# Jean Zhao's Patents and Publications

###### tags: `Patents and Publications`

[TOC]
## Patents
1. Yoshikuni Y, Wang G, ==Zhao Z==, Coates RC, Cheng JF, Robinson D, Pathway Integration and Expression in Host Cells, US 20190048354, publication date: Feb 14, ==2019==
2. Chen F, Peng Z, ==Zhao Z==, Nath N, Froula JL, Method for Making Mate-Pair Libraries, US Patent 13/535,167, date issued Jun 27, ==2012==

## Publications
1. Panich J, Toppari E, Tejedor-Sanz S, Fong B, Dugan E, Chen Y, Petzold J, ==Zhao Z==, Yoshikuni Y, Savage DF, Singer SW, Functional plasticity of HCO3- uptake and CO2 fixation in Cupriavidus necator H16. ==Bioresource Technology==, 2024, doi.org/10.1016/j.biortech.2024.131214

2. Gauttam R, Eng T, ==Zhao Z==, Rana QUA, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer, SW, Development of genetic tools for heterologous protein expression in a pentose‐utilizing environmental isolate of Pseudomonas putida. ==Microb. Biotechnol.==, 2023, doi.org/10.1111/1751-7915.14205

3. Rekha S, Roux S, Huber KJ, Wu D, Yu S, Udwary D, ==Zhao Z==, …,Ivanova NN, Expanding the Genomic Encyclopedia of Actinobacteria with 824 Isolate Reference Genomes. ==Cell Genomics==, 2022, https://doi.org/10.1016/j.xgen.2022.100213.

4. ==Zhao Z==, and Yoshikuni Y, Discovering Untapped Biochemistry in Microorganisms from Hidden Corners, ==Nature Reviews Microbiology==, 2022, doi.org/10.1038/s41579-022-00795-w. (invited)

5. ==Zhao Z==, Cheng JF, and Yoshikuni Y, Chromosomal Integration of Complex DNA Constructs Using CRAGE and CRAGE-Duet Systems, ==STAR Protocols==, 2022, doi.org/10.1016/j.xpro.2022.101546. (invited)

6. Ke J, ==Zhao Z==, Coates R, …, Yoshikuni Y, Development of Platforms for Functional Characterization and Production of Phenazines Using a Multi-Chassis Approach via CRAGE, ==Metabolic Engineering==, 2022, doi.org/10.1016/j.ymben.2021.11.012

7. Jabusch JK, Kim PW, Chiniquy D., ==Zhao Z==, Wang B., Boqwn B., Kang AJ, Yoshikuni Y, Deutschbauer AM, Singh AK, Northern TR, Microfabrication of a Chamber for High-Resolution, in-situ Imaging of the Whole Root for Plant-microbe Interactions, ==International Journal of Molecular Sciences==, 2021, doi.org/10.3390/ijms22157880

8. Noonan AJC, Qiu Y, Ho JCH, Ocampo J, Vreugdenhil KA, Marr RA, ==Zhao Z==, Yoshikuni Y, Hallam SJ, CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli, ==Oxford Academy Synthetic Biology==, 2020, doi.org/10.1093/synbio/ysaa015

9. Wang B*, ==Zhao Z*==, Chiniquy D, Ono K, Conway J, Zhang Z, Wang G, Robinson D, Cheng JF, Dangl J, Northen TR, Jabusch L, Yoshikuni Y, CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant-Microbe Interactions, ==ACS Synthetic Biology==, 2020, doi.org/10.1021/acssynbio.0c00280 (==Cover page image==)

10. Wang G*, ==Zhao Z*==, Ke J*, Engel Y*, Shi Y*, …, Bode HB, Yoshikuni Y, Chassis-independent recombinase- assisted genome engineering enables rapid activation of biosynthetic gene clusters in undomesticated bacteria, ==Nature Microbiology==, 2019, doi.org/10.1038/s41564-019-0573-8.

11. Coates RC, Bowen BP, Oberortner E, Thomashow L, Hadjithomas M, ==Zhao Z==, Ke J, Silva L, Louie K, Wang G, Robinson D, Tarver A, Hamilton M, Lubbe A, Feltcher M, Dangl J, Pati A, Weller D, Northen T, Yoshikuni Y, An integrated workflow for phenazine-modifying enzyme characterization, ==Journal of Industrial Microbiology & Biotechnology==, 2018 Jul;45(7):567-577

12. Peng Z, Nath N, ==Zhao Z==, Froula JL, Cheng JF, Chen F, Preparing Mate-Paired Illumina Libraries Using Cre Recombinase, ==Methods in Molecular Biology==, 2017 August, 1642:247-261

13. Haitjema C, Gilmore S, Henske J, Solomon K, Groot R, Kuo A, Mondo S, Salamov A, Labutti K, ==Zhao Z==, Chiniquy J, Barry K, Brewer H, Purvine S, Wright A, Hainaut M, Boxma B, Hackstein J, O'Malley M. A parts list for fungal cellulosomes revealed by comparative genomics. ==Nature Microbiology==, 2017, 2. doi.org/10.1038/nmicrobiol.2017.87.

14. Blow M, Clark T, Daum C, Deutschbauer A, Fomenkov A, Fries R, Froula JL, Kang D, Malmstrom R, Morgan R, Posfai J, Singh K, Visel A, Wetmore K, ==Zhao Z==, Rubin E, Korlach J, Pennacchio L, Roberts, Richard. The Epigenomic Landscape of Prokaryotes. ==PLOS genetics==. 2016, 12.e1005854.10.1371/ journal. pgen.1005854.

15. Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, ==Zhao Z==, Dang D, Underwood J, Grigoriev IV, Figueroa M, Schilling JS, Chen F, Wang Z. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing, ==PLOS ONE==, 2015, 10(7): e0132628.

16. ==Zhao Z==, Tsai YC, Clum A, Munson K, Daum C, Turner SW, Korlach J, Pennacchio LA, Chen F, PacBio only Assembly with Low Genomic DNA Input, ==eScholarship.org==, 2013

17. Peng Z*, ==Zhao Z*==, Clum A, Pennacchio LA, Chen F., Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach, ==PLOS One==, 2012, Jan 09

* co-first author