Publications in VIVO

Co-author Network

Gill, Ryan T. The Wilfred and Caroline Slade Endowed Professor

Positions

Professor, Renewable & Sustainable Energy Institute (RASEI)

Research Areas

Research

research overview

Dr. Gill's research is focused on the development of novel technologies for genome-scale engineering. The technologies are applied to a broad variety of areas relevant to renewable and sustainable energy, advanced materials, and human health.

keywords

directed evolution, synthetic biology, genomics, metabolic engineering

Publications

selected publications

chapter
conference proceeding
- Strategy for genome design, redesign, and optimization of ethylene production in E. coli. ACS National Meeting Book of Abstracts. 2014
journal article
- Deep scanning lysine metabolism in Escherichia coli. Molecular Systems Biology. 2018
- Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnology and Bioengineering. 2120-2138. 2018
- Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering. Metabolic Engineering. 10-20. 2018
- Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production. Metabolic Engineering. 303-313. 2018
- Renewable acrylonitrile production. Science. 1307-1310. 2017
- The Tolerome: A Database of Transcriptome-Level Contributions to Diverse Escherichia coli Resistance and Tolerance Phenotypes. ACS Synthetic Biology. 2302-2315. 2017
- A communal catalogue reveals Earth's multiscale microbial diversity. Nature: New biology. 457-+. 2017
- ROS mediated selection for increased NADPH availability in Escherichia coli. Biotechnology and Bioengineering. 2685-2689. 2017
- Refactoring the Genetic Code for Increased Evolvability. mBio. 2017
- CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metabolic Engineering. 1-10. 2017
- Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli. Biotechnology and Bioengineering. 885-893. 2017
- Quantitative Tracking of Combinatorially Engineered Populations with Multiplexed Binary Assemblies. ACS Synthetic Biology. 619-627. 2017
- Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nature Biotechnology. 48-55. 2017
- Quantifying complexity in metabolic engineering using the LASER database.. Metabolic Engineering Communications. 227-233. 2016
- The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes. ACS Synthetic Biology. 1566-1577. 2016
- A Web Interface for Codon Compression. ACS Synthetic Biology. 1021-1023. 2016
- Rapid and Efficient One-Step Metabolic Pathway Integration in E-coli. ACS Synthetic Biology. 561-568. 2016
- Directed evolution and synthetic biology applications to microbial systems. Current Opinion in Biotechnology. 126-133. 2016
- integrating entire metabolic pathways in e coli. Cell Systems. 289-289. 2016
- Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli. PLoS ONE. 2016
- Overcoming substrate limitations for improved production of ethylene in E. coli. Biotechnology for Biofuels. 2016
- Ch. 9: Biotechnological strategies for advanced biofuel production: enhancing tolerance phenotypes through genome scale modifications. 227-263. 2016
- Genome wide mapping of mutations and single nucleotide resolution for protein, pathway, and genome engineering.. Nature Biotechnology. 2016
- Synthesis aided design: The biological design-build-test engineering paradigm?. Biotechnology and Bioengineering. 7-10. 2016
- Complex systems in metabolic engineering. Current Opinion in Biotechnology. 107-114. 2015
- Bacterial Recombineering: Genome Engineering via Phage-Based Homologous Recombination. ACS Synthetic Biology. 1176-1185. 2015
- Genome scale engineering techniques for metabolic engineering. Metabolic Engineering. 143-154. 2015
- Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits. ACS Synthetic Biology. 1244-1253. 2015
- The emergence of commodity-scale genetic manipulation. Current Opinion in Chemical Biology. 150-155. 2015
- Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli. ACS Synthetic Biology. 776-780. 2015
- Multiplexed tracking of combinatorial genomic mutations in engineered cell populations. Nature Biotechnology. 631-+. 2015
- Codon Compression Algorithms for Saturation Mutagenesis. ACS Synthetic Biology. 604-614. 2015
- Comparison of Genome-Wide Selection Strategies to Identify Furfural Tolerance Genes in Escherichia Coli. Biotechnology and Bioengineering. 129-140. 2015
- CONSTRICTOR: Constraint Modification Provides Insight into Design of Biochemical Networks. PLoS ONE. 2014
