A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids
- Sierra M Brooks, Celeste Marsan, Kevin B Reed, …, Nathan Ballinger, Alshakim Nelson, Hal S Alper
- Nat Commun, 10.1038/s41467-023-40242-9
Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction
- Widianti Sugianto, Gokce Altin-Yavuzarslan, Benjamin I Tickman, …, Hal S Alper, Alshakim Nelson, James M Carothers
- None, 10.1016/j.mtbio.2023.100677
Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica
- Emily K Bowman, Phuong T Nguyen Hoang, Angela R Gordillo Sierra, …, Angela R Gordillo Sierra, Karoline M Vieira Nogueira, Hal S Alper
- Lab Chip, 10.1039/d3lc00020f
Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica
- Ya-Hue Valerie Soong, Sarah M Coleman, Na Liu, …, Carl Lawton, Hal S Alper, Dongming Xie
- Biotechnol Adv, 10.1016/j.biotechadv.2023.108128
Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing
- Blake J Rasor, Ashty S Karim, Hal S Alper, …, Ashty S Karim, Hal S Alper, Michael C Jewett
- ACS Synth Biol, 10.1021/acssynbio.2c00685
Complementary actions of finerenone and SGLT2-i on renal outcomes?: An urgent need for more information
- Eleni Rebelos, Nikolaos Tentolouris, Eleni Rebelos, …, Nikolaos Tentolouris, Eleni Rebelos, Nikolaos Tentolouris
- Nephrology (Carlton), 10.1111/nep.14124
Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs
- Kristin V Presnell, Omar Melhem, Nicholas J Morse, …, Omar Melhem, Nicholas J Morse, Hal S Alper
- ACS Synth Biol, 10.1021/acssynbio.2c00327
Valorization of Caribbean Sargassum biomass as a source of alginate and sugars for de novo biodiesel production
- Angela R Gordillo Sierra, Luis Fernando Amador-Castro, Andreé E RamÃrez-Partida, Tomás GarcÃa-Cayuela, Danay Carrillo-Nieves, Hal S Alper
- J Environ Manage, 10.1016/j.jenvman.2022.116364
Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism
- Cheng Cheng, Wei-Bin Wang, Meng-Lin Sun, …, Long Bai, Hal S Alper, Xin-Qing Zhao
- None, 10.3389/fmicb.2022.960114
Using fungible biosensors to evolve improved alkaloid biosyntheses
- Wantae Kim, Nathaniel T Burkholder, Kamyab Javanmardi, …, Yan Zhang, Hal S Alper, Andrew D Ellington
- Nat Chem Biol, 10.1038/s41589-022-01072-w
Machine learning-aided engineering of hydrolases for PET depolymerization
- Hongyuan Lu, Daniel J Diaz, Natalie J Czarnecki, …, Nathaniel A Lynd, Andrew D Ellington, Hal S Alper
- Nature, 10.1038/s41586-022-04599-z
Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level
- Shenghu Zhou, Hal S Alper, Jingwen Zhou, …, Hal S Alper, Jingwen Zhou, Yu Deng
- Crit Rev Biotechnol, 10.1080/07388551.2022.2040415
Shifting the distribution: modulation of the lipid profile in Yarrowia lipolytica via iron content
- Lauren T Cordova, Claire M Palmer, Hal S Alper
- Appl Microbiol Biotechnol, 10.1007/s00253-022-11800-w
Evolving a Generalist Biosensor for Bicyclic Monoterpenes
- Simon d’Oelsnitz, Vylan Nguyen, Hal S Alper, Andrew D Ellington
- ACS Synth Biol, 10.1021/acssynbio.1c00402
Enabling commercial success of industrial biotechnology
- Bradley W Biggs, Hal S Alper, Brian F Pfleger, …, Christine N S Santos, Parayil Kumaran Ajikumar, Gregory Stephanopoulos
- Science, 10.1126/science.abj5040
Mapping enzyme catalysis with metabolic biosensing
- Linfeng Xu, Kai-Chun Chang, Emory M Payne, …, Robert T Kennedy, Dale S Cornett, Adam R Abate
- Nat Commun, 10.1038/s41467-021-27185-9
Microbial valorization of underutilized and nonconventional waste streams
- Beena C Lad, Sarah M Coleman, Hal S Alper
- J Ind Microbiol Biotechnol, 10.1093/jimb/kuab056
An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts
- Blake J Rasor, Xiunan Yi, Hunter Brown, …, Hunter Brown, Hal S Alper, Michael C Jewett
- Nat Commun, 10.1038/s41467-021-25233-y
Development of a growth coupled and multi-layered dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin biosynthesis in Escherichia coli
- Shenghu Zhou, Shuo-Fu Yuan, Priya H Nair, Hal S Alper, Yu Deng, Jingwen Zhou
- Metab Eng, 10.1016/j.ymben.2021.05.007
