Eleftherios Papoutsakis

TitleEugene duPont Chaired Professor
InstitutionUniversity of Delaware
DepartmentChemical and Biomolecular Engineering
Address15 Innovation Way
Newark DE 19716
Phone302-831-8376
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Delaware
    DepartmentBiological Sciences


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    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. Foster C, Charubin K, Papoutsakis ET, Maranas CD. Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture. mSystems. 2021 Feb 23; 6(1). PMID: 33622858.
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    2. Bennett RK, Gregory GJ, Gonzalez JE, Har JRG, Antoniewicz MR, Papoutsakis ET. Improving the Methanol Tolerance of an Escherichia coli Methylotroph via Adaptive Laboratory Evolution Enhances Synthetic Methanol Utilization. Front Microbiol. 2021; 12:638426. PMID: 33643274.
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    3. Har JRG, Agee A, Bennett RK, Papoutsakis ET, Antoniewicz MR. Adaptive laboratory evolution of methylotrophic Escherichia coli enables synthesis of all amino acids from methanol-derived carbon. Appl Microbiol Biotechnol. 2021 Jan; 105(2):869-876. PMID: 33404828.
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    4. Kyle Bennett R, Agee A, Har JRG, von Hagel B, Antoniewicz MR, Papoutsakis ET. Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli. Biotechnol Bioeng. 2020 Sep 02. PMID: 32876943.
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    5. Charubin K, Modla S, Caplan JL, Papoutsakis ET. Interspecies Microbial Fusion and Large-Scale Exchange of Cytoplasmic Proteins and RNA in a Syntrophic Clostridium Coculture. mBio. 2020 Sep 01; 11(5). PMID: 32873766.
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    6. Charubin K, Streett H, Papoutsakis ET. Development of new strong anaerobic fluorescent reporters for Clostridium acetobutylicum and Clostridium ljungdahlii using HaloTag and SNAP-tag proteins. Appl Environ Microbiol. 2020 Aug 07. PMID: 32769192.
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    7. Bennett RK, Agee A, Gerald Har JR, von Hagel B, Siu KH, Antoniewicz MR, Papoutsakis ET. Triggering the stringent response enhances synthetic methanol utilization in Escherichia coli. Metab Eng. 2020 Apr 28; 61:1-10. PMID: 32360074.
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    8. Bennett RK, Dillon M, Gerald Har JR, Agee A, von Hagel B, Rohlhill J, Antoniewicz MR, Papoutsakis ET. Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production. Metab Eng. 2020 Mar 13; 60:45-55. PMID: 32179162.
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    9. Escobar C, Kao CY, Das S, Papoutsakis ET. Human megakaryocytic microparticles induce de novo platelet biogenesis in a wild-type murine model. Blood Adv. 2020 Mar 10; 4(5):804-814. PMID: 32119736.
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    10. Rohlhill J, Gerald Har JR, Antoniewicz MR, Papoutsakis ET. Improving synthetic methylotrophy via dynamic formaldehyde regulation of pentose phosphate pathway genes and redox perturbation. Metab Eng. 2020 Jan; 57:247-255. PMID: 31881281.
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    11. Streett HE, Kalis KM, Papoutsakis ET. A strongly fluorescing anaerobic reporter and protein-tagging system for Clostridium organisms based on the Fluorescence-Activating and Absorption-Shifting Tag (FAST) protein. Appl Environ Microbiol. 2019 May 10. PMID: 31076434.
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    12. Kao CY, Papoutsakis ET. Extracellular vesicles: exosomes, microparticles, their parts, and their targets to enable their biomanufacturing and clinical applications. Curr Opin Biotechnol. 2019 Mar 06; 60:89-98. PMID: 30851486.
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    13. Diaz CAC, Bennett RK, Papoutsakis ET, Antoniewicz MR. Deletion of four genes in Escherichia coli enables preferential consumption of xylose and secretion of glucose. Metab Eng. 2019 Mar; 52:168-177. PMID: 30529131.
