Koffas Group at RPI

Publications

Recent

Raethong, N., Thananusak, R., Cheawchanlertfa, P., Prabhakaran, P., Rattanaporn, K., Laoteng, K., Koffas, M. and Vongsangnak, W., 2023. Functional genomics and systems biology of Cordyceps species for biotechnological applications. Current Opinion in Biotechnology, 81, p.102939.

Connor, A., Wigham, C., Bai, Y., Rai, M., Nassif, S., Koffas, M. and Zha, R.H., 2023. Novel insights into construct toxicity, strain optimization, and primary sequence design for producing recombinant silk fibroin and elastin-like peptide in E. coli. Metabolic Engineering Communications, 16, p.e00219.

Paliya, B.S., Sharma, V.K., Tuohy, M.G., Singh, H.B., Koffas, M., Benhida, R., Tiwari, B.K., Kalaskar, D.M., Singh, B.N. and Gupta, V.K., 2023. Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans. Biotechnology Advances, p.108180.

Connor, A., Lamb, J., Delferro, M., Koffas, M. and Zha, R., 2023. Microbial Upcycling of Polyethylene into Recombinant Proteins.

Xiao, Z., Connor, A.J., Worland, A.M., Tang, Y.J., Zha, R.H. and Koffas, M., 2023. Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress. Metabolic Engineering, 77, pp.231-241.

KIM, D.H., HWANG, H.G., NOH, M.H., KOFFAS, M.A., Sungho, J.A.N.G. and JUNG, G.Y., 2023. Precise Rebalancing of the Naringenin Biosynthetic Pathway with Artificial RNA BiosensorguidedHigh-throughput Screening. pp.685-685.

Watthanasakphuban, N., Nguyen, L.V., Cheng, Y.S., Show, P.L., Sriariyanun, M., Koffas, M. and Rattanaporn, K., 2023. Development of a Molasses-Based Medium for Agrobacterium tumefaciens Fermentation for Application in Plant-Based Recombinant Protein Production. Fermentation, 9(2), p.149.

Zha, J., Zhao, Z., Xiao, Z., Eng, T., Mukhopadhyay, A., Koffas, M.A. and Tang, Y.J., 2023. Biosystem design of Corynebacterium glutamicum for bioproduction. Current Opinion in Biotechnology, 79, p.102870.

Jeandet, P., Uddin, M.S., Clement, C., Aziz, A., Jacquard, C., Khan, H., Shah, M.A., Barka, E.A., Koffas, M., Nabavi, S.M. and Sobarzo-Sanchez, E., 2023. Production of high molecular-ordered stilbene oligomers for the study of their biological activity: total synthesis, bio-catalyzed synthesis and production by plant systems. Natural Product Reports, 40(5), pp.1045-1057.

2022

Thananusak, R., Laoteng, K., Raethong, N., Koffas, M. and Vongsangnak, W., 2022. Dissecting Metabolic Regulation in Mycelial Growth and Fruiting Body Developmental Stages of Cordyceps militaris through Integrative Transcriptome Analysis. Biotechnology and Bioprocess Engineering, pp.1-13.

Gupta, M., Wong, M., Jawed, K., Gedeon, K., Barrett, H., Bassalo, M., Morrison, C., Eqbal, D., Yazdani, S.S., Gill, R.T. and Huang, J., 2022. Isobutanol production by combined in vivo and in vitro metabolic engineering. Metabolic Engineering Communications, 15, p.e00210.

Xiu, Y., Zhang, N., Prabhakaran, P., Jang, S., Yuan, Q., Breneman, C.M., Jung, G.Y., Vongsangnak, W. and Koffas, M.A., 2022. Parallel screening and cheminformatics modeling of flavonoid activated aptasensors. Synthetic and Systems Biotechnology, 7(4), pp.1148-1158.

Wu, X., Liu, J., Liu, D., Yuwen, M., Koffas, M.A. and Zha, J., 2022. Biosynthesis of eriodictyol from tyrosine by Corynebacterium glutamicum. Microbial Cell Factories, 21(1), pp.1-11.

Bu, X., Lin, J.Y., Duan, C.Q., Koffas, M.A. and Yan, G.L., 2022. Dual regulation of lipid droplet-triacylglycerol metabolism and ERG9 expression for improved beta carotene production in Saccharomyces cerevisiae. Microbial Cell Factories, 21(1), pp.1-13.

Dodds, D.R., Armiger, W.B. and Koffas, M., BIOCHEMINSIGHTS Inc, 2020. Methods and systems for 1-butanol production. U.S. Patent 10,696,988.

Perl, A., Rai, M., Dalton, H., Nathan, R., Koffas, M. and Chen, W., 2022, November. Dynamic Regulation of Metabolic Pathways with Toehold-Gated dCas9 Regulators. In 2022 AIChE Annual Meeting. AIChE.

Awofiranye, A.E., Dhar, C., He, P., Varki, A., Koffas, M.A. and Linhardt, R.J., 2022. N-glycolylated carbohydrates in nature. Glycobiology, 32(11), pp.921-932.

Badri, A., KOFFAS, M.A., Linhardt, R.J. and Williams, A.J., Rensselaer Polytechnic Institute, 2022. Recombinant microorganisms for in vivo production of sulfated glycosaminoglycans. U.S. Patent Application 17/641,675.

Phujumpa, P., Muangham, S., Jatuponwiphat, T., Koffas, M., Nakphaichit, M. and Vongsangnak, W., 2022. Comparative genomics-based probiotic relevance of Limosilactobacillus fermentum KUB-D18. Gene, 840, p.146747.

Gupta, V.K., Pandey, A., Koffas, M., Mussatto, S.I. and Khare, S., 2022. Biobased biorefineries: sustainable bioprocesses and bioproducts from biomass/bioresources special issue. Renewable and Sustainable Energy Reviews, 167, p.112683.

Cheawchanlertfa, P., Chitcharoen, S., Raethong, N., Liu, Q., Chumnanpuen, P., Soommat, P., Song, Y., Koffas, M., Laoteng, K. and Vongsangnak, W., 2022. Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris. Journal of Fungi, 8(8), p.887.

Akdemir, H., Liu, Y., Zhuang, L., Zhang, H. and Koffas, M.A., 2022. Utilization of microbial cocultures for converting mixed substrates to valuable bioproducts. Current Opinion in Microbiology, 68, p.102157.

Awofiranye, A.E., Hudson, J., Tithi, A.D., Linhardt, R.J., Vongsangnak, W. and Koffas, M.A., 2022. Chondroitin sulfate and its derivatives: A review of microbial and other production methods. Fermentation, 8(7), p.323.

Fang, Z., Tang, Y.J. and Koffas, M.A., 2022. Harnessing electrical-to-biochemical conversion for microbial synthesis. Current Opinion in Biotechnology, 75, p.102687.

Liu, W., Li, H., Zhang, J.X., Xu, Y.N., Zhang, X.M., Shi, J.S., Koffas, M.A.G. and Xu, Z.H., 2022. Whole-genome analyses and metabolic modification of Mycobacterium sp. LY-1 to enhance yield of 9a-OH-AD. Systems Microbiology and Biomanufacturing, pp.1-11.

Laurens, L. and Koffas, M., 2022, May. Biochemical Conversion for Chemical and Material Precursors. In 44th Symposium on Biomaterials, Fuels and Chemicals. SIMB.

Finkelstein, J., Swartz, J. and Koffas, M., 2022. Bioelectrosynthesis systems. Current Opinion in Biotechnology, 74, pp.211-219.

Dhakal, D., Kim, E.S. and Koffas, M., 2022. Engineering the Microbial Platform for the Production of Biologics and Small-Molecule Medicines, Volume II. Frontiers in Microbiology, 13, p.827181.

