Thomas Jefferson University

Eleftherios Papoutsakis

TitleAssoc Prof CHP
InstitutionThomas Jefferson University
DepartmentNursing - Undergraduate
Address15 Innovation Way
Newark DE 19716
Phone302-831-8376
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    Other Positions
    TitleAssoc Prof CHP
    InstitutionThomas Jefferson University
    DepartmentNursing - Undergraduate


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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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Reddy JV, Leibiger T, Singh SK, Lee KH, Papoutsakis E, Ierapetritou M. A Novel, Site-Specific N-Linked Glycosylation Model Provides Mechanistic Insights Into the Process-Condition Dependent Distinct Fab and Fc Glycosylation of an IgG1 Monoclonal Antibody Produced by CHO VRC01 Cells. Biotechnol Bioeng. 2024 Dec 30. PMID: 39740206.
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    2. Reddy JV, Singh SK, Leibiger T, Lee KH, Ierapetritou M, Papoutsakis ET. Flux balance analysis and peptide mapping elucidate the impact of bioreactor pH on Chinese Hamster Ovary (CHO) cell metabolism and N-linked glycosylation in the Fab and Fc regions of the produced IgG. Metab Eng. 2024 Nov 20. PMID: 39577620.
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    3. Seo H, Capece SH, Hill JD, Otten JK, Papoutsakis ET. Butyrate as a growth factor of Clostridium acetobutylicum. Metab Eng. 2024 Oct 15; 86:194-207. PMID: 39413987.
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    4. Das S, Thompson W, Papoutsakis ET. Engineered and hybrid human megakaryocytic extracellular vesicles for targeted non-viral cargo delivery to hematopoietic (blood) stem and progenitor cells. Front Bioeng Biotechnol. 2024; 12:1435228. PMID: 39386042.
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    5. Hill JD, Papoutsakis ET. Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures. mSystems. 2024 Oct 22; 9(10):e0057224. PMID: 39254339.
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    6. Charubin K, Hill JD, Papoutsakis ET. DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture. mBio. 2024 Jan 12; e0313323. PMID: 38214507.
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    7. Belliveau J, Thompson W, Papoutsakis ET. Kinetic and functional analysis of abundant microRNAs in extracellular vesicles from normal and stressed cultures of Chinese hamster ovary cells. Biotechnol Bioeng. 2023 Oct 20. PMID: 37859509.
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    8. Thompson W, Papoutsakis ET. Similar but distinct: The impact of biomechanical forces and culture age on the production, cargo loading, and biological efficacy of human megakaryocytic extracellular vesicles for applications in cell and gene therapies. Bioeng Transl Med. 2023 Sep; 8(5):e10563. PMID: 37693047.
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    9. Reddy JV, Raudenbush K, Papoutsakis ET, Ierapetritou M. Cell-culture process optimization via model-based predictions of metabolism and protein glycosylation. Biotechnol Adv. 2023 May 29; 67:108179. PMID: 37257729.
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    10. Thompson W, Papoutsakis ET. The role of biomechanical stress in extracellular vesicle formation, composition and activity. Biotechnol Adv. 2023 Apr 25; 66:108158. PMID: 37105240.
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    11. Jang YS, Kim WJ, Im JA, Palaniswamy S, Yao Z, Lee HL, Yoon YR, Seong HJ, Papoutsakis ET, Lee SY. Efforts to install a heterologous Wood-Ljungdahl pathway in Clostridium acetobutylicum enable the identification of the native tetrahydrofolate (THF) cycle and result in early induction of solvents. Metab Eng. 2023 Apr 11; 77:188-198. PMID: 37054966.
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    12. Funk MA, Malo CS, Lavine MS, Papoutsakis ET, Gagn? MR, Simonti C, Hurtley SM, Alderton G, Osborne IS, Scanlon ST, Ferrarelli LK, Olingy C. In Science Journals. Science. 2023 Mar 17; 379(6637):1110-1112. PMID: 36927024.
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    13. Belliveau J, Papoutsakis ET. The microRNomes of Chinese Hamster Ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress. Biotechnol Bioeng. 2023 Feb 14. PMID: 36788116.
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    14. Das S, Harris JC, Winter EJ, Kao CY, Day ES, Papoutsakis ET. Megakaryocyte membrane-wrapped nanoparticles for targeted cargo delivery to hematopoietic stem and progenitor cells. Bioeng Transl Med. 2023 May; 8(3):e10456. PMID: 37206243.
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    15. Otten JK, Zou Y, Papoutsakis ET. The potential of caproate (hexanoate) production using Clostridium kluyveri syntrophic cocultures with Clostridium acetobutylicum or Clostridium saccharolyticum. Front Bioeng Biotechnol. 2022; 10:965614. PMID: 36072287.
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    16. Kao CY, Jiang J, Thompson W, Papoutsakis ET. miR-486-5p and miR-22-3p Enable Megakaryocytic Differentiation of Hematopoietic Stem and Progenitor Cells without Thrombopoietin. Int J Mol Sci. 2022 May 11; 23(10). PMID: 35628168.