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    14. Kao CY, Papoutsakis ET. Engineering human megakaryocytic microparticles for targeted delivery of nucleic acids to hematopoietic stem and progenitor cells. Sci Adv. 2018 Nov; 4(11):eaau6762. PMID: 30417099.
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    15. Charubin K, Papoutsakis ET. Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO2 fixation, superior metabolite yields, and an expanded metabolic space. Metab Eng. 2019 Mar; 52:9-19. PMID: 30391511.
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    16. Luff SA, Kao CY, Papoutsakis ET. Role of p53 and transcription-independent p53-induced apoptosis in shear-stimulated megakaryocytic maturation, particle generation, and platelet biogenesis. PLoS One. 2018; 13(9):e0203991. PMID: 30231080.
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    17. Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng. 2018 Jul 25. PMID: 30055325.
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    18. Jones AJ, Fast AG, Clupper M, Papoutsakis ET. Small and Low but Potent: the Complex Regulatory Role of the Small RNA SolB in Solventogenesis in Clostridium acetobutylicum. Appl Environ Microbiol. 2018 Jul 15; 84(14). PMID: 29728392.
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    19. Fast AG, Papoutsakis ET. Functional Expression of the Clostridium ljungdahlii Acetyl-CoA Synthase in Clostridium acetobutylicum as Demonstrated by a Novel In Vivo CO Exchange Activity, on the Way to Heterologous Installation of a Functional Wood-Ljungdahl Pathway. Appl Environ Microbiol. 2018 Jan 26. PMID: 29374033.
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    20. Bennett RK, Gonzalez JE, Whitaker WB, Antoniewicz MR, Papoutsakis ET. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. Metab Eng. 2018 Jan; 45:75-85. PMID: 29203223.
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    21. Bennett RK, Steinberg LM, Chen W, Papoutsakis ET. Engineering the bioconversion of methane and methanol to fuels and chemicals in native and synthetic methylotrophs. Curr Opin Biotechnol. 2017 Dec 04; 50:81-93. PMID: 29216497.
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    22. Carlson ED, Papoutsakis ET. Heterologous expression of the Clostridium carboxidivorans CO dehydrogenase alone or together with the acetyl-CoA synthase enables Clostridium acetobutylicum to both reduce CO2 and oxidize CO. Appl Environ Microbiol. 2017 Jun 16. PMID: 28625981.
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    23. Dong M, Gonzalez TD, Klems MM, Steinberg LM, Chen W, Papoutsakis ET, Bahnson BJ. In vitro methanol production from methyl coenzyme M using the Methanosarcina barkeri MtaABC protein complex. Biotechnol Prog. 2017 May 27. PMID: 28556629.
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    24. Rohlhill J, Sandoval NR, Papoutsakis ET. Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol. ACS Synth Biol. 2017 08 18; 6(8):1584-1595. PMID: 28463494.
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    25. Jiang J, Kao CY, Papoutsakis ET. How do megakaryocytic microparticles target and deliver cargo to alter the fate of hematopoietic stem cells? J Control Release. 2017 Feb 10; 247:1-18. PMID: 28024915.
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    26. Whitaker WB, Jones JA, Bennett RK, Gonzalez JE, Vernacchio VR, Collins SM, Palmer MA, Schmidt S, Antoniewicz MR, Koffas MA, Papoutsakis ET. Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli. Metab Eng. 2016 Nov 1. PMID: 27815193.
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    27. Price JV, Chen L, Whitaker WB, Papoutsakis E, Chen W. Scaffoldless engineered enzyme assembly for enhanced methanol utilization. Proc Natl Acad Sci U S A. 2016 Oct 24. PMID: 27791059.
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    28. Jones SW, Fast AG, Carlson ED, Wiedel CA, Au J, Antoniewicz MR, Papoutsakis ET, Tracy BP. CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nat Commun. 2016 Sep 30; 7:12800. PMID: 27687501.
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    29. Sandoval NR, Papoutsakis ET. Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes. Curr Opin Microbiol. 2016 Oct; 33:56-66. PMID: 27376665.
