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 2021-11-01 to 2025-11-01.)

Article	Citations
Elucidation and engineering of Sphingolipid biosynthesis pathway in Yarrowia lipolytica for enhanced production of human-type sphingoid bases and glucosylceramides	122
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria	117
Engineering Yarrowia lipolytica for sustainable ricinoleic acid production: A pathway to free fatty acid synthesis	109
Butyrate as a growth factor of Clostridium acetobutylicum	78
Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism	78
Editorial Board	72
Heterologous biosynthesis of betanin triggers metabolic reprogramming in tobacco	70
Engineering carbon source division of labor for efficient α-carotene production in Corynebacterium glutamicum	67
Efficient production of (S)-limonene and geraniol in Saccharomyces cerevisiae through the utilization of an Erg20 mutant with enhanced GPP accumulation capability	64
Alternative routes for production of the drug candidate d-chiro-inositol with Corynebacterium glutamicum using endogenous or promiscuous plant enzymes	63
Editorial Board	62
Biosensor-informed engineering of Cupriavidus necator H16 for autotrophic D-mannitol production	58
Engineering sub-organelles of a diploid Saccharomyces cerevisiae to enhance the production of 7-dehydrocholesterol	57
Introduction of acetyl-phosphate bypass and increased culture temperatures enhanced growth-coupled poly-hydroxybutyrate production in the marine cyanobacterium Synechococcus sp. PCC7002	57
Engineering Halomonas bluephagenesis for pilot production of terpolymers containing 3-hydroxybutyrate, 4-hydroxybutyrate and 3-hydroxyvalerate from glucose	56
Quantifying supply and demand in the pea aphid-Buchnera symbiosis reveals the metabolic Achilles’ heels of this interaction	56
Optimized production of concanamycins using a rational metabolic engineering strategy	55
Biosynthesis of 12-aminododecanoic acid from biomass sugars	54
Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus	52
Development of a Streptomyces-based system for facile thioholgamide library generation and analysis	52
Integrating metabolome dynamics and process data to guide cell line selection in biopharmaceutical process development	51
13C-Metabolic flux analysis of 3T3-L1 adipocytes illuminates its core metabolism under hypoxia	50
Versatile xylose and arabinose genetic switches development for yeasts	50
The flocculant Saccharomyces cerevisiae strain gains robustness via alteration of the cell wall hydrophobicity	49
Engineering an SspB-mediated degron for novel controllable protein degradation	49

Metabolic engineering of the oleaginous alga Nannochloropsis for enriching eicosapentaenoic acid in triacylglycerol by combined pulling and pushing strategies	48
Pathway elucidation and microbial synthesis of proaporphine and bis-benzylisoquinoline alkaloids from sacred lotus (Nelumbo nucifera)	47
De novo 2′-fucosyllactose biosynthesis using glucose as the sole carbon source by multiple engineered Bacillus subtilis	47
Inferring secretory and metabolic pathway activity from omic data with secCellFie	47
Consistent biosynthesis of D-glycerate from variable mixed substrates	46
Coordinating caffeic acid and salvianic acid A pathways for efficient production of rosmarinic acid in Escherichia coli	46
Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production	46
Synergistic experimental and computational approach identifies novel strategies for polyhydroxybutyrate overproduction	46
Coupling cell growth and biochemical pathway induction in Saccharomyces cerevisiae for production of (+)-valencene and its chemical conversion to (+)-nootkatone	46
Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy	45
Auto-inducible synthetic pathway in E. coli enhanced sustainable indigo production from glucose	44
Unlocking lager's flavour palette by metabolic engineering of Saccharomyces pastorianus for enhanced ethyl ester production	44
Metabolic engineering of Escherichia coli for N-methylserotonin biosynthesis	44
Consolidated bioprocessing for bioethanol production by metabolically engineered cellulolytic fungus Myceliophthora thermophila	44
Rethinking 13C-metabolic flux analysis – The Bayesian way of flux inference	44
CelloSelect – A synthetic cellobiose metabolic pathway for selection of stable transgenic CHO cell lines	43
Engineering diverse fatty acid compositions of phospholipids in Escherichia coli	43
A Pseudomonas taiwanensis malonyl-CoA platform strain for polyketide synthesis	42
Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress	42
Metabolic engineering of commensal bacteria for gut butyrate delivery and dissection of host-microbe interaction	42
COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling	42
A reactive species reactions module for integration into genome-scale metabolic models for improved insights: Application to cancer	42
Boosting titers of engineered triketide and tetraketide synthases to record levels through T7 promoter tuning	41
Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library	38
Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers	38
Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO2 assimilation	38
Membrane transporter identification and modulation via adaptive laboratory evolution	38
A novel step towards the heterologous biosynthesis of paclitaxel: Characterization of T1βOH taxane hydroxylase	37
Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate	37
Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering	35
Biosynthesis of diverse α,ω-diol-derived polyhydroxyalkanoates by engineered Halomonas bluephagenesis	34
Deep learning for NAD/NADP cofactor prediction and engineering using transformer attention analysis in enzymes	34
Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida	34
Selective microbial production of lacto-N-fucopentaose I in Escherichia coli using engineered α-1,2-fucosyltransferases	33
Corrigendum to “Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to β-ketoadipic acid by Pseudomonas putida KT2440” (Metab. Eng. 67 (2021) 250–261)	33
Verazine biosynthesis from simple sugars in engineered Saccharomyces cerevisiae	33
Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology	33
Editorial Board	33
Hybrid biological-chemical strategy for converting polyethylene into a recyclable plastic monomer using engineered Corynebacterium glutamicum	32
Targeting cofactors regeneration in methylation and hydroxylation for high level production of Ferulic acid	32
Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield	32
Editorial Board	32
Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae	31
Endogenous BiP reporter system for simultaneous identification of ER stress and antibody production in Chinese hamster ovary cells	31
Metabolic engineering of artificially modified transcription factor SmMYB36-VP16 for high-level production of tanshinones and phenolic acids	31
Manufacturing specialized wax esters in plants	31
Establishing recombinant production of pediocin PA-1 in Corynebacterium glutamicum	31
Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids	30
Repurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast	30
High-yield production of FK228 and new derivatives in a Burkholderia chassis	30

Systems metabolic engineering of Corynebacterium glutamicum eliminates all by-products for selective and high-yield production of the platform chemical 5-aminovalerate	30
Stress-driven dynamic regulation of multiple genes to reduce accumulation of toxic aldehydes	30
Systems metabolic engineering upgrades Corynebacterium glutamicum for selective high-level production of the chiral drug precursor and cell-protective extremolyte L-pipecolic acid	30
Efficient production of natural sunscreens shinorine, porphyra-334, and mycosporine-2-glycine in Saccharomyces cerevisiae	29
Ectoine hyperproduction by engineered Halomonas bluephagenesis	29
Electrical-biological hybrid system for carbon efficient isobutanol production	29
Engineering of insect juvenile hormone III biosynthesis in the plant Nicotiana benthamiana	29
Developing a Bacillus licheniformis platform for de novo production of γ-aminobutyric acid and other glutamate-derived chemicals	29
KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states	29
Sustainable production through spatial niche partitioning in engineered light-driven microbial community	28
Biomass accumulation in chondrocyte metabolic modelling: Incorporating extracellular matrix proxies to predict tissue engineering outcomes	28
Genetic and biocatalytic basis of formate dependent growth of Escherichia coli strains evolved in continuous culture	27
Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	27
High-level and -yield production of L-leucine in engineered Escherichia coli by multistep metabolic engineering	27
Kinetically guided, ratiometric tuning of fatty acid biosynthesis	27
Engineering 5-hydroxymethylfurfural (HMF) oxidation in Pseudomonas boosts tolerance and accelerates 2,5-furandicarboxylic acid (FDCA) production	27
Biosynthesis of β-lactam nuclei in yeast	27
Metabolic engineering of Corynebacterium glutamicum for increased cis, cis-muconate production from plant-derived p-hydroxycinnamates via deregulated pathway flux and increased CoA intermediate availa	27
Metabolic engineering of Saccharomyces cerevisiae for gram-scale diosgenin production	27
