol pathway of Paenibacillus polymyxa DSM 365	38
Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway	37
Enhancement of the flavone contents of Scutellaria baicalensis hairy roots via metabolic engineering using maize Lc and Arabidopsis PAP1 transcription factors	36
Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1	36
Engineering Saccharomyces cerevisiae for isoprenol production	36
K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data	36
Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942	35
INCA 2.0: A tool for integrated, dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis	35
High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities	35
High-level sustainable production of the characteristic protopanaxatriol-type saponins from Panax species in engineered Saccharomyces cerevisiae	35
Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly	34
Development of Klebsiella pneumoniae J2B as microbial cell factory for the production of 1,3-propanediol from glucose	34
Quorum sensing-mediated protein degradation for dynamic metabolic pathway control in Saccharomyces cerevisiae	34
Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450	34
Integrated knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction	34
Comprehensive study on Escherichia coli genomic expression: Does position really matter?	34
Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression	33

Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production	33
Highly efficient production of L-homoserine in Escherichia coli by engineering a redox balance route	33
In vivo evolutionary engineering of riboswitch with high-threshold for N-acetylneuraminic acid production	33
Rewiring carbon flux in Escherichia coli using a bifunctional molecular switch	33
Engineering Halomonas bluephagenesis for L-Threonine production	32
A hybrid mechanistic-empirical model for in silico mammalian cell bioprocess simulation	32
Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions	32
Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound	31
Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida	31
Heterologous production of the epoxycarotenoid violaxanthin in Saccharomyces cerevisiae	31
A genetic toolbox for metabolic engineering of Issatchenkia orientalis	31
Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering	31
Animal-free heme production for artificial meat in Corynebacterium glutamicum via systems metabolic and membrane engineering	31
Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties	31
Structure-guided reshaping of the acyl binding pocket of ‘TesA thioesterase enhances octanoic acid production in E. coli	31
Transportome-wide engineering of Saccharomyces cerevisiae	30
Constructing an ethanol utilization pathway in Escherichia coli to produce acetyl-CoA derived compounds	30
Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products	30
Metabolic engineering for valorization of macroalgae biomass	30
Enhanced 2′-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate	30
Optimization of heterologous Darobactin A expression and identification of the minimal biosynthetic gene cluster	30
Overexpression of native ORANGE (OR) and OR mutant protein in Chlamydomonas reinhardtii enhances carotenoid and ABA accumulation and increases resistance to abiotic stress	29
Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves	29
Engineering adipic acid metabolism in Pseudomonas putida	28
Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor	28
Engineering cyanobacteria as cell factories for direct trehalose production from CO2	28
Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers	28
Adaptive laboratory evolution of Escherichia coli lacking cellular byproduct formation for enhanced acetate utilization through compensatory ATP consumption	28
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network	28
The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system	28
Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli	28
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms	28
Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	28
Design of a genetically encoded biosensor to establish a high-throughput screening platform for L-cysteine overproduction	27
Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics	27
Heterologous biosynthesis of lutein in S. cerevisiae enabled by temporospatial pathway control	27
Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways	27
A modular autoinduction device for control of gene expression in Bacillus subtilis	27
Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis	27
Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs	27
Isobutanol production in Corynebacterium glutamicum: Suppressed succinate by-production by pckA inactivation and enhanced productivity via the Entner–Doudoroff pathway	27
Engineering yeast for high-level production of diterpenoid sclareol	27
Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties	27
Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes	27
Development of bifunctional biosensors for sensing and dynamic control of glycolysis flux in metabolic engineering	27
Metabolic engineering of E. coli for pyocyanin production	26
Control of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFE	26
Engineering a powerful green cell factory for robust photoautotrophic diterpenoid production	26
Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs	26
Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose	26
Systematic identification of Ocimum sanctum sesquiterpenoid synthases and (−)-eremophilene overproduction in engineered yeast	25
Coupling cell growth and biochemical pathway induction in Saccharomyces cerevisiae for production of (+)-valencene and its chemical conversion to (+)-nootkatone	25
Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate	25
Single-gene regulated non-spore-forming Bacillus subtilis: Construction, transcriptome responses, and applications for producing enzymes and surfactin	25
Metabolic engineering of Escherichia coli W3110 for efficient production of homoserine from glucose	25
Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis	25
Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch	25
Multilevel metabolic engineering of Bacillus licheniformis for de novo biosynthesis of 2-phenylethanol	25
Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound	25
Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass	25
CRISPR-based metabolic pathway engineering	25
A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae	25
Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens	24
Protocatechuate overproduction by Corynebacterium glutamicum via simultaneous engineering of native and heterologous biosynthetic pathways	24
Reprint of Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	24
Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae	24
High-throughput screening for high-efficiency small-molecule biosynthesis	24
Microbial synthesis of wax esters	24
Simultaneous tracers and a unified model of positional and mass isotopomers for quantification of metabolic flux in liver	24
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models	24
Targeting cofactors regeneration in methylation and hydroxylation for high level production of Ferulic acid	23
Metabolic engineering of β-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanone	23
Four-carbon dicarboxylic acid production through the reductive branch of the open cyanobacterial tricarboxylic acid cycle in Synechocystis sp. PCC 6803	23
CRISPR-derived genome editing technologies for metabolic engineering	23
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato	23