OOIR: Observatory of International Research

Papers

(The TQCC of Metabolic Engineering is 18. 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 2021-02-01 to 2025-02-01.)

Article	Citations
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria	183
Resource allocation modeling for autonomous prediction of plant cell phenotypes	96
Efficient production of (S)-limonene and geraniol in Saccharomyces cerevisiae through the utilization of an Erg20 mutant with enhanced GPP accumulation capability	83
Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory	80
Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose	75
Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells	73
Scalable, robust, high-throughput expression & purification of nanobodies enabled by 2-stage dynamic control	67
Rational design of a bacterial import system for new-to-nature molecules	66
Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution	57
CHOGlycoNET: Comprehensive glycosylation reaction network for CHO cells	55
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model	55
A smart RBS library and its prediction model for robust and accurate fine-tuning of gene expression in Bacillus species	51
KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states	49
Engineering Yarrowia lipolytica for sustainable ricinoleic acid production: A pathway to free fatty acid synthesis	48
Directed evolution of biomass intensive CHO cells by adaptation to sub-physiological temperature	47
Building a highly efficient Streptomyces super-chassis for secondary metabolite production by reprogramming naturally-evolved multifaceted shifts	46
Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine	45
Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli	44
Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites	44
Metabolic engineering of Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids	44
Engineering 5-hydroxymethylfurfural (HMF) oxidation in Pseudomonas boosts tolerance and accelerates 2,5-furandicarboxylic acid (FDCA) production	44
Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis	44
Combinatorial optimization and spatial remodeling of CYPs to control product profile	43
Large-scale pathway reconstruction and colorimetric screening accelerate cellular metabolism engineering	42
Engineering carbon source division of labor for efficient α-carotene production in Corynebacterium glutamicum	40

Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: A modular metabolic engineering approach	40
A coculture-coproduction system designed for enhanced carbon conservation through inter-strain CO2 recycling	40
Control of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFE	40
Alternative routes for production of the drug candidate d-chiro-inositol with Corynebacterium glutamicum using endogenous or promiscuous plant enzymes	38
Editorial Board	38
Metabolic engineering of “last-line antibiotic” colistin in Paenibacillus polymyxa	38
A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and intracellular flux distributions in CHO clonal variations	38
Editorial Board	37
Overexpression of peroxisome proliferator-activated receptor co-activator-1⍺ (PGC-1⍺) in Chinese hamster ovary cells increases oxidative metabolism and IgG productivity	37
Minimized antibiotic-free plasmid vector for gene therapy utilizing a new toxin-antitoxin system	37
Corrigendum to “Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440” [Metab. Eng. 59 (2020) 64–75]	37
Fluctuating pH for efficient photomixotrophic succinate production	37
Biosynthesis of β-lactam nuclei in yeast	36
G6P-capturing molecules in the periplasm of Escherichia coli accelerate the shikimate pathway	36
Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules	35
Editorial Board	35
Genetic and biocatalytic basis of formate dependent growth of Escherichia coli strains evolved in continuous culture	35
Microbial synthesis of wax esters	35
Phenotype-centric modeling for rational metabolic engineering	34
Editorial Board	34
Metabolic engineering of tomato fruit enriched in L-DOPA	33
Introduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanol	33
Sustainable production of genistin from glycerol by constructing and optimizing Escherichia coli	33
Editorial Board	33
Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440	33
Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast	32
Microbial production of the plant-derived fungicide physcion	32
Rational genome and metabolic engineering of Candida viswanathii by split CRISPR to produce hundred grams of dodecanedioic acid	32
Active and machine learning-based approaches to rapidly enhance microbial chemical production	32
Transcription factor DegU-mediated multi-pathway regulation on lichenysin biosynthesis in Bacillus licheniformis	32
Reconstructing a recycling and nonauxotroph biosynthetic pathway in Escherichia coli toward highly efficient production of L-citrulline	31
Engineering Halomonas bluephagenesis via small regulatory RNAs	31
Engineering sub-organelles of a diploid Saccharomyces cerevisiae to enhance the production of 7-dehydrocholesterol	31
Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network	31
Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution	31
A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes	30
Enhancing acid tolerance of Escherichia coli via viroporin-mediated export of protons and its application for efficient whole-cell biotransformation	30
Improved production of human hemoglobin in yeast by engineering hemoglobin degradation	30
Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties	30
De novo biosynthesis of carminic acid in Saccharomyces cerevisiae	29
Investigation of putative genes for the production of medium-chained acids and alcohols in autotrophic acetogenic bacteria	29
Metabolic engineering of the malonyl-CoA pathway to efficiently produce malonate in Saccharomyces cerevisiae	29
Biosensor-informed engineering of Cupriavidus necator H16 for autotrophic D-mannitol production	29
In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product	29
Engineering a solar formic acid/pentose (SFAP) pathway in Escherichia coli for lactic acid production	29
High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities	28
Helicase-AID: A novel molecular device for base editing at random genomic loci	28
Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion	28
Metabolic engineering to produce palmitic acid or palmitoleic acid in an oleic acid-producing Corynebacterium glutamicum strain	27
Metabolic engineering of Escherichia coli for high production of 1,5-pentanediol via a cadaverine-derived pathway	27