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    30. Lee J, Jang YS, Papoutsakis ET, Lee SY. Stable and enhanced gene expression in Clostridium acetobutylicum using synthetic untranslated regions with a stem-loop. J Biotechnol. 2016 Jul 20; 230:40-3. PMID: 27188957.
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    31. Luff SA, Papoutsakis ET. Megakaryocytic Maturation in Response to Shear Flow Is Mediated by the Activator Protein 1 (AP-1) Transcription Factor via Mitogen-activated Protein Kinase (MAPK) Mechanotransduction. J Biol Chem. 2016 Apr 8; 291(15):7831-43. PMID: 26814129.
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    32. Sandoval NR, Venkataramanan KP, Groth TS, Papoutsakis ET. Whole-genome sequence of an evolved Clostridium pasteurianum strain reveals Spo0A deficiency responsible for increased butanol production and superior growth. Biotechnol Biofuels. 2015; 8:227. PMID: 26705421.
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    33. Zingaro KA, Papoutsakis ET. Building cellular pathways and programs enabled by the genetic diversity of allo-genomes and meta-genomes. Curr Opin Biotechnol. 2015 Dec; 36:16-31. PMID: 26318075.
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    34. Papoutsakis ET, Pronk JT. Editorial overview: Energy biotechnology. Curr Opin Biotechnol. 2015 Jun; 33:viii-xi. PMID: 25998091.
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    35. Gaida SM, Sandoval NR, Nicolaou SA, Chen Y, Venkataramanan KP, Papoutsakis ET. Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries. Nat Commun. 2015; 6:7045. PMID: 25944046.
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    36. Whitaker WB, Sandoval NR, Bennett RK, Fast AG, Papoutsakis ET. Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. Curr Opin Biotechnol. 2015 Jun; 33:165-75. PMID: 25796071.
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    37. Al-Hinai MA, Jones SW, Papoutsakis ET. The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiol Mol Biol Rev. 2015 Mar; 79(1):19-37. PMID: 25631287.
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    38. Dash S, Mueller TJ, Venkataramanan KP, Papoutsakis ET, Maranas CD. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model. Biotechnol Biofuels. 2014; 7(1):144. PMID: 25379054.
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    39. Yuan Y, Bi C, Nicolaou SA, Zingaro KA, Ralston M, Papoutsakis ET. Overexpression of the Lactobacillus plantarum peptidoglycan biosynthesis murA2 gene increases the tolerance of Escherichia coli to alcohols and enhances ethanol production. Appl Microbiol Biotechnol. 2014 Oct; 98(19):8399-411. PMID: 25173692.
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    40. Jiang J, Woulfe DS, Papoutsakis ET. Shear enhances thrombopoiesis and formation of microparticles that induce megakaryocytic differentiation of stem cells. Blood. 2014 Sep 25; 124(13):2094-103. PMID: 24948658.
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    41. Jang YS, Han MJ, Lee J, Im JA, Lee YH, Papoutsakis ET, Bennett G, Lee SY. Proteomic analyses of the phase transition from acidogenesis to solventogenesis using solventogenic and non-solventogenic Clostridium acetobutylicum strains. Appl Microbiol Biotechnol. 2014 Jun; 98(11):5105-15. PMID: 24743985.
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    42. Zingaro KA, Nicolaou SA, Yuan Y, Papoutsakis ET. Exploring the heterologous genomic space for building, stepwise, complex, multicomponent tolerance to toxic chemicals. ACS Synth Biol. 2014 Jul 18; 3(7):476-86. PMID: 24933690.
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    43. Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC, Papoutsakis ET. The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics. 2013; 14:849. PMID: 24299206.
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    44. Wang Q, Venkataramanan KP, Huang H, Papoutsakis ET, Wu CH. Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. BMC Syst Biol. 2013; 7:120. PMID: 24196194.
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    45. Al-Hinai MA, Jones SW, Papoutsakis ET. sK of Clostridium acetobutylicum Is the First Known Sporulation-Specific Sigma Factor with Two Developmentally Separated Roles, One Early and One Late in Sporulation. J Bacteriol. 2014 Jan; 196(2):287-99. PMID: 24187083.
