171.   Kevin Reed, Sierra Brooks, Jordan Wells, Kristin Blake, Minye Zhao, Kira Placido, Simon d'Oelsnitz, Adit Trivedi, Shruti Gadhiyar, and Hal Alper, 2024. A Modular and Synthetic Biosynthesis Platform for de novo Production of Diverse Halogenated Tryptophan-Derived Molecules Nature Communications 15, 3188. Link to paper

170.   Kristin Presnell, Omar Melhem, Sarah Coleman, Nicholas Morse, and Hal Alper, 2024. Design and synthesis of synthetic promoters for consistency of gene expression across growth phases and scale in S. cerevisiae Synthetic and Systems Biotechnology Accepted/In Press. Link to paper

169.   Kevin Reed, Simon d’Oelsnitz, Sierra Brooks, Jordan Wells, Minye Zhao, Adit Trivedi, Selina Eshraghi, and Hal Alper, 2024. Fluorescence-based Screens for engineering enzymes linked to halogenated tryptophan ACS Synthetic Biology Accepted/In Press. Link to paper

168.   Celeste Marsan, Sung Gyung Lee, Ankim Nguyen, Angela Gordillo-Sierra, Sarah Coleman, Sierra Brooks, and Hal Alper, 2024. Leveraging a Yarrowia lipolytica naringenin chassis for biosynthesis of apigenin and associated glucoside isovitexin Metabolic Engineering Accepted/In Press. Link to paper

167.   Andreé E. Ramírez-Partida, Luis Fernando Amador-Castro, Tomás García-Cayuela, Hal Alper, and Danay Carrillo-Nieves, 2024. Towards a biorefinery processing Sargassum seaweed: Techno- economic assessment of alginate and fucoidan production through SuperPro Designer® process simulation Environmental Technology & Innovation Accepted/In Press. Link to paper

166.   Simon d’Oelsnitz, Daniel Diaz, Mason Schechter, Daniel Acosta, Matthew Minus, James Howard, James Loy, Hannah Do, Hal Alper, and Andrew Ellington, 2024. Biosensor and Machine Learning-Aided Engineering of an Amaryllidaceae Enzyme Nature Communications 15, 2084. Link to paper

165.   Gokce Altin-Yavuzarslan, Naroa Sadaba, Sierra Brooks, Hal Alper, and Alshakim Nelson, 2024. Engineered Living Material Bioreactors with Tunable Mechanical Properties using Vat Photopolymerization Small Accepted/In Press. Link to paper


164.   Daniel Acosta and Hal Alper, 2023. Advances in enzymatic and organismal technologies for the recycling and upcycling of petroleum-derived plastic waste Current Opinion in Biotechnology 84:103021 Link to paper

163.   Xiunan Yi, Blake Rasor, Nathalie Boadi, Katherine Louie, Trent Northen, Ashty Karim, Michael Jewett, and Hal Alper, 2023. Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping Metabolic Engineering 80, 241-253. Link to paper

162.   Sierra Brooks, Celeste Marsan, Kevin Reed, Shuo-Fu Yuan, Dustin-Dat Nguyen, Adit Trivedi, Gokce Altin-Yavuzarslan, Nathan Ballinger, Alshakim Nelson, and Hal Alper, 2023. A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids Nature Communications 14, 4448 (2023). Link to paper

161.   Widianti Sugianto, Gokce Altin-Yavuzarslan, Benjamin Tickman, Cholpisit Kiattisewee, Shuo-Fu Yuan, Sierra Brooks, Jitkanya Wong, Hal Alper, Alshakim Nelson, and James Carothers, 2023. Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction Materials Today Bio 20, 100677. Link to paper

160.   Emily Bowman, Phuong Nguyen Hoang, Angela Gordillo Sierra, Karoline Nogueira, and Hal Alper, 2023. Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica Lab on a Chip 23, 2249 – 2256. Link to paper

159.   Ya-Hue Valerie Soong, Sarah Coleman, Na Liu, Jiansong Qin, Carl Lawton, Hal Alper, and Dongming Xie, 2023. Using Oils and Fats to Replace Sugars as Feedstocks for Biomanufacturing: Challenges and Opportunities for the Yeast Yarrowia lipolytica Biotechnology Advances 65, 108128.Link to paper

158.   Gokce Altin-Yavuzarslan, Sierra Brooks, Shuo-Fu Yuan, James Park, Hal Alper, and Alshakim Nelson, 2023. Additive Manufacturing of Engineered Living Materials with Bio- Augmented Mechanical Properties and Resistance to Degradation Advanced Functional Materials 330(24), 2300332. Link to paper

157.   Blake Rasor, Ashty Karim, Hal Alper, and Michael Jewett, 2023. Cell extracts from bacteria and yeast retain metabolic activity after extended storage and repeated thawing ACS Synthetic Biology 12(3), 904–908. Link to paper

156.   Sarah Coleman, Lauren Cordova, Beena Lad, Sabah Ali, Esha Ramanan, James Collett, and Hal Alper, 2023. Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste Applied Microbiology and Biotechnology 107, 2011–2025. Link to paper

155.   Sierra Brooks, Kevin Reed, Shuo-Fu Yuan, Ryan Shafranek, Gokce Altin-Yavuzarslan, Alshakim Nelson, and Hal Alper, 2023. Enhancing long-term storage and stability of engineered living materials through desiccant storage and trehalose treatment Biotechnology and Bioengineering 120(2), 572-582. Link to paper


