Senior Director Quality Control

STEPHEN R. HUGHES, PhD

Contact Information

** ******* ***** ****: 309-***-****

Chatham, NJ 07928 Email: ***@***.***

Technical and Leadership Competencies

•Oversee all scientific functions and execution of company platforms as part of senior management, including basic and applied research projects, as well as the development and licensing of new processes, technologies, or products to promote the efficiency, profitability, sustainability, and competitive position of the company.

•Provide the overall tactical leadership for the establishment and implementation of high-volume new product platforms associated with optimizing profitable operational performance and compliance for development, manufacturing, and testing of large-scale, super-coiled, low-endotoxin plasmids.

•Design integrated hardware and software automation systems for low-cost manufacturing of raw materials to rapidly produce gene open reading frames for GMP grade dsDNA, ssDNA, and IVT templates used for homogeneous production of RNA for gene therapies.

•Constructed automated platform in LEED platinum building operation using electronic GMP training, batch, TM, TS, SOP, and IND documentation; all processes and documents for digital FDA review remotely.

•Developed company expansion capacity models and execute resourcing strategies to ensure delivery of activities and scopes of work from various internal teams and external consultants/vendors/contractors.

•Lead development and execution of automated experimental workflows for scientific manufacturing processes, including budgeting, bulk reagent and disposable ordering, procurement of capital equipment and facility (> 30 million dollars), validation, safety, and status.

•Provide the strategic leadership to establish and build an integrated automation infrastructure for executing repetitive/high-throughput processes for research, preclinical, and clinical GMP grade DNA production.

•Design and provide technical support; recruited and developed diverse expert teams for manufacturing positive strand only AAV virus, CAR T lentivirus, and DNA for direct transfection in vaccines and biological countermeasures.

•Focus areas include optimized nucleic acid production for episomal high-level gene expression, dual prime editing and gene writing, and large-scale AAV production for systemic therapy using AAV synthetic positive-strand only ssDNA; coordinated and implemented with marketing, quality/regulatory, sales in USA and international sales operations in China and India.

•Produced ultra-stable ultra-high expression amplicons for COVID vaccines for homogeneous DNA templates for hydrodynamic and electroporation use.

•Created high expression linear amplicons for use with CD19 CAR T using linear dsDNA templates for clinical scale and use in clinical trials.

•Generated dsDNA with modified ends for DNA self-transduction strategies to use in point of diagnosis ultra-personal gene and cell therapies using poly SUMO expression cassettes for cCAR T or one promoter polyprotein cassettes for cTCR T.

•Investigated nanospike delivery of linear dsDNA for use in microfluidic production of gene therapies on single patient CD34+ STEM cells.

•Contributed documentation for Type II Master File for linear dsDNA gene therapies produced via PCR from High Expression Amplicons (HEA).

•Designed processes for treating relapse after CD19 CAR-T using NK::HAC cCAR T expressing CD19-CD22-CD20-CD38 cCAR episomally to avoid memory cell production.

•Explored application of IVT templates to generate pegRNA guides for TwinPrime editing to add therapeutic payload with nebulized LNP particle containing two pegRNA guides and one CAS-RT RNA.

•Work with FDA to expedite approval of cell and gene therapies that use same equipment or device for manufacture or delivery using regulatory guidance on combination products.

•Possess unique combination of upstream and downstream DNA plasmid production and purification experience for industrial, preclinical, and clinical fully automated operations.

•Familiar with regulatory requirements for cGMP compliance of automated systems.

•Effectively help to recruit, retain, and develop a team of professionals to accomplish company objectives including establishment of procedures and practices for operation of a newly established department.

•Collaborate with business development, project management, supply chain, quality, and manufacturing sciences, and technology to evaluate manufacturing proposals, technologies, and processes.

•Lead development of DNA assembly team carrying out company scientific goals in developing novel undefeated oligo assembly process for large >4 kb gene assembly for production of synthetic euchromatin assembly unit with novel process defined in an invention disclosure/ patent written around this process for improved gene assembly effectiveness and open reading frame expression efficiency.

•Responsible for technology enabling very-large-scale production of DNA using proprietary undefeated PCR methods, which allow designed or sequenced DNA sequences to be produced directly from synthetic genomics platforms.

