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Ryan T. Gill

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemical & Biological Engin
Phone303/492-2627
    Other Positions
    TitleEndowed or Named Professor
    InstitutionUniversity of Colorado Boulder
    DepartmentCollege Engineering & App Sci


    Collapse Research 
    Collapse research activities and funding
    R21AI055773     (GILL, RYAN T)May 1, 2003 - Apr 30, 2006
    NIH/NIAID
    Using Genomics to Identify Antibiotic Sensitivity Genes
    Role: Principal Investigator

    K25AI064338     (GILL, RYAN T)Jun 1, 2005 - Apr 30, 2010
    NIH/NIAID
    BioMolecular Networks in Antibiotic Resistance Evolution
    Role: Principal Investigator

    R01AI106721     (FELDHEIM, DAN L.)Jul 1, 2014 - Jun 30, 2019
    NIH/NIAID
    Gold Nanocrystal Antibiotics for the Treatment of Multidrug-resistant Gram Negati
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT. ROS mediated selection for increased NADPH availability in Escherichia coli. Biotechnol Bioeng. 2017 Jul 15. PMID: 28710857.
      View in: PubMed
    2. Liang L, Liu R, Garst AD, Lee T, Nogué VSI, Beckham GT, Gill RT. CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab Eng. 2017 May; 41:1-10. PMID: 28216108.
      View in: PubMed
    3. Zeitoun RI, Pines G, Grau WC, Gill RT. Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies. ACS Synth Biol. 2017 Apr 21; 6(4):619-627. PMID: 28103008.
      View in: PubMed
    4. Groot J, Cepress-Mclean SC, Robbins-Pianka A, Knight R, Gill RT. Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli. Biotechnol Bioeng. 2017 Apr; 114(4):885-893. PMID: 27861733.
      View in: PubMed
    5. Garst AD, Bassalo MC, Pines G, Lynch SA, Halweg-Edwards AL, Liu R, Liang L, Wang Z, Zeitoun R, Alexander WG, Gill RT. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol. 2017 Jan; 35(1):48-55. PMID: 27941803.
      View in: PubMed
    6. Gill RT, Thornton SF, Harbottle MJ, Smith JW. Sustainability assessment of electrokinetic bioremediation compared with alternative remediation options for a petroleum release site. J Environ Manage. 2016 Dec 15; 184(Pt 1):120-131. PMID: 27511828.
      View in: PubMed
    7. Winkler JD, Halweg-Edwards AL, Erickson KE, Choudhury A, Pines G, Gill RT. The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes. ACS Synth Biol. 2016 12 16; 5(12):1566-1577. PMID: 27438180.
      View in: PubMed
    8. Halweg-Edwards AL, Pines G, Winkler JD, Pines A, Gill RT. A Web Interface for Codon Compression. ACS Synth Biol. 2016 Sep 16; 5(9):1021-3. PMID: 27169595.
      View in: PubMed
    9. Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin AP, Gill RT. Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli. ACS Synth Biol. 2016 07 15; 5(7):561-8. PMID: 27072506.
      View in: PubMed
    10. Bassalo MC, Liu R, Gill RT. Directed evolution and synthetic biology applications to microbial systems. Curr Opin Biotechnol. 2016 Jun; 39:126-33. PMID: 27054950.
      View in: PubMed
    11. Weiss SJ, Mansell TJ, Mortazavi P, Knight R, Gill RT. Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli. PLoS One. 2016; 11(1):e0146916. PMID: 26771672; PMCID: PMC4714920.
    12. Lynch S, Eckert C, Yu J, Gill R, Maness PC. Overcoming substrate limitations for improved production of ethylene in E. coli. Biotechnol Biofuels. 2016; 9:3. PMID: 26734073; PMCID: PMC4700776.
    13. Gill RT, Halweg-Edwards AL, Clauset A, Way SF. Synthesis aided design: The biological design-build-test engineering paradigm? Biotechnol Bioeng. 2016 Jan; 113(1):7-10. PMID: 26580431.
