Alper, Hal Ph.D.

Z.D. Bonner Professorship in Chemical Engineering

Office: CPE 5.408 Mailing Address:
Phone: (512) 471-4417 The University of Texas at Austin
Fax: (512) 471-7060 McKetta Department of Chemical Engineering
Email: 200 E Dean Keeton St. Stop C0400
UT Mail: C0400 Austin, TX 78712-1589

Research Areas: Biotechnology and Energy

Research Group Website

Educational qualifications

Ph.D., Chemical Engineering, Massachusetts Institute of Technology  (2006)
B.S., Chemical Engineering, University of Maryland, College Park (2002)
Postdoctoral Research Associate, Whitehead Institute for Biomedical Research (2006-2008)
Postdoctoral Research Associate, Shire Human Genetic Therapies (2007-2008)

Courses Taught

CHE 317 Introduction to Chemical Engineering Analysis
CHE 372 Chemical Reactor Analysis and Design
CHE 379/384 Biochemical, Cellular, and Metabolic Engineering: Principles and Practices
UGS 302 Freshman Signature Course: Engineering Biology: Prospects for biofuels to biomedicine
CHE 185 Graduate Student Seminar Series


Biotechnology, Metabolic and Cellular Engineering, Biofuels, Synthetic Biology, and Systems Biology.


Our group focuses on engineering biology to produce organic molecules of interest such as biofuels, commodity and specialty chemicals, and protein pharmaceuticals.  To accomplish these tasks, traditional pathway engineering approaches are merged with novel synthetic biology tools, protein engineering strategies, systems biology paradigms and applied genetic engineering capabilities.  We utilize a variety of host systems including microbial (eg. Escherichia coli), fungal (eg. the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica), and mammalian cells (eg. Chinese Hamster Ovary (CHO) cells and Human HEK293) to produce a diverse array of products.  Specifically, our lab focusses on developing the methodologies and tools for altering cells and “hijacking” basic metabolism.  The goal is to “rewire” cellular systems into industrially-relevant biochemical factories.  In doing so, we are heavily invested in developing novel synthetic biology and directed evolution approaches aimed at increasing our capacity to engineer cells.

Awards & Honors

Society for Industrial Microbiology and Biotechnology Young Investigator Award (2015)
Jay Bailey Young Investigator Award in Metabolic Engineering (2014)
Camille Dreyfus Teacher-Scholar Award (2014)
Biotechnology and Bioengineering Daniel I.C. Wang Award (2013)
Regents’ Outstanding Teaching Award (selected by the UT System) (2012)
Office of Naval Research Young Investigator Award (2011)
DuPont Young Professor Award (2010)
Invited Participant, National Academies Keck Futures Initiative Conference, Synthetic Biology: Building on Nature’s Inspiration (2009)
Protégé, The 6th Annual Conference of The Academy of Medicine, Engineering & Science of Texas-attendance based on nomination by National Academy Member (2009)
Texas Exes Teaching Award (2008)
Camille and Henry Dreyfus New Faculty Award (2008)
Merck Student/Young Investigator Poster Award for Best Poster (Metabolic Engineering Conference, 2004)


Selected Publications

  • Heidi Redden and Hal Alper, The development and characterization of synthetic minimal yeast promoters, Nature Communications, 6:7810, July 2015.
  • Kathleen Curran, Nicholas Morse, Kelly Markham, Allison Wagman, Akash Gupta, and Hal Alper, 2105, Short, Synthetic Terminators for Improved Heterologous Gene Expression in Yeast, ACS Synthetic Biology, 4(7), 824–832, July 2015.
  • Leqian Liu, Anny Pan, Caitlin Spofford, Nijia Zhou, and Hal Alper, An Evolutionary Metabolic Engineering Approach for Enhancing Lipogenesis in Yarrowia lipolytica, Metabolic Engineering, 29, 36-45, May 2015.
  • 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, May 2014.
  • John Blazeck, Andrew Hill, Leqian Liu, Rebecca Knight, Jarrett Miller, Anny Pan, Peter Otoupal, and Hal Alper, Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production, Nature Communications, 5:3131, January 2014.
  • Eric Young, Alice Tong, Hang Bui, Caitlin Spofford, and Hal Alper, Rewiring yeast sugar transporter preference through modifying a conserved protein motif, PNAS, 111(1), 131-136, January 2014.
  • Kathleen Curran, John Leavitt, Ashty Karim, and Hal Alper, Metabolic Engineering of Muconic Acid Production in Saccharomyces cerevisiae, Metabolic Engineering, 15(1), 55-66, January 2013.
  • John Blazeck, Rishi Garg, Ben Reed, and Hal Alper, Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters, Biotechnology and Bioengineering, 109(11), 2884-2895, November, 2012.
  •  Sun-mi Lee, Taylor Jellison, and Hal Alper, Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae, Applied and Environmental Microbiology, 78(16), 5708-5716, August 2012.
  • Eric Young, Austin Comer, Huashu Huang, and Hal Alper, A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae, Metabolic Engineering, 14(4), 401-411, July 2012.
  • Amanda Lanza, John Blazeck, Nathan Crook, and Hal Alper, Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach, PLoS ONE, 7(4), e36193, April 2012.
  • John Blazeck, Leqian Liu, Heidi Redden, and Hal Alper, Tuning Gene Expression in Yarrowia lipolytica using a Hybrid Promoter Approach, Applied and Environmental Microbiology, 77(22), 7905–7914, November 2011.
  • Nathan Crook, Elizabeth Freeman, and Hal Alper, Re-engineering Multicloning Sites for Function and Convenience, Nucleic Acids Research, doi: 10.1093/nar/gkr346, May 2011.
  • Eric Young, Ashley Poucher, Austin Comer, Alexandra Bailey, and Hal Alper, Functional Survey for Heterologous Sugar Transport Proteins, using Saccharomyces cerevisiae as a Host, Applied and Environmental Microbiology, 77(10), 3311–3319, May 2011.
  • John Blazeck and Hal Alper, Systems Metabolic Engineering: Genome-Scale Models and Beyond, Biotechnology Journal, 5(7), 647-659, July 2010.
  • Hal Alper and Gregory Stephanopoulos, Engineering microbes for biofuels: Exploiting innate cellular capacity or importing biosynthetic potential?, Nature Reviews Microbiology, 7(10), 715-723, October 2009.
  • Hal Alper, Joel Moxley, Elke Nevoigt, Gerald Fink, and Gregory Stephanopoulos, Engineering yeast transcription machinery for improved ethanol tolerance and production, Science, 314(5805), 1565 – 1568, December 2006.
  • Hal Alper, Curt Fischer, Elke Nevoigt, and Gregory Stephanopoulos, Tuning Genetic Control through Promoter Engineering, PNAS, 102(36), 12678-12683, September 2006.
  • Hal Alper, Kohei Miyaoku, and Gregory Stephanopoulos, Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets, Nature Biotechnology, 23(5), 612 – 616, May 2005.


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