Research output per year
Research output per year
- 1 - 50 out of 237 results
Search results
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2025
Impacts of blending advanced treated water and traditional groundwater supply on lead and copper concentrations and microbial diversity in premise plumbing
Mishrra, A., Zhang, L., Junior, J., Ling, F., Blute, N. K. & Giammar, D. E., Jan 1 2025, In: Water Research. 268, 122726.Research output: Contribution to journal › Article › peer-review
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Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) intended for river stocking
Andres, K. J., Liu, B., Johnson, L. E., Kapuscinski, K. L., Moerke, A. H., Ling, F. & Knouft, J. H., Jan 15 2025, In: Aquaculture. 594, 741469.Research output: Contribution to journal › Article › peer-review
Open Access -
MAGMA: Microbial and Algal Growth Modeling Application
Xu, V. A., Lee, H., Long, B., Yuan, J. & Tang, Y. J., Mar 25 2025, In: New Biotechnology. 85, p. 16-22 7 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Metabolic analyses of Yarrowia lipolytica for biopolymer production reveals roadblocks and strategies for microbial utilizing volatile fatty acids as sustainable feedstocks
Xiao, Z., Xiong, X., Sun, Y., Tourang, M., Chen, S. & Tang, Y. J., Feb 2025, In: Bioresource Technology. 417, 131855.Research output: Contribution to journal › Article › peer-review
Open Access -
Network for knowledge Organization (NEKO): An AI knowledge mining workflow for synthetic biology research
Xiao, Z., Pakrasi, H. B., Chen, Y. & Tang, Y. J., Jan 2025, In: Metabolic Engineering. 87, p. 60-67 8 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2024
A hybrid in silico/in-cell controller that handles process-model mismatches using intracellular biosensing
Ohkubo, T., Sakumura, Y., Zhang, F. & Kunida, K., Dec 2024, In: Scientific reports. 14, 1, 27252.Research output: Contribution to journal › Article › peer-review
Open Access -
ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction
Mu, X., Evans, T. D. & Zhang, F., Dec 2024, In: Nature communications. 15, 1, 5299.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Biological upgrading of biogas assisted with membrane supplied hydrogen gas in a three-phase upflow reactor
Rao, Y., Lin, T. Y., Ling, F. & He, Z., Feb 2024, In: Bioresource Technology. 394, 130260.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
Blending recombinant amyloid silk proteins generates composite fibers with tunable mechanical properties
Subramani, S. V., Li, J., Lee, K. Z., Fisher, N. & Zhang, F., Feb 21 2024, In: Materials Advances. 5, 8, p. 3506-3516 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: How cells balance acetyl-CoA and excess reducing equivalents
Worland, A. M., Han, Z., Maruwan, J., Wang, Y., Du, Z. Y., Tang, Y. J., Su, W. W. & Roell, G. W., Sep 2024, In: Metabolic Engineering. 85, p. 1-13 13 p.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
Evaluating GPT Models for Automated Literature Screening in Wastewater-Based Epidemiology
Chibwe, K., Mantilla-Calderon, D. & Ling, F., 2024, (Accepted/In press) In: ACS Environmental Au.Research output: Contribution to journal › Article › peer-review
Open Access -
Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators
Anthony, W. E., Geng, W., Diao, J., Carr, R. R., Wang, B., Ning, J., Moon, T. S., Dantas, G. & Zhang, F., Dec 2024, In: Biotechnology for Biofuels and Bioproducts. 17, 1, 83.Research output: Contribution to journal › Article › peer-review
Open Access -
Intra-hospital microbiome variability is driven by accessibility and clinical activities
Chibwe, K., Sundararaju, S., Zhang, L., Tsui, C., Tang, P. & Ling, F., Aug 2024, In: Microbiology spectrum. 12, 8Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
The ability in managing reactive oxygen species affects Escherichia coli persistence to ampicillin after nutrient shifts
Zhang, R., Hartline, C. & Zhang, F., Nov 2024, In: mSystems. 9, 11, e01295-24.Research output: Contribution to journal › Article › peer-review
Open Access -
The use of a benign fast-growing cyanobacterial species to control microcystin synthesis from Microcystis aeruginosa
Lee, H., Xu, V., Diao, J., Zhao, R., Chen, M., Moon, T. S., Liu, H., Parker, K. M., Jun, Y. S. & Tang, Y. J., 2024, In: Frontiers in Microbiology. 15, 1461119.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism
Roell, G. W., Schenk, C., Anthony, W. E., Carr, R. R., Ponukumati, A., Kim, J., Akhmatskaya, E., Foston, M., Dantas, G., Moon, T. S., Tang, Y. J. & García Martín, H., Jun 16 2023, In: ACS synthetic biology. 12, 6, p. 1632-1644 13 p.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
An algal-bacterial symbiotic system of carbon fixation using formate as a carbon source
