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.
selected publications chapter A strategy for directed searching of combinatorial mutation space at the genome-scale 2012 Construction of Genomic Libraries 2010 After a Decade of Progress, an Expanded Role for Metabolic Engineering 2009 Green biosynthesis of polyhydroxyalkanoates: Engineering of cyanobacteria for biopolymer production 2000 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
courses taught CHEM 6901 Research in Chemistry (Spring 2019) CHEM 8991 Doctoral Dissertation (Spring 2019) CHEN 2840 Independent Study (Spring 2019) CHEN 3840 Independent Study (Spring 2019) CHEN 4840 Independent Study (Spring 2019) CHEN 5840 Independent Study (Spring 2019) CHEN 5919 Special Topics in CHBE (Spring 2019) CHEN 6950 Master's Thesis (Spring 2019) CHEN 8990 Doctoral Thesis (Spring 2019) MCDB 8990 Doctoral Dissertation (Spring 2019) CHEM 6901 Research in Chemistry (Fall 2018) CHEM 8991 Doctoral Dissertation (Fall 2018) CHEN 2840 Independent Study (Fall 2018) CHEN 3840 Independent Study (Fall 2018) CHEN 4840 Independent Study (Fall 2018) CHEN 5840 Independent Study (Fall 2018) CHEN 5919 Special Topics in CHBE (Fall 2018) CHEN 6950 Master's Thesis (Fall 2018) CHEN 8990 Doctoral Thesis (Fall 2018) MCDB 8990 Doctoral Dissertation (Fall 2018) CHEM 6901 Research in Chemistry (Summer 2018) CHEM 8991 Doctoral Dissertation (Summer 2018) CHEN 2840 Independent Study (Summer 2018) CHEN 3840 Independent Study (Summer 2018) CHEN 4840 Independent Study (Summer 2018) CHEN 5840 Independent Study (Summer 2018) CHEN 5919 Special Topics in CHBE (Summer 2018) CHEN 6950 Master's Thesis (Summer 2018) CHEN 8990 Doctoral Thesis (Summer 2018) MCDB 8990 Doctoral Dissertation (Summer 2018) CHEM 6901 Research in Chemistry (Spring 2018) CHEM 8991 Doctoral Dissertation (Spring 2018) CHEN 2840 Independent Study (Spring 2018) CHEN 3840 Independent Study (Spring 2018) CHEN 4803 Metabolic Engineering (Spring 2018) CHEN 4840 Independent Study (Spring 2018) CHEN 5840 Independent Study (Spring 2018) CHEN 5919 Special Topics in CHBE (Spring 2018) CHEN 6950 Master's Thesis (Spring 2018) CHEN 8990 Doctoral Thesis (Spring 2018) MCDB 8990 Doctoral Dissertation (Spring 2018)
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
global connections related to teaching and scholarly work (in recent years) China Country Denmark Country Europe Continent Spain Country Switzerland Country United Kingdom Country