154.   Kristin Presnell, Omar Melhem, Nicholas Morse, and Hal Alper, 2022. Modular, synthetic Boolean logic gates enabled in Saccharomyces cerevisiae through T7 polymerases / CRISPR dCas9 designs ACS Synthetic Biology 11(10), 3414–3425. Link to paper

153.   Angela R. Gordillo Sierra, Luis Fernando Amador-Castro, Andreé E. Ramírez-Partida, Tomás García-Cayuela, Danay Carrillo-Nieves, and Hal Alper, 2022. Valorization of Caribbean Sargassum biomass as a source of alginate and sugars for de novo biodiesel production Journal of Environmental Management 324, 116364. Link to paper

152.   Shuo-Fu Yuan, Priya Nair, Dominic Borbon, Sarah Coleman, Po-Hsun Fan, Wen-Ling Lin, and Hal Alper, 2022. Metabolic engineering of E. coli for β-alanine production using a multi-biosensor enabled approach Metabolic Engineering 74, 24-35. Link to paper

151.   Cheng Cheng, Wei-Bin Wang, Meng-Lin Sun, Rui-Qi Tang, Long Bai, Hal Alper and Xinqing Zhao, 2022. Deletion of NGG1 in the recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism Frontiers in Microbiology 13:960114. Link to paper

150.   Simon d’Oelsnitz, Wantae Kim, Nathaniel Burkholder, Kamyab Javanmardi, Ross Thyer, Yan Zhang, Hal Alper, Andrew Ellington, 2022. Using fungible biosensors to evolve improved alkaloid biosyntheses Nature Chemical Biology 18, 981–989. Link to paper

149.   Hongyuan Lu, Daniel Diaz, Natalie Czarnecki, Congzhi Zhu, Wantae Kim, Raghav Shroff, Daniel Acosta, Brad Alexander, Hannah Cole, Yan Jessie Zhang, Nathaniel Lynd, Andrew Ellington, and Hal Alper, 2022. Machine learning-aided engineering of hydrolases for PET depolymerization Nature 604, 662–667 Link to paper

148.   Shenghu Zhou, Hal Alper, Jingwen Zhou, and Yu Deng, 2022. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level Critical Reviews in Biotechnology 10.1080/07388551.2022.2040415, 1-18 Link to paper

147.   Xiunan Yi and Hal Alper, 2022. Considering strain variation and non-type strains for yeast metabolic engineering applications Life 12 (4), 10.3390/life12040510 Link to paper

146.   Lauren Cordova, Claire Palmer, and Hal Alper, 2022. Shifting the Distribution: Modulation of the Lipid Profile in Yarrowia lipolytica via Iron Content Applied Microbiology and Biotechnology 106, 1571–1581 Link to paper

145.   Simon d’Oelsnitz, Vylan Nguyen, Hal Alper, Andrew Ellington, 2022. Evolving a generalist biosensor for bicyclic monoterpenes ACS Synthetic Biology 11 (1), 265–272. Link to paper

144.   Kelly Miller, Sarah Springthorpe, Jennifer Imbrogno, David Walker, Shruti Gadiyar, Benjamin Keitz, Andrew Ellington, Nathaniel Lynd, and Hal Alper, 2022. Biocompatible materials enabled by bio-based production of pyomelanin isoforms using an engineered Yarrowia lipolytica Advanced Functional Materials 32 (7), 2109366. Link to paper


143.   Linfeng Xu, Kai-Chun Chang, Emory Payne, Cyrus Modavi, Leqian Liu, Claire Palmer, Nannan Tao, Hal Alper, Robert Kennedy, Dale Cornett and Adam Abate, 2021. Mapping enzyme catalysis with metabolic biosensing Nature Communications 12, 6803(2021). Link to paper

142.   Beena Lad, Sarah Coleman, and Hal Alper, 2021. Microbial valorization of underutilized and nonconventional waste streams Journal of Industrial Microbiology and Biotechnology kuab056. Link to paper

141.   Emily Bowman, James Wagner, Shuo-Fu Yuan, Matt Deaner, Claire Palmer, Simon D’Oelsnitz, Lauren Cordova, Xin Li, Frank F. Craig and Hal Alper, 2021. Sorting for secreted molecule production using a biosensor-in-microdroplet approach PNAS 118 (36) e2106818118. Link to paper

140.   Blake Rasor, Xiunan Yi, Hunter Brown, Hal Alper, and Michael Jewett, 2021. An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts Nature Communications 12, 5139. Link to paper

139.   Lauren Cordova, Hannah Walton, Eletria Biswas, Khristal Monroe, Rafael Quirino, and Hal Alper, 2021. A data-driven approach to decipher the role of triglyceride composition on thermo-mechanical properties of thermosetting polymers using vegetable and microbial oils ACS Applied Polymer Materials 3 (9), 4485–4494 Link to paper

138.   Shenghu Zhou, Shuo-Fu Yuan, Priya Nair, Hal Alper, Yu Deng, and Jingwen Zhou, 2021. Development of a growth coupled and multi-layered dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin biosynthesis in Escherichia coli Metabolic Engineering 67, 41-52. Link to paper

137.   Kevin Reed and Hal Alper, 2021. Modular biocatalysis for polyamines Nature Catalysis 4, 449-450. Link to paper

136.   James Wagner, Claire Palmer, Maya Venkataraman, Lars Lauffer, Joshua Wiggers, Eden Williams, Xiunan Yi, and Hal Alper, 2021. Genome Engineering of Yarrowia lipolytica with the PiggyBac Transposon System, Yarrowia lipolytica: methods and protocols, ed. Ian Wheeldon and Mark Blenner. Methods in Molecular Biology Series Volume 2307, 1-24. Link to paper