•Managed all scientific personnel, expenditures, and strategies to support high-throughput functional proteomics operations at USDA, ARS, Peoria.

•Developed strategies to optimize genes and improve microbial strains to convert renewable agricultural materials into sustainable commercial products for increased profitability of biorefining operations.

•Provided expertise individually and as team leader in areas of automated molecular biology techniques, gene/chromosome assembly, integrated robotic platforms, biofuel processes, and coordination of multi-faceted collaborative projects.

•Recognized as an expert in the areas of heterologous protein expression, gene optimization, design of platforms for automated molecular biology routines, development of high-throughput assays, and improvement of industrial microbial strains; represented research and development group across other department areas communicating company objectives, inspiring scientific participation in gene therapy DNA platforms, bringing solutions to downstream processing of linear dsDNa and ssDNA to company and resolving issues with these company platforms.

•Collaborated with engineers and scientists at universities, industries, and government institutions to implement automated molecular biology protocols, develop optimized genes, create novel vectors, engineer host cell lines, support continuous screening operations, and design integrated biorefineries.

•Created innovative efficient high-throughput microbial gene expression systems combined with novel gene/chromosome synthesis approaches including verified codon optimization for automated platforms to create improved commercially viable stable industrial strains for kg-scale recombinant protein and peptide commercial GMP production for pharmaceutical, cosmetic, and agricultural uses.

•Authored 49 peer-reviewed journal articles, 18 as first author; authored or co-authored 10 book chapters.

•Listed as inventor on 6 patents.

•Delivered more than 20 international and national invited presentations.

•Organized first Advanced Biofuels Leadership Conference, Washington, DC.

•Presented 2 invited seminars at Mitsubishi headquarters in Tokyo, Japan on biofuels and biorefineries.

•Organized 5 cooperative research and development agreements (CRADAs) with companies and universities, 1 international.

•Member of editorial board of 3 journals.

•President of ACS Illinois Heartland Section, 2006; won Chem Luminary award for mid-size section that year.

•Participated in review panels for DOE Advanced Research Projects Agency-Energy, for USDA Research Position Evaluation System, and for NSF Center for Biorenewable Chemicals.

•Serve on the Advisory Board for the Center for Bioprocessing Research and Development (CBRD) as part of the governor’s initiative for economic development in South Dakota.

Specific Accomplishments and Impact

•Negotiated with equipment suppliers and integrators to build fully automated high-throughput manufacturing facility to produce gene therapy materials as part of expansion of technology facilities and capabilities required to support current development, manufacture, and technical operations for several pharmaceutical companies.

•Established accurate cost evaluations within budget and on time for fully in-house automated and semi-automated options; successfully bid nine laboratory and robotic integrators for final designs.

•Facility will optimize the full potential of the space available and build in flexibility and utilities to enable spaces to be easily reconfigured and redeployed as required by the technical development functions and to address new needs in relatively short time frame.

•Designed and directed building of an integrated industrial robotic platform for rapid cGMP manufacture of gene therapy materials in a scheduled fashion that will operate unattended to minimize cross-contamination and that will be the core for production of raw materials for all therapies.

•Assembled laboratory to support high-throughput functional proteomics operations involving over one million dollars in capital expenditures using government specific cooperative agreement.

•Constructed first-in-kind integrated plasmid-based functional proteomic robotic platform to perform high-throughput cloning, transformation, expression, and assay operations for screening mutagenized genes to use in engineering improved industrial yeast strains for efficient biofuel production.

•Produced library of mutagenized insecticidal peptide genes expressed and screened in cellulosic ethanol yeast using automated protocols for gene assembly in first demonstration of completely automated high-throughput molecular biology platform.

•Constructed first 3-plasmid expression system on a fully automated molecular biology platform that produced high levels of three soluble functional proteins in Saccharomyces cerevisiae and screened the recombinant strains for improved growth on xylose to demonstrate optimization of an industrial yeast strain by expression of a valuable co-product and high levels of enzymes needed to utilize pentose sugars from cellulosic biomass. Publication received award for most-cited paper for 2009 and 2010.

•Conceived and implemented a unique high-throughput yeast mating strategy that identified native yeast genes whose over-expression improved anaerobic growth of S. cerevisiae on xylose to obtain optimum growth on sugars from biomass.