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    46. Zingaro KA, Nicolaou SA, Papoutsakis ET. Dissecting the assays to assess microbial tolerance to toxic chemicals in bioprocessing. Trends Biotechnol. 2013 Nov; 31(11):643-53. PMID: 24094862.
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    47. Nicolaou SA, Fast AG, Nakamaru-Ogiso E, Papoutsakis ET. Overexpression of fetA (ybbL) and fetB (ybbM), Encoding an Iron Exporter, Enhances Resistance to Oxidative Stress in Escherichia coli. Appl Environ Microbiol. 2013 Dec; 79(23):7210-9. PMID: 24038693.
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    48. Gaida SM, Al-Hinai MA, Indurthi DC, Nicolaou SA, Papoutsakis ET. Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acids Res. 2013 Oct; 41(18):8726-37. PMID: 23892399.
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    49. Hou S, Jones SW, Choe LH, Papoutsakis ET, Lee KH. Workflow for quantitative proteomic analysis of Clostridium acetobutylicum ATCC 824 using iTRAQ tags. Methods. 2013 Jun 15; 61(3):269-76. PMID: 23523702.
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    50. Panuganti S, Schlinker AC, Lindholm PF, Papoutsakis ET, Miller WM. Three-stage ex vivo expansion of high-ploidy megakaryocytic cells: toward large-scale platelet production. Tissue Eng Part A. 2013 Apr; 19(7-8):998-1014. PMID: 23190353.
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    51. Lindsey S, Papoutsakis ET. The Evolving Role of the Aryl Hydrocarbon Receptor (AHR) in the Normophysiology of Hematopoiesis. Stem Cell Rev. 2012 Dec; 8(4):1223-35. PMID: 22628113.
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    52. Zingaro KA, Papoutsakis ET. Toward a semisynthetic stress response system to engineer microbial solvent tolerance. MBio. 2012; 3(5). PMID: 23033472.
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    53. Jiang J, Papoutsakis ET. Stem-Cell Niche Based Comparative Analysis of Chemical and Nano-mechanical Material Properties Impacting Ex Vivo Expansion and Differentiation of Hematopoietic and Mesenchymal Stem Cells. Adv Healthc Mater. 2013 Jan; 2(1):25-42. PMID: 23184458.
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    54. Al-Hinai MA, Fast AG, Papoutsakis ET. Novel system for efficient isolation of clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration. Appl Environ Microbiol. 2012 Nov; 78(22):8112-21. PMID: 22983967.
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    55. Nicolaou SA, Gaida SM, Papoutsakis ET. Exploring the combinatorial genomic space in Escherichia coli for ethanol tolerance. Biotechnol J. 2012 Nov; 7(11):1337-45. PMID: 22847918.
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    56. Apostolidis PA, Lindsey S, Miller WM, Papoutsakis ET. Proposed megakaryocytic regulon of p53: the genes engaged to control cell cycle and apoptosis during megakaryocytic differentiation. Physiol Genomics. 2012 Jun 15; 44(12):638-50. PMID: 22548738.
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    57. Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol. 2012 Jun; 23(3):364-81. PMID: 22079352.
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    58. Apostolidis PA, Woulfe DS, Chavez M, Miller WM, Papoutsakis ET. Role of tumor suppressor p53 in megakaryopoiesis and platelet function. Exp Hematol. 2012 Feb; 40(2):131-42.e4. PMID: 22024107.
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    59. Nicolaou SA, Gaida SM, Papoutsakis ET. Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes. Nucleic Acids Res. 2011 Dec; 39(22):e152. PMID: 21976725.
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    60. Bi C, Jones SW, Hess DR, Tracy BP, Papoutsakis ET. SpoIIE is necessary for asymmetric division, sporulation, and expression of sigmaF, sigmaE, and sigmaG but does not control solvent production in Clostridium acetobutylicum ATCC 824. J Bacteriol. 2011 Oct; 193(19):5130-7. PMID: 21784928.
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    61. Jones SW, Tracy BP, Gaida SM, Papoutsakis ET. Inactivation of sF in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division and abolishes sE and sG protein expression but does not block solvent formation. J Bacteriol. 2011 May; 193(10):2429-40. PMID: 21421765.