135.   Sierra Brooks and Hal Alper, 2021. Applications, challenges, and needs for employing synthetic biology beyond the lab Nature Communications 12, 1390 Link to paper

134.   Fernando Amador-Castro, Tomás García-Cayuela, Hal Alper, Veronica Rodriguez-Martinez, and Danay Carrillo-Nieves, 2021. Valorization of pelagic Sargassum biomass into sustainable applications: current trends and challenges Journal of Environmental Management 283, 112013 Link to paper

133.   Shuo-Fu Yuan, Sierra Brooks, Annalee Nguyen, Wen-Ling Lin, Trevor Johnston, Jennifer Maynard, Alshakim Nelson, and Hal Alper, 2021. Bioproduced Proteins On Demand (Bio-POD) in hydrogels using Pichia pastoris Bioactive Materials 6 (8), 2390-2399 Link to paper

132.   Lichao Sun, Fengjiao Xin, and Hal Alper, 2021. Bio-synthesis of food additives and colorants-a growing trend in future food Biotechnology Advances 47, 107694 Link to paper


131.   Rui-Qi Tang, James M. Wagner, Hal S. Alper, Xin-Qing Zhao, and Feng-Wu Bai, 2020. 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), 2714–2722 Link to paper

130.   Emily Bowman, Matthew Deaner, Jan-Fang Cheng, Robert Evans, Ernst Oberortner, Yasuo Yoshikuni, and Hal Alper, 2020. Bi-directional Titration of Yeast Gene Expression using a Pooled CRISPR Guide RNA Approach PNAS 117 (31) 18424-18430 Link to paper

129.   Angela Gordillo Sierra and Hal Alper, 2020. Progress in the metabolic engineering of bio-based lactams and their ω-amino acids precursors Biotechnology Advances 43, 107587 Link to paper

128.   Shuo-Fu Yuan, Xiunan Yi, Trevor Johnston, and Hal Alper, 2020. De novo resveratrol production through modular engineering of an Escherichia coli–Saccharomyces cerevisiae co-culture Microbial Cell Factories 19, 143 (2020) Link to paper

127.   Lauren Cordova, Beena Lad, Sabah Ali, Andrew Schmidt, Justin Billing, Kyle Pomraning, Beth Hofstad, Marie Swita, James Collett, and Hal Alper, 2020. Valorizing a Hydrothermal Liquefaction Aqueous Phase through co-production of chemicals and lipids using the oleaginous yeast Yarrowia lipolytica Bioresource Technology 313, 123639 Link to paper

126.   Lichao Sun and Hal Alper, 2020. Non-conventional hosts for the production of fuels and chemicals Current Opinion in Chemical Biology 59, 15-22 Link to paper

125.   Trevor Johnston, Shuo-Fu Yuan, James Wagner, Xiunan Yi, Abhijit Saha, Patrick Smith, Alshakim Nelson and Hal Alper, 2020. Compartmentalized microbes and co-cultures in hydrogels for on-demand bioproduction and preservation Nature Communications 11, 563 (2020) Link to paper

124.   Claire Palmer, Kelly Miller, Ankim Nguyen, and Hal Alper, 2020. Engineering 4-coumaroyl-CoA derived polyketide production in Yarrowia lipolytica through a b-oxidation mediated strategy Metabolic Engineering 57, 174-181 Link to paper

123.   Emily Bowman and Hal Alper, 2020. Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications Trends in Biotechnology 38(7), 701-714 Link to paper

122.   Lauren Cordova, Jonathan Butler, and Hal Alper, 2020. Direct production of fatty alcohols from glucose using engineered strains of Yarrowia lipolytica Metabolic Engineering Communications 10, e00105 Link to paper

121.   Haibo Li and Hal Alper, 2020. Producing biochemicals in Yarrowia lipolytica from xylose through a strain mating approach Biotechnology Journal 15(2), 1900304 Link to paper

120.   Shuo-Fu Yuan and Hal Alper, 2020. Improving Spinach2- and Broccoli-based biosensors for single and double analytes Biotechnology Notes 1, 2-8 Link to paper


119.   Matthew Deaner and Hal Alper, 2019. Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae FEMS Yeast Research 19(7), foz076 Link to paper

118.   Kelly Miller and Hal Alper, 2019. Yarrowia lipolytica: More Than an Oleaginous Workhorse Applied Microbiology and Biotechnology 103(23-24), 9251–9262 Link to paper

117.   Ruiqi Tang, Peiliang Ye, Hal Alper, Zhanying Liu, Xinqing Zhao, and Fengwu Bai, 2019. Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome Applied Microbiology and Biotechnology 103(23-24) 9465–9477 Link to paper

116.   James Wagner, Kevin Reed, Simon d’Oelsnitz, Joshua Wiggers, and Hal Alper, 2019. Improving Ionic Liquid Tolerance in Saccharomyces cerevisiae Through Heterologous Expression and Directed Evolution of an ILT1 Homolog from Yarrowia lipolytica Journal of Industrial Microbiology and Biotechnology 46(12), 1715–1724 Link to paper

115.   Cory Schwartz, Jan-Fang Cheng, Robert Evans, Christopher Schwartz, James Wagner, Scott Anglin, Adam Beitz, Weihua Pan, Stefano Lonardi, Mark Blenner, Hal Alper, Yasuo Yoshikuni, and Ian Wheeldon, 2019. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica Metabolic Engineering 55, 102-110 Link to paper

114.   Joseph Cheng, Nicholas Morse, James Wagner, Scott Tucker, and Hal Alper, 2019. Design and evaluation of synthetic terminators for regulating mammalian cell transgene expression ACS Synthetic Biology 8(6), 1263-1275 Link to paper