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    17. Dahle ML, Papoutsakis ET, Antoniewicz MR. 13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions. Metab Eng. 2022 Mar 18; 72:161-170. PMID: 35307558.
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    18. Belliveau J, Papoutsakis ET. Extracellular vesicles facilitate large-scale dynamic exchange of proteins and RNA among cultured Chinese hamster ovary and human cells. Biotechnol Bioeng. 2022 Feb 04. PMID: 35120270.
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    19. Gregory GJ, Bennett RK, Papoutsakis ET. Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs. Metab Eng. 2021 Sep 20. PMID: 34547453.
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    20. Streett H, Charubin K, Papoutsakis ET. Anaerobic fluorescent reporters for cell identification, microbial cell biology and high-throughput screening of microbiota and genomic libraries. Curr Opin Biotechnol. 2021 Oct; 71:151-163. PMID: 34375813.
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    21. Athaley A, Zhang Y, Papoutsakis ET, Ierapetritou M. Techno-economic and Life Cycle Analysis of MixAlco® Processes for Mixed Alcohol Production from Brown Algae. Appl Biochem Biotechnol. 2021 Sep; 193(9):2964-2982. PMID: 34019250.
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    22. 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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    23. 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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    24. 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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    25. 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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    26. 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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    27. 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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    28. 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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    29. 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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    30. 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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    31. 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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    32. 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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    33. 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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    34. 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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    35. 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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    36. 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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    37. 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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    38. 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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    39. 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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    40. 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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    41. 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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    42. 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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    43. Gonzalez JE, Bennett RK, Papoutsakis ET, Antoniewicz MR. Methanol assimilation in Escherichia coli is improved by co-utilization of threonine and deletion of leucine-responsive regulatory protein. Metab Eng. 2018 01; 45:67-74. PMID: 29203222.
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    44. 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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    45. 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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    46. 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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    47. Cho C, Choe D, Jang YS, Kim KJ, Kim WJ, Cho BK, Papoutsakis ET, Bennett GN, Seung DY, Lee SY. Genome analysis of a hyper acetone-butanol-ethanol (ABE) producing Clostridium acetobutylicum BKM19. Biotechnol J. 2017 Feb; 12(2). PMID: 27918147.
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    48. 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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    49. 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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    50. 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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    51. 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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    52. 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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    53. 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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    54. 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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    55. 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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    56. 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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    57. Venkataramanan KP, Min L, Hou S, Jones SW, Ralston MT, Lee KH, Papoutsakis ET. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum. Biotechnol Biofuels. 2015; 8:81. PMID: 26269711.
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    58. Papoutsakis ET, Pronk JT. Editorial overview: Energy biotechnology. Curr Opin Biotechnol. 2015 Jun; 33:viii-xi. PMID: 25998091.
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    59. 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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    60. 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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    61. 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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    62. 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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    63. 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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    64. 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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    65. 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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    66. Lindsey S, Jiang J, Woulfe D, Papoutsakis ET. Platelets from mice lacking the aryl hydrocarbon receptor exhibit defective collagen-dependent signaling. J Thromb Haemost. 2014 Mar; 12(3):383-94. PMID: 24410994.
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    67. 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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    68. 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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    69. 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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    70. 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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    71. 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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    72. 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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    73. 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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    74. 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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    75. 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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    76. Konieczna IM, Panuganti S, Deluca TA, Papoutsakis ET, Eklund EA, Miller WM. Administration of nicotinamide does not increase platelet levels in mice. Blood Cells Mol Dis. 2013 Mar; 50(3):171-6. PMID: 23265740.
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    77. 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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    78. 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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    79. 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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    80. 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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    81. 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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    82. 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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    83. Lee J, Jang YS, Choi SJ, Im JA, Song H, Cho JH, Seung do Y, Papoutsakis ET, Bennett GN, Lee SY. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl Environ Microbiol. 2012 Mar; 78(5):1416-23. PMID: 22210214.
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    84. 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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    85. 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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    86. 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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    87. 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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    88. 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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    89. 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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    90. 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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    91. 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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    92. 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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    93. 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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    94. Sepúlveda 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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    95. 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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    96. 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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    97. 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.
      Citations:    
    98. 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.
      Citations:    
    99. 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.
      Citations:    
    100. 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.
      Citations:    
    101. 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.
      Citations:    
    102. 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.
      Citations:    
    103. 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.
      Citations:    
    104. 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.
      Citations:    
    105. 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.
      Citations:    
    106. 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.
      Citations:    
    107. 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.
      Citations:    
    108. 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.
      Citations:    
    109. Papoutsakis ET. Engineering solventogenic clostridia. Curr Opin Biotechnol. 2008 Oct; 19(5):420-9. PMID: 18760360.
      Citations:    
    110. 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.
      Citations:    
    111. 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.
      Citations:    
    112. 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.
      Citations:    
    113. 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.
      Citations:    
    114. 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.
      Citations:    
    115. 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.
      Citations:    
    116. 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.