Xu, Y., Geng, L., Zhang, Y., Jones, J.A., Zhang, M., Chen, Y., Tan, R., Koffas, M.A., Wang, Z. and Zhao, S., 2022. De novo biosynthesis of salvianolic acid B in Saccharomyces cerevisiae engineered with the rosmarinic acid biosynthetic pathway. Journal of Agricultural and Food Chemistry, 70(7), pp.2290-2302.

Perl, A., Dalton, H., Yoo, Y. and Koffas, M.A., 2022. Methods for the development of recombinant microorganisms for the production of natural products. Plant Metabolic Engineering: Methods and Protocols, pp.1-17.

Xu, G., Shi, X., Gao, Y., Wang, J., Cheng, H., Liu, Y., Chen, Y., Li, J., Xu, X., Zha, J. and Xia, K., 2022. Semi-rational evolution of pyruvate carboxylase from Rhizopus oryzae for elevated fumaric acid synthesis in Saccharomyces cerevisiae. Biochemical Engineering Journal, 177, p.108238.

Wong, M., 2022. Cell Free Production of Isobutanol. Rensselaer Polytechnic Institute.

2021

Xu, G., Wang, J., Gu, L., Zhu, Y., Zha, J., Zhang, X., Zhang, X., Cheng, Z., Yuan, Z., Cui, W. and Shi, J., 2021. Functional Caracterization of CapBCA in Controlling Poly-y-Glutamic Acid Synthesis in Corynebacterium Glutamicum.

Wong, M., Badri, A., Gasparis, C., Belfort, G. and Koffas, M., 2021. Modular optimization in metabolic engineering. Critical Reviews in Biochemistry and Molecular Biology, 56(6), pp.587-602.

Fang, Z., Zhou, J., Zhou, X. and Koffas, M.A., 2021. Abiotic-biotic hybrid for CO2 biomethanation: From electrochemical to photochemical process. Science of The Total Environment, 791, p.148288.

Rathnasinghe, R., Karlicek Jr, R.F., Schotsaert, M., Koffas, M., Arduini, B.L., Jangra, S., Wang, B., Davis, J.L., Alnaggar, M., Costa, A. and Vincent, R., 2021. Scalable, effective, and rapid decontamination of SARS-CoV-2 contaminated N95 respirators using germicidal ultraviolet C (UVC) irradiation device. Scientific Reports, 11(1), p.19970.

HWANG, H.G., NOH, M.H., KOFFAS, M.A., Sungho, J.A.N.G. and JUNG, G.Y., 2021. Multi-level Rebalancing of the Naringenin Biosynthetic Pathway Using Synthetic RNA Biosensors. pp.162-162.

KOFFAS, M., 2021. The Road to Animal Free Sulfated Glycosaminoglycans: Production of Chondroitin and Heparin Using Recombinant Bacteria. pp.30-30.

Hwang, H.G., Noh, M.H., Koffas, M.A., Jang, S. and Jung, G.Y., 2021. Multi-level rebalancing of the naringenin pathway using riboswitch-guided high-throughput screening. Metabolic Engineering, 67, pp.417-427.

Koffas, M. and Jones, J.A., Rensselaer Polytechnic Institute, 2021. Microbial polycultures and methods of use thereof. U.S. Patent 10,954,543.

Zan, X., Sun, J., Chu, L., Cui, F., Huo, S., Song, Y. and Koffas, M.A., 2021. Improved glucose and xylose co-utilization by overexpression of xylose isomerase and/or xylulokinase genes in oleaginous fungus Mucor circinelloides. Applied Microbiology and Biotechnology, 105, pp.5565-5575.

Wu, X., Han, J., Gong, G., Koffas, M.A. and Zha, J., 2021. Wall teichoic acids: physiology and applications. FEMS Microbiology Reviews, 45(4), p.fuaa064.

Morrison, C.S., Armiger, W.B., Dodds, D.R. and Koffas, M., BIOCHEMINSIGHTS Inc, 2021. Method for using electrochemical bioreactor module with recovery of cofactor. U.S. Patent 10,927,395.

Connor, A.J., Zha, R.H. and Koffas, M., 2021. Bioproduction of biomacromolecules for antiviral applications. Current Opinion in Biotechnology, 69, pp.263-272.

Koffas, M. and Jones, J.A., Rensselaer Polytechnic Institute, 2021. Microbial polycultures and methods of use thereof. U.S. Patent 10,954,543.

Badri, A., Williams, A., Awofiranye, A., Datta, P., Xia, K., He, W., Fraser, K., Dordick, J.S., Linhardt, R.J. and Koffas, M.A., 2021. Complete biosynthesis of a sulfated chondroitin in Escherichia coli. Nature Communications, 12(1), p.1389.

da Silva, A.J., de Souza Cunha, J., Hreha, T., Micocci, K.C., Selistre-de-Araujo, H.S., Barquera, B. and Koffas, M.A., 2021. Metabolic engineering of E. coli for pyocyanin production. Metabolic Engineering, 64, pp.15-25.

Morrison, C.S., Armiger, W.B., Dodds, D.R. and Koffas, M., BIOCHEMINSIGHTS Inc, 2021. Method for using electrochemical bioreactor module with recovery of cofactor. U.S. Patent 10,927,395.

Hreha, T.N., Foreman, S., Duran-Pinedo, A., Morris, A.R., Diaz-Rodriguez, P., Jones, J.A., Ferrara, K., Bourges, A., Rodriguez, L., Koffas, M.A. and Hahn, M., 2021. The three NADH dehydrogenases of Pseudomonas aeruginosa: Their roles in energy metabolism and links to virulence. Plos one, 16(2), p.e0244142.

Li, H., Shi, W., Li, C., Zhang, X., Gong, J., Shi, J., Koffas, M.A. and Xu, Z., 2021. Impact of ethylene glycol on DHEA dihydroxylation in Colletotrichum lini: Increasing the expression of cytochrome P450 and 6-phosphogluconate dehydrogenase and enhancing the generation of NADPH. Biochemical Engineering Journal, 166, p.107860.

Jeandet, P., Vannozzi, A., Sobarzo-Sánchez, E., Uddin, M. S., Bru, R., Martínez-Márquez, A., ... & Nabavi, S. M. (2021). Phytostilbenes as agrochemicals: biosynthesis, bioactivity, metabolic engineering and biotechnology. Natural Product Reports.

Badri, A., Williams, A., Awofiranye, A., Datta, P., Xia, K., He, W., ... & Koffas, M. A. (2021). Complete biosynthesis of a sulfated chondroitin in Escherichia coli. Nature communications, 12(1), 1-10.

da Silva, A. J., de Souza Cunha, J., Hreha, T., Micocci, K. C., Selistre-de-Araujo, H. S., Barquera, B., & Koffas, M. A. (2021). Metabolic engineering of E. coli for pyocyanin production. Metabolic Engineering, 64, 15-25.

Connor, A. J., Zha, R. H., & Koffas, M. (2021). Bioproduction of biomacromolecules for antiviral applications. Current Opinion in Biotechnology, 69, 263-272.

Hreha, T. N., Foreman, S., Duran-Pinedo, A., Morris, A. R., Diaz-Rodriguez, P., Jones, J. A., ... & Barquera, B. (2021). The three NADH dehydrogenases of Pseudomonas aeruginosa: Their roles in energy metabolism and links to virulence. PloS one, 16(2), e0244142.

Li, H., Shi, W., Li, C., Zhang, X., Gong, J., Shi, J., ... & Xu, Z. (2021). Impact of ethylene glycol on DHEA dihydroxylation in Colletotrichum lini: Increasing the expression of cytochrome P450 and 6-phosphogluconate dehydrogenase and enhancing the generation of NADPH. Biochemical Engineering Journal, 166, 107860.

