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 2021-04-01 to 2025-04-01.)

Article	Citations
Introduction of acetyl-phosphate bypass and increased culture temperatures enhanced growth-coupled poly-hydroxybutyrate production in the marine cyanobacterium Synechococcus sp. PCC7002	200
Exploring and increased acetate biosynthesis in Synechocystis PCC 6803 through insertion of a heterologous phosphoketolase and overexpressing phosphotransacetylase	118
Scalable, robust, high-throughput expression & purification of nanobodies enabled by 2-stage dynamic control	101
Engineering Halomonas bluephagenesis via small regulatory RNAs	99
Reconstructing a recycling and nonauxotroph biosynthetic pathway in Escherichia coli toward highly efficient production of L-citrulline	94
Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution	87
A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes	81
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model	75
Directed evolution of biomass intensive CHO cells by adaptation to sub-physiological temperature	70
Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli	63
Large-scale pathway reconstruction and colorimetric screening accelerate cellular metabolism engineering	62
Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: A modular metabolic engineering approach	62
Editorial Board	59
A coculture-coproduction system designed for enhanced carbon conservation through inter-strain CO2 recycling	59
Fluctuating pH for efficient photomixotrophic succinate production	57
Minimized antibiotic-free plasmid vector for gene therapy utilizing a new toxin-antitoxin system	57
Editorial Board	55
Biosynthesis of β-lactam nuclei in yeast	54
G6P-capturing molecules in the periplasm of Escherichia coli accelerate the shikimate pathway	50
Editorial Board	49
Genetic and biocatalytic basis of formate dependent growth of Escherichia coli strains evolved in continuous culture	49
Editorial Board	49
Introduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanol	48
Sustainable production of genistin from glycerol by constructing and optimizing Escherichia coli	48
Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440	48

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network	47
Microbial production of the plant-derived fungicide physcion	46
Metabolic engineering of tomato fruit enriched in L-DOPA	46
Improved production of human hemoglobin in yeast by engineering hemoglobin degradation	46
Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid	44
Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules	44
Engineering sub-organelles of a diploid Saccharomyces cerevisiae to enhance the production of 7-dehydrocholesterol	44
Metabolic engineering of “last-line antibiotic” colistin in Paenibacillus polymyxa	44
Evolution-assisted engineering of E. coli enables growth on formic acid at ambient CO2 via the Serine Threonine Cycle	44
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network	42
Engineering a solar formic acid/pentose (SFAP) pathway in Escherichia coli for lactic acid production	42
Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose	42
Elucidation and engineering of Sphingolipid biosynthesis pathway in Yarrowia lipolytica for enhanced production of human-type sphingoid bases and glucosylceramides	41
Efficient production of (S)-limonene and geraniol in Saccharomyces cerevisiae through the utilization of an Erg20 mutant with enhanced GPP accumulation capability	41
Fine-tuning of p-coumaric acid synthesis to increase (2S)-naringenin production in yeast	41
Rational design of a bacterial import system for new-to-nature molecules	41
Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells	40
Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites	40
Biosynthesis of a rosavin natural product in Escherichia coli by glycosyltransferase rational design and artificial pathway construction	39
Butyrate as a growth factor of Clostridium acetobutylicum	39
Optimized genome-wide CRISPR screening enables rapid engineering of growth-based phenotypes in Yarrowia lipolytica	39
A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and intracellular flux distributions in CHO clonal variations	38
Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida	38
Control of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFE	38
Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis	38
Metabolic engineering of Escherichia coli for high production of 1,5-pentanediol via a cadaverine-derived pathway	38
CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion	38
Metabolic engineering of Saccharomyces cerevisiae for de novo production of odd-numbered medium-chain fatty acids	38
In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product	37
KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states	37
Microbial synthesis of wax esters	37
Metabolic engineering of Escherichia coli for the production of an antifouling agent zosteric acid	36
Transcription factor DegU-mediated multi-pathway regulation on lichenysin biosynthesis in Bacillus licheniformis	35
Corrigendum to “Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440” [Metab. Eng. 59 (2020) 64–75]	35
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria	35
Kinetically guided, ratiometric tuning of fatty acid biosynthesis	35
Engineering Yarrowia lipolytica for sustainable ricinoleic acid production: A pathway to free fatty acid synthesis	35
Phenotype-centric modeling for rational metabolic engineering	34
CHOGlycoNET: Comprehensive glycosylation reaction network for CHO cells	34
Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast	33
Engineering carbon source division of labor for efficient α-carotene production in Corynebacterium glutamicum	33
Role of cyanobacterial phosphoketolase in energy regulation and glucose secretion under dark anaerobic and osmotic stress conditions	33
Combinatorial optimization and spatial remodeling of CYPs to control product profile	32
Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida	32
A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes	32
Enhancing acid tolerance of Escherichia coli via viroporin-mediated export of protons and its application for efficient whole-cell biotransformation	32
Alternative routes for production of the drug candidate d-chiro-inositol with Corynebacterium glutamicum using endogenous or promiscuous plant enzymes	32
Metabolic engineering to produce palmitic acid or palmitoleic acid in an oleic acid-producing Corynebacterium glutamicum strain	32
-Substituted 3-hydroxy acid production from glucose in Escherichia coli	31
Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold	31