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    62. Chen Y, Indurthi DC, Jones SW, Papoutsakis ET. Small RNAs in the genus Clostridium. MBio. 2011; 2(1):e00340-10. PMID: 21264064.
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    63. Lindsey S, Papoutsakis ET. The aryl hydrocarbon receptor (AHR) transcription factor regulates megakaryocytic polyploidization. Br J Haematol. 2011 Feb; 152(4):469-84. PMID: 21226706.
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    64. Tracy BP, Jones SW, Papoutsakis ET. Inactivation of sE and sG in Clostridium acetobutylicum illuminates their roles in clostridial-cell-form biogenesis, granulose synthesis, solventogenesis, and spore morphogenesis. J Bacteriol. 2011 Mar; 193(6):1414-26. PMID: 21217008.
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    65. Crown SB, Indurthi DC, Ahn WS, Choi J, Papoutsakis ET, Antoniewicz MR. Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis. Biotechnol J. 2011 Mar; 6(3):300-5. PMID: 21370473.
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    66. Panuganti S, Papoutsakis ET, Miller WM. Bone marrow niche-inspired, multiphase expansion of megakaryocytic progenitors with high polyploidization potential. Cytotherapy. 2010 Oct; 12(6):767-82. PMID: 20482285.
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    67. SepĂșlveda DE, Andrews BA, Papoutsakis ET, Asenjo JA. Metabolic flux analysis of embryonic stem cells using three distinct differentiation protocols and comparison to gene expression patterns. Biotechnol Prog. 2010 Sep-Oct; 26(5):1222-9. PMID: 20945480.
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    68. Alsaker KV, Paredes C, Papoutsakis ET. Metabolite stress and tolerance in the production of biofuels and chemicals: gene-expression-based systems analysis of butanol, butyrate, and acetate stresses in the anaerobe Clostridium acetobutylicum. Biotechnol Bioeng. 2010 Apr 15; 105(6):1131-47. PMID: 19998280.
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    69. Nicolaou SA, Gaida SM, Papoutsakis ET. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng. 2010 Jul; 12(4):307-31. PMID: 20346409.
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    70. Tracy BP, Gaida SM, Papoutsakis ET. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotechnol. 2010 Feb; 21(1):85-99. PMID: 20206495.
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    71. Borden JR, Jones SW, Indurthi D, Chen Y, Papoutsakis ET. A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab Eng. 2010 May; 12(3):268-81. PMID: 20060060.
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    72. Wang M, Senger RS, Paredes C, Banik GG, Lin A, Papoutsakis ET. Microarray-based gene expression analysis as a process characterization tool to establish comparability of complex biological products: scale-up of a whole-cell immunotherapy product. Biotechnol Bioeng. 2009 Nov 1; 104(4):796-808. PMID: 19591186.
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    73. Lee JY, Jang YS, Lee J, Papoutsakis ET, Lee SY. Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J. 2009 Oct; 4(10):1432-40. PMID: 19830716.
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    74. Giammona LM, Panuganti S, Kemper JM, Apostolidis PA, Lindsey S, Papoutsakis ET, Miller WM. Mechanistic studies on the effects of nicotinamide on megakaryocytic polyploidization and the roles of NAD+ levels and SIRT inhibition. Exp Hematol. 2009 Nov; 37(11):1340-1352.e3. PMID: 19715739.
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    75. Kunas KT, Papoutsakis ET. Damage mechanisms of suspended animal cells in agitated bioreactors with and without bubble entrainment. Biotechnol Bioeng 1990; 36:476-83. Biotechnol Bioeng. 2009 Mar 1; 102(4):980-87; discussion 977-9. PMID: 19156925.
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    76. Sillers R, Al-Hinai MA, Papoutsakis ET. Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations. Biotechnol Bioeng. 2009 Jan 1; 102(1):38-49. PMID: 18726959.
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    77. Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol Bioeng. 2008 Dec 1; 101(5):1053-71. PMID: 18767191.