2020

Naseri, G., & Koffas, M. A. (2020). Application of combinatorial optimization strategies in synthetic biology. Nature communications, 11(1), 1-14.Naseri, G., & Koffas, M. A. (2020). Application of combinatorial optimization strategies in synthetic biology. Nature communications, 11(1), 1-14.

Wang, R., Zhao, S., Wang, Z., & Koffas, M. A. (2020). Recent advances in modular co-culture engineering for synthesis of natural products. Current opinion in biotechnology, 62, 65-71.

Xu, P., Marsafari, M., Zha, J., & Koffas, M. (2020). Microbial coculture for flavonoid synthesis. Trends in Biotechnology, 38(7), 686-688.

Marsafari, M., Ma, J., Koffas, M., & Xu, P. (2020). Genetically-encoded biosensors for analyzing and controlling cellular process in yeast. Current opinion in biotechnology, 64, 175-182.

Marsafari, M., Samizadeh, H., Rabiei, B., Mehrabi, A., Koffas, M., & Xu, P. (2020). Biotechnological production of flavonoids: an update on plant metabolic engineering, microbial host selection, and genetically encoded biosensors. Biotechnology journal, 15(8), 1900432.

Jeandet, P., Sobarzo-Sánchez, E., Silva, A. S., Clément, C., Nabavi, S. F., Battino, M., ... & Nabavi, S. M. (2020). Whole-cell biocatalytic, enzymatic and green chemistry methods for the production of resveratrol and its derivatives. Biotechnology advances, 39, 107461.

Czajka, J. J., Okumuş, B., Koffas, M. A., Blenner, M., & Tang, Y. J. (2020). Mitigation of host cell mutations and regime shift during microbial fermentation: a perspective from flux memory. Current Opinion in Biotechnology, 66, 227-235.

Schilling, C., Badri, A., Sieber, V., Koffas, M., & Schmid, J. (2020). Metabolic engineering for production of functional polysaccharides. Current Opinion in Biotechnology, 66, 44-51.

Wang, X., Li, Z., Policarpio, L., Koffas, M. A., & Zhang, H. (2020). De novo biosynthesis of complex natural product sakuranetin using modular co-culture engineering. Applied microbiology and biotechnology, 104(11), 4849-4861.

Olmsted, Z. T., Stigliano, C., Badri, A., Zhang, F., Williams, A., Koffas, M. A., ... & Paluh, J. L. (2020). Fabrication of homotypic neural ribbons as a multiplex platform optimized for spinal cord delivery. Scientific reports, 10(1), 1-18.

Wu, X., Zha, J., & Koffas, M. A. (2020). Microbial production of bioactive chemicals for human health. Current Opinion in Food Science, 32, 9-16.

Wu, X., Han, J., Gong, G., Koffas, M. A., & Zha, J. (2020). Wall teichoic acids: Physiology and applications. FEMS Microbiology Reviews.

Shastry, D. G., Irudayanathan, F. J., Williams, A., Koffas, M., Linhardt, R. J., Nangia, S., & Karande, P. (2020). Rational identification and characterisation of peptide ligands for targeting polysialic acid. Scientific reports, 10(1), 1-15.

Schilling, C., Koffas, M. A., Sieber, V., & Schmid, J. (2020). Novel Prokaryotic CRISPR-Cas12a-Based Tool for Programmable Transcriptional Activation and Repression. ACS Synthetic Biology, 9(12), 3353-3363.

Jawed, K., Abdelaal, A. S., Koffas, M. A., & Yazdani, S. S. (2020). Improved butanol production using FASII pathway in E. coli. ACS Synthetic Biology, 9(9), 2390-2398.

Zha, J., Wu, X., & Koffas, M. A. (2020). Making brilliant colors by microorganisms. Current opinion in biotechnology, 61, 135-141.

Bu, X., Lin, J. Y., Cheng, J., Yang, D., Duan, C. Q., Koffas, M., & Yan, G. L. (2020). Engineering endogenous ABC transporter with improving ATP supply and membrane flexibility enhances the secretion of β-carotene in Saccharomyces cerevisiae. Biotechnology for biofuels, 13(1), 1-14.

Whitehead, T. A., Banta, S., Bentley, W. E., Betenbaugh, M. J., Chan, C., Clark, D. S., ... & Wheeldon, I. (2020). The importance and future of biochemical engineering. Biotechnology and bioengineering, 117(8), 2305-2318.

Zhang, X., Gao, Y., Chen, Z., Xu, G., Zhang, X., Li, H., ... & Xu, Z. (2020). High-yield production of L-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum. Microbial cell factories, 19, 1-14.

Morrison, C. S., Paskaleva, E. E., Rios, M. A., Beusse, T. R., Blair, E. M., Lin, L. Q., ... & Koffas, M. A. (2020). Improved soluble expression and use of recombinant human renalase. Plos one, 15(11), e0242109.

Hussain, S. A., Garcia, A., Khan, M., Kabir, A., Nosheen, S., Zhang, Y., ... & Song, Y. (2020). Increased Accumulation of Medium-Chain Fatty Acids by Dynamic Degradation of Long-Chain Fatty Acids in Mucor circinelloides. Genes, 11(8), 890.

Awofiranye, A. E., Baytas, S. N., Xia, K., Badri, A., He, W., Varki, A., ... & Linhardt, R. J. (2020). N-glycolyl chondroitin synthesis using metabolically engineered E. coli. AMB Express, 10(1), 1-9.

Rathnasinghe, R., Karlicek, R. F., Schotsaert, M., Koffas, M. A., Arduini, B., Jangra, S., ... & Balchandani, P. (2020). Scalable, effective, and rapid decontamination of SARS-CoV-2 contaminated N95 respirators using germicidal ultra-violet C (UVC) irradiation device. medRxiv.

Yang, Y., Pan, Y., Liu, G., Dong, G., Zhan, C., Koffas, M. A., ... & Bai, Z. (2020). Glycerol transporter 1 (Gt1) and zinc-regulated transporter 1 (Zrt1) function in different modes for zinc homeostasis in Komagataella phaffii (Pichia pastoris). Biotechnology Letters, 42(11), 2413-2423.

2019

Wong, M., Zha, J., Sorci, M., Gasparis, C., Belfort, G. & Koffas, M.A.G. (2019) Cell-free production of isobutanol: A completely immobilized system Biores. Tech 294. 122104. doi: 10.1016/j.biortech.2019.122104.

Wu, X., Zha, J., Koffas, M.A.G. & Dordick, J.S. (2019) Reducing Staphylococcus aureus resistance to lyostaphin using CRISPR-dCas9 Biotechnol. Bioengg. 116:12. 3149-3159. doi: 10.1002/bit.27143.

Jeandet, P., Sobaro-Sanchez, E., Silva, A.S., Clement, C., Nabavi, S.F., Battino, M., Rasekhian, M., Belwal, T., Habtemariam, S., Koffas, M.A.G. & Nabavi, S.M. (2019) Whole-cell biocatalytic, enzymatic and green chemistry methods for the production of resveratrol and its derivatives. Biotechnol. Adv. 107461. doi: 10.1016/j.biotechadv.2019.107461.

Zha, J., Wu, X. Gong, G. & Koffas, M.A.G. (2019) Pathway enzyme engineering for flavonoid production in recombinant microbes. Metabolic Engg. Comm. e00104. doi: 10.1016/j.mec.2019.e00104.

Lv, Y., Marsafari, M., Koffas, M.A.G., Zhou, J. & Xu. P. (2019) Optimizing oleaginous yeast cell factories for flavonoids and hydroxylated flavonoids biosynthesis ACS Syn. Bio. 8:11 2514-2523. doi: 10.1021/acssynbio.9b00193.