•Implemented novel assembly method for large genes on the robotic platform, constructed and expressed active synthetic lipase enzyme, an important industrial biocatalyst, in yeast, and used the resin-bound enzyme to catalyze formation of fatty acid esters (biodiesel) from ethanol and corn oil.

•Applied UV-C irradiation to produce Kluyveromyces marxianus mutant strains that grew anaerobically at 46 C on substrates that are constituents of biomass and therefore have potential application in biofuel production at elevated temperature from starch, sucrose, pectins, and cellulosic biomass.

•Designed automated assembly process to produce a synthetic yeast chromosome containing a multi-gene cassette for expression of enzymes to enhance xylose utilization and stably introduced this chromosome into a yeast strain without affecting integrity of host strain.

•Developed multi-stage biorefinery concept for sustainable conversion of coffee and other crop wastes to biofuels and bioproducts using coupled biochemical and thermochemical processes and collaborated with Cenicafe in Colombia, South America to apply this concept for converting waste produced at coffee pulping stations to valuable biofuels and bioproducts.

•Assembled synthetic chromosome containing yeast-codon-optimized gene for brazzein, a promising non-caloric sugar substitute, and demonstrated feasibility of expression in S. cerevisiae as a potential valuable co-product to improve profitability of biofuel production.

•Designed and implemented functional proteomics platform to express all full-length cDNA libraries isolated from cancer cell line mRNA into functional proteins to provide arrays for high-throughput screening to identify binding targets of compounds of interest.

•Developed and scaled up high-yield expression systems in yeast and E. coli for production of industrially and therapeutically important nucleases and proteases, coordinated project to produce recombinant Protein A in a batched production from E. coli for a large pharmaceutical company, responsible for in-process and release testing of all biochemical and molecular biology products in accordance with applicable GLP and cGMP regulations, developed and conducted assays for characterization of enzymes and related protein products utilizing more than 70 different assays.

•Developed and conducted assays to evaluate safety of biologics, specifically PCR and RT-PCR detection of viral and mycoplasma contaminants and QC-PCR quantitation of gene therapy vectors, evaluated cell lines with respect to integration site, copy number, and sequence of expressed message to verify post-production stability; sequenced gene therapy vectors, conducted work in compliance with GLP/GMP regulations and other applicable FDA requirements, managed work performed by contract testing facilities.

•Engineered novel two-hybrid technology to identify protein-protein interactions involving the plaque-forming Aβ peptide implicated in Alzheimer’s disease and used the technique to characterize Aβ peptide monomer-monomer interactions and to study the mechanism of these interactions by mutagenesis of the regions important to Aβ aggregation.

Education and Training

Hoechst Marion Roussel

Neuroscience Department

Postdoctoral

1993 – 1996

Publication: Two-hybrid system as a model to study the interaction of beta-amyloid peptide monomers. Proc Natl Acad Sci USA 93:2065-2070.

University of Cincinnati, College of Medicine

Department of Molecular Genetics, Biochemistry, and Microbiology

PhD

1987 – 1993

Thesis: Investigation of cis-acting elements involved in alternative splicing of rat alpha-tropomyosin pre-RNA using expression constructs derived from genomic DNA.

Rutgers University

Major: Biology/Genetics

BA

1983 – 1987

Senior Project: Genetic linkage analysis of mitotic mutants in the filamentous fungus, Aspergillus nidulans.

Professional Experience

2021-present Director, New Platform Development, GenScript USA Inc., Piscataway, NJ

Developed and built novel DNA assembly line for DNA fragments undefeated to 4 kb

Designed and built 1000-maxiprep DNA platform for Kingsbridge Rd, Piscataway site for GenScript

Designed and started linear DNA production facility at East Hanover NJ site for GenScript existing processes to produce mDNA, dsDNA, ssDNA, and nanoDNA for use in therapies using AAV, lenti, CRISPR editing, nonviral, twin prime editing, cCAR-T, cTCR-T, and lcDNA gene and cell therapy manufacture

2020-2021 Preclinical Automation Lead, Spark Therapeutics, Inc., Philadelphia, PA

Designed and built full preclinical production line from oligonucleotide to AAV production line for 300 Market St Philadelphia for Spark to produce 100 human doses per week

2019-2020 Director, Vector Manufacturing, GenScript USA Inc., Piscataway, NJ

Designed and built high-throughput manufacturing robot platforms for GenScript to produce ultra-high output from small footprint operation using robust manufacturing automation

Developed new classes of manufacturing robots for gene and cell therapies, IVT vaccines, and industrial-scale pDNA and linear DNA production

2017-2019 Director, DNA Programs, Applied DNA Sciences, Stony Brook, NY

Designed and rebuilt continuous robotic platform for production of linear HEA DNA production at LIHTI on SUNY Stony Brook campus.

