Articles

2023

25. Transcriptomics elucidates metabolic regulation and functional promoters in the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938

E.E. Tobin*, J.H. Collins*, C.B. Marsan, G.T. Nadeau, K. Mori, A. Lipzen, S. Mondo, I.V. Grigoriev, E.M. Young
* = equal contribution
Preprint, under review

24. A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris

B. Yang, B. Vaisvil, D. Schmitt, J.H. Collins, E.M. Young, V. Kapatral, R. Rao
Preprint, under review

23.  Systematic part transfer by extending a modular toolkit to diverse bacteria

K.W. Keating and E.M. Young
ACS Synthetic Biology
bioRxiv

22.  Microstructure properties of optically clear bacterial cellulose produced using an alternative carbon source  

E.M. van Zyl, M.A. Kennedy, W. Nason, R. Liu, S.J. Fenlon, E.M. Young, L.J. Smith, S.R. Bhatia, and J.M. Coburn
Biomaterials Advances

21.  Genetic basis for probiotic phenotypes revealed by nanopore sequencing

J.H. Collins*, L. Kunyeit*, S. Weintraub, N. Sharma, C. White, N. Haq, K.A. Anu-Appaiah, R.P. Rao*, and E.M. Young*
* = equal contribution
Genes, Genomes, Genetics

20. Draft genome of the Ogataea polymorpha type strain CBS 4732

J.H. Collins and E.M. Young
Microbiology Resource Announcements.

2022

19. Discovering content through text mining for a Synthetic Biology Knowledge System

B.T. McInnes, J.S. Downie, Y. Hao, J. Jett, K. Keating, G. Nakum, S. Ranjan, N.E. Rodriguez, J. Tang, D. Xiang, E.M. Young, and M.H. Nguyen
ACS Synthetic Biology

18. Multicolor plater reader fluorescence calibration

J. Beal, C.A. Telmer, A. Vignoni, Y. Boada, G.S. Baldwin, L. Hallett, T. Lee, V. Selvarajah, S. Billerbeck, B. Brown, G. Cai, L. Cai, E. Eisenstein, D. Kiga, D. Ross, N. Alperovich, N. Sprent, J. Thompson, E.M. Young, D. Endy, T. Haddock-Angelli
Synthetic Biology

2021

17. Engineered yeast genomes accurately assembled from pure and mixed samples

J. H. Collins, K. W. Keating, T. R. Jones, S. Balaji, C. B. Marsan, M. Como, Z. J. Newlon, T. Mitchell, B. Bartley, A. Adler, N. Roehner, and E. M. Young 
​Nature Communications

16. Secondary metabolite production in plant cell culture: a new epigenetic frontier (Book Chapter)

C. Brzycki, E. M. Young, and S. Roberts
Ed. Sonia Malik
Exploring Plant Cells for the Production of Compounds of Interest, ISBN: 9783030582708​

15. Synthetic Biology Knowledge System

J. Mante, Y. Hao, J. Jett, U. Joshi, K.W. Keating, X. Lu, G. Nakum, N.E. Rodriguez, J. Tang, L. Terry, X. Wu, E. Yu, J.S. Downie, B.T. McInnes, M.H. Nguyen, B. Sepulvado, E.M. Young, and C.J. Myers
ACS Synthetic Biology

14. Curation principles derived from the analysis of the SBOL iGEM dataset

J. Mante, N. Roehner, K.W. Keating, J. McLaughlin, E.M. Young, J. Beal, C.J. Myers​
ACS Synthetic Biology

2020

13.  Genetic circuit design automation for yeast

Y. Chen, S. Zhang, E. M. Young, T. S. Jones, D. Densmore, and C. A. Voigt
Nature Microbiology

2019

12. Synthetic biology for bio-derived structural materials ​(Review)

K. W. Keating and E. M. Young 
Current Opinion in Chemical Engineering

2018

11. Genetic engineering of host organisms for pharmaceutical synthesis ​(Review)

J. H. Collins and E. M. Young 
Current Opinion in Biotechnology

10. Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast

E. M. Young, Z. Zhao, B. E. M. Gielesen, L. Wu, D. B. Gordon, J. A. Roubos, C. A. Voigt
Metabolic Engineering

9. A pressure test to make 10 molecules in 90 days: External evaluation of methods to engineer biology​

A. Casini*, F.-Y. Chang*, R. Eleure*, A. King*, E. M. Young*, Q. M. Dudley, A. Karim, K. Pratt, C.  Bristol, A. Forget, A. Ghodasara, R. Warden-Rothman, R. Gan, A. Cristofaro, A. E. Borujeni, M.-H. Ryu, J. Li, Y.-C. Kwon, H. Wang, E. Tatsis, C. Rodriguez-Lopez, S. O’Connor, M. H. Mdema, M. A. Fischbach, M. C. Jewett, C. A. Voigt , and D. B. Gordon           (* = Equal contribution)
Journal of the American Chemical Society

2017

8. Formation of nitrogenase nifDK tetramers in the mitochondria of Saccharomyces cerevisiae

S. Buren, E. M. Young, E. Sweeny, C. A. Voigt, and L. Rubio
ACS Synthetic Biology

2016

7. DoubleDutch: a tool for designing combinatorial libraries of metabolic pathway variants

N. Roehner, E. M. Young, C. A. Voigt, D. B. Gordon, and D. Densmore
​ACS Synthetic Biology

2015

6. Chapter 12: Remaining challenges in the metabolic engineering of yeasts for biofuels (Book Chapter)

S.-M. Lee, E. M. Young, and H. S. Alper
Editor: M. E. Himmel
Direct Microbial Conversion of Biomass to Advanced Biofuels, ISBN: 9780444595928​

2014

5. Rewiring yeast sugar transporter preference through modifying a conserved protein motif

E. M. Young, A. Tong, H. Bui, C. Spofford, and H. S. Alper
Proceedings of the National Academies of Science of the United States of America

2012

4. A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae

E. M. Young, A. D. Comer, H. Huang, and H. S. Alper
Metabolic Engineering

2011

3. Functional survey for heterologous sugar transport proteins, using Saccharomyces cerevisiae as a host

E. M. Young, A. Poucher, A. D. Comer, A. Bailey, and H. S. Alper
Applied and Environmental Microbiology

2010

2. Synthetic biology: Tools to design, build, and optimize cellular processes  (Review)

E. M. Young and H. S. Alper
Journal of Biomedicine and Biotechnology

1. Optimizing pentose utilization in yeast: the need for novel tools and approaches (Review​)

E. M. Young, S.-M. Lee, and H. S. Alper
​Biotechnology for Biofuels

Patents

2. ​Methods for Engineering Sugar Transporter Preferences

H. S. Alper and E. M. Young
Board of Regents, University of Texas System
​​U.S. Patent #9,926,347
​WO2015069796

1. Engineered Xylose Transporters with Reduced Glucose Inhibition

H. S. Alper, E. M. Young, and S.-M. Lee
Board of Regents, University of Texas System
​U.S. Patent #9,695,223
WO2015179701