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	31
Generation of a Vibrio-based platform for efficient conversion of raffinose through Adaptive Laboratory Evolution on a solid medium	31
Development of a vitamin B5 hyperproducer in Escherichia coli by multiple metabolic engineering	30
Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale	29
Engineering 5-hydroxymethylfurfural (HMF) oxidation in Pseudomonas boosts tolerance and accelerates 2,5-furandicarboxylic acid (FDCA) production	28
Multilevel metabolic engineering of Bacillus licheniformis for de novo biosynthesis of 2-phenylethanol	28
Improved terephthalic acid production from p-xylene using metabolically engineered Pseudomonas putida	28
Overexpression of peroxisome proliferator-activated receptor co-activator-1⍺ (PGC-1⍺) in Chinese hamster ovary cells increases oxidative metabolism and IgG productivity	28
Helicase-AID: A novel molecular device for base editing at random genomic loci	28
A smart RBS library and its prediction model for robust and accurate fine-tuning of gene expression in Bacillus species	28
Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution	28
De novo biosynthesis of carminic acid in Saccharomyces cerevisiae	27
Active and machine learning-based approaches to rapidly enhance microbial chemical production	27
Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose	27
Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties	27
Overproduction of medicinal ergot alkaloids based on a fungal platform	27
Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida	26
Investigation of putative genes for the production of medium-chained acids and alcohols in autotrophic acetogenic bacteria	26
Biosensor-informed engineering of Cupriavidus necator H16 for autotrophic D-mannitol production	26
Resource allocation modeling for autonomous prediction of plant cell phenotypes	26
Metabolic engineering of Saccharomyces cerevisiae for gram-scale diosgenin production	26
High-level and -yield production of L-leucine in engineered Escherichia coli by multistep metabolic engineering	26
Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions	26
Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags	25
High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities	25
Rational genome and metabolic engineering of Candida viswanathii by split CRISPR to produce hundred grams of dodecanedioic acid	25
Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory	25
Metabolic engineering of the malonyl-CoA pathway to efficiently produce malonate in Saccharomyces cerevisiae	24
Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine	24
Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion	24
Heterologous biosynthesis of betanin triggers metabolic reprogramming in tobacco	24
Hyperproduction of 7-dehydrocholesterol by rewiring the post-squalene module in lipid droplets of Saccharomyces cerevisiae	24
Building a highly efficient Streptomyces super-chassis for secondary metabolite production by reprogramming naturally-evolved multifaceted shifts	24
A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae	24
A novel WRKY34-bZIP3 module regulates phenolic acid and tanshinone biosynthesis in Salvia miltiorrhiza	24
De novo 2′-fucosyllactose biosynthesis using glucose as the sole carbon source by multiple engineered Bacillus subtilis	23
Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production	23
Editorial Board	23
Optimized production of concanamycins using a rational metabolic engineering strategy	23
Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate	23
Efficient production of protocatechuic acid using systems engineering of Escherichia coli	23
Synthetic translational coupling system for accurate and predictable polycistronic gene expression control in bacteria	23
Engineering an SspB-mediated degron for novel controllable protein degradation	23
Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida	23
Biosynthesis of 10-Hydroxy-2-Decenoic Acid in Escherichia coli	22
Metabolic engineering of Halomonas bluephagenesis for high-level mevalonate production from glucose and acetate mixture	22
Corrigendum to “Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound” [Metab. Eng. 65 (2021) 1–10]	22
Designing a microbial factory suited for plant chloroplast-derived enzymes to efficiently and green synthesize natural products: Capsanthin and capsorubin as examples	22
Editorial Board	22
Metabolic engineering of CHO cells towards cysteine prototrophy and systems analysis of the ensuing phenotype	22
Integrating metabolome dynamics and process data to guide cell line selection in biopharmaceutical process development	22
Developing a novel heme biosensor to produce high-active hemoproteins in Pichia pastoris through comparative transcriptomics	22
Editorial Board	22
Mitigating transcriptional bottleneck using a constitutively active transcription factor, VP16-CREB, in mammalian cells	21
Engineering Halomonas bluephagenesis for synthesis of polyhydroxybutyrate (PHB) in the presence of high nitrogen containing media	21
A multiscale hybrid modelling methodology for cell cultures enabled by enzyme-constrained dynamic metabolic flux analysis under uncertainty	21
Modularized Engineering of Shewanella oneidensis MR-1 for Efficient and Directional Synthesis of 5-Aminolevulinic Acid	21
A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato	21
Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose	21
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast	21
Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae	21
Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels	20
Production of cholesterol-like molecules impacts Escherichia coli robustness, production capacity, and vesicle trafficking	20
Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism	20
Production of the infant formula ingredient 1,3-olein-2-palmitin in Arabidopsis thaliana seeds	20
Editorial Board	20
A quantitative metabolic analysis reveals Acetobacterium woodii as a flexible and robust host for formate-based bioproduction	20
A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)	20
Single cell mutant selection for metabolic engineering of actinomycetes	20
Editorial Board	20
Editorial Board	20
Editorial Board	20
Versatile xylose and arabinose genetic switches development for yeasts	20