Identified operations to make euchromatine and chromatin for episomal expression to prevent integration in T-cell therapies

2012-2017 Research Molecular Biologist GS-15, USDA, ARS, Peoria, IL

Engineered yeast artificial chromosomes to make high-value sweeteners in cellulosic ethanologenic yeast

2006-2012 Research Molecular Biologist GS-14, USDA, ARS, Peoria, IL

Engineered yeast to produce CALB and Lyt-1 for high-value ethanol operations

2003-2006 Research Molecular Biologist GS-13, USDA, ARS, Peoria, IL

Produced the first hands free molecular biology platform for assembling synthetic genes and transforming yeast

2001-2003 Staff Scientist, Cell Pathways, Inc., Horsham, PA

Screened entire colon cancer library using HTP-IVT followed by drug binding to identify mechanism of lead CP461 compound

2000-2001 Senior Research Scientist, Worthington Biochemical Corp., Lakewood, NJ

Made bulk recombinant expression platform in E coli and yeast to produce valuable nuclease and proteases

1998-2000 Molecular Biology and Quality Control Manager, Worthington Biochemical Corp., Lakewood, NJ

1998-1998 Sales Manager, Hudson Robotics, Inc., Springfield, NJ

1997-1998 Research Scientist, Neuroscience Dept., Hoechst Marion Roussel, Inc., Somerville, NJ

1996-1997 Senior Scientist, Molecular Biology, Quality Biotech, Inc., Camden, NJ

Peer-Reviewed Journal Articles and Book Chapters

1.Hughes SR, Jones MA. 2020. The global demand for biofuels and biotechnology-derived commodity chemicals: technologies, markets, and challenges. In: Vertès AA, Qureshi N, Blaschek HP, Yukawa H, editors. Green Energy to Sustainability: Strategies for Global Industries. John Wiley & Sons Ltd. pp. 137-156.

2.Hughes SR, Jones MA. 2020. Fuel ethanol production from lignocellulosic materials using recombinant yeasts. In: Vertès AA, Qureshi N, Blaschek HP, Yukawa H, editors. Green Energy to Sustainability: Strategies for Global Industries. John Wiley & Sons Ltd. pp. 269-282

3.Hughes SR, Qureshi N, López-Núñez JC, Jones MA. 2017. Utilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals World J Microbiol Biotechnol. 33(4):78. doi: 10.1007/s11274-017-2241-6. Epub 2017 Mar 24.

4.Liu S, Qureshi N, Hughes SR. 2017. Progress and perspectives on improving butanol tolerance. World J Microbiol Biotechnol. 33(3):51. doi: 10.1007/s11274-017-2220-y. Epub 2017 Feb 11

5.Pinkelman RJ, Hughes SR, Lindquist MR, Cox EJ, Jones MA, Bischoff KM, Liu S, Butt TR, Saha BC, Qureshi N, Bang SS. 2017. Construction of a yeast artificial chromosome containing a yeast-codon-optimized brazzein gene and expression in Saccharomyces cerevisiae. [submitted].

6.Galindo-Leva LA, Hughes SR, López-Núñez JC, Jarodsky JM, Erickson A, Lindquist MR, Cox EJ, Bischoff KM, Hoecker EC, Liu S, Qureshi N, Jones MA. 2016. Growth, ethanol production, and inulinase activity on various inulin substrates by mutant Kluyveromyces marxianus strains NRRL Y 50798 and NRRL Y 50799. J Ind Microbiol Biotechnol 43(7):927-939.

7.Liu S, Skory C, Qureshi N, Hughes SR. 2016. The yajC gene from Lactobacillus buchneri and Escherichia coli its role in ethanol tolerance. J. Ind. Microbiol. Biotechnol. 43(4):441-50.