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    78. Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol Bioeng. 2008 Dec 1; 101(5):1036-52. PMID: 18767192.
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    79. Wang M, Windgassen D, Papoutsakis ET. A global transcriptional view of apoptosis in human T-cell activation. BMC Med Genomics. 2008; 1:53. PMID: 18947405.
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    80. Tracy BP, Gaida SM, Papoutsakis ET. Development and application of flow-cytometric techniques for analyzing and sorting endospore-forming clostridia. Appl Environ Microbiol. 2008 Dec; 74(24):7497-506. PMID: 18931289.
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    81. Sepulveda DE, Andrews BA, Asenjo JA, Papoutsakis ET. Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells. Tissue Eng Part A. 2008 Oct; 14(10):1603-14. PMID: 18433312.
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    82. Papoutsakis ET. Engineering solventogenic clostridia. Curr Opin Biotechnol. 2008 Oct; 19(5):420-9. PMID: 18760360.
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    83. Sillers R, Chow A, Tracy B, Papoutsakis ET. Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab Eng. 2008 Nov; 10(6):321-32. PMID: 18725313.
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    84. Jones SW, Paredes CJ, Tracy B, Cheng N, Sillers R, Senger RS, Papoutsakis ET. The transcriptional program underlying the physiology of clostridial sporulation. Genome Biol. 2008; 9(7):R114. PMID: 18631379.
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    85. Wang M, Windgassen D, Papoutsakis ET. Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-cell activation. BMC Genomics. 2008; 9:225. PMID: 18485203.
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    86. Fuhrken PG, Apostolidis PA, Lindsey S, Miller WM, Papoutsakis ET. Tumor suppressor protein p53 regulates megakaryocytic polyploidization and apoptosis. J Biol Chem. 2008 Jun 6; 283(23):15589-600. PMID: 18397889.
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    87. Fuhrken PG, Chen C, Apostolidis PA, Wang M, Miller WM, Papoutsakis ET. Gene Ontology-driven transcriptional analysis of CD34+ cell-initiated megakaryocytic cultures identifies new transcriptional regulators of megakaryopoiesis. Physiol Genomics. 2008 Apr 22; 33(2):159-69. PMID: 18252802.
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    88. Chen C, Fuhrken PG, Huang LT, Apostolidis P, Wang M, Paredes CJ, Miller WM, Papoutsakis ET. A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis. BMC Genomics. 2007; 8:384. PMID: 17953764.
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    89. Pascoe DE, Arnott D, Papoutsakis ET, Miller WM, Andersen DC. Proteome analysis of antibody-producing CHO cell lines with different metabolic profiles. Biotechnol Bioeng. 2007 Oct 1; 98(2):391-410. PMID: 17461427.
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    90. Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET. A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinformatics. 2007; 8:228. PMID: 17603872.
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    91. Huang LT, Paredes CJ, Papoutsakis ET, Miller WM. Gene expression analysis illuminates the transcriptional programs underlying the functional activity of ex vivo-expanded granulocytes. Physiol Genomics. 2007 Sep 19; 31(1):114-25. PMID: 17550995.
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    92. Paredes CJ, Senger RS, Spath IS, Borden JR, Sillers R, Papoutsakis ET. A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum. Appl Environ Microbiol. 2007 Jul; 73(14):4631-8. PMID: 17526797.
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    93. Borden JR, Papoutsakis ET. Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum. Appl Environ Microbiol. 2007 May; 73(9):3061-8. PMID: 17337545.
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    94. Fuhrken PG, Chen C, Miller WM, Papoutsakis ET. Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation. Exp Hematol. 2007 Mar; 35(3):476-489. PMID: 17309828.
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    95. Ray D, Terao Y, Fuhrken PG, Ma ZQ, DeMayo FJ, Christov K, Heerema NA, Franks R, Tsai SY, Papoutsakis ET, Kiyokawa H. Deregulated CDC25A expression promotes mammary tumorigenesis with genomic instability. Cancer Res. 2007 Feb 1; 67(3):984-91. PMID: 17283130.