113.   Kristin Presnell, Madeleine Flexer-Harrison, and Hal Alper, 2019. Design and synthesis of synthetic UP elements for modulation of gene expression in Escherichia coli Synthetic and Systems Biotechnology 4(2), 99–106 Link to paper

112.   Kristin Presnell and Hal Alper, 2019. Systems Metabolic Engineering Meets Machine Learning: A new era for data-driven metabolic engineering Biotechnology Journal 14(9), 1800416 Link to paper

111.   Shuo-Fu Yuan and Hal Alper, 2019. Metabolic engineering of microbial cell factories for production of nutraceuticals Microbial Cell Factories 18:46 Link to paper

110.   Jyun-Liang Lin, Holly Ekas, Matthew Deaner, and Hal Alper, 2019. CRISPR-PIN: Modifying gene position in the nucleus via dCas9-mediated tethering Synthetic and Systems Biotechnology 4(2), 73-78 Link to paper

109.   Hui Wei, Wei Wang, Hal S. Alper, Qi Xu, Eric P. Knoshaug, Stefanie Van Wychen, Chien-Yuan Lin, Yonghua Luo, Stephen R. Decker, Michael E. Himmel, and Min Zhang, 2019. Ameliorating the metabolic burden of the co-expression of secreted fungal cellulases in a high lipid-accumulating Yarrowia lipolytica strain by medium C/N ratio and a chemical chaperone Frontiers in Microbiology 9:3276 Link to paper

108.   Holly Ekas, Matthew Deaner, and Hal Alper, 2019. Recent advancements in fungal-derived fuel and chemical production and commercialization Current Opinion in Biotechnology 57, 1-9 Link to paper

107.   Shenghu Zhou and Hal Alper, 2018. Strategies for directed and adapted evolution as part of microbial strain engineering Journal of Chemical Technology and Biotechnology 94(2), 366-376  Link to paper

106.   Claire Palmer and Hal Alper, 2018. Expanding the chemical palette of industrial microbes: metabolic engineering for type III PKS-derived polyketides Biotechnology Journal 14(1), 1700463 Link to paper


105.   Claire Palmer and Hal Alper, 2018. Navigating genetic diversity by painting the bacteria red PNAS 115(43), 10824-10826 Link to paper

104.   Lauren Cordova and Hal Alper, 2018. Production of α-linolenic acid in Yarrowia lipolytica using a low temperature fermentation Applied Microbiology and Biotechnology 102(20), 8809–8816 Link to paper

103.   Tengfei Niu, Yanfeng Liu, Jianghua Li, Mattheos Koffas, Guocheng Du, Hal Alper, Jian Chen, Long Liu, 2018. 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), 2423-2435 Link to paper

102.   Shuo-Fu Yuan, Teng-Chieh Hsu, Chun-An Wang, Ming-Feng Jang, Yang-Cheng Kuo, Hal Alper, Gia-Luen Guo, and Wen-Song Hwang, 2018. Production of optically pure L(+)-Lactic acid from waste plywood chips using an isolated thermotolerant Enterococcus faecalis SI at a pilot scale Journal of Industrial Microbiology and Biotechnology 45(11), 961–970 Link to paper

101.   Jyun-Liang Lin, Holly Ekas, Kelly Markham and Hal Alper, 2018. An enzyme-coupled assay enables rapid protein engineering for geraniol production in yeast Biochemical Engineering Journal 139, 95-100 Link to paper

100.   Kelly Markham and Hal Alper, 2018. Engineering Yarrowia lipolytica for the production of cyclopropanated fatty acids Journal of Industrial Microbiology and Biotechnology 45(10), 881–888 Link to paper

99.   Ahmad Abdel-Mawgoud, Kelly Markham, Claire Palmer, Nian Liu, Gregory Stephanopoulos, and Hal Alper, 2018. Metabolic engineering in the host Yarrowia lipolytica Metabolic Engineering 50, 192-208 Link to paper

98.   Kelly Markham, Sofia Vazquez, and Hal Alper, 2018. High efficiency transformation of Yarrowia lipolytica using electroporation FEMS Yeast Research 18(7), foy081 Link to paper

97.   Kelly Markham and Hal Alper, 2018. Synthetic biology expands the industrial potential of Yarrowia lipolytica Trends in Biotechnology 36(10), 1085-1095 Link to paper

96.   James Wagner, Leqian Liu, Shuo-Fu Yuan, Maya Venkataraman, Adam Abate, and Hal Alper, 2018. A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: riboflavin overproduction in Yarrowia lipolytica Metabolic Engineering 47, 346-356 Link to paper

95.   Matthew Deaner, Allison Holzman, and Hal Alper, 2018. Modular Ligation Extension of Guide RNA Operons (LEGO) for multiplexed dCas9 regulation of metabolic pathways in Saccharomyces cerevisiae Biotechnology Journal 13(9) Link to paper

94.   Liang Xiong, Yu Zeng, Ruiqi Tang, Hal Alper, Fengwu Bai, and Xinqing Zhao, 2018. Condition-specific promoter activities in Saccharomyces cerevisiae Microbial Cell Factories 17:58 Link to paper

93.   Nicholas Morse, James Wagner, Kevin Reed, Madan Gopal, Lars Lauffer, and Hal Alper, 2018. T7 Polymerase Expression of Guide RNAs in vivo Allows Exportable CRISPR-Cas9 Editing in Multiple Yeast Hosts ACS Synthetic Biology 7(4), 1075-1084 Link to paper