      Citations:    
    117. 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.
      Citations:    
    118. 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.
      Citations:    
    119. 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.
      Citations:    
    120. Wang H, Lu Y, Huang W, Papoutsakis ET, Fuhrken P, Eklund EA. HoxA10 activates transcription of the gene encoding mitogen-activated protein kinase phosphatase 2 (Mkp2) in myeloid cells. J Biol Chem. 2007 Jun 1; 282(22):16164-76. PMID: 17430893.
      Citations:    
    121. 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.
      Citations:    
    122. Ramsborg CG, Papoutsakis ET. Global transcriptional analysis delineates the differential inflammatory response interleukin-15 elicits from cultured human T cells. Exp Hematol. 2007 Mar; 35(3):454-464. PMID: 17309826.
      Citations:    
    123. 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.
      Citations:    
    124. 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.
      Citations:    
    125. 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.
      Citations:    
    126. 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.
      Citations:    
    127. 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.
      Citations:    
    128. 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:    
    129. 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:    
    130. 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:    
    131. 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:    
    132. 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:    
    133. 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:    
    134. 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:    
    135. Paredes CJ, Rigoutsos I, Papoutsakis ET. Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res. 2004; 32(6):1973-81. PMID: 15060177.
      Citations:    
    136. 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:    
    137. 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:    
    138. 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:    
    139. 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:    
    140. 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:    
    141. Yang H, Haddad H, Tomas C, Alsaker K, Papoutsakis ET. A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis. Proc Natl Acad Sci U S A. 2003 Feb 4; 100(3):1122-7. PMID: 12529501.
      Citations:    
    142. 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:    
    143. 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:    
    144. Yang H, Miller WM, Papoutsakis ET. Higher pH promotes megakaryocytic maturation and apoptosis. Stem Cells. 2002; 20(4):320-8. PMID: 12110701.
      Citations:    
    145. Harris LM, Blank L, Desai RP, Welker NE, Papoutsakis ET. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J Ind Microbiol Biotechnol. 2001 Nov; 27(5):322-8. PMID: 11781808.
      Citations:    
    146. Chow DC, Wenning LA, Miller WM, Papoutsakis ET. Modeling pO(2) distributions in the bone marrow hematopoietic compartment. I. Krogh's model. Biophys J. 2001 Aug; 81(2):675-84. PMID: 11463616.
      Citations:    
    147. Chow DC, Wenning LA, Miller WM, Papoutsakis ET. Modeling pO(2) distributions in the bone marrow hematopoietic compartment. II. Modified Kroghian models. Biophys J. 2001 Aug; 81(2):685-96. PMID: 11463617.
      Citations:    
    148. Mostafa SS, Papoutsakis ET, Miller WM. Oxygen tension modulates the expression of cytokine receptors, transcription factors, and lineage-specific markers in cultured human megakaryocytes. Exp Hematol. 2001 Jul; 29(7):873-83. PMID: 11438210.
      Citations:    
    149. Yang H, Papoutsakis ET, Miller WM. Model-based estimation of myeloid hematopoietic progenitor cells in ex vivo cultures for cell and gene therapies. Biotechnol Bioeng. 2001 Jan 20; 72(2):144-55. PMID: 11114652.
      Citations:    
    150. Haddad H, Papoutsakis ET. Low oxygen tension and autologous plasma enhance T-cell proliferation and CD49d expression density in serum-free media. Cytotherapy. 2001; 3(6):435-47. PMID: 11953028.
      Citations:    
    151. Mostafa SS, Miller WM, Papoutsakis ET. Oxygen tension influences the differentiation, maturation and apoptosis of human megakaryocytes. Br J Haematol. 2000 Dec; 111(3):879-89. PMID: 11122151.
      Citations:    
    152. Carswell KS, Papoutsakis ET. Extracellular pH affects the proliferation of cultured human T cells and their expression of the interleukin-2 receptor. J Immunother. 2000 Nov-Dec; 23(6):669-74. PMID: 11186155.
      Citations:    
    153. Hevehan DL, Wenning LA, Miller WM, Papoutsakis ET. Dynamic model of ex vivo granulocytic kinetics to examine the effects of oxygen tension, pH, and interleukin-3. Exp Hematol. 2000 Sep; 28(9):1016-28. PMID: 11008014.
      Citations:    
    154. Patel SD, Papoutsakis ET, Winter JN, Miller WM. The lactate issue revisited: novel feeding protocols to examine inhibition of cell proliferation and glucose metabolism in hematopoietic cell cultures. Biotechnol Prog. 2000 Sep-Oct; 16(5):885-92. PMID: 11027185.
      Citations:    
    155. Carswell KS, Papoutsakis ET. Culture of human T cells in stirred bioreactors for cellular immunotherapy applications: shear, proliferation, and the IL-2 receptor. Biotechnol Bioeng. 2000 May 5; 68(3):328-38. PMID: 10745201.
      Citations:    
    156. Hevehan DL, Papoutsakis ET, Miller WM. Physiologically significant effects of pH and oxygen tension on granulopoiesis. Exp Hematol. 2000 Mar; 28(3):267-75. PMID: 10720691.