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    96. Giammona LM, Fuhrken PG, Papoutsakis ET, Miller WM. Nicotinamide (vitamin B3) increases the polyploidisation and proplatelet formation of cultured primary human megakaryocytes. Br J Haematol. 2006 Nov; 135(4):554-66. PMID: 17054670.
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    97. Paredes CJ, Alsaker KV, Papoutsakis ET. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol. 2005 Dec; 3(12):969-78. PMID: 16261177.
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    98. Alsaker KV, Papoutsakis ET. Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum. J Bacteriol. 2005 Oct; 187(20):7103-18. PMID: 16199581.
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    99. Borden JR, Paredes CJ, Papoutsakis ET. Diffusion, mixing, and associated dye effects in DNA-microarray hybridizations. Biophys J. 2005 Nov; 89(5):3277-84. PMID: 16100268.
      Citations:    
    100. Zhao Y, Tomas CA, Rudolph FB, Papoutsakis ET, Bennett GN. Intracellular butyryl phosphate and acetyl phosphate concentrations in Clostridium acetobutylicum and their implications for solvent formation. Appl Environ Microbiol. 2005 Jan; 71(1):530-7. PMID: 15640230.
      Citations:    
    101. Ramsborg CG, Windgassen D, Fallon JK, Paredes CJ, Papoutsakis ET. Molecular insights into the pleiotropic effects of plasma on ex vivo-expanded T cells using DNA-microarray analysis. Exp Hematol. 2004 Oct; 32(10):970-90. PMID: 15504553.
      Citations:    
    102. Haddad H, Windgassen D, Ramsborg CG, Paredes CJ, Papoutsakis ET. Molecular understanding of oxygen-tension and patient-variability effects on ex vivo expanded T cells. Biotechnol Bioeng. 2004 Aug 20; 87(4):437-50. PMID: 15286980.
      Citations:    
    103. Thomas R, Mehrotra S, Papoutsakis ET, Hatzimanikatis V. A model-based optimization framework for the inference on gene regulatory networks from DNA array data. Bioinformatics. 2004 Nov 22; 20(17):3221-35. PMID: 15247105.
      Citations:    
    104. Alsaker KV, Spitzer TR, Papoutsakis ET. Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J Bacteriol. 2004 Apr; 186(7):1959-71. PMID: 15028679.
      Citations:    
    105. Tomas CA, Beamish J, Papoutsakis ET. Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J Bacteriol. 2004 Apr; 186(7):2006-18. PMID: 15028684.
      Citations:    
    106. Tummala SB, Junne SG, Paredes CJ, Papoutsakis ET. Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicumstrains. Biotechnol Bioeng. 2003 Dec 30; 84(7):842-54. PMID: 14708125.
      Citations:    
    107. Tomas CA, Alsaker KV, Bonarius HP, Hendriksen WT, Yang H, Beamish JA, Paredes CJ, Papoutsakis ET. DNA array-based transcriptional analysis of asporogenous, nonsolventogenic Clostridium acetobutylicum strains SKO1 and M5. J Bacteriol. 2003 Aug; 185(15):4539-47. PMID: 12867463.
      Citations:    
    108. Tomas CA, Welker NE, Papoutsakis ET. Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell's transcriptional program. Appl Environ Microbiol. 2003 Aug; 69(8):4951-65. PMID: 12902291.
      Citations:    
    109. Tummala SB, Junne SG, Papoutsakis ET. Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations. J Bacteriol. 2003 Jun; 185(12):3644-53. PMID: 12775702.
      Citations:    
    110. Tummala SB, Welker NE, Papoutsakis ET. Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J Bacteriol. 2003 Mar; 185(6):1923-34. PMID: 12618456.
      Citations:    
    111. Harris LM, Welker NE, Papoutsakis ET. Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824. J Bacteriol. 2002 Jul; 184(13):3586-97. PMID: 12057953.
      Citations:    
    112. Hevehan DL, Miller WM, Papoutsakis ET. Differential expression and phosphorylation of distinct STAT3 proteins during granulocytic differentiation. Blood. 2002 Mar 1; 99(5):1627-37. PMID: 11861277.
      Citations:    
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