92.   James Wagner, Eden Williams, and Hal Alper, 2018. Developing a piggyBac transposon system and compatible selection markers for insertional mutagenesis and genome engineering in Yarrowia lipolytica Biotechnology Journal 13(5), 1800022 Link to paper

91.   Kelly Markham, Claire Palmer, Malgorzata Chwatko, James Wagner, Clare Murray, Sofia Vazquez, Arvind Swaminathan, Ishani Chakravarty, Nathaniel Lynd, and Hal Alper, 2018. Rewiring Yarrowia lipolytica toward triacetic acid lactone for novel materials generation PNAS 115 (9) 2096-2101 Link to paper

90.   Ja Kyong Ko, Je Hyeong Jung, Fredy Altpeter, Hal Alper, Youngsoon Um, and Sun-Mi Lee, 2018. Largely enhanced bioethanol production through the combined use of lignin-modified sugarcane and xylose fermenting yeast strain Bioresource Technology 256, 312-320 Link to paper

89.   Kevin Reed and Hal Alper, 2018. Expanding beyond canonical metabolism: interfacing alternative elements, synthetic biology, and metabolic engineering Synthetic and Systems Biotechnology 3(1), 20-33 Link to paper

88.   Kristin Presnell and Hal Alper, 2018. Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: Promoter and aptamer designs Molecular Systems Design & Engineering 3, 19 - 37 Link to paper


87.   Nicholas Morse, Madan Gopal, James Wagner, and Hal Alper, 2017. Yeast terminator function can be modulated and designed based on predictions of nucleosome occupancy ACS Synthetic Biology 6 (11), 2086-2095 Link to paper

86.   Matthew Deaner, Julio Mejia, and Hal Alper, 2017. Enabling graded and large-scale multiplex of desired genes using a dual-mode dCas9 activator in Saccharomyces cerevisiae ACS Synthetic Biology 6 (10), 1931-1943 Link to paper

85.   Jyun-Liang Lin, James M. Wagner, Hal S. Alper, 2017. Enabling Tools for High-throughput Detection of Metabolites: Metabolic Engineering and Directed Evolution Applications Biotechnology Advances 35(8), 950-970 Link to paper

84.   Joseph Abatemarco, Maen Sarhan, James Wagner, Jyun-Liang Lin, Leqian Liu, Wafa Hassouneh, Shuo-Fu Yuan, Hal Alper, and Adam Abate. RNA-Aptamer-In-Droplet (RAPID) High-Throughput Screening of Secretory Phenotypes Nature Communications 8, 332 Link to paper

83.   Kelly Markham, Lauren Cordova, Andrew Hill, and Hal Alper, 2017. Yarrowia lipolytica as a Cell Factory for Oleochemical Biotechnology Handbook of Hydrocarbon and Lipid Microbiology, 1-18 Link to paper

82.   John Leavitt, James Wagner, Cuong Chi Tu, Alice Tong, Yanyi Liu, and Hal Alper, 2017. Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae Biotechnology Journal 12(10), 1600687 Link to paper

81.   Matthew Deaner and Hal Alper, 2017. Systematic Testing of Enzyme Perturbation Sensitivities via Graded dCas9 Modulation Metabolic Engineering 40, 14-22 Link to paper

80.   Jie Sun and Hal Alper, 2017. Synthetic Biology: An Emerging Approach for Strain Engineering Industrial Biotechnology: Microorganisms, 85-110 Link to paper


79.   Haibo Li, Olivia Schmitz, and Hal Alper, 2016. Enabling glucose/xylose co-transport in yeast through the directed evolution of a sugar transporter Applied Microbiology and Biotechnology 100(23), 10215-10223 Link to paper

78.   Nathan Crook, Joseph Abatemarco, Jie Sun, James Wagner, Alexander Schmitz, and Hal Alper, 2016. in vivo continuous evolution of genes and pathways in yeast Nature Communications 7, 13051 Link to paper

77.   Lauren Cordova and Hal Alper, 2016. Central metabolic nodes for diverse biochemical production Current Opinion in Chemical Biology 35, 37-42 Link to paper

76.   Nathan Crook, Jie Sun, Nicholas Morse, Alexander Schmitz, and Hal Alper, 2016. Identification of gene knockdown targets conferring enhanced isobutanol and 1-butanol tolerance to Saccharomyces cerevisiae using a tunable RNAi screening approach Applied Microbiology and Biotechnology 100(23), 10005-10018 Link to paper

75.   Matthew Deaner and Hal Alper, 2016. Promoter and Terminator Discovery and Engineering Advances in Biochemical Engineering/Biotechnology, 1-24 Link to paper

74.   Haibo Li and Hal Alper, 2016. Enabling xylose utilization in Yarrowia lipolytica for lipid production Biotechnology Journal 11(9), 1230-1240 Link to paper

73.   Joseph Cheng and Hal Alper, 2016. Transcriptomics-guided design of synthetic promoters for a mammalian system ACS Synthetic Biology 5(12), 1455-1465 Link to paper

72.   Joseph Cheng, Amanda Lewis, Do Soon Kim, Timothy Dyess, and Hal Alper, 2016. Identifying and Retargeting Transcriptional Hot Spots in the Human Genome Biotechnology Journal 11(8), 1100-1109 Link to paper

71.   John Leavitt, Alice Tong, Joyce Tong, Jonathan Pattie, and Hal Alper, 2016. Coordinated Transcription Factor and Promoter Engineering to Establish Strong Expression Elements in Saccharomyces cerevisiae Biotechnology Journal 11(7), 866-876 Link to paper