Zheng, Y., Czajka, J. J., Daiek, C., Yang, Z., Sun, L., Tang, Y. J., Liu, Y. & Liao, W., May 2023, In: Algal Research. 72, 103103.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
Backman, T. W. H., Schenk, C., Radivojevic, T., Ando, D., Singh, J., Czajka, J. J., Costello, Z., Keasling, J. D., Tang, Y., Akhmatskaya, E. & Martin, H. G., Nov 2023, In: PLoS computational biology. 19, 11 November, e1011111.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Bi-terminal fusion of intrinsically-disordered mussel foot protein fragments boosts mechanical strength for protein fibers
Li, J., Jiang, B., Chang, X., Yu, H., Han, Y. & Zhang, F., Dec 2023, In: Nature communications. 14, 1, 2127.Research output: Contribution to journal › Article › peer-review
Open Access20 Scopus citations -
Characterizing a Propionate Sensor in E. coli Nissle 1917
Amrofell, M. B. & Moon, T. S., Jun 16 2023, In: ACS synthetic biology. 12, 6, p. 1868-1873 6 p.Research output: Contribution to journal › Article › peer-review
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Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia
Rottinghaus, A. G., Vo, S. & Moon, T. S., Jan 3 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 1, e2213154120.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
Conditional protein degradation in Yarrowia lipolytica using the auxin-inducible degron
Han, Z., Maruwan, J., Tang, Y. & Su, W. W., 2023, In: Frontiers in Bioengineering and Biotechnology. 11, 1188119.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Engineering E. coli strains using antibiotic-resistance-gene-free plasmids
Amrofell, M. B., Rengarajan, S., Vo, S. T., Ramirez Tovar, E. S., LoBello, L., Dantas, G. & Moon, T. S., Dec 18 2023, In: Cell Reports Methods. 3, 12, 100669.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Engineering the Future through Synthetic Biology
Moon, T. S., Dec 2023, In: Biotechnology and Bioprocess Engineering. 28, 6, p. 889-891 3 p.Research output: Contribution to journal › Article › peer-review
2 Scopus citations -
Generative Artificial Intelligence GPT-4 Accelerates Knowledge Mining and Machine Learning for Synthetic Biology
Xiao, Z., Li, W., Moon, H., Roell, G. W., Chen, Y. & Tang, Y. J., Oct 20 2023, In: ACS synthetic biology. 12, 10, p. 2973-2982 10 p.Research output: Contribution to journal › Article › peer-review
Open Access20 Scopus citations -
Genetically Engineered Protein-Based Bioadhesives with Programmable Material Properties
Jeon, J., Lee, K. Z., Zhang, X., Jaeger, J., Kim, E., Li, J., Belaygorod, L., Arif, B., Genin, G. M., Foston, M. B., Zayed, M. A. & Zhang, F., 2023, (Accepted/In press) In: ACS Applied Materials and Interfaces.Research output: Contribution to journal › Article › peer-review
2 Scopus citations -
Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Han, Y., Li, W., Filko, A., Li, J. & Zhang, F., Dec 2023, In: Nature communications. 14, 1, 5757.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Microbial thermogenesis is dependent on ATP concentrations and the protein kinases ArcB, GlnL, and YccC
Dhatt, P. S., Chiu, S. & Moon, T. S., Oct 2023, In: PLoS biology. 21, 10, e3002180.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress
Xiao, Z., Connor, A. J., Worland, A. M., Tang, Y. J., Zha, R. H. & Koffas, M., May 2023, In: Metabolic Engineering. 77, p. 231-241 11 p.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
Ten simple rules for managing laboratory information
Berezin, C. T., Aguilera, L. U., Billerbeck, S., Bourne, P. E., Densmore, D., Freemont, P., Gorochowski, T. E., Hernandez, S. I., Hillson, N. J., King, C. R., Köpke, M., Ma, S., Miller, K. M., Moon, T. S., Moore, J. H., Munsky, B., Myers, C. J., Nicholas, D. A., Peccoud, S. J. & Zhou, W. & 1 others, , Dec 2023, In: PLoS computational biology. 19, 12, e1011652.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Upcycling of poly(ethylene terephthalate) to produce high-value bio-products
Diao, J., Hu, Y., Tian, Y., Carr, R. & Moon, T. S., Jan 31 2023, In: Cell Reports. 42, 1, 111908.Research output: Contribution to journal › Article › peer-review
Open Access50 Scopus citations -
2022
A comparative evaluation of machine learning algorithms for predicting syngas fermentation outcomes
Roell, G. W., Sathish, A., Wan, N., Cheng, Q., Wen, Z., Tang, Y. J. & Bao, F. S., Aug 2022, In: Biochemical Engineering Journal. 186, 108578.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630
Diao, J., Carr, R. & Moon, T. S., Dec 2022, In: Communications Biology. 5, 1, 1109.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Emerging investigator series: meta-analyses on SARS-CoV-2 viral RNA levels in wastewater and their correlations to epidemiological indicators