      View in: PubMed
    14. Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin AP, Knight R, Gill RT. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits. ACS Synth Biol. 2015 Nov 20; 4(11):1244-53. PMID: 26478262.
      View in: PubMed
    15. Liu R, Bassalo MC, Zeitoun RI, Gill RT. Genome scale engineering techniques for metabolic engineering. Metab Eng. 2015 Nov; 32:143-54. PMID: 26453944.
      View in: PubMed
    16. Winkler JD, Erickson K, Choudhury A, Halweg-Edwards AL, Gill RT. Complex systems in metabolic engineering. Curr Opin Biotechnol. 2015 Dec; 36:107-14. PMID: 26319897.
      View in: PubMed
    17. Halweg-Edwards AL, Grau WC, Winkler JD, Garst AD, Gill RT. The emergence of commodity-scale genetic manipulation. Curr Opin Chem Biol. 2015 Oct; 28:150-5. PMID: 26302383.
      View in: PubMed
    18. Pines G, Freed EF, Winkler JD, Gill RT. Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination. ACS Synth Biol. 2015 Nov 20; 4(11):1176-85. PMID: 25856528.
      View in: PubMed
    19. Zeitoun RI, Garst AD, Degen GD, Pines G, Mansell TJ, Glebes TY, Boyle NR, Gill RT. Multiplexed tracking of combinatorial genomic mutations in engineered cell populations. Nat Biotechnol. 2015 Jun; 33(6):631-7. PMID: 25798935.
      View in: PubMed
    20. Reynolds TS, Gill RT. Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli. ACS Synth Biol. 2015 Jul 17; 4(7):776-80. PMID: 25763604.
      View in: PubMed
    21. Erickson KE, Gill RT, Chatterjee A. CONSTRICTOR: constraint modification provides insight into design of biochemical networks. PLoS One. 2014; 9(11):e113820. PMID: 25422896; PMCID: PMC4244162.
    22. Pines G, Pines A, Garst AD, Zeitoun RI, Lynch SA, Gill RT. Codon compression algorithms for saturation mutagenesis. ACS Synth Biol. 2015 May 15; 4(5):604-14. PMID: 25303315.
      View in: PubMed
    23. Glebes TY, Sandoval NR, Gillis JH, Gill RT. Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli. Biotechnol Bioeng. 2015 Jan; 112(1):129-40. PMID: 24981318.
      View in: PubMed
    24. Gill RT, Harbottle MJ, Smith JW, Thornton SF. Electrokinetic-enhanced bioremediation of organic contaminants: a review of processes and environmental applications. Chemosphere. 2014 Jul; 107:31-42. PMID: 24875868.
      View in: PubMed
    25. Eckert C, Xu W, Xiong W, Lynch S, Ungerer J, Tao L, Gill R, Maness PC, Yu J. Ethylene-forming enzyme and bioethylene production. Biotechnol Biofuels. 2014 Mar 03; 7(1):33. PMID: 24589138; PMCID: PMC3946592.
    26. Glebes TY, Sandoval NR, Reeder PJ, Schilling KD, Zhang M, Gill RT. Genome-wide mapping of furfural tolerance genes in Escherichia coli. PLoS One. 2014; 9(1):e87540. PMID: 24489935; PMCID: PMC3905028.
    27. Garst A, Lynch M, Evans R, Gill RT. Strategies for the multiplex mapping of genes to traits. Microb Cell Fact. 2013 Oct 30; 12:99. PMID: 24171944; PMCID: PMC3842685.
    28. Chaput C, Spindler E, Gill RT, Zychlinsky A. O-antigen protects gram-negative bacteria from histone killing. PLoS One. 2013; 8(8):e71097. PMID: 23951089; PMCID: PMC3738592.