70.   Jinsuk Lee, Nathan Crook, Jie Sun, and Hal S. Alper, 2016. Improvement of lactic acid production by a deletion of ssb1 in Saccharomyces cerevisiae, Journal of Industrial Microbiology and Biotechnology 43(1), 87-96 Link to paper

69.   Sun-mi Lee, Taylor Jellison, and Hal Alper, 2016. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae, Applied Microbiology and Biotechnology 100(5), 2487-2498 Link to paper

68.   James Wagner and Hal Alper, 2015, Synthetic Biology and Molecular Genetics in Non-Conventional Yeasts: Current Tools and Future Advances, Fungal Genetics and Biology 89, 126-136 Link to paper

67.   Nicholas Morse and Hal Alper, 2016, Gene Expression Engineering, Metabolic Engineering for Bioprocess Commercialization, 7-30 Link to paper


66.   John Blazeck, Andrew Hill, Mariam Jamoussi, Anny Pan, Jarrett Miller, and Hal Alper, 2015. Metabolic Engineering of Yarrowia lipolytica for itaconic acid production. Metabolic Engineering 32, 66-73 Link to paper

65.   Leqian Liu, Kelly Markham, John Blazeck, Nijia Zhou, Dacia Leon, Peter Otoupal, and Hal Alper, 2015. Surveying the lipogenesis landscape in Yarrowia lipolytica through understanding the function of a Mga2p regulatory protein mutant. Metabolic Engineering 31, 102-111 Link to paper

64.   Heidi Redden and Hal Alper, 2015. The development and characterization of synthetic minimal yeast promoters. Nature Communications 6:7810 Link to paper

63.   Leqian Liu, Anny Pan, Caitlin Spofford, Nijia Zhou, and Hal Alper, 2015. An Evolutionary Metabolic Engineering Approach for Enhancing Lipogenesis in Yarrowia lipolytica. Metabolic Engineering 29, 36-45 Link to paper

62.   Kathleen Curran, Nicholas Morse, Kelly Markham, Allison Wagman, Akash Gupta, and Hal Alper, 2015. Short, Synthetic Terminators for Improved Heterologous Gene Expression in Yeast. ACS Synthetic Biology 4(7), 824-832 Link to paper

61.   Kelly Markham and Hal Alper, 2015. Synthetic Biology for Specialty Chemicals. Annual Review of Chemical and Biomolecular Engineering 6, 35-52 Link to paper

60.   Sun-mi Lee, Taylor Jellison, and Hal Alper, 2015. Xylan catabolism is improved by blending bioprospecting and metabolic pathway engineering in Saccharomyces cerevisiae. Biotechnology Journal 10:575 Link to paper

59.   John Leavitt and Hal Alper, 2015. Advances and Current Limitations in Transcript-Level Control of Gene Expression. Current Opinion in Biotechnology 34, 98-104 Link to paper

58.   Heidi Redden, Nicholas Morse, and Hal Alper, 2015. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Research 15(1), 1-10 Link to paper


57.   Jie Sun and Hal Alper, 2014. Metabolic Engineering of Strains: from industrial-scale to lab-scale chemical production. Journal of Industrial Microbiology and Biotechnology 42(3), 423-436 Link to paper

56.   Leqian Liu, Peter Otoupal, Anny Pan, and Hal Alper, 2014. Increasing expression level and copy number of a Yarrowia lipolytica plasmid through regulated centromere function. FEMS Yeast Research 14(7), 1124-1127 Link to paper

55.   Sun-mi Lee, Taylor Jellison, and Hal Alper, 2014. Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnology for Biofuels 7:122 Link to paper

54.   Leqian Liu and Hal S. Alper, 2014. Draft genome sequence of the oleaginous yeast Yarrowia lipolytica PO1f, a commonly used metabolic engineering host. Genome Announcements 2(4), e00652-14 Link to paper

53.   John Blazeck, Jarrett Miller, Anny Pan, Jon Gengler, Clinton Holden, Mariam Jamoussi, and Hal Alper, 2014. Metabolic Engineering of Saccharomyces cerevisiae for itaconic acid production. Applied Microbiology and Biotechnology 98(19), 8155-8164 Link to paper

52.   Joseph Cheng and Hal Alper, 2014. The genome editing toolbox: A spectrum of approaches for targeted modification. Current Opinion in Biotechnology 30, 87-94 Link to paper

51.   Kathleen Curran, Nathan Crook, Ashty Karim, Akash Gupta, Allison Wagman, and Hal Alper, 2014. Design of synthetic yeast promoters via tuning of nucleosome architecture. Nature Communications 5:4002 Link to paper

50.   Amanda Lanza, Kathleen Curran, Lindsey Rey, and Hal Alper, 2014. A Condition-Specific Codon Optimization Approach for Improved Heterologous Gene Expression in Saccharomyces cerevisiae. BMC Systems Biology 8:33 Link to paper

49.   John Blazeck, Andrew Hill, Leqian Liu, Rebecca Knight, Jarrett Miller, Anny Pan, Peter Otoupal, and Hal Alper, 2014. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nature Communications 5:3131 Link to paper

48.   Nathan Crook, Alexander Schmitz, and Hal Alper, 2014. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synthetic Biology 3(5), 307–313 Link to paper

47.   Eric Young, Alice Tong, Hang Bui, Caitlin Spofford, and Hal Alper, 2014. Rewiring yeast sugar transporter preference through modifying a conserved protein motif. PNAS 111(1), 131-136. Link to paper


46.   Kathleen Curran, Ashty Karim, Akash Gupta, and Hal Alper, 2013. Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metabolic Engineering 19, 88-97. Link to paper

