OOIR: Observatory of International Research

Papers

(The TQCC of Metabolic Engineering is 20. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Towards bio-upcycling of polyethylene terephthalate	183
Machine learning for metabolic engineering: A review	166
Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator	114
Dynamic control in metabolic engineering: Theories, tools, and applications	111
Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440	96
Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production	89
A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications	84
Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica	83
The metabolic potential of plastics as biotechnological carbon sources – Review and targets for the future	80
Development of a growth coupled and multi-layered dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin biosynthesis in Escherichia coli	75
Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid	75
Metabolic compartmentalization in yeast mitochondria: Burden and solution for squalene overproduction	73
Engineering yeast subcellular compartments for increased production of the lipophilic natural products ginsenosides	67
Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid	66
Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator	66
High-yield production of L-valine in engineered Escherichia coli by a novel two-stage fermentation	58
Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide	57
Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis	55
Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry	55
Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool	55
Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags	55
Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida	51
Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol	49
Engineering carotenoid production in mammalian cells for nutritionally enhanced cell-cultured foods	49
Automated engineering of synthetic metabolic pathways for efficient biomanufacturing	48

Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy	48
Engineering of Corynebacterium glutamicum for high-level γ-aminobutyric acid production from glycerol by dynamic metabolic control	47
Tailored biosynthesis of gibberellin plant hormones in yeast	46
INCA 2.0: A tool for integrated, dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis	45
Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1	45
Synergistic improvement of N-acetylglucosamine production by engineering transcription factors and balancing redox cofactors	44
High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica	44
Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol	44
High-level sustainable production of the characteristic protopanaxatriol-type saponins from Panax species in engineered Saccharomyces cerevisiae	44
Enhancement of the flavone contents of Scutellaria baicalensis hairy roots via metabolic engineering using maize Lc and Arabidopsis PAP1 transcription factors	43
Comprehensive study on Escherichia coli genomic expression: Does position really matter?	43
Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	42
Production of moth sex pheromones for pest control by yeast fermentation	41
Development of Klebsiella pneumoniae J2B as microbial cell factory for the production of 1,3-propanediol from glucose	40
Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose	40
Quorum sensing-mediated protein degradation for dynamic metabolic pathway control in Saccharomyces cerevisiae	40
High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities	40
Overexpression of native ORANGE (OR) and OR mutant protein in Chlamydomonas reinhardtii enhances carotenoid and ABA accumulation and increases resistance to abiotic stress	40
Animal-free heme production for artificial meat in Corynebacterium glutamicum via systems metabolic and membrane engineering	40
Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions	38
Engineering yeast for high-level production of diterpenoid sclareol	38
Highly efficient production of L-homoserine in Escherichia coli by engineering a redox balance route	38
Engineering Saccharomyces cerevisiae for isoprenol production	38
Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs	37
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network	37
Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450	37
A hybrid mechanistic-empirical model for in silico mammalian cell bioprocess simulation	37
Integrated knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction	37
Transportome-wide engineering of Saccharomyces cerevisiae	36
Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida	36
Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes	35
Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products	35
Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties	35
Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly	35
Engineering adipic acid metabolism in Pseudomonas putida	35
Design of a genetically encoded biosensor to establish a high-throughput screening platform for L-cysteine overproduction	35
Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways	34
Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties	34
Optimization of heterologous Darobactin A expression and identification of the minimal biosynthetic gene cluster	34
Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli	33
CRISPR-based metabolic pathway engineering	33
Constructing an ethanol utilization pathway in Escherichia coli to produce acetyl-CoA derived compounds	33
Reprint of Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	33
Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers	33
Metabolic engineering for valorization of macroalgae biomass	33
Metabolic engineering of E. coli for pyocyanin production	32
Multilevel metabolic engineering of Bacillus licheniformis for de novo biosynthesis of 2-phenylethanol	32
Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate	32
A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae	32
Heterologous biosynthesis of lutein in S. cerevisiae enabled by temporospatial pathway control	32