    29. Pandhal J, Woodruff LB, Jaffe S, Desai P, Ow SY, Noirel J, Gill RT, Wright PC. Inverse metabolic engineering to improve Escherichia coli as an N-glycosylation host. Biotechnol Bioeng. 2013 Sep; 110(9):2482-93. PMID: 23568537.
      View in: PubMed
    30. Nordwald EM, Garst A, Gill RT, Kaar JL. Accelerated protein engineering for chemical biotechnology via homologous recombination. Curr Opin Biotechnol. 2013 Dec; 24(6):1017-22. PMID: 23540421.
      View in: PubMed
    31. Boyle NR, Reynolds TS, Evans R, Lynch M, Gill RT. Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing. Biotechnol J. 2013 May; 8(5):515-22. PMID: 23436787.
      View in: PubMed
    32. Spindler EC, Boyle NR, Hancock RE, Gill RT. Genome-wide identification of genes conferring energy related resistance to a synthetic antimicrobial peptide (Bac8c). PLoS One. 2013; 8(1):e55052. PMID: 23383054; PMCID: PMC3561415.
    33. Woodruff LB, Boyle NR, Gill RT. Engineering improved ethanol production in Escherichia coli with a genome-wide approach. Metab Eng. 2013 May; 17:1-11. PMID: 23376594.
      View in: PubMed
    34. Woodruff LB, May BL, Warner JR, Gill RT. Towards a metabolic engineering strain "commons": an Escherichia coli platform strain for ethanol production. Biotechnol Bioeng. 2013 May; 110(5):1520-6. PMID: 23322646.
      View in: PubMed
    35. Mansell TJ, Warner JR, Gill RT. Trackable multiplex recombineering for gene-trait mapping in E. coli. Methods Mol Biol. 2013; 985:223-46. PMID: 23417807.
      View in: PubMed
    36. Woodruff LB, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT. Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metab Eng. 2013 Jan; 15:124-33. PMID: 23164575.
      View in: PubMed
    37. Sandoval NR, Kim JY, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, Gill RT. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):10540-5. PMID: 22689973; PMCID: PMC3387050.
    38. Boyle NR, Gill RT. Tools for genome-wide strain design and construction. Curr Opin Biotechnol. 2012 Oct; 23(5):666-71. PMID: 22357141.
      View in: PubMed
    39. Warnecke TE, Lynch MD, Lipscomb ML, Gill RT. Identification of a 21 amino acid peptide conferring 3-hydroxypropionic acid stress-tolerance to Escherichia coli. Biotechnol Bioeng. 2012 May; 109(5):1347-52. PMID: 22161628.
      View in: PubMed
    40. Lynch SA, Gill RT. Synthetic biology: new strategies for directing design. Metab Eng. 2012 May; 14(3):205-11. PMID: 22227399.
      View in: PubMed
    41. Woodruff LB, Gill RT. Engineering genomes in multiplex. Curr Opin Biotechnol. 2011 Aug; 22(4):576-83. PMID: 21592776.
      View in: PubMed
    42. Spindler EC, Hale JD, Giddings TH, Hancock RE, Gill RT. Deciphering the mode of action of the synthetic antimicrobial peptide Bac8c. Antimicrob Agents Chemother. 2011 Apr; 55(4):1706-16. PMID: 21282431; PMCID: PMC3067151.
    43. Sandoval NR, Mills TY, Zhang M, Gill RT. Elucidating acetate tolerance in E. coli using a genome-wide approach. Metab Eng. 2011 Mar; 13(2):214-24. PMID: 21163359.
      View in: PubMed
    44. Handke P, Lynch SA, Gill RT. Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals. Metab Eng. 2011 Jan; 13(1):28-37. PMID: 21056114.
      View in: PubMed
    45. Singh A, Cher Soh K, Hatzimanikatis V, Gill RT. Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metab Eng. 2011 Jan; 13(1):76-81. PMID: 21040799.
      View in: PubMed
    46. Warner JR, Reeder PJ, Karimpour-Fard A, Woodruff LB, Gill RT. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol. 2010 Aug; 28(8):856-62. PMID: 20639866.