- Implications of variable fluid resistance caused by start-up flow in microfluidic networks. Microfluidics and Nanofluidics. 473-482. 2014
- Genome-Wide Mapping of Furfural Tolerance Genes in Escherichia coli. PLoS ONE. 2014
- Accelerated protein engineering for chemical biotechnology via homologous recombination. Current Opinion in Biotechnology. 1017-1022. 2013
- Strategies for the multiplex mapping of genes to traits. Microbial Cell Factories. 2013
- Inverse Metabolic Engineering to Improve Escherichia coli as an N-Glycosylation Host. Biotechnology and Bioengineering. 2482-2493. 2013
- O-Antigen Protects Gram-Negative Bacteria from Histone Killing. PLoS ONE. 2013
- Engineering improved ethanol production in Escherichia coli with a genome-wide approach. Metabolic Engineering. 1-11. 2013
- Recombineering to homogeneity: extension of multiplex recombineering to large-scale genome editing. Biotechnology Journal. 515-522. 2013
- Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production. Biotechnology and Bioengineering. 1520-1526. 2013
- Genome-Wide Identification of Genes Conferring Energy Related Resistance to a Synthetic Antimicrobial Peptide (Bac8c). PLoS ONE. 2013
- Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metabolic Engineering. 124-133. 2013
- Trackable multiplex recombineering for gene-trait mapping in E. coli.. Methods in Molecular Biology. 223-246. 2013
- Tools for genome-wide strain design and construction. Current Opinion in Biotechnology. 666-671. 2012
- Strategy for directing combinatorial genome engineering in Escherichia coli. Proceedings of the National Academy of Sciences. 10540-10545. 2012
- Identification of a 21 amino acid peptide conferring 3-hydroxypropionic acid stress-tolerance to Escherichia coli. Biotechnology and Bioengineering. 1347-1352. 2012
- Synthetic biology: New strategies for directing design. Metabolic Engineering. 205-211. 2012
- Genomics-driven elucidation and construction of combinatorial mutants for hydrolysate tolerance in Escherichia coli. ACS National Meeting Book of Abstracts. 2012
- Engineering genomes in multiplex. Current Opinion in Biotechnology. 576-583. 2011
- Deciphering the Mode of Action of the Synthetic Antimicrobial Peptide Bac8c. Antimicrobial Agents and Chemotherapy. 1706-1716. 2011
- Trackable recombination-based directed evolution. ACS National Meeting Book of Abstracts. 2011
- Using genome-wide and targeted tools to engineer acetate tolerance in E. coli for improved cellulosic biofuel production. ACS National Meeting Book of Abstracts. 2011
- Elucidating acetate tolerance in E. coli using a genome-wide approach. Metabolic Engineering. 214-224. 2011
- Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals. Metabolic Engineering. 28-37. 2011
- Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metabolic Engineering. 76-81. 2011
- Increased Mutation Frequency in Redox-Impaired Escherichia coli Due to RelA- and RpoS-Mediated Repression of DNA Repair. Applied and Environmental Microbiology. 5463-5470. 2010
- Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nature Biotechnology. 856-U138. 2010
- Broad-Host-Range Vectors for Protein Expression Across Gram Negative Hosts. Biotechnology and Bioengineering. 326-332. 2010
- Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes. Metabolic Engineering. 241-250. 2010
- Identification and characterization of a bacterial cytochrome P450 for the metabolism of diclofenac. Applied Microbiology and Biotechnology. 625-633. 2010
- Genome-Scale Identification Method Applied to Find Cryptic Aminoglycoside Resistance Genes in Pseudomonas aeruginosa. PLoS ONE. A6-A15. 2009
- Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metabolic Engineering. 347-354. 2009
- Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli. Biotechnology for Biofuels. 2009
- BIOT 167-Elucidating mechanisms of acetate tolerance in E. coli with genome-wide tools. ACS National Meeting Book of Abstracts. 2009
- BIOT 400-Molecular biorefining to liquid alkanes and alcohols. ACS National Meeting Book of Abstracts. 2009
- Genomics enabled approaches in strain engineering. Current Opinion in Microbiology. 223-230. 2009
- Parallel mapping of genotypes to phenotypes contributing to overall biological fitness. Metabolic Engineering. 382-393. 2008
- Predicting protein linkages in bacteria: Which method is best depends on task. BMC Bioinformatics. 2008
- 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 Infectious Diseases. 2008