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	27
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network	27
Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida	27
Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida	27
A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae	27
Metabolic engineering of Saccharomyces cerevisiae for gram-scale diosgenin production	27
Improved terephthalic acid production from p-xylene using metabolically engineered Pseudomonas putida	27
Model reduction of genome-scale metabolic models as a basis for targeted kinetic models	27
Fine-tuning of p-coumaric acid synthesis to increase (2S)-naringenin production in yeast	26
Multilevel metabolic engineering of Bacillus licheniformis for de novo biosynthesis of 2-phenylethanol	26
Metabolic engineering of Escherichia coli for the production of an antifouling agent zosteric acid	26
Overproduction of medicinal ergot alkaloids based on a fungal platform	25
Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale	25
Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags	24
Biosynthesis of a rosavin natural product in Escherichia coli by glycosyltransferase rational design and artificial pathway construction	24
Kinetically guided, ratiometric tuning of fatty acid biosynthesis	24
A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes	24
CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion	24
High-level and -yield production of L-leucine in engineered Escherichia coli by multistep metabolic engineering	24
A novel WRKY34-bZIP3 module regulates phenolic acid and tanshinone biosynthesis in Salvia miltiorrhiza	24
Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid	23
Elucidation and engineering of Sphingolipid biosynthesis pathway in Yarrowia lipolytica for enhanced production of human-type sphingoid bases and glucosylceramides	23
Role of cyanobacterial phosphoketolase in energy regulation and glucose secretion under dark anaerobic and osmotic stress conditions	23
Development of a vitamin B5 hyperproducer in Escherichia coli by multiple metabolic engineering	23
-Substituted 3-hydroxy acid production from glucose in Escherichia coli	23
Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida	23
Generation of a Vibrio-based platform for efficient conversion of raffinose through Adaptive Laboratory Evolution on a solid medium	23
Flux balance analysis and peptide mapping elucidate the impact of bioreactor pH on Chinese hamster ovary (CHO) cell metabolism and N-linked glycosylation in the fab and Fc regions of the produced IgG	23
Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold	22
Butyrate as a growth factor of Clostridium acetobutylicum	22
Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose	22
Optimized genome-wide CRISPR screening enables rapid engineering of growth-based phenotypes in Yarrowia lipolytica	22
Hyperproduction of 7-dehydrocholesterol by rewiring the post-squalene module in lipid droplets of Saccharomyces cerevisiae	22
Heterologous biosynthesis of betanin triggers metabolic reprogramming in tobacco	22
Integrating metabolome dynamics and process data to guide cell line selection in biopharmaceutical process development	21
Multi-level rebalancing of the naringenin pathway using riboswitch-guided high-throughput screening	21
Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals	20
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals	20
Editorial Board	20
High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica	20
Serial propagation in water-in-oil emulsions selects for Saccharomyces cerevisiae strains with a reduced cell size or an increased biomass yield on glucose	20
Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production	20
Metabolic engineering of Halomonas bluephagenesis for high-level mevalonate production from glucose and acetate mixture	20
Rational orthologous pathway and biochemical process engineering for adipic acid production using Pseudomonas taiwanensis VLB120	20
Unraveling productivity-enhancing genes in Chinese hamster ovary cells via CRISPR activation screening using recombinase-mediated cassette exchange system	20
Dynamic upregulation of the rate-limiting enzyme for valerolactam biosynthesis in Corynebacterium glutamicum	19
A dynamic kinetic model captures cell-free metabolism for improved butanol production	19
Reprint of Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	19
Development of an efficient yeast platform for cannabigerolic acid biosynthesis	19
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato	19
Versatile xylose and arabinose genetic switches development for yeasts	19
Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch	19
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast	19
Riboswitch-guided chalcone synthase engineering and metabolic flux optimization for enhanced production of flavonoids	19
A tunable metabolic valve for precise growth control and increased product formation in Pseudomonas putida	19
Editorial Board	19
Switching metabolic flux by engineering tryptophan operon-assisted CRISPR interference system in Klebsiella pneumoniae	19
Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry	19
Coordinating caffeic acid and salvianic acid A pathways for efficient production of rosmarinic acid in Escherichia coli	19
Rational search of genetic design space for a heterologous terpene metabolic pathway in Streptomyces	19
Metabolic engineering of the oleaginous alga Nannochloropsis for enriching eicosapentaenoic acid in triacylglycerol by combined pulling and pushing strategies	18
Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440	18
Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction	18
Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida	18
Engineering a powerful green cell factory for robust photoautotrophic diterpenoid production	18
Combinational quorum sensing devices for dynamic control in cross-feeding cocultivation	18