Hal S Alper

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 62

Top Topics

Machine Learning

Saccharomyces Cerevisiae

Top Venues

Nature communications

ACS synthetic biology

Proceedings of the National Academy of Sciences of the United States of America

Applied microbiology and biotechnology

This page only lists publications with an associated author ORCID identifier.

Publications

Kevin B Reed, Wantae Kim, Hongyuan Lu, Clayton T Larue, Shirley Guo, Sierra M Brooks, Michael R Montez, James W Wagner, Yan Jessie Zhang, Hal S Alper
Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Kevin B Reed, Wantae Kim, Hongyuan Lu, Clayton T Larue, Shirley Guo, Sierra M Brooks, Michael R Montez, James W Wagner, Yan Jessie Zhang, Hal S Alper
Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Amelia R Bergeson, Ashli J Silvera, Hal S Alper
Bottlenecks in biobased approaches to plastic degradation. Nature communications 15 (1) (2024)
Kevin B Reed, Simon d'Oelsnitz, Sierra M Brooks, Jordan Wells, Minye Zhao, Adit Trivedi, Selina Eshraghi, Hal S Alper
Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS synthetic biology (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Amelia R Bergeson, Ashli J Silvera, Hal S Alper
Bottlenecks in biobased approaches to plastic degradation. Nature communications 15 (1) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
Author Correction: A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Kevin B Reed, Simon d'Oelsnitz, Sierra M Brooks, Jordan Wells, Minye Zhao, Adit Trivedi, Selina Eshraghi, Hal S Alper
Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS synthetic biology 13 (4) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
Author Correction: A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Kevin B Reed, Simon d'Oelsnitz, Sierra M Brooks, Jordan Wells, Minye Zhao, Adit Trivedi, Selina Eshraghi, Hal S Alper
Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS synthetic biology 13 (4) (2024)
Amelia R Bergeson, Ashli J Silvera, Hal S Alper
Bottlenecks in biobased approaches to plastic degradation. Nature communications 15 (1) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Amelia R Bergeson, Ashli J Silvera, Hal S Alper
Bottlenecks in biobased approaches to plastic degradation. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Kevin B Reed, Simon d'Oelsnitz, Sierra M Brooks, Jordan Wells, Minye Zhao, Adit Trivedi, Selina Eshraghi, Hal S Alper
Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS synthetic biology 13 (4) (2024)
Kevin B Reed, Wantae Kim, Hongyuan Lu, Clayton T Larue, Shirley Guo, Sierra M Brooks, Michael R Montez, James W Wagner, Yan Jessie Zhang, Hal S Alper
Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system. Proceedings of the National Academy of Sciences of the United States of America 121 (35) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Kevin B Reed, Sierra M Brooks, Jordan Wells, Kristin J Blake, Minye Zhao, Kira Placido, Simon D'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, Hal S Alper
A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Simon D'Oelsnitz, Daniel J Diaz, Wantae Kim, Daniel J Acosta, Tyler L Dangerfield, Mason W Schechter, Matthew B Minus, James R Howard, Hannah Do, James M Loy, Hal S Alper, Yan Jessie Zhang, Andrew D Ellington
Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nature communications 15 (1) (2024)
Blake J Rasor, Ashty S Karim, Hal S Alper, Michael C Jewett
Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS synthetic biology (2023)
Sarah M Coleman, Lauren T Cordova, Beena C Lad, Sabah A Ali, Esha Ramanan, James R Collett, Hal S Alper
Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste. Applied microbiology and biotechnology 107 (5-6) (2023)
Sarah M Coleman, Lauren T Cordova, Beena C Lad, Sabah A Ali, Esha Ramanan, James R Collett, Hal S Alper
Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste. Applied microbiology and biotechnology (2023)
Blake J Rasor, Ashty S Karim, Hal S Alper, Michael C Jewett
Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS synthetic biology 12 (3) (2023)
Gokce Altin-Yavuzarslan, Naroa Sadaba, Sierra M Brooks, Hal S Alper, Alshakim Nelson
Engineered Living Material Bioreactors with Tunable Mechanical Properties using Vat Photopolymerization. Small (Weinheim an der Bergstrasse, Germany) 20 (22) (2023)
Sarah M Coleman, Lauren T Cordova, Beena C Lad, Sabah A Ali, Esha Ramanan, James R Collett, Hal S Alper
Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste. Applied microbiology and biotechnology 107 (5-6) (2023)
Sierra M Brooks, Celeste Marsan, Kevin B Reed, Shuo-Fu Yuan, Dustin-Dat Nguyen, Adit Trivedi, Gokce Altin-Yavuzarslan, Nathan A Ballinger, Alshakim Nelson, Hal S Alper
A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids. Nature communications 14 (1) (2023)
Emily K Bowman, Phuong T Nguyen Hoang, Angela R Gordillo Sierra, Karoline M Vieira Nogueira, Hal S Alper
Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica . Lab on a chip (2023)
Blake J Rasor, Ashty S Karim, Hal S Alper, Michael C Jewett
Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS synthetic biology 12 (3) (2023)
Sarah M Coleman, Lauren T Cordova, Beena C Lad, Sabah A Ali, Esha Ramanan, James R Collett, Hal S Alper
Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste. Applied microbiology and biotechnology 107 (5-6) (2023)
Gokce Altin-Yavuzarslan, Naroa Sadaba, Sierra M Brooks, Hal S Alper, Alshakim Nelson
Engineered Living Material Bioreactors with Tunable Mechanical Properties using Vat Photopolymerization. Small (Weinheim an der Bergstrasse, Germany) (2023)
Xiunan Yi, Hal S Alper
Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications. Life (Basel, Switzerland) 12 (4) (2022)
Simon D'Oelsnitz, Wantae Kim, Nathaniel T Burkholder, Kamyab Javanmardi, Ross Thyer, Yan Jessie Zhang, Hal S Alper, Andrew D Ellington
Using fungible biosensors to evolve improved alkaloid biosyntheses. Nature chemical biology 18 (9) (2022)
Sierra M Brooks, Kevin B Reed, Shuo-Fu Yuan, Gokce Altin-Yavuzarslan, Ryan Shafranek, Alshakim Nelson, Hal S Alper
Enhancing long-term storage and stability of engineered living materials through desiccant storage and trehalose treatment. Biotechnology and bioengineering (2022)
Kristin V Presnell, Omar Melhem, Nicholas J Morse, Hal S Alper
Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs. ACS synthetic biology 11 (10) (2022)
Emily K Bowman, James M Wagner, Shuo-Fu Yuan, Matthew Deaner, Claire M Palmer, Simon D'Oelsnitz, Lauren T Cordova, Xin Li, Frank F Craig, Hal S Alper
Sorting for secreted molecule production using a biosensor-in-microdroplet approach. Proceedings of the National Academy of Sciences of the United States of America 118 (36) (2022)
Simon D'Oelsnitz, Vylan Nguyen, Hal S Alper, Andrew D Ellington
Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS synthetic biology 11 (1) (2022)
Hongyuan Lu, Daniel J Diaz, Natalie J Czarnecki, Congzhi Zhu, Wantae Kim, Raghav Shroff, Daniel J Acosta, Bradley R Alexander, Hannah O Cole, Yan Jessie Zhang, Nathaniel A Lynd, Andrew D Ellington, Hal S Alper
Machine learning-aided engineering of hydrolases for PET depolymerization. Nature 604 (7907) (2022)
Beena C Lad, Sarah M Coleman, Hal S Alper
Microbial valorization of underutilized and nonconventional waste streams. Journal of industrial microbiology & biotechnology (2021)
Linfeng Xu, Kai-Chun Chang, Emory M Payne, Cyrus Modavi, Leqian Liu, Claire M Palmer, Nannan Tao, Hal S Alper, Robert T Kennedy, Dale S Cornett, Adam R Abate
Mapping enzyme catalysis with metabolic biosensing. Nature communications 12 (1) (2021)