8.Hughes SR, Cox EJ, Bang SS, Pinkelman RJ, López-Núñez JC, Saha BC, Qureshi N, Gibbons WR, Fry MR, Moser BR, Bischoff KM, Liu S, Sterner DE, Butt TR, Riedmuller SB, Jones MA, Riaño-Herrera NM. 2015. Process for assembly and transformation into Saccharomyces cerevisiae of a synthetic yeast artificial chromosome containing a multigene cassette to express enzymes that enhance xylose utilization designed for an automated platform. J Lab Autom 20(6):621–635 pii: 2211068215573188. This article was featured on front cover of December 2015 issue of the journal.

9.Lindquist MR, López-Núñez JC, Jones MA, Cox EJ,, Pinkelman RJ, Bang SS, Moser BR, Jackson MA, Iten LB, Kurtzman CP, Bischoff KM, Liu S, Qureshi N, Tasaki K, Rich JO, Cotta MA, Saha BC, Hughes SR. 2015. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates. Appl Microbiol Biotechnol 99(22):9723-9743.

10.Hughes SR, López-Núñez JC, Jones MA, Moser BR, Cox EJ, Lindquist M, Galindo-Leva LA, Riaño-Herrera NM, Rodriguez-Valencia N, Gast F, Cedeño DL, Tasaki K, Brown RC, Darzins A, Brunner L. 2014. Sustainable conversion of coffee and other crop wastes to biofuels and bioproducts using coupled biochemical and thermochemical processes in a multi-stage biorefinery concept. Appl Microbiol Biotechnol 98(20):8413-8431. doi:10.1007/s00253-014-5991-1

11.Khatibi PA, Roach DR, Donovan DM, Hughes SR, Bischoff KM. 2014. Saccharomyces cerevisiae expressing bacteriophage endolysins reduce Lactobacillus contamination during fermentation. Biotechnol Biofuels 7:104.

12.Hughes SR, Riedmuller SB. 2014. Integrated automation for continuous high-throughput synthetic chromosome assembly and transformation to identify improved yeast strains for industrial production of biofuel and bio-based chemicals. In Van den Berg MA, Maruthachalam K, editors. Genetic Transformation Systems in Fungi, Volume 2. Cham Heidelberg New York Dordrecht London: Springer. pp 183-200.

13.Hughes SR, Qureshi N 2014. Biomass for biorefining: Resources, allocation, utilization, and policies. In: Qureshi, N., Hodge, D., Vertes, A., editors. Biorefineries: Integrated Biochemical Processes for Liquid Biofuels. Amsterdam, The Netherlands: Elsevier. pp 37-58.

14.Johnson ET, Dowd PF, Hughes SR. 2014. Expression of a wolf spider toxin in tobacco inhibits the growth of microbes and insects. Biotechnol Lett 36(8):1735-1742. doi:10.1007/s10529-014-1536-z

15.Bergdale TE, Hughes SR, Bang SS. 2014. Thermostable hemicellulases of a bacterium, Geobacillus sp. DC3, isolated from the former Homestake gold mine in Lead, South Dakota. Appl Biochem Biotechnol 172(7):3488-3501. doi:10.1007/s12010-014-0784-7

16.Gibbons W, Hughes SR, Moser BR. 2014. Moving toward energy security and sustainability in 2050 by reconfiguring biofuel production. In: Songstad DD, Hatfield JL, Tomes DT, editors. Convergence of Food Security, Energy Security and Sustainable Agriculture. New York Dordrecht Heidelberg London: Springer. pp 15-30.

17.Hughes SR, Bang SS, Cox EJ, Schoepke A, Ochwat K, Pinkelman R, Nelson D, Qureshi N, Gibbons WR, Kurtzman CP, Bischoff KM, Liu S, Cote GL, Rich JO, Jones MA, Cedeño D, Doran-Peterson J, Riaño-Herrera NM, Rodríguez-Valencia N, López-Núñez JC. 2013. Automated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars. J Lab Autom 18(4):276-290.

18.Hughes SR, Gibbons WR, Moser BR, Rich JO. 2013. Sustainable Multipurpose Biorefineries for Third-Generation Biofuels and Value-Added Co-Products, In: Biofuels - Economy, Environment and Sustainability, Fang Z (Ed.), ISBN: 978-***-**-****-1, InTech, DOI: 10.5772/54804.