      Citations:    
    157. Harris LM, Desai RP, Welker NE, Papoutsakis ET. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition? Biotechnol Bioeng. 2000 Jan 5; 67(1):1-11. PMID: 10581430.
      Citations:    
    158. Patel SD, Miller WM, Winter JN, Papoutsakis ET. Cell density-dependent proliferation in frequently-fed peripheral blood mononuclear cell cultures. Cytotherapy. 2000; 2(4):267-80. PMID: 12042036.
      Citations:    
    159. Patel SD, Guo R, Miller WM, Papoutsakis ET, Minster NI, Baum CM, Winter JN. Clinical-scale production of granulocyte progenitor and post-progenitor cells using daniplestim, leridistim, Progenipoietin, Promegapoietin and autologous plasma. Cytotherapy. 2000; 2(2):85-94. PMID: 12042045.
      Citations:    
    160. Carswell KS, Weiss JW, Papoutsakis ET. Low oxygen tension enhances the stimulation and proliferation of human T lymphocytes in the presence of IL-2. Cytotherapy. 2000; 2(1):25-37. PMID: 12042052.
      Citations:    
    161. Tummala SB, Welker NE, Papoutsakis ET. Development and characterization of a gene expression reporter system for Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol. 1999 Sep; 65(9):3793-9. PMID: 10473377.
      Citations:    
    162. Desai RP, Harris LM, Welker NE, Papoutsakis ET. Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by Clostridium acetobutylicum. Metab Eng. 1999 Jul; 1(3):206-13. PMID: 10937935.
      Citations:    
    163. Desai RP, Nielsen LK, Papoutsakis ET. Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. J Biotechnol. 1999 May 28; 71(1-3):191-205. PMID: 10483106.
      Citations:    
    164. Desai RP, Papoutsakis ET. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl Environ Microbiol. 1999 Mar; 65(3):936-45. PMID: 10049845.
      Citations:    
    165. Nair RV, Green EM, Watson DE, Bennett GN, Papoutsakis ET. Regulation of the sol locus genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor. J Bacteriol. 1999 Jan; 181(1):319-30. PMID: 9864345.
      Citations:    
    166. Guo M, Miller WM, Papoutsakis ET, Patel S, James C, Goolsby C, Winter JN. Ex-vivo expansion of CFU-GM and BFU-E in unselected PBMC cultures with Flt3L is enhanced by autologous plasma. Cytotherapy. 1999; 1(3):183-94. PMID: 12881174.
      Citations:    
    167. Collins PC, Patel SD, Papoutsakis ET, Miller WM. Nuclei-size distributions as predictive tools of hematopoietic cell proliferation. Cytotherapy. 1999; 1(2):99-109. PMID: 19746586.
      Citations:    
    168. Collins PC, Patel SD, Miller WM, Papoutsakis ET. Initiation, maintenance, and quantification of human hematopoietic cell cultures. Methods Mol Med. 1999; 18:271-92. PMID: 21370184.
      Citations:    
    169. Nielsen LK, Bender JG, Miller WM, Papoutsakis ET. Population balance model of in vivo neutrophil formation following bone marrow rescue therapy. Cytotechnology. 1998 Nov; 28(1-3):157-62. PMID: 19003417.
      Citations:    
    170. McAdams TA, Miller WM, Papoutsakis ET. pH is a potent modulator of erythroid differentiation. Br J Haematol. 1998 Nov; 103(2):317-25. PMID: 9827900.
      Citations:    
    171. McDowell CL, Papoutsakis ET. Increased agitation intensity increases CD13 receptor surface content and mRNA levels, and alters the metabolism of HL60 cells cultured in stirred tank bioreactors. Biotechnol Bioeng. 1998 Oct 20; 60(2):239-50. PMID: 10099425.
      Citations:    
    172. McDowell CL, Carver RT, Papoutsakis ET. Effects of methocel A15LV, polyethylene glycol, and polyvinyl alcohol on CD13 and CD33 receptor surface content and metabolism of HL60 cells cultured in stirred tank bioreactors. Biotechnol Bioeng. 1998 Oct 20; 60(2):251-8. PMID: 10099426.
      Citations:    
    173. McDowell CL, Papoutsakis ET. Serum increases the CD13 receptor expression, reduces the transduction of fluid-mechanical forces, and alters the metabolism of HL60 cells cultured in agitated bioreactors. Biotechnol Bioeng. 1998 Oct 20; 60(2):259-68. PMID: 10099427.
      Citations:    
    174. Collins PC, Miller WM, Papoutsakis ET. Stirred culture of peripheral and cord blood hematopoietic cells offers advantages over traditional static systems for clinically relevant applications. Biotechnol Bioeng. 1998 Sep 5; 59(5):534-43. PMID: 10099369.
      Citations:    
    175. Horner M, Miller WM, Ottino JM, Papoutsakis ET. Transport in a grooved perfusion flat-bed bioreactor for cell therapy applications. Biotechnol Prog. 1998 Sep-Oct; 14(5):689-98. PMID: 9758657.
      Citations:    
    176. LaIuppa JA, Papoutsakis ET, Miller WM. Oxygen tension alters the effects of cytokines on the megakaryocyte, erythrocyte, and granulocyte lineages. Exp Hematol. 1998 Aug; 26(9):835-43. PMID: 9694504.
      Citations:    
    177. McDowell CL, Papoutsakis ET. Decreasing extracellular pH increases CD13 receptor surface content and alters the metabolism of HL60 cells cultured in stirred tank bioreactors. Biotechnol Prog. 1998 Jul-Aug; 14(4):567-72. PMID: 9694677.
      Citations:    
    178. Collins PC, Nielsen LK, Patel SD, Papoutsakis ET, Miller WM. Characterization of hematopoietic cell expansion, oxygen uptake, and glycolysis in a controlled, stirred-tank bioreactor system. Biotechnol Prog. 1998 May-Jun; 14(3):466-72. PMID: 9622528.
      Citations:    
    179. Bermejo LL, Welker NE, Papoutsakis ET. Expression of Clostridium acetobutylicum ATCC 824 genes in Escherichia coli for acetone production and acetate detoxification. Appl Environ Microbiol. 1998 Mar; 64(3):1079-85. PMID: 9501448.
      Citations:    
    180. LaIuppa JA, McAdams TA, Papoutsakis ET, Miller WM. Culture materials affect ex vivo expansion of hematopoietic progenitor cells. J Biomed Mater Res. 1997 Sep 5; 36(3):347-59. PMID: 9260106.
      Citations:    
    181. Cornillot E, Nair RV, Papoutsakis ET, Soucaille P. The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain. J Bacteriol. 1997 Sep; 179(17):5442-7. PMID: 9286999.
      Citations:    
    182. Collins PC, Nielsen LK, Wong CK, Papoutsakis ET, Miller WM. Real-time method for determining the colony-forming cell content of human hematopoietic cell cultures. Biotechnol Bioeng. 1997 Aug 20; 55(4):693-700. PMID: 18636579.
      Citations:    
    183. McAdams TA, Miller WM, Papoutsakis ET. Variations in culture pH affect the cloning efficiency and differentiation of progenitor cells in ex vivo haemopoiesis. Br J Haematol. 1997 Jun; 97(4):889-95. PMID: 9217193.
      Citations:    
    184. LaIuppa JA, Papoutsakis ET, Miller WM. Ex vivo expansion of hematopoietic stem and progenitor cells for transplantation. Cancer Treat Res. 1997; 77:159-86. PMID: 9071503.
      Citations:    
    185. LaIuppa JA, Papoutsakis ET, Miller WM. Evaluation of cytokines for expansion of the megakaryocyte and granulocyte lineages. Stem Cells. 1997; 15(3):198-206. PMID: 9170211.
      Citations:    
    186. Sandstrom CE, Collins PC, McAdams TA, Bender JG, Papoutsakis ET, Miller WM. Comparison of whole serum-deprived media for ex vivo expansion of hematopoietic progenitor cells from cord blood and mobilized peripheral blood mononuclear cells. J Hematother. 1996 Oct; 5(5):461-73. PMID: 8938518.
      Citations:    
    187. McAdams TA, Winter JN, Miller WM, Papoutsakis ET. Hematopoietic cell culture therapies (Part II): Clinical aspects and applications. Trends Biotechnol. 1996 Oct; 14(10):388-96. PMID: 8987637.
      Citations:    
    188. McAdams TA, Miller WM, Papoutsakis ET. Hematopoietic cell culture therapies (Part I): Cell culture considerations. Trends Biotechnol. 1996 Sep; 14(9):341-9. PMID: 8818288.
      Citations:    
    189. Michaels JD, Mallik AK, Papoutsakis ET. Sparging and agitation-induced injury of cultured animals cells: Do cell-to-bubble interactions in the bulk liquid injure cells? Biotechnol Bioeng. 1996 Aug 20; 51(4):399-409. PMID: 18629792.
      Citations:    
    190. Green EM, Boynton ZL, Harris LM, Rudolph FB, Papoutsakis ET, Bennett GN. Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824. Microbiology. 1996 Aug; 142 ( Pt 8):2079-86. PMID: 8760920.
      Citations:    
    191. Sandstrom CE, Bender JG, Miller WM, Papoutsakis ET. Development of novel perfusion chamber to retain nonadherent cells and its use for comparison of human "mobilized" peripheral blood mononuclear cell cultures with and without irradiated bone marrow stroma. Biotechnol Bioeng. 1996 Jun 5; 50(5):493-504. PMID: 18627011.
      Citations:    
    192. Collins PC, Papoutsakis ET, Miller WM. Ex vivo culture systems for hematopoietic cells. Curr Opin Biotechnol. 1996 Apr; 7(2):223-30. PMID: 8791333.
      Citations:    
    193. Michaels JD, Nowak JE, Mallik AK, Koczo K, Wasan DT, Papoutsakis ET. Analysis of cell-to-bubble attachment in sparged bioreactors in the presence of cell-protecting additives. Biotechnol Bioeng. 1995 Aug 20; 47(4):407-19. PMID: 18623417.
      Citations:    
    194. Michaels JD, Nowak JE, Mallik AK, Koczo K, Wasan DT, Papoutsakis ET. Interfacial properties of cell culture media with cell-protecting additives. Biotechnol Bioeng. 1995 Aug 20; 47(4):420-30. PMID: 18623418.
      Citations:    
    195. Sandstrom CE, Bender JG, Papoutsakis ET, Miller WM. Effects of CD34+ cell selection and perfusion on ex vivo expansion of peripheral blood mononuclear cells. Blood. 1995 Aug 1; 86(3):958-70. PMID: 7542506.
      Citations:    
    196. McAdams TA, Sandstrom CE, Miller WM, Bender JG, Papoutsakis ET. Ex vivo expansion of primitive hematopoietic cells for cellular therapies: An overview. Cytotechnology. 1995 Jan; 18(1-2):133-46. PMID: 22358646.
      Citations:    
    197. Borys MC, Linzer DI, Papoutsakis ET. Cell aggregation in a Chinese hamster ovary cell microcarrier culture affects the expression rate and N-linked glycosylation of recombinant mouse placental lactogen-1. Ann N Y Acad Sci. 1994 Nov 30; 745:360-71. PMID: 7832523.
      Citations:    
    198. Nair RV, Papoutsakis ET. Expression of plasmid-encoded aad in Clostridium acetobutylicum M5 restores vigorous butanol production. J Bacteriol. 1994 Sep; 176(18):5843-6. PMID: 8083176.
      Citations:    
    199. Mermelstein LD, Welker NE, Petersen DJ, Bennett GN, Papoutsakis ET. Genetic and metabolic engineering of Clostridium acetobutylicum ATCC 824. Ann N Y Acad Sci. 1994 May 2; 721:54-68. PMID: 8010697.
      Citations:    
    200. Walter KA, Mermelstein LD, Papoutsakis ET. Studies of recombinant Clostridium acetobutylicum with increased dosages of butyrate formation genes. Ann N Y Acad Sci. 1994 May 2; 721:69-72. PMID: 8010698.
      Citations:    
    201. Sandstrom CE, Miller WM, Papoutsakis ET. Serum-free media for cultures of primitive and mature hematopoietic cells. Biotechnol Bioeng. 1994 Apr 5; 43(8):706-33. PMID: 18615795.
      Citations:    
    202. Borys MC, Linzer DI, Papoutsakis ET. Ammonia affects the glycosylation patterns of recombinant mouse placental lactogen-I by chinese hamster ovary cells in a pH-dependent manner. Biotechnol Bioeng. 1994 Mar 15; 43(6):505-14. PMID: 18615748.
      Citations:    
    203. Nair RV, Bennett GN, Papoutsakis ET. Molecular characterization of an aldehyde/alcohol dehydrogenase gene from Clostridium acetobutylicum ATCC 824. J Bacteriol. 1994 Feb; 176(3):871-85. PMID: 8300540.
      Citations:    
    204. Walter KA, Nair RV, Cary JW, Bennett GN, Papoutsakis ET. Sequence and arrangement of two genes of the butyrate-synthesis pathway of Clostridium acetobutylicum ATCC 824. Gene. 1993 Nov 30; 134(1):107-11. PMID: 8244020.
      Citations:    
    205. Mermelstein LD, Papoutsakis ET, Petersen DJ, Bennett GN. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for increased solvent production by enhancement of acetone formation enzyme activities using a synthetic acetone operon. Biotechnol Bioeng. 1993 Nov 5; 42(9):1053-60. PMID: 18613233.
      Citations:    
    206. Borys MC, Linzer DI, Papoutsakis ET. Culture pH affects expression rates and glycosylation of recombinant mouse placental lactogen proteins by Chinese hamster ovary (CHO) cells. Biotechnology (N Y). 1993 Jun; 11(6):720-4. PMID: 7763675.
      Citations:    
    207. Lee SY, Mermelstein LD, Papoutsakis ET. Determination of plasmid copy number and stability in Clostridium acetobutylicum ATCC 824. FEMS Microbiol Lett. 1993 Apr 15; 108(3):319-23. PMID: 8514119.
      Citations:    
    208. Lakhotia S, Bauer KD, Papoutsakis ET. Fluid-mechanical forces in agitated bioreactors reduce the CD13 and CD33 surface protein content of HL60 cells. Biotechnol Bioeng. 1993 Apr 15; 41(9):868-77. PMID: 18609635.
      Citations:    
    209. Mermelstein LD, Papoutsakis ET. In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi 3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol. 1993 Apr; 59(4):1077-81. PMID: 8386500.
      Citations:    
    210. Koller MR, Bender JG, Miller WM, Papoutsakis ET. Expansion of primitive human hematopoietic progenitors in a perfusion bioreactor system with IL-3, IL-6, and stem cell factor. Biotechnology (N Y). 1993 Mar; 11(3):358-63. PMID: 7680209.
      Citations:    
    211. Papoutsakis ET, Bennett GN. Cloning, structure, and expression of acid and solvent pathway genes of Clostridium acetobutylicum. Biotechnology. 1993; 25:157-99. PMID: 7691287.
      Citations:    
    212. Walter KA, Bennett GN, Papoutsakis ET. Molecular characterization of two Clostridium acetobutylicum ATCC 824 butanol dehydrogenase isozyme genes. J Bacteriol. 1992 Nov; 174(22):7149-58. PMID: 1385386.
      Citations:    
    213. Lakhotia S, Bauer KD, Papoutsakis ET. Damaging agitation intensities increase DNA synthesis rate and alter cell-cycle phase distributions of CHO cells. Biotechnol Bioeng. 1992 Oct 20; 40(8):978-90. PMID: 18601205.
      Citations:    
    214. Koller MR, Bender JG, Papoutsakis ET, Miller WM. Beneficial effects of reduced oxygen tension and perfusion in long-term hematopoietic cultures. Ann N Y Acad Sci. 1992 Oct 13; 665:105-16. PMID: 1416596.
      Citations:    
    215. Lee SY, Mermelstein LD, Bennett GN, Papoutsakis ET. Vector construction, transformation, and gene amplification in Clostridium acetobutylicum ATCC 824. Ann N Y Acad Sci. 1992 Oct 13; 665:39-51. PMID: 1416617.
      Citations:    
    216. Koller MR, Bender JG, Papoutsakis ET, Miller WM. Effects of synergistic cytokine combinations, low oxygen, and irradiated stroma on the expansion of human cord blood progenitors. Blood. 1992 Jul 15; 80(2):403-11. PMID: 1627798.
      Citations:    
    217. Mermelstein LD, Welker NE, Bennett GN, Papoutsakis ET. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. Biotechnology (N Y). 1992 Feb; 10(2):190-5. PMID: 1368230.
      Citations:    
    218. Koller MR, Bender JG, Miller WM, Papoutsakis ET. Reduced oxygen tension increases hematopoiesis in long-term culture of human stem and progenitor cells from cord blood and bone marrow. Exp Hematol. 1992 Feb; 20(2):264-70. PMID: 1544397.
      Citations:    
    219. Lakhotia S, Papoutsakis ET. Agitation induced cell injury in microcarrier cultures. Protective effect of viscosity is agitation intensity dependent: Experiments and modeling. Biotechnol Bioeng. 1992 Jan 5; 39(1):95-107. PMID: 18600891.
      Citations:    
    220. Borys MC, Papoutsakis ET. Formation of bridges and large cellular clumps in CHO-cell microcarrier cultures: effects of agitation, dimethyl sulfoxide and calf serum. Cytotechnology. 1992; 8(3):237-48. PMID: 1368821.
      Citations:    
    221. Petersen DJ, Welch RW, Walter KA, Mermelstein LD, Papoutsakis ET, Rudolph FB, Bennett GN. Cloning of an NADH-dependent butanol dehydrogenase gene from Clostridium acetobutylicum. Ann N Y Acad Sci. 1991 Dec 27; 646:94-8. PMID: 1809209.
      Citations:    
    222. Papoutsakis ET. Fluid-mechanical damage of animal cells in bioreactors. Trends Biotechnol. 1991 Dec; 9(12):427-37. PMID: 1367747.
      Citations:    
    223. Papoutsakis ET. Media additives for protecting freely suspended animal cells against agitation and aeration damage. Trends Biotechnol. 1991 Sep; 9(9):316-24. PMID: 1367617.
      Citations:    
    224. Michaels JD, Papoutsakis ET. Polyvinyl alcohol and polyethylene glycol as protectants against fluid-mechanical injury of freely-suspended animal cells (CRL 8018). J Biotechnol. 1991 Jul; 19(2-3):241-57. PMID: 1367239.
      Citations:    
    225. Michaels JD, Petersen JF, McIntire LV, Papoutsakis ET. Protection mechanisms of freely suspended animal cells (CRL 8018) from fluid-mechanical injury. Viscometric and bioreactor studies using serum, pluronic F68 and polyethylene glycol. Biotechnol Bioeng. 1991 Jun 20; 38(2):169-80. PMID: 18600747.
      Citations:    
    226. Kunas KT, Papoutsakis ET. Damage mechanisms of suspended animal cells in agitated bioreactors with and without bubble entrainment. Biotechnol Bioeng. 1990 Aug 20; 36(5):476-83. PMID: 18595104.
      Citations:    
    227. Kunas KT, Papoutsakis ET. The protective effect of serum against hydrodynamic damage of hybridoma cells in agitated and surface-aerated bioreactors. J Biotechnol. 1990 Jul; 15(1-2):57-69. PMID: 1366688.