Generation of a Vibrio-based platform for efficient conversion of raffinose through Adaptive Laboratory Evolution on a solid medium	26
Evolution-assisted engineering of E. coli enables growth on formic acid at ambient CO2 via the Serine Threonine Cycle	26
CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion	26
Editorial Board	25
Overexpression of peroxisome proliferator-activated receptor co-activator-1⍺ (PGC-1⍺) in Chinese hamster ovary cells increases oxidative metabolism and IgG productivity	25
Metabolic engineering of Escherichia coli for high production of 1,5-pentanediol via a cadaverine-derived pathway	25
Fluctuating pH for efficient photomixotrophic succinate production	25
Editorial Board	25
Minimized antibiotic-free plasmid vector for gene therapy utilizing a new toxin-antitoxin system	25
Sustainable production of genistin from glycerol by constructing and optimizing Escherichia coli	25
Unraveling productivity-enhancing genes in Chinese hamster ovary cells via CRISPR activation screening using recombinase-mediated cassette exchange system	25
Engineering of Escherichia coli cytoplasm and periplasm for efficient synthesis of salvianic acid A	24
Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production	24
A dynamic kinetic model captures cell-free metabolism for improved butanol production	24
Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases	24
Rational search of genetic design space for a heterologous terpene metabolic pathway in Streptomyces	24
Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction	24
A tunable metabolic valve for precise growth control and increased product formation in Pseudomonas putida	24
Development of an efficient yeast platform for cannabigerolic acid biosynthesis	24
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato	24
Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator	24
Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production	23
Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate	23
A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)	23
Coordinated reprogramming of ATP metabolism strongly enhances adipic acid production in Escherichia coli	23
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals	23
Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida	23
Demonstration and technoeconomic analysis of dodecanol production from acetate using metabolically engineered Escherichia coli	23
Rational orthologous pathway and biochemical process engineering for adipic acid production using Pseudomonas taiwanensis VLB120	23
AI-based automated construction of high-precision Geobacillus thermoglucosidasius enzyme constraint model	23
Advances in metabolic engineering of Vibrio natriegens as an unconventional host for biotechnology	22
Encapsulation of select violacein pathway enzymes in the 1,2-propanediol utilization bacterial microcompartment to divert pathway flux	22
Modulating fatty acid metabolism and composition of CHO cells by feeding high levels of fatty acids complexed using methyl-β-cyclodextrin	22
Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii	22
Engineering ethanologenicity into the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiriuptor) bescii	21
dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation	21
Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains promotes synthetic formate assimilation	21
A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models	21
Engineering metabolic flux for the microbial synthesis of aromatic compounds	21
Cyanobacterial phycobilisomes as a platform for the stable production of heterologous enzymes and other proteins	21
Multi-omic based production strain improvement (MOBpsi) for bio-manufacturing of toxic chemicals	21
Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink	21
Editorial Board	21
Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions	21
Metabolic engineering improves transduction efficiency and downstream vector isolation by altering the lipid composition of extracellular vesicle-enclosed AAV	21
Big data and machine learning: Metabolic engineering special issue	21
Combinatorial iterative method for metabolic engineering of Yarrowia lipolytica: Application for betanin biosynthesis	20
Metabolic engineering of human gut microbiome: Recent developments and future perspectives	20
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning	20
Metabolic impact of heterologous protein production in Pseudomonas putida: Insights into carbon and energy flux control	20
Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs	20
Enhancing oil feedstock utilization for high-yield low-carbon polyhydroxyalkanoates industrial bioproduction	20
Establishing a coumarin production platform by protein and metabolic engineering	20