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 Accepted/In Press

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 Accepted/In Press 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 Accepted/In Press 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 Accepted/In Press 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