45.   Joseph Abatemarco, Andrew Hill, and Hal Alper, 2013. Expanding the Metabolic Engineering Toolbox with Directed Protein Evolution. Biotechnology Journal 8(12), 1397-1410 Link to paper

44.   John Blazeck, Leqian Liu, Rebecca Knight, and Hal Alper, 2013. Heterologous Production of Pentane in the Oleaginous Yeast Yarrowia lipolytica. Journal of Biotechnology 165(3-4), 184-194 Link to paper

43.   Leqian Liu, Heidi Redden, and Hal Alper, 2013. Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces. Current Opinion in Biotechnology 24(6), 1023-1030 Link to paper

42.   Amanda Lanza, Do Soon Kim, and Hal Alper, 2013. Evaluating the Influence of Selection Markers on Obtaining Selected Pools and Stable Cell Lines in Human Cells. Biotechnology Journal 8(7), 811-821 Link to paper

41.   Nathan Crook and Hal Alper, 2013. Model-Based Design of Synthetic, Biological Systems. Chemical Engineering Science 103, 15 November 2013, 2-11. Link to paper

40.   Kathleen Curran, John Leavitt, Ashty Karim, and Hal Alper, 2013. Metabolic Engineering of Muconic Acid Production in Saccharomyces cerevisiae. Metabolic Engineering 15(1), 55-66 Link to paper

39.   Nathan Crook and Hal Alper, 2013. Classical Strain Improvement. Engineering Complex Phenotypes in Industrial Strains, First Edition 1-33. Edited by Ranjan Patnaik. John Wiley & Sons, Inc. Link to paper

38.   Ashty Karim, Kathleen Curran, and Hal Alper, 2013. Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications. FEMS Yeast Research 13(1), 107-116. Link to paper

37.   John Blazeck, Ben Reed, Rishi Garg, Rachelle Gerstner, Annie Pan, Vaibhav Agarwala, and Hal Alper, 2013. Generalizing a Hybrid Synthetic Promoter Approach in Yarrowia lipolytica. Applied Microbiology and Biotechnology 97(7), 3037-3052 Link to paper

36.   John Blazeck and Hal Alper, 2013. Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnology Journal 8(1), 46-58. Link to paper


35.   Amanda Lanza, Joseph Cheng, and Hal Alper, 2012. Emerging Synthetic Biology Tools for Engineering Mammalian Cell Systems and Expediting Cell Line Development. Current Opinion in Chemical Engineering 1(4), 403-410, November 2012. Link to paper

34.   Sun-mi Lee, Taylor Jellison, and Hal Alper, 2012. Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae. Applied and Environmental Microbiology 78(16), 5708-5716 Link to paper

33.   John Blazeck, Rishi Garg, Ben Reed, and Hal Alper, 2012. Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnology and Bioengineering 109(11), 2884-2895 Link to paper

32.   Amanda Lanza, Timothy Dyess, and Hal Alper, 2012. Using the Cre/lox System for Targeted Integration into the Human Genome: loxFAS-loxP Pairing and Delayed Introduction of Cre DNA Improve Gene Swapping Efficiency. Biotechnology Journal 7(7), 898-908 Link to paper

31.   Kathleen Curran and Hal Alper, 2012. Expanding the Chemical Palate of Cells by Combining Systems Biology and Metabolic Engineering. Metabolic Engineering 14(4), 289-297 Link to paper

30.   Amanda Lanza, John Blazeck, Nathan Crook, and Hal Alper, 2012. Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach. PLoS ONE 7(4), e36193. Link to paper

29.   Eric Young, Austin Comer, Huashu Huang, and Hal Alper, 2012. A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae. Metabolic Engineering 14(4), 401-411 Link to paper

28.   Ben Reed, John Blazeck, and Hal Alper, 2012. Evolution of an Alkane-Inducible Biosensor for Increased Responsiveness to Short-Chain Alkanes. Journal of Biotechnology 158(3), 75-79. Link to paper

27.   Amanda Lanza, Nathan Crook, and Hal Alper, 2012. Innovation at the Intersection of Synthetic and Systems Biology. Current Opinion in Biotechnology 23(5), 712-717. Link to paper

26.   Kathleen Curran, Nathan Crook, and Hal Alper, 2012. Using Flux Balance Analysis to Guide Microbial Metabolic Engineering. Methods in Molecular Biology v. 834: Microbial Metabolic Engineering 197-216. Link to paper

25.   Amanda Lanza and Hal Alper, 2012. Using Transcription Machinery to Elicit Complex Cellular Phenotypes. Methods in Molecular Biology v. 813: Synthetic Gene Networks 229-248. Link to paper


24.   John Blazeck, Leqian Liu, Heidi Redden, and Hal Alper, 2011. Tuning Gene Expression in Yarrowia lipolytica using a Hybrid Promoter Approach. Applied and Environmental Microbiology 77(42), 7905-7914. Link to paper

23.   Nathan Crook, Elizabeth Freeman, and Hal Alper, 2011. Re-Engineering Multicloning Sites for Function and Convenience. Nucleic Acids Research 39(14), e92. Link to paper

22.   Amanda Lanza and Hal Alper, 2011. Global Strain Engineering by Mutant Transcription Factors. Methods in Molecular Biology v. 765: Strain Engineering 253-274. Link to paper

21.   Eric Young, Ashley Poucher, Austin Comer, Alexandra Bailey, and Hal Alper, 2011. Functional Survey for Heterologous Sugar Transport Proteins using Saccharomyces cerevisiae as a Host. Applied and Environmental Microbiology 77(10), 3311-3319. Link to paper