Williams, A., Gedeon, K.S., Vaidyanathan,D., Yu,Y., Collins, C.H., Dordick, J.S., Linhardt, R.J. & Koffas, M.A.G. (2019) Metabolic engineering of Bacillus megaterium for heparosan biosynthesis using Pasteurella multocida heparosan synthase, PmHS2 Microb. Cell Fact. 18:1 doi: 10.1186/s12934-019-1187-9.

Roell, G.W., Zha, J., Carr, R.R., Koffas, M.A.G., Fong, S.S. & Tang, Y.J. (2019) Engineering microbial consortia by division of labor. Microb. Cell Fact. 18:1 doi: 10.1186/s12934-019-1083-3.

Xu, G., Zha, J., Cheng, H., Ibrahim, M.H.A., Yang, F., Dalton, H., Cao, R., Zhu, Y., Fang, J., Chi, K., Zheng, P., Zhang, X., Shi, J., Xu, Z., Gross, R.A. & Koffas, M.A.G. (2019) Engineering Corynebacterium glutamicum for the de novo biosynthesis of tailored poly-γ-glutamic acid Met. Engg. In Press. doi: 10.1016/j.ymben.2019.08.011.

Wang, R., Cress, B.F., Yang, Z., Hordines, J.C., Zhao, S., Jung, G.Y., Wang, Z. & Koffas, M.A.G. (2019) Design and characterization of biosensors for the screening of modular assembled naringenin biosynthetic library in Saccharomyces cerevisiae. ACS Synth. Biol. In Press. doi: 10.1021/acssynbio.9b00212.

Wu, X., Zha, J., Koffas, M.A.G. & Dordick, J.S. (2019) Reducing Staphylococcus aureus Resistance to Lysostaphin using CRISPR‐dCas9. Biotechnol. Bioengg. Just Accepted Article doi: 10.1002/bit.27143.

Badri, A., Williams, A., Xia, K., Linhardt, R.J. & Koffas, M.A.G. (2019) Increased 3’‐phosphoadenosine‐5’‐phosphosulfate levels in engineered Escherichia coli cell lysate facilitates in vitro synthesis of Chondroitin Sulfate A. Biotechnol. J. 1800436. doi: 10.1002/biot.201800436.

Maynard, A., Butler, N.L., Ito, T., da Silva, A.J., Murai, M., Chen, T., Koffas, M.A.G., Miyoshi, H., & Barquera, B. (2019) The antibiotic korormicin A kills bacteria by producing reactive oxygen species. J. Bacteriol. doi: 10.1128/JB.00718-18.

Hanson, A.D., Hibberd, J.M., Koffas, M.A.G., Kopka, J., & Wurtzel, E.T. (2019) Focus Issue Editorial: Synthetic Biology. Plant Physiol. 179:3. doi: 10.1104/pp.19.00074.

Zhou, S., Lyu, Y., Li, H., Koffas, M.A.G., & Zhou, J. (2019) Fine‐tuning the (2S)‐naringenin synthetic pathway using an iterative high‐throughput balancing strategy Biotech. Bioengg. Just Accepted Article. doi: 10.1002/bit.26941.

Yu, Y., Williams, A., Zhang, X., Fu, L., Xia, K., Xu, Y., Zhang, F., Liu, J., Koffas, M.A.G. & Linhardt, R.J. (2019) Specificity and action pattern of heparanase Bp, a β-glucuronidase from Burkholderia pseudomallei. Glycobiology 29:8. 572-581. doi:10.1093/glycob/cwz039.

Akdemir, H., Silva, A., Zha, J., Zagorevski, D.V. & Koffas, M.A.G. (2019) Production of pyranoanthocyanins using Escherichia coli co-cultures. Met. Engg. 55. 290-298. doi:10.1016/j.ymben.2019.05.008.

Jawed, K., Yazdani, S.S. & Koffas, M.A.G. (2019) Advances in the development and application of microbial consortia for metabolic engineering. Met. Engg. Comm. In Press. e00095. doi:10.1016/j.mec.2019.e00095.

Singh, B.N., Raghubanshi, A.S., Koffas, M.A.G. & Gupta V.K. (2019) Microbial engineering biotechnologies. Biotechnol. Adv. 37:6 107399. doi:10.1016/j.biotechadv.2019.05.005.

Cress, B.F., Bhaskar, U., Vaidyanathan, D., Williams, A., Cai, C., Liu, X., Fu, L., Chari, V.M., Zhang, F., Mousa, S.A., Dordick, J.S., Koffas, M.A.G., & Linhardt, R.J. (2019) Heavy heparin: A stable isotope‐enriched, chemoenzymatically‐synthesized, poly‐component drug Angew. Chem. doi: 10.1002/ange.201900768.

Zang, Y., Zha, J., Wu, X., Zheng, Z., Ouyang, J. & Koffas, M.A.G. (2019) In vitro Naringenin Biosynthesis from p-Coumaric Acid Using Recombinant Enzymes. J. Agri. Food Chem. doi:10.1021/acs.jafc.9b00413

Tokuyama, K., Toya, Y., Matsuda, F., Cress, B.F., Koffas, M.A.G., & Shimizu, H. (2019) Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli. Met. Engg. 52. doi: 10.1016/j.ymben.2018.12.002.

Zhang, X., Lai, L., Xu, G., Zhang, X., Shi, J., Koffas, M.A.G., & Xu, Z. (2019) Rewiring the Central Metabolic Pathway for High‐Yield L‐Serine Production in Corynebacterium Glutamicum by Using Glucose Biotech J. Just Accepted Article. doi: 10.1002/biot.201800497.

Sharma, K., Zha, J., Chouhan, S., Guleria, S., & Koffas, M.A.G. (2019) Biosynthesis of Polyphenols in Recombinant Micro‐organisms Recent Adv. in Polyphenol Res. 237-262. Ed. Halbwirth, H., Stich, K., Cheynier, V., Quideaudoi, S.

Sarnaik, A., Abernathy, M.H., Han, X., Ouyang, Y., Xia, K., Chen, Y., Cress, B., Zhang, F., Lali, A., Pandit, R., Linhardt, R.J., Tang, Y.J., & Koffas, M.A.G. (2019) Metabolic engineering of cyanobacteria for photoautotrophic production of heparosan, a pharmaceutical precursor of heparin. Algal Res. 37 57-63. doi: 10.1016/j.algal.2018.11.010.

2018

Zha, J., Zang, Y., Mattozzi, M., Plassmeier, J., Gupta, M., Wu, X., Clarkson, S., & Koffas, M.A.G. (2018) Metabolic engineering of Corynebacterium glutamicum for anthocyanin production. Microb Cell Fact 17:143. doi: 10.1186/s12934-018-0990-z.

Koffas, M.A.G. & Linhardt, R.J. (2018) Metabolic bioengineering: glycans and glycoconjugates. Emerging Topics in Life Sciences 2:3 333-335. doi:10.1042/ETLS20180091.

Williams, A., Linhardt, R.J., & Koffas, M.A.G. (2018) Metabolic engineering of capsular polysaccharides. Emerging Topics in Life Sciences. doi: 10.1042/ETLS20180003.

Badri, A., Williams, A., Linhardt, R.J., & Koffas, M.A.G. (2018) The Road to Animal-Free Glycosaminoglycan Production: Current Efforts and Bottlenecks. Curr Opi Biotechnol. 53. 85-92. doi:10.1016/j.copbio.2017.12.018.

Gupta, M., Zha, J., Zhang, X., Jung, G.Y., Linhardt, R.J., & Koffas, M.A.G. (2018) Production of Deuterated Cyanidin 3-O-Glucoside from Recombinant Escherichia coli. ACS omega 3:9 11643-11648. doi:10.1021/acsomega.8b01134.

Kalbarczyk, K.Z., Mazeau, E.J., Rapp, K.M., Marchand, N., Koffas, M.A.G., & Collins, C.H. (2018) Engineering Bacillus megaterium strains to secrete cellulases for synergistic cellulose degradation in a microbial community. ACS Synth Biol. Just Accepted Manuscript. doi: 10.1021/acssynbio.8b00186.