19.Rastogi G, Gurram RN., Bhalla A, Gonzalez R, Bischoff KM, Hughes SR, Kumar S, Sani RK. 2013. Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South Dakota. Frontiers in Microbiology 4(2):1-8.

20.Liu S, Bischoff KM, Leathers TD, Qureshi N, Rich JO, Hughes SR. 2013. Butyric acid from anaerobic fermentation of lignocellulosic biomass hydrolysates by Clostridium tyrobutyricum strain RPT-4213. Bioresource Technol 143:322-329.

21.Tudor KW, Jones MA, Hughes SR, Holt JP, Wiegand BR. 2013. Effect of fermentation with Saccharomyces cerevisiae strain PJ69-4 on the phytic acid, raffinose, and stachyose contents of soybean meal. Professional Animal Scientist 29(5):529-534.

22.Roach DR, Khatibi PA, Bischoff KM, Hughes SR, Donovan DM. 2013. Bacteriophage-encoded lytic enzymes control growth of contaminating Lactobacillus found in fuel ethanol fermentations. Biotechnol Biofuels 6(1):20. doi:10.1186/175*-****-*-**

23.Hughes SR, Gibbons WR, Bang SS, Pinkelman RJ, Bischoff KM, Slininger PJ, Qureshi N, Kurtzman CP, Liu S, Saha BC, Jackson JS, Cotta MA, Rich JO, Javers JE. 2012. Random UV-C mutagenesis of Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars. J Ind Microbiol Biotechnol 39(1):163–173.

24.Hughes SR, Moser BR, Robinson S, Cox EJ, Harmsen AJ, Friesen JA, Bischoff KM, Jones MA, Pinkelman RJ, Bang SS, Tasaki K, Doll KM, Qureshi N, Liu S, Saha BC, Jackson JS, Cotta MA, Rich JO, Caimi P. 2012. Synthetic resin-bound truncated Candida antarctica lipase B for production of fatty acid alkyl esters by transesterification of corn and soybean oils with ethanol or butanol. J Biotechnol 159:69-77. doi:10.1016/j.jbiotec.2012.01.025

25.Liu S, Wilkinson BJ, Bischoff KM, Hughes SR, Rich JO, Cotta MA. 2012. Novel antibacterial polypeptide laparaxin produced by Lactobacillus paracasei strain NRRL B-50314 via fermentation. J Pet Environ Biotechnol 3:121.

26.Qureshi N, Dien BS, Liu S, Saha BC, Hector RE, Cotta MA, Hughes SR. 2012. Genetically engineered Escherichia coli FBR5: Part I. Comparison of high cell density bioreactors for enhanced ethanol production from xylose. Biotechnol Progr 28(5):1167-1178.

27.Qureshi N, Dien BS, Liu S, Saha BC, Cotta MA, Hughes SR, Hector R. 2012. Genetically engineered Escherichia coli FBR5: Part II. Ethanol production from xylose and simultaneous product recovery. Biotechnol Progr 28(5):1179-1185.

28.Hughes SR, Dowd PF, Johnson ET. 2012. Cell-penetrating recombinant peptides for potential use in agricultural pest control applications. Pharmaceuticals (Basel) 5(10):1054-63. doi:10.3390/ph5101054

29.Geiger M, Gibbons J, West T, Hughes SR, Gibbons W. 2012. Evaluation of UV-C mutagenized Scheffersomyces stipitis strains for ethanol production. J Lab Autom 17(6):417-424. doi:10.1177/2211068212452873

30.Bergdale TE, Pinkelman RJ, Hughes SR, Zambelli B, Ciurli S, Bang SS. 2012. Engineered biosealant strains producing inorganic and organic biopolymers. J Biotechnol 161(3):181-189. doi:10.1016/j.jbiotec.2012.07.001

31.Hughes SR, Butt TR, Bartolett S, Riedmuller SB. 2012. Automated plasmid-based functional proteomics to improve microbes for biofuel production. In Liu ZL, editor. Microbial Stress Tolerance for Biofuels. New York Dordrecht Heidelberg London: Springer. pp 259-278.