Genome Engineering of Yarrowia lipolytica with the PiggyBac Transposon System
- James M Wagner, Claire M Palmer, Maya V Venkataraman, …, Eden V Williams, Xiunan Yi, Hal S Alper
- Methods Mol Biol, 10.1007/978-1-0716-1414-3_1
Applications, challenges, and needs for employing synthetic biology beyond the lab
- Sierra M Brooks, Hal S Alper, Sierra M Brooks, Hal S Alper
- Nat Commun, 10.1038/s41467-021-21740-0
Bioproduced Proteins On Demand (Bio-POD) in hydrogels using Pichia pastoris
- Shuo-Fu Yuan, Sierra M Brooks, Annalee W Nguyen, …, Jennifer A Maynard, Alshakim Nelson, Hal S Alper
- None, 10.1016/j.bioactmat.2021.01.019
Valorization of pelagic sargassum biomass into sustainable applications: Current trends and challenges
- Fernando Amador-Castro, Tomás GarcÃa-Cayuela, Hal S Alper, Verónica Rodriguez-Martinez, Danay Carrillo-Nieves
- J Environ Manage, 10.1016/j.jenvman.2021.112013
Bio-synthesis of food additives and colorants-a growing trend in future food
- Lichao Sun, Fengjiao Xin, Hal S Alper
- Biotechnol Adv, 10.1016/j.biotechadv.2020.107694
Design, Evolution, and Characterization of a Xylose Biosensor in Escherichia coli Using the XylR/ xylO System with an Expanded Operating Range
- Rui-Qi Tang, James M Wagner, Hal S Alper, Xin-Qing Zhao, Feng-Wu Bai
- ACS Synth Biol, 10.1021/acssynbio.0c00225
Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach
- Emily K Bowman, Matthew Deaner, Jan-Fang Cheng, …, Ernst Oberortner, Yasuo Yoshikuni, Hal S Alper
- Proc Natl Acad Sci U S A, 10.1073/pnas.2007413117
Non-conventional hosts for the production of fuels and chemicals
- Lichao Sun, Hal S Alper
- Curr Opin Chem Biol, 10.1016/j.cbpa.2020.03.004
Compartmentalized microbes and co-cultures in hydrogels for on-demand bioproduction and preservation
- Trevor G Johnston, Shuo-Fu Yuan, James M Wagner, …, Patrick Smith, Alshakim Nelson, Hal S Alper
- Nat Commun, 10.1038/s41467-020-14371-4
Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications
- Emily K Bowman, Hal S Alper
- Trends Biotechnol, 10.1016/j.tibtech.2019.11.002
Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome
- Ruiqi Tang, Peiliang Ye, Hal S Alper, Zhanying Liu, Xinqing Zhao, Fengwu Bai
- Appl Microbiol Biotechnol, 10.1007/s00253-019-10161-1
Yarrowia lipolytica: more than an oleaginous workhorse
- Kelly K Miller, Hal S Alper
- Appl Microbiol Biotechnol, 10.1007/s00253-019-10200-x
Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae
- Matthew Deaner, Hal S Alper
- FEMS Yeast Res, 10.1093/femsyr/foz076
Systems Metabolic Engineering Approaches for Rewiring Cells
- Hal S Alper, Christoph Wittmann
- Biotechnol J, 10.1002/biot.201900312
Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica
- Kevin B Reed, James M Wagner, Simon d’Oelsnitz, Joshua M Wiggers, Hal S Alper
- J Ind Microbiol Biotechnol, 10.1007/s10295-019-02228-9
Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica
- Cory Schwartz, Jan-Fang Cheng, Robert Evans, …, Hal S Alper, Yasuo Yoshikuni, Ian Wheeldon
- Metab Eng, 10.1016/j.ymben.2019.06.007
Design and Evaluation of Synthetic Terminators for Regulating Mammalian Cell Transgene Expression
- Joseph K Cheng, Nicholas J Morse, James M Wagner, Scott K Tucker, Hal S Alper
- ACS Synth Biol, 10.1021/acssynbio.8b00285
Design and synthesis of synthetic UP elements for modulation of gene expression in Escherichia coli
- Kristin V Presnell, Madeleine Flexer-Harrison, Hal S Alper
- None, 10.1016/j.synbio.2019.04.002
Metabolic engineering of microbial cell factories for production of nutraceuticals
- Shuo-Fu Yuan, Hal S Alper
- Microb Cell Fact, 10.1186/s12934-019-1096-y
CRISPR-PIN: Modifying gene position in the nucleus via dCas9-mediated tethering
- Jyun-Liang Lin, Holly Ekas, Matthew Deaner, Hal S Alper
- None, 10.1016/j.synbio.2019.02.001
Recent advancements in fungal-derived fuel and chemical production and commercialization
- Holly Ekas, Matthew Deaner, Hal S Alper
- Curr Opin Biotechnol, 10.1016/j.copbio.2018.08.014