Koffas, M.A.G. & Cirino P.C. (2018) Editorial overview: Chemical biotechnology. Curr. Op. in Biot. doi:10.1016/j.copbio.2018.08.010.

Niu, T., Liu, Y., Li, J., Koffas, M.A.G., Du, G., Alper, H.S., & Liu, L. (2018) Engineering a glucosamine-6-phosphate responsive gloms ribozyme switch enables dynamic control of metabolic flux in Bacillus subtilis for overproduction of N-acetylglucosamine. ACS Synth Biol. Just Accepted Manuscript. doi: 10.1021/acssynbio.8b00196.

Kim, S.G., Noh, M.H., Lim, H.G., Jang, S., Jang, S., Koffas, M.A.G. & Jung, G.Y. (2018) Molecular parts and genetic circuits for metabolic engineering of microorganisms. FEMS Microbiol Lett. 365:17. doi: 10.1093/femsle/fny187.

Zhang, X., Xu, G., Shi, J., Koffas, M.A.G, & Xu, Z. (2018) Microbial Production of l-Serine from Renewable Feedstocks. Trends Biotechnol. 36:7. 700-712. ISSN 0167-7799, doi: 10.1016/j.tibtech.2018.02.001

Zhao, M., Huang, D., Zhang, X., Koffas, M.A.G., Zhou,J., & Deng, Y. (2018) Metabolic engineering of Escherichia coli for producing adipic acid through the reverse adipate-degradation pathway. Metab Eng. 47. 254-262. doi: 10.1016/j.ymben.2018.04.002.

Fang, Z., Jones, J.A., Zhou, J., & Koffas, M.A.G. (2018) Engineering Escherichia coli Co-cultures for Production of Curcuminoids From Glucose. Biotechnol J. 13:5. doi: 10.1002/biot.201700576.

Zha, J., & Koffas, M.A.G. (2018) Anthocyanin Production in Engineered Microorganisms. In: Schwab W., Lange B., Wüst M. (eds) Biotechnology of Natural Products. Springer, Cham. 81-97. ISBN: 978-3-319-67902-0. doi: 10.1007/978-3-319-67903-7_4

Morrison, C., Heitmann, E., Armiger, W., Dodds, D., & Koffas, M.A.G. Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis. Adv. in Applied Microbiol. 105 51-86. doi:10.1016/bs.aambs.2018.07.001.

2017

Zha, J., & Koffas, M.A.G. (2017) Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives. Synth. and Sys. Biotechnol. 2:4. 259-266. ISSN 2405-805X. doi: 10.1016/j.synbio.2017.10.005

Chouhan, S., Sharma, K., Zha, J., Guleria, S., & Koffas, M.A.G. (2017) Recent Advances in the Recombinant Biosynthesis of Polyphenols. Front. Microbiol. 8:2259. doi: 10.3389/fmicb.2017.02259

Rütering, M., Cress, B.F., Schilling, M., Rühmann, B., Koffas, M.A.G., Sieber, V., & Schmid, J. (2017) Tailor-made exopolysaccharides — CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa. Synthetic Biology, 2:1. 1-12. doi: 10.1093/synbio/ysx007

Morrison, C.S., Armiger, W.B., Dodds, D.R., Dordick, J.S., & Koffas, M.A.G (2017) Improved strategies for electrochemical 1,4-NAD(P)H2 regeneration: A new era of bioreactors for industrial biocatalysis. Biotechnol. Adv. 36:1 120-131. doi: 10.1016/j.biotechadv.2017.10.003

Englaender, J.A., Zhu, Y.Y., Shirke, A.N., Lin, L., Liu, X., Zhang, F., Gross, R.A., Koffas, M.A.G., & Linhardt, R.J. (2017). Expression and secretion of glycosylated heparin biosynthetic enzymes using Komagataella pastoris. Appl Microbiol Biotechnol, 101, 2843-2851. doi: 10.1007/s00253-016-8047-x.

Guleria, S., Zhou, J., & Koffas, M.A.G. (2017). Nutraceuticals (Vitamin C, Carotenoids, Resveratrol). Industrial Biotechnology: Product and Processes. 309-336. ISBN: 978-3-527-34181-8.

Wang, H., He, W., Jiang, P., Yu, Y., Lin, L., Sun, Z., Koffas, M., Zhang, F., & Linhardt, R.J. (2017). Construction and functional characterization of truncated versions of recombinant keratanase II from Bacillus circulans. Glycoconj J, 34, 643-649. doi: 10.1007/s10719-017-9786-3.

He, W., Zhu, Y., Shirke, A., Sun, Z., Liu, J., Gross, R.A., Koffas, M.A.G., Linhardt, R.J., & Li, M. (2017). Expression of chondroitin-4-O-sulfotransferase in Escherichia coli and Pichia pastoris. Appl Microbiol Biotechnol, 101, 6919-6928. doi: 10.1007/s00253-017-8411-5.

Williams, A., He, W., Cress, B.F., Liu, X., Alexandria, J., Yoshizawa, H., Nishimura, K., Toida, T., Koffas, M.A.G., & Linhardt, R.J. (2017). Cloning and Expression of Recombinant Chondroitinase ACII and Its Comparison to the Arthrobacter aurescens Enzyme. Biotechnology Journal. doi: 10.1002/biot.201700239.

Jang, S., Jang, S., Xiu, Y., Kang, T.K., Lee, S.-H., Koffas, M.A.G., & Jung, G.Y. (2017). Development of Artificial Riboswitches for Monitoring of Naringenin In Vivo. ACS Synthetic Biology. doi: 10.1021/acssynbio.7b00128.

Jones, J.A., Vernacchio, V.R., Collins, S.M., Shirke, A.N., Xiu, Y., Englaender, J.A., Cress, B.F., McCutcheon, C., Linhardt, R.J., Gross, R., & Koffas M.A.G. (2017) Complete biosynthesis of anthocyanins using E. coli polycultures. mBio, 8(3), e00621-17. doi: 10.1128/mBio.00621-17.

Xiu, Y., Jang, S., Jones, J.A., Zill, N.A., Linhardt, R.J., Jung, G.Y., Yuan, Q., & Koffas, M.A.G. (2017) Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures. Biotechnology and Bioengineering, 114(4), 2235-2244. doi: 10.1002/bit.26340.

Ito, T., Murai, M., Ninokura, S., Kitazumi, Y., Mezic, K.G., Cress, B.F., Koffas, M.A.G., Morgan, J.E., Barquera B., & Miyoshi, H. (2017). Identification of the binding sites for ubiquinone and inhibitors in the Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae by photoaffinity labeling. J Biol Chem, 292(19), 7727-7742. doi: 10.1074/jbc.M117.781393.

Cress, B.F., Leitz, Q.D., Kim, D.C., Amore, T.D., Suzuki, J.Y., Linhardt, R.J., & Koffas, M.A. (2017). CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production. Microbial Cell Factories.

Englaender, J.A., Jones, J.A., Cress, B.F., Kuhlman, T.E., Linhardt, R.J., & Koffas, M.A. (2017). Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli. ACS Synthetic Biology.

He, L., Xiu, Y., Jones, J.A., Baidoo, E.E., Keasling, J.D., Tang, Y.J., & Koffas, M.A. (2017). Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions. Metabolic Engineering.

Whitaker, W.B., Jones, J.A., Bennett, K., Gonzalez, J., Vernacchio, V.R., Collins, S.M., Palmer, M.A., Schmidt, S., Antoniewicz, M.R., Koffas, M.A. & Papoutsakis, E.T. (2017). Engineering the Biological Conversion of Methanol to Specialty Chemicals in Escherichia coli. Metabolic Engineering. doi:10.1016/j.ymben.2016.10.015.