Mantilla-Calderon, D., Huang, K., Li, A., Chibwe, K., Yu, X., Ye, Y., Liu, L. & Ling, F., May 4 2022, In: Environmental Science: Water Research and Technology. 8, 7, p. 1391-1407 17 p.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Engineering diverse fatty acid compositions of phospholipids in Escherichia coli
Bai, W., Anthony, W. E., Hartline, C. J., Wang, S., Wang, B., Ning, J., Hsu, F. F., Dantas, G. & Zhang, F., Nov 2022, In: Metabolic Engineering. 74, p. 11-23 13 p.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals
Rottinghaus, A. G., Xi, C., Amrofell, M. B., Yi, H. & Moon, T. S., Mar 16 2022, In: Cell Systems. 13, 3, p. 204-214.e4Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Genetically stable CRISPR-based kill switches for engineered microbes
Rottinghaus, A. G., Ferreiro, A., Fishbein, S. R. S., Dantas, G. & Moon, T. S., Dec 2022, In: Nature communications. 13, 1, 672.Research output: Contribution to journal › Article › peer-review
Open Access85 Scopus citations -
Meter-scale variation within a single transect demands attention to taxon accumulation curves in riverine microbiome studies
Liu, Z., Zhang, L., Knouft, J. H. & Ling, F., May 2022, In: Frontiers of Environmental Science and Engineering. 16, 5, 64.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Microbial electrochemical ammonia recovery from anaerobic digester centrate and subsequent application to fertilize Arabidopsis thaliana
Liu, F., Worland, A., Tang, Y., Moustafa, H., Hassouna, M. S. E. D. & He, Z., Jul 15 2022, In: Water Research. 220, 118667.Research output: Contribution to journal › Article › peer-review
Open Access19 Scopus citations -
MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes
Zhang, L., Chen, L., Yu, X., Duvallet, C., Isazadeh, S., Dai, C., Park, S., Frois-Moniz, K., Duarte, F., Ratti, C., Alm, E. J. & Ling, F., Sep 2022, In: PLoS computational biology. 18, 9, e1010472.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Mineral-hydrogel composites for mitigating harmful algal bloom and supplying phosphorous for photo-biorefineries
Xiao, Z., Tan, A. X., Xu, V., Jun, Y. S. & Tang, Y. J., Nov 15 2022, In: Science of the Total Environment. 847, 157533.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels
Zhao, R., Sengupta, A., Tan, A. X., Whelan, R., Pinkerton, T., Menasalvas, J., Eng, T., Mukhopadhyay, A., Jun, Y. S., Pakrasi, H. B. & Tang, Y. J., Dec 2022, In: Scientific reports. 12, 1, 22163.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Re-Programing Glucose Catabolism in the Microalga Chlorella sorokiniana under Light Condition
Li, T., Pang, N., He, L., Xu, Y., Fu, X., Tang, Y., Shachar-Hill, Y. & Chen, S., Jul 2022, In: Biomolecules. 12, 7, 939.Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations -
The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors
Hartline, C. J. & Zhang, F., Jul 15 2022, In: ACS synthetic biology. 11, 7, p. 2247-2258 12 p.Research output: Contribution to journal › Article › peer-review
9 Scopus citations -
Trade-Offs in Biosensor Optimization for Dynamic Pathway Engineering
Verma, B. K., Mannan, A. A., Zhang, F. & Oyarzún, D. A., Jan 21 2022, In: ACS synthetic biology. 11, 1, p. 228-240 13 p.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
Transient Antibiotic Tolerance Triggered by Nutrient Shifts From Gluconeogenic Carbon Sources to Fatty Acid
Hartline, C. J., Zhang, R. & Zhang, F., Mar 11 2022, In: Frontiers in Microbiology. 13, 854272.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production
Czajka, J. J., Banerjee, D., Eng, T., Menasalvas, J., Yan, C., Munoz, N. M., Poirier, B. C., Kim, Y. M., Baker, S. E., Tang, Y. J. & Mukhopadhyay, A., Dec 2022, In: Metabolic Engineering Communications. 15, e00206.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
2021
A Biosynthetic Hybrid Spidroin-Amyloid-Mussel Foot Protein for Underwater Adhesion on Diverse Surfaces
Kim, E., Jeon, J., Zhu, Y., Hoppe, E. D., Jun, Y. S., Genin, G. M. & Zhang, F., Oct 20 2021, In: ACS Applied Materials and Interfaces. 13, 41, p. 48457-48468 12 p.Research output: Contribution to journal › Article › peer-review
Open Access36 Scopus citations -
An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus
Delorenzo, D. M., Diao, J., Carr, R., Hu, Y. & Moon, T. S., Apr 16 2021, In: ACS synthetic biology. 10, 4, p. 786-798 13 p.Research output: Contribution to journal › Article › peer-review
15 Scopus citations -
Development of a kinetic model to describe six types of symbiotic interactions in a formate utilizing microalgae-bacteria cultivation system
Xiao, Z., Zheng, Y., Gudi, C. R., Liu, Y., Liao, W. & Tang, Y. J., Oct 2021, In: Algal Research. 58, 102372.Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations