Laboratory for Cellular and Metabolic Engineering

Laboratory for Cellular and Metabolic Engineering

Department of Chemical Engineering

Publications

 

 

Publications (Peer-Reviewed)

 

1. 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.

2. 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.

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

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

5. 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.

6. 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), 5266-73.

7. 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.

8. 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

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

10. 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.

11. Hal Alper, Yong-su Jin, J. Moxley, and G. Stephanopoulos, 2005.  Identifying gene targets for the metabolic engineering of Escherichia coli.  Metab Eng.  7(3), 155-164.

12. 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.

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

14. Gregory Stephanopoulos, Hal Alper, and Joel Moxley, 2004.  Exploiting Biological Complexity for Strain Improvement through Systems Biology.  Nat Biotechnology. 22(10), 1261-7.

 

Manuscripts Under Preparation/Under Review

 

1. Joel Moxley, Michael Jewett, Silas Villas-Boas, Maciek Antoniewicz, Hal Alper, Robert Wheeler, Alan Hinnebusch, Trey Ideker, Jens Nielsen, and Gregory Stephanopoulos, 2007.  Systematically bridging transcriptional regulation and metabolic phenotype. (Submitted)

2. Hal Alper and Gregory Stephanopoulos, 2007.  Increasing cellular tolerances through global Transcription Machinery Engineering. (Submitted).

3. Hal Alper, Joel Moxley, and Gregory Stephanopoulos, 2007. A multi-level analysis of cellular perturbations imparted by global Transcription Machinery Engineering-mediated ethanol tolerance.  (Under Preparation).

 

Publications (Non-Peer Reviewed)

 

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.