Sierra M Brooks, Hal S Alper
Applications, challenges, and needs for employing synthetic biology beyond the lab. Nature communications 12 (1) (2021)
Blake J Rasor, Xiunan Yi, Hunter Brown, Hal S Alper, Michael C Jewett
An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nature communications 12 (1) (2021)
Rui-Qi Tang, James M Wagner, Hal S Alper, Xin-Qing Zhao, Feng-Wu Bai
Design, Evolution, and Characterization of a Xylose Biosensor in Escherichia coli Using the XylR/xylO System with an Expanded Operating Range. ACS synthetic biology 9 (10) (2020)
Emily K Bowman, Matthew Deaner, Jan-Fang Cheng, Robert Evans, Ernst Oberortner, Yasuo Yoshikuni, Hal S Alper
Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach. Proceedings of the National Academy of Sciences of the United States of America 117 (31) (2020)
Shuo-Fu Yuan, Xiunan Yi, Trevor G Johnston, Hal S Alper
De novo resveratrol production through modular engineering of an Escherichia coli-Saccharomyces cerevisiae co-culture. Microbial cell factories 19 (1) (2020)
Joseph K Cheng, Nicholas J Morse, James M Wagner, Scott K Tucker, Hal S Alper
Design and Evaluation of Synthetic Terminators for Regulating Mammalian Cell Transgene Expression. ACS synthetic biology 8 (6) (2019)
Kevin B Reed, James M Wagner, Simon d'Oelsnitz, Joshua M Wiggers, Hal S Alper
Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica. Journal of industrial microbiology & biotechnology 46 (12) (2019)
Kelly K Miller, Hal S Alper
Yarrowia lipolytica: more than an oleaginous workhorse. Applied microbiology and biotechnology 103 (23-24) (2019)
Haibo Li, Hal S Alper
Producing Biochemicals in Yarrowia lipolytica from Xylose through a Strain Mating Approach. Biotechnology journal 15 (2) (2019)
Shuo-Fu Yuan, Hal S Alper
Metabolic engineering of microbial cell factories for production of nutraceuticals. Microbial cell factories 18 (1) (2019)
Tengfei Niu, Yanfeng Liu, Jianghua Li, Mattheos A G Koffas, Guocheng Du, Hal S Alper, Long Liu
Engineering a Glucosamine-6-phosphate Responsive glmS Ribozyme Switch Enables Dynamic Control of Metabolic Flux in Bacillus subtilis for Overproduction of N-Acetylglucosamine. ACS synthetic biology 7 (10) (2018)
Kelly A Markham, Hal S Alper
Engineering Yarrowia lipolytica for the production of cyclopropanated fatty acids. Journal of industrial microbiology & biotechnology 45 (10) (2018)
Lauren T Cordova, Hal S Alper
Production of α-linolenic acid in Yarrowia lipolytica using low-temperature fermentation. Applied microbiology and biotechnology 102 (20) (2018)
Kelly A Markham, Claire M Palmer, Malgorzata Chwatko, James M Wagner, Clare Murray, Sofia Vazquez, Arvind Swaminathan, Ishani Chakravarty, Nathaniel A Lynd, Hal S Alper
Rewiring Yarrowia lipolytica toward triacetic acid lactone for materials generation. Proceedings of the National Academy of Sciences of the United States of America 115 (9) (2018)
Claire M Palmer, Hal S Alper
Navigating genetic diversity by painting the bacteria red. Proceedings of the National Academy of Sciences of the United States of America 115 (43) (2018)
Nicholas J Morse, James M Wagner, Kevin B Reed, Madan R Gopal, Lars H Lauffer, Hal S Alper
T7 Polymerase Expression of Guide RNAs in vivo Allows Exportable CRISPR-Cas9 Editing in Multiple Yeast Hosts. ACS synthetic biology 7 (4) (2018)
Matthew Deaner, Julio Mejia, Hal S Alper
Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae. ACS synthetic biology 6 (10) (2017)
Nicholas J Morse, Madan R Gopal, James M Wagner, Hal S Alper
Yeast Terminator Function Can Be Modulated and Designed on the Basis of Predictions of Nucleosome Occupancy. ACS synthetic biology 6 (11) (2017)
John M Leavitt, James M Wagner, Cuong C Tu, Alice Tong, Yanyi Liu, Hal S Alper
Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae. Biotechnology journal 12 (10) (2017)