Shirke, A.N., Su, A., Jones, J.A., Butterfoss, G.L., Koffas, M.A., Kim, J.R., & Gross, R.A. (2017). Comparative thermal inactivation analysis of Aspergillus oryzae and Thiellavia terrestris cutinase: Role of glycosylation. Biotechnology and Bioengineering. doi:10.1002/bit.26052.

Earlier

Guleria, S., Zhou, J., & Koffas, M.A. (2016). Nutraceuticals (Vitamin C, Carotenoids, Resveratrol). Industrial Biotechnology: Products and Processes, 309-336.

Englaender, J.A., Zhu, Y., Shirke, A.N., Lin, L., Liu, X., Zhang, F., Gross, R., Koffas, M.A.G., & Linhardt, R.J. (2016). Expression and secretion of glycosylated heparin biosynthetic enzymes using Komagataella pastoris. Applied Microbiology and Biotechnology, 1-9.

Ibrahim, M.H., Cress, B.F., Linhardt, R.J., Koffas, M.A., & Gross, R.A. (2016). Draft Genome Sequence of Bacillus subtilis Ia1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production. Genome Announcements, 4(6), e01361-16.

Vaidyanathan, D., Williams, A., Dordick, J.S., Koffas, M.A., & Linhardt, R.J. (2016). Engineered heparins as new anticoagulant drugs. Bioengineering & Translational Medicine. doi:10.1002/btm2.10042.

Zhang, X., Khalidi, O., Kim, S.Y., Wang, R., Schultz, V., Cress, B.F., Gross, R.A., Koffas, M.A. & Linhardt, R.J., (2016). Synthesis and biological evaluation of 5,7-dihydroxyflavanone derivatives as antimicrobial agents. Bioorg Med Chem Lett, 26(13), 3089-3092. doi:10.1016/j.bmcl.2016.05.003.

Cress, B.F., Jones, J.A., Kim, D.C., Leitz, Q.D., Englaender, J.A., Collins, S.M., Linhardt, R.J., & Koffas, M.A.G. (2016). Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Research. doi:10.1093/nar/gkw231.

Wu, G., Yan, Q., Jones, J.A., Tang, Y.J., Fong, S.S. & Koffas, M.A. (2016). Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications. Trends in Biotechnology. doi:10.1016/j.tibtech.2016.02.010.

Jones, J.A. & Koffas, M.A.G. (2016). Optimizing Metabolic Pathways for the Improved Production of Natural Products. Methods in Enzymology. doi:10.1016/bs.mie.2016.02.010.

Pandey, R.P., Parajuli, P., Koffas, M.A. & Sohng, J.K. (2016). Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology. Biotechnology Advances. doi:10.1016/j.biotechadv.2016.02.012.

Jones, J.A., Vernacchio, V.R., Sinkoe, A.L., Collins, S.M., Ibrahim, M.H., Lachance, D.M., Hahn, J. & Koffas, M.A. (2016). Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metabolic Engineering, 35, 55-63. doi:10.1016/j.ymben.2016.01.006.

Wang, J., Guleria, S., Koffas, M.A. & Yan, Y. (2016). Microbial production of value-added nutraceuticals. Current Opinion in Biotechnology, 37, 97-104. doi:10.1016/j.copbio.2015.11.003.

Jones, J.A., Collins, S.M., Vernacchio, V.R., Lachance, D.M. & Koffas, M.A. (2015). Optimization of naringenin and p‐coumaric acid hydroxylation using the native E. coli hydroxylase complex, HpaBC. Biotechnology progress. doi:10.1002/btpr.2185.

Cress, B.F., Trantas, E.A., Ververidis, F., Linhardt, R.J. & Koffas, M.A. (2015). Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways. Current opinion in biotechnology, 36, 205-214. doi:10.1007/s00253-015-6821-9.

Lim, C. G., Wong, L., Bhan, N., Dvora, H., Xu, P., Venkiteswaran, S. & Koffas, M.A.G. (2015). Development of a Recombinant Escherichia coli Strain for Overproduction of the Plant Pigment Anthocyanin. Applied and environmental microbiology, 81(18), 6276-6284. doi:10.1128/AEM.01448-15.

Suflita, M., Fu, L., He, W., Koffas, M. & Linhardt, R.J. (2015). Heparin and related polysaccharides: synthesis using recombinant enzymes and metabolic engineering. Applied microbiology and biotechnology, 99, 7465-7479. doi:10.1007/s00253-015-6821-9.

Mora‐Pale, M., Bhan, N., Masuko, S., James, P., Wood, J., McCallum, S., Linhardt, R.J., Dordick, J.S. & Koffas, M.A.G. (2015). Antimicrobial mechanism of resveratrol‐trans‐dihydrodimer produced from peroxidase‐catalyzed oxidation of resveratrol. Biotechnology and bioengineering, 9999, 1-13. doi:10.1002/bit.25686.

Bhan, N., Li, L., Cai, C., Xu, P., Linhardt, R. J. & Koffas, M.A.G. (2015). Enzymatic formation of a resorcylic acid by creating a structure‐guided single‐point mutation in stilbene synthase. Protein Science, 24(2), 167-173. doi:10.1002/pro.2600.

Bhan, N., Cress, B.F., Linhardt, R. J. & Koffas, M.A.G. (2015). Expanding the chemical space of polyketides through structure guided mutagenesis of Vitis vinifera stilbene synthase. Biochimie, 115, 136-143. doi:10.1016/j.biochi.2015.05.019.

Trantas, E.A., Koffas, M.A.G., Xu, P. & Koffas, M.A.G. (2015). When plants produce not enough or at all: metabolic engineering of flavonoids in microbial hosts. Frontiers in Plant Science, 6, 1-16. doi:10.3389/fpls.2015.00007.

Jones J. A., Vernacchio V. R., Lachance D. M., Lebovich M., Fu L., Shirke A., Schultz V., Cress B., Linhardt, R. J. & Koffas, M.A.G. (2015). ePathOptimize: A combinatorial approach for transcriptional balancing of metabolic pathways. Scientific Reports, 5(11301), 1-10. doi:10.1038/srep11301.

Cress, B.F., Toparlak, O.D., Guleria, S., Lebovich, M., Stieglitz, J.T., Englaender, JA., Jones, J.A., Linhardt, R. J. & Koffas, M.A.G. (2015). CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli. ACS synthetic biology. doi:10.1021/acssynbio.5b00012.

Zhao, S., Jones, J. A., Lachance, D. M., Bhan, N., Khalidi, O., Venkataraman, S., Wang, Z., & Koffas, M.A.G. (2015). Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering. Metabolic Engineering, 28, 43-53. doi:10.1016/j.ymben.2014.12.002.

He, W., Fu, L., Li, G., Jones, A.J., Linhardt, R.J., & Koffas, M. (2015). Production of chondroitin in metabolically engineered E. coli. Metabolic Engineering, 27, 92-100. doi:0.1016/j.ymben.2014.11.003.

Jones, A.J., Toparlak, Ö.D., & Koffas, M. A. G. (2015). Metabolic pathway balancing and its role in the production of biofuels and chemicals. Current Opinion in Biotechnology, 33, 52-59. doi:10.1016/j.copbio.2014.11.013. ePub ahead of print.

Bhan, N., Li, L., Cai, C., Xu, P., Linhardt, R.J., & Koffas, M.A.G. (2014). Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase. Protein Science, 1-34. doi:10.1002/pro.2600.

Xu, P., Li, L., Zhang, F., Stephanopoulos, G., & Koffas, M. A. G. (2014). Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. PNAS, 1-6. doi:10.1073/pnas.1406401111. ePub ahead of print.