- BIOT 274-Multiplex recombineering: Progress toward the multigenic insertion of regulatory elements and potential applications in metabolic engineering. ACS National Meeting Book of Abstracts. 2008
- BIOT 299-Engineering bacteria for the production of human drug metabolites. ACS National Meeting Book of Abstracts. 2008
- BIOT 375-Enhancing Succinic acid production by improving fitness of E.coli production strains. ACS National Meeting Book of Abstracts. 2008
- BIOT 433-Elucidating mechanisms of acetate tolerance in E. coli using SCALES. ACS National Meeting Book of Abstracts. 2008
- The topology of the bacterial co-conserved protein network and its implications for predicting protein function. BMC Genomics. 2008
- A genomics approach to improve the analysis and design of strain selections. Metabolic Engineering. 154-165. 2008
- Genome-scale analysis of anti-metabolite directed strain engineering. Metabolic Engineering. 109-120. 2008
- Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiology Letters. 83-92. 2007
- Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics. 2007
- Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biology. 2007
- SCALEs: multiscale analysis of library enrichment. Nature Methods. 87-93. 2007
- BIOT 281-Engineering heterologous drug metabolism in Gram negative bacteria. ACS National Meeting Book of Abstracts. 2006
- BIOT 290-Identification of succinic acid tolerance genes in E.coli. ACS National Meeting Book of Abstracts. 2006
- BIOT 35-Engineering of organic acid tolerance genes in E. coli for biorefinery applications. ACS National Meeting Book of Abstracts. 2006
- BIOT 360-Co-conservation analysis of bacterial genes across phyla reveals that this method can be reliably used to predict gene function. ACS National Meeting Book of Abstracts. 2006
- Reverse engineering antibiotic sensitivity in a multidrug-resistant Pseudomonas aeruginosa isolate. Antimicrobial Agents and Chemotherapy. 2506-2515. 2006
- Broad host range vectors for stable genornic library construction. Biotechnology and Bioengineering. 151-158. 2006
- A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli. Metabolic Engineering. 227-239. 2006
- A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray. BMC Genomics. 2006
- Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications. Microbial Cell Factories. 2005
- Amino acid content of recombinant proteins influences the metabolic burden response. Biotechnology and Bioengineering. 116-126. 2005
- Inverse metabolic engineering antibiotic sensitivity in resistant bacteria.. ACS National Meeting Book of Abstracts. U224-U224. 2005
- Metabolic engineering bacteria to produce human drug metabolites.. ACS National Meeting Book of Abstracts. U223-U223. 2005
- Mixed-library parallel gene trait mapping: A quantitative micro-array technique for the genome-wide identification of trait conferring genes.. ACS National Meeting Book of Abstracts. U202-U202. 2005
- Post-genomics approach to understanding E. Coli network architecture.. ACS National Meeting Book of Abstracts. U227-U227. 2005
- Tools and applications for directed genome evolution: Combining inverse and constructive metabolic engineering.. ACS National Meeting Book of Abstracts. U197-U198. 2005
- Antibiotic resistance as a model for strain engineering. Computers and Chemical Engineering. 509-517. 2005
- Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metabolic Engineering. 45-52. 2005
- Mapping phenotypic landscapes using DNA micro-arrays. Metabolic Engineering. 177-185. 2004
- Special issue on inverse metabolic engineering. Metabolic Engineering. 175-176. 2004
- Evolution, characterization, and engineering of bacterial traits.. ACS National Meeting Book of Abstracts. U254-U254. 2004
- Genomic analysis of the metabolic burden response.. ACS National Meeting Book of Abstracts. U225-U226. 2004
- Inverse metabolic engineering antibiotic sensitivity in resistant bacteria.. ACS National Meeting Book of Abstracts. U225-U225. 2004
- Enabling inverse metabolic engineering through genomics. Current Opinion in Biotechnology. 484-490. 2003
- Diagnosing biopharmaceutical fermentations using transcriptional profiling. ACS National Meeting Book of Abstracts. U222-U222. 2003
- Metabolic and evolutionary engineering in the era of genomics: Antibiotic resistance as a model for engineering new microbial behaviors.. ACS National Meeting Book of Abstracts. U204-U205. 2003
- Genome-wide screening for trait conferring genes using DNA microarrays. Proceedings of the National Academy of Sciences. 7033-7038. 2002