32.Gibbons W, Hughes SR. 2011. Integrated biorefineries with engineered microbes and high-value co-products for profitable biofuels production. In: Tomes D, Lakshmanan P, Songstad D, editors. Biofuels: Global Impact on Renewable Energy, Production Agriculture, and Technological Advancements. New York Dordrecht Heidelberg London: Springer. pp. 265-284.

33.Bischoff KM, De Rezende ST, Larson TM, Liu S, Hughes SR, Rich JO. 2011. Purification and characterization of arabinofuranosidase from the corn endophyte Acremonium zeae. Biotechnol Lett 33(10):2013-2018. DOI: 10.1007/s10529-011-0658-9

34.Hector RE, Mertens JA, Bowman MJ, Nichols NN, Cotta MA, Hughes SR. 2011. Saccharomyces cerevisiae engineered for xylose metabolism requires gluconeogenesis and the oxidative branch of the pentose phosphate pathway for aerobic xylose assimilation. Yeast 28:645-660.

35.Hughes SR, Moser BR, Harmsen AJ, Robinson S, Bischoff KM, Jones MA, Pinkelman RJ, Bang SS, Tasaki K, Doll KM, Qureshi N, Liu S, Saha BC, Jackson JS, Cotta MA, Rich JO, Caimi P. 2011. Production of Candida antarctica lipase B gene open reading frame using automated PCR gene assembly protocol on robotic workcell and expression in an ethanologenic yeast for use as resin- bound biocatalyst in biodiesel production. J Lab Autom 16(1):17-37.

36.Hughes SR, Butt TR, Bartolett S, Riedmuller SB, Farrelly P. 2011. Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications. J Lab Autom 16(4):292-307.

37.Hughes SR, Qureshi N. 2010. Biofuel demand realization. In: Vertes A, Qureshi N, Blascheck HP, Yukawa H, editors. Biomass to Biofuels: Strategies for Global Industries. UK: John Wiley & Sons Limited. pp 55-69.

38.Hughes SR, Gibbons W, Kohl S. 2010. Advanced biorefineries for production of fuel ethanol. In: Vertes A, Qureshi N, Blaschek HP, Yukawa H, editors. Biomass to Biofuels: Strategies for Global Industries. UK: John Wiley & Sons Limited. pp 71-88.

39.Rastogi G, Bhalla A, Adhikari A, Bischoff KM, Hughes SR, Christopher LP, Sani RK. 2010. Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains. Bioresource Technol 101(22):8798-8806.

40.Qureshi N, Saha BC, Hector RE, Dien B, Hughes SR, Liu S, Iten L, Bowman MJ, Sarath G, Cotta MA. 2010. Production of butanol (a Biofuel) from agricultural residues: Part II - Use of corn stover and switchgrass hydrolysates. Biomass Bioenerg 34(4):566-571.

41.Bischoff KM, Liu S, Hughes SR, Rich JO. 2010. Fermentation of corn fiber hydrolysate to lactic acid by the moderate thermophile Bacillus coagulans. Biotechnol Lett 32:823-828.

42.Liu S, Bischoff KM, Qureshi N, Hughes SR, Rich JO. 2010. Functional expression of the thiolase gene THl from Clostridium beijerinckii P260 in Lactococcus lactis and Lactobacillus buchneri. New Biotechnol 27(4):283-288.

43.Hughes SR, Rich JO, Bischoff KM, Hector RE, Qureshi N, Saha BC, Dien BS, Liu S, Jackson JS, Sterner D., Butt TR, Labaer J, Cotta MA. 2009. Automated yeast transformation protocol to engineer Saccharomyces cerevisiae strains for cellulosic ethanol production with open reading frames that express proteins binding to xylose isomerase identified using robotic two-hybrid screen. J Assoc Lab Autom 14(4):200-212.

44.Hughes SR, Hector RE, Rich JO, Qureshi N, Bischoff KM, Dien BS, Saha BC, Liu S, Cox EJ, Jackson JS, Sterner DE. Butt TR, LaBaer J, Cotta MA. 2009. Automated yeast mating protocol using open reading frames from Saccharomyces cerevisiae genome to improve yeast strains for cellulosic ethanol production. J Assoc Lab Autom 14(4):190-199.

45.Hughes SR, Sterner DE, Bischoff KM, Hector RE,

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