      View in: PubMed
    47. Singh A, Karimpour-Fard A, Gill RT. Increased mutation frequency in redox-impaired Escherichia coli due to RelA- and RpoS-mediated repression of DNA repair. Appl Environ Microbiol. 2010 Aug; 76(16):5463-70. PMID: 20581184; PMCID: PMC2918982.
    48. Prior JE, Lynch MD, Gill RT. Broad-host-range vectors for protein expression across gram negative hosts. Biotechnol Bioeng. 2010 Jun 01; 106(2):326-32. PMID: 20148414.
      View in: PubMed
    49. Gill R, Datta S, Datta S. A statistical framework for differential network analysis from microarray data. BMC Bioinformatics. 2010 Feb 19; 11:95. PMID: 20170493; PMCID: PMC2838870.
    50. Warnecke TE, Lynch MD, Karimpour-Fard A, Lipscomb ML, Handke P, Mills T, Ramey CJ, Hoang T, Gill RT. Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes. Metab Eng. 2010 May; 12(3):241-50. PMID: 20060059.
      View in: PubMed
    51. Struble JM, Gill RT. Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa. PLoS One. 2009 Nov 11; 4(11):e6576. PMID: 19907650; PMCID: PMC2771283.
    52. Prior JE, Shokati T, Christians U, Gill RT. Identification and characterization of a bacterial cytochrome P450 for the metabolism of diclofenac. Appl Microbiol Biotechnol. 2010 Jan; 85(3):625-33. PMID: 19636551.
      View in: PubMed
    53. Singh A, Lynch MD, Gill RT. Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metab Eng. 2009 Nov; 11(6):347-54. PMID: 19628049.
      View in: PubMed
    54. Warner JR, Patnaik R, Gill RT. Genomics enabled approaches in strain engineering. Curr Opin Microbiol. 2009 Jun; 12(3):223-30. PMID: 19467921.
      View in: PubMed
    55. Karimpour-Fard A, Leach SM, Gill RT, Hunter LE. Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics. 2008 Sep 24; 9:397. PMID: 18816389; PMCID: PMC2570368.
    56. Drevinek P, Holden MT, Ge Z, Jones AM, Ketchell I, Gill RT, Mahenthiralingam E. Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infect Dis. 2008 Sep 19; 8:121. PMID: 18801206; PMCID: PMC2559838.
    57. Gall S, Lynch MD, Sandoval NR, Gill RT. Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metab Eng. 2008 Nov; 10(6):382-93. PMID: 18789396.
      View in: PubMed
    58. Karimpour-Fard A, Leach SM, Hunter LE, Gill RT. The topology of the bacterial co-conserved protein network and its implications for predicting protein function. BMC Genomics. 2008 Jun 30; 9:313. PMID: 18590549; PMCID: PMC2488357.
    59. Warnecke TE, Lynch MD, Karimpour-Fard A, Sandoval N, Gill RT. A genomics approach to improve the analysis and design of strain selections. Metab Eng. 2008 May-Jul; 10(3-4):154-65. PMID: 18514004.
      View in: PubMed
    60. Bonomo J, Lynch MD, Warnecke T, Price JV, Gill RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metab Eng. 2008 Mar; 10(2):109-20. PMID: 18093856.
      View in: PubMed
    61. Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW. Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiol Lett. 2007 Nov; 276(1):83-92. PMID: 17937666.
      View in: PubMed
    62. Karimpour-Fard A, Hunter L, Gill RT. Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics. 2007 Oct 29; 8:393. PMID: 17967189; PMCID: PMC2204017.
    63. Karimpour-Fard A, Detweiler CS, Erickson KD, Hunter L, Gill RT. Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol. 2007; 8(9):R185. PMID: 17803817; PMCID: PMC2375023.
    64. Lynch MD, Warnecke T, Gill RT. SCALEs: multiscale analysis of library enrichment. Nat Methods. 2007 Jan; 4(1):87-93. PMID: 17099705.