Teaching

courses taught

CHEM 6901 Research in Chemistry (Spring 2019 UC Boulder)
CHEM 8991 Doctoral Dissertation (Spring 2019 UC Boulder)
CHEN 2840 Independent Study (Spring 2019 UC Boulder)
CHEN 3840 Independent Study (Spring 2019 UC Boulder)
CHEN 4840 Independent Study (Spring 2019 UC Boulder)
CHEN 5840 Independent Study (Spring 2019 UC Boulder)
CHEN 5919 Special Topics in CHBE (Spring 2019 UC Boulder)
CHEN 6950 Master's Thesis (Spring 2019 UC Boulder)
CHEN 8990 Doctoral Thesis (Spring 2019 UC Boulder)
CHEM 6901 Research in Chemistry (Fall 2018 UC Boulder)
CHEM 8991 Doctoral Dissertation (Fall 2018 UC Boulder)
CHEN 2840 Independent Study (Fall 2018 UC Boulder)
CHEN 3840 Independent Study (Fall 2018 UC Boulder)
CHEN 4840 Independent Study (Fall 2018 UC Boulder)
CHEN 5840 Independent Study (Fall 2018 UC Boulder)
CHEN 5919 Special Topics in CHBE (Fall 2018 UC Boulder)
CHEN 6950 Master's Thesis (Fall 2018 UC Boulder)
CHEN 8990 Doctoral Thesis (Fall 2018 UC Boulder)
MCDB 8990 Doctoral Dissertation (Fall 2018 UC Boulder)
CHEM 6901 Research in Chemistry (Summer 2018 UC Boulder)
CHEM 8991 Doctoral Dissertation (Summer 2018 UC Boulder)
CHEN 2840 Independent Study (Summer 2018 UC Boulder)
CHEN 3840 Independent Study (Summer 2018 UC Boulder)
CHEN 4840 Independent Study (Summer 2018 UC Boulder)
CHEN 5840 Independent Study (Summer 2018 UC Boulder)
CHEN 5919 Special Topics in CHBE (Summer 2018 UC Boulder)
CHEN 6950 Master's Thesis (Summer 2018 UC Boulder)
CHEN 8990 Doctoral Thesis (Summer 2018 UC Boulder)
MCDB 8990 Doctoral Dissertation (Summer 2018 UC Boulder)
CHEM 6901 Research in Chemistry (Spring 2018 UC Boulder)
CHEM 8991 Doctoral Dissertation (Spring 2018 UC Boulder)
CHEN 2840 Independent Study (Spring 2018 UC Boulder)
CHEN 3840 Independent Study (Spring 2018 UC Boulder)
CHEN 4803 Metabolic Engineering (Spring 2018 UC Boulder)
CHEN 4840 Independent Study (Spring 2018 UC Boulder)
CHEN 5840 Independent Study (Spring 2018 UC Boulder)
CHEN 5919 Special Topics in CHBE (Spring 2018 UC Boulder)
CHEN 6950 Master's Thesis (Spring 2018 UC Boulder)
CHEN 8990 Doctoral Thesis (Spring 2018 UC Boulder)
MCDB 8990 Doctoral Dissertation (Spring 2018 UC Boulder)

Background

education and training

Ph.D., University of Maryland College Park Campus 1999
M.S., University of Maryland College Park Campus 1997
B.S., Johns Hopkins University 1993

awards and honors

Provost's Faculty Achievement Award for Tenured Faculty (Academic Affairs), conferred by Academic Affairs, 2011
Inventor of the Year (Office of Technology Transfer), conferred by Office of Technology Transfer, 2010
Fellow (Renewable & Sustainable Energy Institute (RASEI)), conferred by Renewable & Sustainable Energy Institute (RASEI), 2009
Provost's Faculty Achievement Award for Pre-Tenure Faculty (Academic Affairs), conferred by Academic Affairs, 2006
Faculty Early Career Development (CAREER) Program (National Science Foundation), conferred by National Science Foundation, 2005

International Activities

global connections related to teaching and scholarly work (in recent years)

China Country
Denmark Country
Europe Continent
Spain Country
Switzerland Country
United Kingdom Country

Other Profiles

ORCID iD

http://orcid.org/0000-0003-1858-1731