20.   Leqian Liu, Ben Reed, and Hal Alper, 2011. From pathways to genomes and beyond: The Metabolic Engineering toolbox and its place in biofuels production. GREEN - The International Journal on Sustainable Energy Conversion and Storage 1(1), 81-95. Link to paper


19.   Eric Young, Sun-Mi Lee and Hal Alper, 2010. Optimizing Pentose Utilization in Yeast: the Need for Novel Tools and Approaches. Biotechnology for Biofuels 3(24) Link to paper

18.   John Blazeck and Hal Alper, 2010. Systems Metabolic Engineering: Genome-Scale Models and Beyond. Biotechnology Journal 5(7), 647-659. Link to paper

17.   Eric Young and Hal Alper, 2010. Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes. Journal of Biomedicine and Biotechnology 2010, #130781. Link to paper


16.   Hal Alper and Gregory Stephanopoulos, 2009. Engineering microbes for biofuels: Exploiting innate cellular capacity or importing biosynthetic potential? Nature Reviews Microbio 7(10), 715-723. Link to paper

15.   Joel Moxley, Michael Jewett, Silas Villas-Boas, Maciek Antoniewicz, Hal Alper, Robert Wheeler, Alan Hinnebusch, Trey Ideker, Jens Nielsen, and Gregory Stephanopoulos, 2009 Linking high resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. PNAS 106(16), 6477-6482. Link to paper


14.   Huimin Yu, Keith Tyo, Hal Alper, Daniel Klein-Marcuschamer, and Gregory Stephanopoulos, 2008. A High Throughput Screen for Hyaluronic Acid Accumulation in Recombinant Escherichia coli Transformed by Libraries of Engineered Transcription Factors. Biotech Bioeng 101(4), 788-796. Link to paper

13.   Hal Alper and Gregory Stephanopoulos, 2008. Uncovering the gene knockout landscape for improved lycopene production in E. coli. Appl Micro Biotech 78(5), 801-810. Link to paper


12.   Hal Alper and Gregory Stephanopoulos, 2007. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng. 9(3), 258-267. Link to paper

11.   Keith Tyo, Hal Alper, and Gregory Stephanopoulos, 2007. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotech. 25(3), 132-137. Link to paper


10.   Hal Alper, Joel Moxley, Elke Nevoigt, Gerald Fink, and Gregory Stephanopoulos, 2006. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314(5805), 1565 - 1568. Link to paper

9.   Elke Nevoigt, Jessica Kohnke, Curt Fischer, Hal Alper, Ulf Stahl and Gregory Stephanopoulos, 2006. Engineering of promoter replacement cassettes for tuning gene expression in yeast. Appl Environ Microbiol 72(8), 5266-5273. Link to paper

8.   Hal Alper, Kohei Miayaoku, and Gregory Stephanopoulos, 2006. Characterization of lycopene overproducing E. coli strains in high cell density fermentations. Appl Micro Biotech 72(5), 968-974. Link to paper

7.   Kyle Jensen*, Hal Alper*, Curt Fischer, and Gregory Stephanopoulos, 2006. Identifying functionally-important mutations from phenotypically diverse sequence data. Appl Environ Microbiol 72(5), 3696-3701. *Equal contribution Link to paper


6.   Hal Alper, Curt Fischer, Elke Nevoigt, and Gregory Stephanopoulos, 2005. Tuning Genetic Control through Promoter Engineering. PNAS. 102(36), 12678-12683. Link to paper

5.   Hal Alper, Kohei Miyaoku, and Gregory Stephanopoulos, 2005. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnology. 23(5), 612 - 616. Link to paper

4.   Hal Alper, Yong-su Jin, Joel Moxley, and Gregory Stephanopoulos, 2005. Identifying gene targets for the metabolic engineering of Escherichia coli. Metab Eng. 7(3), 155-164. Link to paper

3.   Yong-Su Jin*, Hal Alper*, Yea-Tyng Yang and Gregory Stephanopoulos, 2005. Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol 71(12), 8249-8256. *Equal contribution Link to paper


2.   Hal Alper and Gregory Stephanopoulos, 2004. Metabolic Engineering Challenges in the Post-Genomic Era. Chemical Engineering Science. 59(22/23), 5009-5017. Link to paper

1.   Gregory Stephanopoulos, Hal Alper, and Joel Moxley, 2004. Exploiting Biological Complexity for Strain Improvement through Systems Biology. Nat Biotechnology. 22(10), 1261-1267. Link to paper

Non-Peer Reviewed

5.   Hal Alper, 2012. Converting Cells into Cellular Factories. Computational and Structural Biotechnology Journal 3(4), e201210001 Link to paper

4.   Hal Alper and Wilfried Weber, 2012. Building synthetic cell systems from the ground up. Current Opinion in Biotechnology 23(5), 641-643 Link to paper

3.   Hal Alper, Patrick Cirino, Elke Nevoigt, and Ganesh Sriram, 2010. Applications of Synthetic Biology in Microbial Biotechnology. Journal of Biomedicine and Biotechnology 2010, #918391. Link to paper

2.   John Blazeck and Hal Alper, 2010. Uncovering latent xylose utilization potential in Saccharomyces cerevisiae. Biofuels 1(5), 681-684. Link to paper

1.   Curt Fischer, Hal Alper, Elke Nevoigt, and Gregory Stephanopoulos, 2006. Response to Hammer et al.: Tuning genetic control - importance of thorough promoter characterization versus generating promoter diversity. Trends Biotech 24(2), 55-56. Link to paper