      View in: PubMed
    65. Struble JM, Gill RT. Reverse engineering antibiotic sensitivity in a multidrug-resistant Pseudomonas aeruginosa isolate. Antimicrob Agents Chemother. 2006 Jul; 50(7):2506-15. PMID: 16801433; PMCID: PMC1489790.
    66. Lynch MD, Gill RT. Broad host range vectors for stable genomic library construction. Biotechnol Bioeng. 2006 May 05; 94(1):151-8. PMID: 16496398.
      View in: PubMed
    67. Leiske DL, Karimpour-Fard A, Hume PS, Fairbanks BD, Gill RT. A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray. BMC Genomics. 2006 Apr 04; 7:72. PMID: 16595014; PMCID: PMC1468409.
    68. Bonomo J, Warnecke T, Hume P, Marizcurrena A, Gill RT. A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli. Metab Eng. 2006 May; 8(3):227-39. PMID: 16497527.
      View in: PubMed
    69. Warnecke T, Gill RT. Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications. Microb Cell Fact. 2005 Aug 25; 4:25. PMID: 16122392; PMCID: PMC1208944.
    70. Bonomo J, Gill RT. Amino acid content of recombinant proteins influences the metabolic burden response. Biotechnol Bioeng. 2005 Apr 05; 90(1):116-26. PMID: 15736162.
      View in: PubMed
    71. Dai M, Ziesman S, Ratcliffe T, Gill RT, Copley SD. Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab Eng. 2005 Jan; 7(1):45-52. PMID: 15974564.
      View in: PubMed
    72. Lynch MD, Gill RT, Stephanopoulos G. Mapping phenotypic landscapes using DNA micro-arrays. Metab Eng. 2004 Jul; 6(3):177-85. PMID: 15256207.
      View in: PubMed
    73. Gill RT. Enabling inverse metabolic engineering through genomics. Curr Opin Biotechnol. 2003 Oct; 14(5):484-90. PMID: 14580577.
      View in: PubMed
    74. Gill RT, Katsoulakis E, Schmitt W, Taroncher-Oldenburg G, Misra J, Stephanopoulos G. Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803. J Bacteriol. 2002 Jul; 184(13):3671-81. PMID: 12057963; PMCID: PMC135141.
    75. Gill RT, Wildt S, Yang YT, Ziesman S, Stephanopoulos G. Genome-wide screening for trait conferring genes using DNA microarrays. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):7033-8. PMID: 11997466; PMCID: PMC124523.
    76. Gill RT, DeLisa MP, Valdes JJ, Bentley WE. Genomic analysis of high-cell-density recombinant Escherichia coli fermentation and "cell conditioning" for improved recombinant protein yield. Biotechnol Bioeng. 2001 Jan 05; 72(1):85-95. PMID: 11084598.
      View in: PubMed
    77. Stephanopoulos G, Gill RT. After a decade of progress, an expanded role for metabolic engineering. Adv Biochem Eng Biotechnol. 2001; 73:1-8. PMID: 11816808.
      View in: PubMed
    78. Gill RT, Valdes JJ, Bentley WE. A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli. Metab Eng. 2000 Jul; 2(3):178-89. PMID: 11056060.
      View in: PubMed
    79. Gill RT, Valdes JJ, Bentley WE. Reverse transcription-PCR differential display analysis of Escherichia coli global gene regulation in response to heat shock. Appl Environ Microbiol. 1999 Dec; 65(12):5386-93. PMID: 10583993; PMCID: PMC91733.
    80. Gill RT, Cha HJ, Jain A, Rao G, Bentley WE. Generating controlled reducing environments in aerobic recombinant Escherichia coli fermentations: effects on cell growth, oxygen uptake, heat shock protein expression, and in vivo CAT activity. Biotechnol Bioeng. 1998 Jul 20; 59(2):248-59. PMID: 10099335.
      View in: PubMed
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