Zhang, H.-J., Fan, X.-G., Qiu, X.-L., Zhang, Q.-X., Wang, W.-Y., Li, S.-X., Deng, L.-H., Koffas, M. A. G., Wei, D.-S., & Yuan, Q.-P. (2014). A novel cleaning process for industrial production of xylose in pilot scale from corncob by using screw-steam-explosive extruder. Bioprocess and Biosystems Engineering, 1-12. doi:10.1007/s00449-014-1219-0.

Xu, P., Wang, W., Li, L., Bhan, N., Zhang, F. & Koffas, M. A. G. (2014). Design and kinetic analysis of a hybrid promoter−regulator system for malonyl-CoA sensing in Escherichia coli. ACS Chemical Biology, 9, 451-458. doi:10.1021/cb400623m.

Cress, B. F., Englaender, J. A., He, W., Kasper, D., Linhardt, R. J. & Koffas, M. A. G. (2014). Masquerading microbial pathogens: capsular polysaccharides mimic host-tissue molecules. FEMS Microbiology Reviews, 1-38. doi:10.1111/1574-6976.12056.

Koffas, M. A. G. & Marienhagen, J. (2014). Editorial overview: Food biotechnology. Current Opinion in Biotechnology, 26, v-vii. doi:10.1016/j.copbio.2014.02.005.

Mora-Pale, M., Sanchez-Rodriguez, S. P., Linhardt, R. J., Dordick, J. S. & Koffas, M. A. G. (2014). Biochemical strategies for enhancing the in vivo production of natural products with pharmaceutical potential. Current Opinion in Biotechnology, 25, 86-94. doi:10.1016/j.copbio.2013.09.009.

Joo, E. J., Cress, B. F. & Koffas, M. A. G. (2014). Using Recombinant microorganisms for the synthesis and modification of flavonoids and stilbenes. In Phenols in Human Health and Disease, 483-488. doi:10.1016/B978-0-12-398456-2.00036-0.

Bhan, N., Xu, P., Khalidi, O., & Koffas, M. A. G. (2013). Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework. Chemical Engineering Science, 103, 109–114. doi:10.1016/j.ces.2012.10.009.

Bhan, N., Xu, P. & Koffas, M. A. G. (2013). Pathway and protein engineering approaches to produce novel and commodity small molecules. Current Opinion in Biotechnology, 24, 1137-1143. doi:10.1016/j.copbio.2013.02.019.

Cress, B. F., Erkert, K. A., Barquera, B. & Koffas, M. A. G. (2013). Draft Genome Sequence of Pseudoalteromonas luteoviolacea Strain B, ATCC 29581. Genome Announcement, 1(2):e00048-13. doi:10.1128/genomeA.00048-13.

Cress, B. F., Greene, Z. R., Linhardt, R. J. & Koffas, M. A. G. (2013). Draft Genome Sequence of Escherichia coli Strain ATCC 23502, serovar O5:K4:H4. Genome Announcement, 1(2):e00046-13. doi:10.1128/genomeA.00046-13.

Cress, B. F., Greene, Z. R., Linhardt, R. J. & Koffas, M. A. G. (2013). Draft Genome Sequence of Escherichia coli Strain ATCC 23506, serovar O10:K5:H4. Genome Announcement, 1(2):e00049-13. doi:10.1128/genomeA.00049-13.

Cress, B. F., Linhardt, R. J. & Koffas, M. A. G. (2013). Draft Genome Sequence of Escherichia coli Strain Nisle 1917, serovar O6:K5:H1. Genome Announcement, 1(2):e00047-13. doi:10.1128/genomeA.00047-13.

Cress, B. F., Linhardt, R. J. & Koffas, M. A. G. (2013). Isoflavonoid production by genetically engineered microorganisms. In Natural Products, Springer-Verlag Berlin Heidelberg, 1647-1681. doi:10.1007/978-3-642-22144-6_53.

Mora-Pale, M., Sanchez-Rodriguez, S. P., Linhardt, R. J., Dordick, J. S. & Koffas, M. A. G. (2013). Metabolic engineering and in vitro biosynthesis of phytochemicals and non-natural analogues. Plant Science, 210, 10-24. doi:10.1016/j.plantsci.2013.05.005.

Wang, W., Englaender, J. A., Xu, P., Mehta, K. K., Suwan, J., Dordick, J. S., Zhang, F., Yuan, Q., Linhardt, R. J. & Koffas, M. A. G. (2013). Expression of low endotoxin 3-O-sulfotransferase in Bacillus subtilis and Bacillus megaterium. Applied Biochemistry and Biotechnology, 171, 954-962. doi:10.1007/s12010-013-0415-8.

Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A. G. W., Collins, C. H. & Koffas, M. A. G. (2013). Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nature Communications, 4, 1409. doi:10.1038/ncomms2425.

Xu, P. & Koffas, M. A. G. (2013). Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors. Synthetic Biology, 1073, Springer Science, 107-129. doi:10.1007/978-1-62703-625-2_10.

Bhan, N. & Koffas, M. A. G. (2012). Non-natural Isoflavonoids. Isoflavones: Chemistry, Analysis, Function and Effects, (5), 83, doi:10.1016/j.copbio.2012.08.010.

Malla, S., Koffas, M. A. G., Kazlauskas, R. J. & Kim, B.-G. (2012). Production of 7-O-methyl aromadendrin, a medicinally valuable flavonoid, in Escherichia coli. Applied and Environmental Microbiology, 78, 684-694, doi:10.1128/aem.06274-11.

Xu, P., Bhan, N. & Koffas, M. A. G. (2012). Engineering plant metabolism into microbes: from systems biology to synthetic biology. Current Opinion in Biotechnology, 24(2), doi:10.1016/j.copbio.2012.08.010.

Xu, P., Vansiri, A., Bhan, N. & Koffas, M. A. G. (2012). ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synthetic Biology, 1, 256-266, doi:10.1021/sb300016b.

Fowler, Z. L., Baron, C. M., Panepinto, J. C. & Koffas, M. A. G. (2011). Melanization of flavonoids by fungal and bacterial laccases. Yeast, 28, 181-188, doi:10.1002/yea.1829.

Fowler, Z. L., Shah, K., Panepinto, J. C., Jacobs, A. & Koffas, M. A. G. (2011). Development of non-natural flavanones as antimicrobial agents. Plos One, 6(10), doi:10.1371/journal.pone.0025681.

Lim, C. G., Fowler, Z. L., Hueller, T., Schaffer, S. & Koffas, M. A. G. (2011). High-yield resveratrol production in engineered Escherichia coli. Applied and Environmental Microbiology, 77(10), 3451-3460, doi:10.1128/aem.02186-10.

Santos, C. N. S., Koffas, M. & Stephanopoulos, G. (2011). Optimization of a heterologous pathway for the production of flavonoids from glucose. Metabolic Engineering, 13, 392-400, doi:10.1016/j.ymben.2011.02.002.

Xu, P., Ranganathan, S., Fowler, Z. L., Maranas, C. D. & Koffas, M. A. G. (2011). Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metabolic Engineering, 13, 578-587, doi:10.1016/j.ymben.2011.06.008 (2011).

Xu, P., Ranganathan, S., Maranas, C. D. & Koffas, M. (2011). An integrated computational and experimental study to increase the intra-cellular malonyl-CoA: application to flavanone synthesis. In Bioengineering Conference (NEBEC), IEEE, 1-2, ISSN 2160-7001, ISBN 9781612848273, doi:10.1109/NEBC.2011.5778699.

Bedekar, A., Shah, K. & Koffas, M. (2010). Natural products for type II diabetes treatment. In Advances in Applied Microbiology, 71, Academic Press, 21-73, ISSN 0065-2164, ISBN 9780123809933, doi:10.1016/S0065-2164(10)71002-9.

Chemler, J. A., Fowler, Z. L., McHugh, K. P. & Koffas, M. A. G. (2010). Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metabolic Engineering, 12, 96-104, doi:10.1016/j.ymben.2009.07.003.

Chemler, J. A., Lim, C. G., Daiss, J. L. & Koffas, M. A. G. (2010). A versatile microbial system for biosynthesis of novel polyphenols with altered estrogen receptor binding activity. Chemistry & Biology, 17, 392-401, doi:10.1016/j.chembiol.2010.03.010.

Fowler, Z. & Koffas, M. (2010). Microbial biosynthesis of fine chemicals: an emerging technology. In The metabolic pathway engineering handbook – tools and applications, CRC Press, 22- 1-30, ISBN 9781420077650.

Lim, C.-G. & Koffas, M. A. G. (2010). Bioavailability and recent advances in the bioactivity of flavonoid and stilbene compounds. Current Organic Chemistry, 14, 1727-1751.

Xu, P & Koffas, M. A. G. (2010). Metabolic engineering of Escherichia coli for biofuel production. Biofuels, 1(3), 493-504, doi:10.4155/bfs.10.13.

Chemler, J. A., Fowler, Z. L., & Koffas, M. A. G. (2009). Trends in microbial synthesis of natural products and biofuels. In Advances in enzymology and related areas of molecular biology: and related areas of molecular biology, 76, 151-217.

Chemler, J. A., Leonard, E. & Koffas, M. A. G. (2009). Flavonoid biotransformations in microorganisms. In Anthocyanins,Springer Science, 191-255, doi:10.1007/978-0-387-77335-3_7.

Fowler, Z. L., Gikandi, W. W. & Koffas, M. A. G. (2009). Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production. Applied and Environmental Microbiology, 75(18), 5831-5839, doi:10.1128/aem.00270-09.

Fowler, Z. L. & Koffas, M. A. G. (2009). Biosynthesis and biotechnological production of flavanones: current state and perspectives. Applied Microbiology and Biotechnology, 83, 799-808, doi:10.1007/s00253-009-2039-z.

Koffas, M. A. G. (2009) Expanding the repertoire of biofuel alternatives through metabolic pathway evolution. Proceedings of the National Academy of Sciences of the United States of America, 106(4), 965-966, doi:10.1073/pnas.0811893106.

Chemler, J. A. & Koffas, M. A. G. (2008). Metabolic engineering for plant natural product biosynthesis in microbes. Current Opinion in Biotechnology, 19, 597-605, doi:10.1016/j.copbio.2008.10.011.

Koffas, M. (2008). Engineering flavonoid biosynthesis in microorganisms. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, 150, S184-S184, doi:10.1016/j.cbpa.2008.04.497.

Leonard, E., Yan, Y., Chemler, J., Matern, U., Martens, S. & Koffas, M. A. G. (2008). Characterization of dihydroflavonol 4-reductases for recombinant plant pigment biosynthesis applications. Biocatalysis and Biotransformation, 26(3), 243-251, doi:10.1080/10242420701685635.

Leonard, E., Yan, Y., Fowler, Z. L., Li, Z., Lim, C.-G., Lim, K.-H. & Koffas, M. A. G. (2008). Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Molecular Pharmaceutics, 5(2), 257-265, doi:10.1021/mp7001472.

Yan, Y., Li, Z. & Koffas, M. A. G. (2008). High-yield anthocyanin biosynthesis in engineered Escherichia coli. Biotechnology and Bioengineering, 100(1), 126-140, doi:10.1002/bit.21721.

Chemler, J. A., Lock, L. T., Koffas, M. A. G. & Tzanakakis, E. S. (2007). Standardized biosynthesis of flavan-3-ols with effects on pancreatic beta-cell insulin secretion. Applied Microbiology and Biotechnology, 77, 797-807, doi:10.1007/s00253-007-1227-y.

Chemler, J. A., Yan, Y., Leonard, E. & Koffas, M. A. G. (2007). Combinatorial mutasynthesis of flavonoid analogues from acrylic acids in microorganisms. Organic Letters, 9(10), 1855-1858, doi:10.1021/ol0703736.

Leonard, E., Fowler, Z. L. & Koffas, M. (2007). Metabolic engineering. Systems Biology, 301-359.

Leonard, E. & Koffas, M. A. G. (2007). Engineering of artificial plant cytochrome p450 enzymes for synthesis of isoflavones by Escherichia coli. Applied and Environmental Microbiology, 73(22), 7246-7251, doi:10.1128/aem.01411-07.

Leonard, E., Lim, K.-H., Saw, P.-N. & Koffas, M. A. G. (2007). Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Applied and Environmental Microbiology, 73(12), 3877-3886, doi:10.1128/aem.00200-07.

Yan, Y., Huang, L. & Koffas, M. A. G. (2007). Biosynthesis of 5-deoxyflavanones in microorganisms. Biotechnology Journal, 2, 1250-1262, doi:10.1002/biot.200700119.

Chemler, J. A., Yan, Y. & Koffas, M. A. G. (2006). Biosynthesis of isoprenoids, polyunsaturated fatty acids and flavonoids in Saccharomyces cerevisiae. Microbial Cell Factories, 5, doi:10.1186/1475-2859-5-20.

Leonard, E., Chemler, J., Lim, K. H. & Koffas, M. A. G. (2006). Expression of a soluble flavone synthase allows the biosynthesis of phytoestrogen derivatives in Escherichia coli. Applied Microbiology and Biotechnology, 70, 85-91, doi:10.1007/s00253-005-0059-x.

Leonard, E., Yan, Y. J. & Koffas, M. A. G. (2006). Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli. Metabolic Engineering, 8, 172-181, doi:10.1016/j.ymben.2005.11.001.

Koffas, M. (2005). Evolutionary metabolic engineering. Metabolic Engineering, 7, 1-3, doi:10.1016/j.ymben.2005.01.001.

Koffas, M. & Stephanopoulos, G. (2005). Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Current Opinion in Biotechnology, 16, 361-366, doi:10.1016/j.copbio.2005.04.010.

Leonard, E., Yan, Y. J., Lim, K. H. & Koffas, M. A. G. (2005). Investigation of two distinct flavone synthases for plant-specific flavone biosynthesis in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 71, 8241-8248, doi:10.1128/aem.71.12.8241-8248.2005.

Yan, Y. J., Chemler, J., Huang, L. X., Martens, S. & Koffas, M. A. G. (2005). Metabolic engineering of anthocyanin biosynthesis in Escherichia coli. Applied and Environmental Microbiology, 71, 3617-3623, doi:10.1128/aem.71.7.3617-3623.2005.

Yan, Y. J., Kohli, A. & Koffas, M. A. G. (2005). Biosynthesis of natural flavanones in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 71, 5610-5613, doi:10.1128/aem.71.9.5610-5613.2005.

Koffas, M. A. G., Jung, G. Y. & Stephanopoulos, G. (2003). Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metabolic Engineering, 5, 32-41, doi:10.1016/s1096-7176(03)00002-8.

Koffas, M. A. G., Jung, G. Y., Aon, J. C. & Stephanopoulos, G. (2002). Effect of pyruvate carboxylase overexpression on the physiology of Corynebacterium glutamicum. Applied and Environmental Microbiology, 68(11), 5422-5428, doi:10.1128/aem.68.11.5422-5428.2002.

Koffas, M., Robervge, C., Lee, K. & Stephanopoulos, G. (1999). Metabolic engineering. Annual Review of Biomedical Engineering, 1, 535-557, doi:10.1146/annurev.bioeng.1.1.535.

Koffas, M. A. G., Ramamoorthi, R., Pine, W. A., Sinskey, A. J. & Stephanopoulos, G. (1998). Sequence of the Corynebacterium glutamicum pyruvate carboxylase gene. Applied Microbiology and Biotechnology, 50, 346-352.