      Citations:    
    228. Cary JW, Petersen DJ, Papoutsakis ET, Bennett GN. Cloning and expression of Clostridium acetobutylicum ATCC 824 acetoacetyl-coenzyme A:acetate/butyrate:coenzyme A-transferase in Escherichia coli. Appl Environ Microbiol. 1990 Jun; 56(6):1576-83. PMID: 2383002.
      Citations:    
    229. Hüsemann MH, Papoutsakis ET. Effects of propionate and acetate additions on solvent production in batch cultures of Clostridium acetobutylicum. Appl Environ Microbiol. 1990 May; 56(5):1497-500. PMID: 2339898.
      Citations:    
    230. Cary JW, Petersen DJ, Bennett GN, Papoutsakis ET. Methods for cloning key primary metabolic enzymes and ancillary proteins associated with the acetone-butanol fermentation of Clostridium acetobutylicum. Ann N Y Acad Sci. 1990; 589:67-81. PMID: 2192667.
      Citations:    
    231. Welch RW, Rudolph FB, Papoutsakis ET. Purification and characterization of the NADH-dependent butanol dehydrogenase from Clostridium acetobutylicum (ATCC 824). Arch Biochem Biophys. 1989 Sep; 273(2):309-18. PMID: 2673038.
      Citations:    
    232. Wiesenborn DP, Rudolph FB, Papoutsakis ET. Phosphotransbutyrylase from Clostridium acetobutylicum ATCC 824 and its role in acidogenesis. Appl Environ Microbiol. 1989 Feb; 55(2):317-22. PMID: 2719475.
      Citations:    
    233. Wiesenborn DP, Rudolph FB, Papoutsakis ET. Coenzyme A transferase from Clostridium acetobutylicum ATCC 824 and its role in the uptake of acids. Appl Environ Microbiol. 1989 Feb; 55(2):323-9. PMID: 2719476.
      Citations:    
    234. Cherry RS, Papoutsakis ET. Modeling of contact-inhibited animal cell growth on flat surfaces and spheres. Biotechnol Bioeng. 1989 Jan 15; 33(3):300-5. PMID: 18587917.
      Citations:    
    235. Wiesenborn DP, Rudolph FB, Papoutsakis ET. Thiolase from Clostridium acetobutylicum ATCC 824 and Its Role in the Synthesis of Acids and Solvents. Appl Environ Microbiol. 1988 Nov; 54(11):2717-22. PMID: 16347774.
      Citations:    
    236. Cherry RS, Papoutsakis ET. Physical mechanisms of cell damage in microcarrier cell culture bioreactors. Biotechnol Bioeng. 1988 Oct 5; 32(8):1001-14. PMID: 18587818.
      Citations:    
    237. Cary JW, Petersen DJ, Papoutsakis ET, Bennett GN. Cloning and expression of Clostridium acetobutylicum phosphotransbutyrylase and butyrate kinase genes in Escherichia coli. J Bacteriol. 1988 Oct; 170(10):4613-8. PMID: 2844725.
      Citations:    
    238. Hüsemann MH, Papoutsakis ET. Solventogenesis in Clostridium acetobutylicum fermentations related to carboxylic acid and proton concentrations. Biotechnol Bioeng. 1988 Sep 20; 32(7):843-52. PMID: 18587795.
      Citations:    
    239. Chu IM, Papoutsakis ET. Growth dynamics of a methylotroph (Methylomonas L3) in continuous cultures. I. Fast transients induced by methanol pulses and methanol accumulation. Biotechnol Bioeng. 1987 Jan; 29(1):55-64. PMID: 18561129.
      Citations:    
    240. Chu IM, Papoutsakis ET. Growth dynamics of a methylotroph (Methylomonas L3) in continuous cultures. II. Growth inhibition and comparison against an unstructured model. Biotechnol Bioeng. 1987 Jan; 29(1):65-71. PMID: 18561130.
      Citations:    
    241. McLaughlin JK, Meyer CL, Papoutsakis ET. Gas chromatography and gateway sensors for on-line state estimation of complex fermentations (butanol-acetone fermentation). Biotechnol Bioeng. 1985 Aug; 27(8):1246-57. PMID: 18553808.
      Citations:    
    242. Roos JW, McLaughlin JK, Papoutsakis ET. The effect of pH on nitrogen supply, cell lysis, and solvent production in fermentations of Clostridium acetobutylicum. Biotechnol Bioeng. 1985 May; 27(5):681-94. PMID: 18553724.
      Citations:    
    243. Papoutsakis ET, Meyer CL. Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations. Biotechnol Bioeng. 1985 Jan; 27(1):50-66. PMID: 18553576.
      Citations:    
    244. Papoutsakis ET, Meyer CL. Fermentation equations for propionic-acid bacteria and production of assorted oxychemicals from various sugars. Biotechnol Bioeng. 1985 Jan; 27(1):67-80. PMID: 18553577.
      Citations:    
    245. Papoutsakis ET. Equations and calculations for fermentations of butyric acid bacteria. Biotechnol Bioeng. 1984 Feb; 26(2):174-87. PMID: 18551704.
      Citations:    
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