Single-gene regulated non-spore-forming Bacillus subtilis: Construction, transcriptome responses, and applications for producing enzymes and surfactin	32
Enhanced 2′-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate	31
Adaptive laboratory evolution of Escherichia coli lacking cellular byproduct formation for enhanced acetate utilization through compensatory ATP consumption	31
Engineering cyanobacteria as cell factories for direct trehalose production from CO2	31
Metabolic engineering of Escherichia coli W3110 for efficient production of homoserine from glucose	31
Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering	31
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato	31
Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves	31
Development of bifunctional biosensors for sensing and dynamic control of glycolysis flux in metabolic engineering	31
Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains promotes synthetic formate assimilation	31
Coupling cell growth and biochemical pathway induction in Saccharomyces cerevisiae for production of (+)-valencene and its chemical conversion to (+)-nootkatone	30
Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch	30
Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound	30
Systematic identification of Ocimum sanctum sesquiterpenoid synthases and (−)-eremophilene overproduction in engineered yeast	30
Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae	29
Systems engineering of Escherichia coli for high-level shikimate production	29
Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis	29
Targeting cofactors regeneration in methylation and hydroxylation for high level production of Ferulic acid	29
Improved production of human hemoglobin in yeast by engineering hemoglobin degradation	29
The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system	29
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms	29
Engineering a powerful green cell factory for robust photoautotrophic diterpenoid production	28
Protocatechuate overproduction by Corynebacterium glutamicum via simultaneous engineering of native and heterologous biosynthetic pathways	28
Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor	28
Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens	27
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models	27
Improved methylation in E. coli via an efficient methyl supply system driven by betaine	27
Control of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFE	27
Microbial production of riboflavin: Biotechnological advances and perspectives	27
Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics	27
Global metabolic rewiring of the nonconventional yeast Ogataea polymorpha for biosynthesis of the sesquiterpenoid β-elemene	27
Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics	27
Cycling between growth and production phases increases cyanobacteria bioproduction of lactate	27
High-throughput screening for high-efficiency small-molecule biosynthesis	27
Systems metabolic engineering of Corynebacterium glutamicum for the efficient production of β-alanine	27
Four-carbon dicarboxylic acid production through the reductive branch of the open cyanobacterial tricarboxylic acid cycle in Synechocystis sp. PCC 6803	26
Metabolic engineering of Escherichia coli for the production of benzoic acid from glucose	26
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals	26
Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass	26
Microbial synthesis of wax esters	25
Novel two-stage processes for optimal chemical production in microbes	25
Model reduction of genome-scale metabolic models as a basis for targeted kinetic models	25
CRISPR-derived genome editing technologies for metabolic engineering	25
Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals	24
Metabolic engineering of tomato fruit enriched in L-DOPA	24
Biosensor-assisted evolution for high-level production of 4-hydroxyphenylacetic acid in Escherichia coli	24
Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida	24
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria	24
Engineering precursor supply for the high-level production of ergothioneine in Saccharomyces cerevisiae	24
A novel WRKY34-bZIP3 module regulates phenolic acid and tanshinone biosynthesis in Salvia miltiorrhiza	24
Biosensor-assisted titratable CRISPRi high-throughput (BATCH) screening for over-production phenotypes	23
Engineering Yarrowia lipolytica for the selective and high-level production of isocitric acid through manipulation of mitochondrial dicarboxylate–tricarboxylate carriers	23
Role of cyanobacterial phosphoketolase in energy regulation and glucose secretion under dark anaerobic and osmotic stress conditions	23
Membrane transporter identification and modulation via adaptive laboratory evolution	23
Improving the production of NAD+ via multi-strategy metabolic engineering in Escherichia coli	23
Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering	23
Biosynthesis of diverse α,ω-diol-derived polyhydroxyalkanoates by engineered Halomonas bluephagenesis	23
Multi-level rebalancing of the naringenin pathway using riboswitch-guided high-throughput screening	23
Adaptive laboratory evolution and reverse engineering enhances autotrophic growth in Pichia pastoris	22
Metabolic engineering of the oleaginous alga Nannochloropsis for enriching eicosapentaenoic acid in triacylglycerol by combined pulling and pushing strategies	22
A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction	22
Metabolic engineering of Saccharomyces cerevisiae for gram-scale diosgenin production	22
Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction	22
Applied evolution: Dual dynamic regulations-based approaches in engineering intracellular malonyl-CoA availability	21
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast	21
Reconstructing a recycling and nonauxotroph biosynthetic pathway in Escherichia coli toward highly efficient production of L-citrulline	21
Metabolic engineering of the acid-tolerant yeast Pichia kudriavzevii for efficient L-malic acid production at low pH	20
Punicic acid production in Brassica napus	20
Stepwise genetic engineering of Pseudomonas putida enables robust heterologous production of prodigiosin and glidobactin A	20
Characterization and directed evolution of propionyl-CoA carboxylase and its application in succinate biosynthetic pathway with two CO2 fixation reactions	20
Coordinating caffeic acid and salvianic acid A pathways for efficient production of rosmarinic acid in Escherichia coli	20
Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria	20
Development of a nonauxotrophic L-homoserine hyperproducer in Escherichia coli by systems metabolic engineering	20
High-yield production of (R)-acetoin in Saccharomyces cerevisiae by deleting genes for NAD(P)H-dependent ketone reductases producing meso-2,3-butanediol and 2,3-dimethylglycerate	20
A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes	20
Two-stage dynamic deregulation of metabolism improves process robustness & scalability in engineered E. coli.	20