Publications & Patents

Hill JD and Papoutsakis ET. 2024. 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. 9(10): DOI10.1128/msystems.00572-24 

Seo, H, Capece, SH, Hill, JD, Otten, JK , Papoutsakis, ET. 2024. Butyrate as a growth factor of Clostridium acetobutylicum. 2024. Metabolic Engineering. 86:194-207 DOI10.1016/j.ymben.2024.10.005 

Willis, NB, and Papoutsakis ET. 2025. Separate Separated and Together: the Transcriptional Program of the Clostridium acetobutylicum- Clostridium ljungdahlii syntrophy leading to interspecies cell fusion. mSystems 10:e00030-25. DOI: 10.1128/msystems.00030-25 

Hill, JD, Seo, H, Papoutsakis ET. 2025. Acetogenic mixotrophy for carbon-neutral and carbon-negative production of chemicals. Current Opinion in Biotechnology 93:103298 

Hill, JD, Seo, H, Papoutsakis ET. 2025. Understanding the complexity of interspecies interactions in acetogenic mixotrophy to harness its potential for carbon-efficient metabolite production Current Opinion in Biotechnology, 93:103311. DOI: 10.1016/j.copbio.2025.103311 

Otten JK, Hill JD, Willis NB, Dalton A, Dougherty J, Papoutsakis ET. 2025. Cross-talk between engineered Clostridium acetobutylicum and Clostridium ljungdahlii in syntrophic cocultures enhances isopropanol and butanol production. Frontiers in Microbiology 16:1674318. DOI: 10.3389/fmicb.2025.1674318 

Willis NB, Otten JK, Seo H, Munasinghe PC, Papoutsakis ET. 2025. Enabling supratheoretical isopropanol yields from carbon-negative glucose fermentations with Clostridium acetobutylicum-Clostridium ljungdahlii cocultures. bioRxiv. DOI: 10.1101/2025.07.14.664808 

Willis NB, Bastek PA, Papoutsakis ET. 2025. Enabling strong acetogenic growth on CO2 and H2: H2 solubility limits Clostridium ljungdahlii growth on CO2 and H2. bioRxiv. DOI: 10.1101/2025.10.22.683911 

Willis NB, Bastek PA, Arunachalam AK, Papoutsakis ET. 2025. Engineering mutualism via nitrogen exchange in mixotrophic cocultures between Clostridium acetobutylicum and Clostridium ljungdahlii. bioRxiv. DOI: 10.1101/2025.10.22.683918 

Reddy JV, Raudenbush, K, Papoutsakis ET and Ierapetritou, M. 2023. Cell-culture process optimization via model-based predictions of metabolism and protein glycosylation, Biotechnology Advances 67: 108179. doi.org/10.1016/j.biotechadv.2023.108179 318. 

Reddy, JV, Singh, SK, Leibiger, T, Lee, KH, Ierapetritou, M, Papoutsakis, ET. 2025. 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. Metabolic Engineering.87: 37-48 DOI10.1016/j.ymben.2024.11.005 323. 

Reddy, JV, Leibiger, T, Singh, SK, Lee, KH, Ierapetritou, M, Papoutsakis, ET. 2025. 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. 122:761–778. DOI 10.1002/bit.28916 335. 

Belliveau J, Thompson, W. & ET Papoutsakis. 2024. Kinetic and functional analysis of abundant microRNAs in extracellular vesicles from normal and stressed cultures of Chinese hamster ovary cells. Biotechn Bioeng. 121:118-130. DOI: 10.1002/bit.28570 322. 

Malinov NG, Barodiya S, MG Ierapetritou and ET Papoutsakis. 2026. Pseudo perfusion of Chinese Hamster Ovary (CHO) cells as a reliable platform for data generation to model and guide continuous perfusion biomanufacturing. Biotechnology & Bioengineering, revised ms submitted (now accepted for publication). 336.

 Reddy, JV, Malinov, NG, Souvaliotis J, ET Papoutsakis & MG Ierapetritou. 2026. A dynamic metabolic flux analysis (DMFA) model for performance predictions of diverse CHO cell culture process modes and conditions. bioRxiv 2026.01.11.698917; doi: https://doi.org/10.64898/2026.01.11.698917 

Kao CY and Papoutsakis ET. 2018. Engineering Human Megakaryocytic Microparticles for Targeted Delivery of Nucleic Acids to Hematopoietic Stem & Progenitor Cells Science Advances. 4, eaau6762 (2018). 

Kao CY & Papoutsakis ET. 2019. Extracellular vesicles: exosomes, microparticles, their parts, and their targets to enable their biomanufacturing and clinical applications. Curr. Opin. Biotech. 60: 89-98. 

Escobar, C, Kao CY, Das, S & Papoutsakis ET. 2020. Human megakaryocytic microparticles induce de novo platelet biogenesis in a wild-type murine model. Blood Advances, 4(5): 804-814. DOI 10.1182/bloodadvances.2019000753. 

Kao CY, Jiang J, Thomson W & ET Papoutsakis. 2021. Combinatorial effect of miR-486-5p & miR-22-3p mimics thrombopoietin’s impact on hematopoietic stem & progenitor cells. Int. J. Mol Sci, 23:5355. https:// doi.org/10.3390/ijms23105355

Das S, Harris JC, Winter EJ, Kao C-Y, Day ES, Papoutsakis ET. 2022. Megakaryocyte membrane-wrapped nanoparticles for targeted cargo delivery to hematopoietic stem and progenitor cells. Bioeng Transl Med.: e10456. doi:10.1002/btm2.10456 

Thompson W, and Papoutsakis ET. 2023. 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. 8: e10563. https://doi.org/10.1002/btm2.10563 

Das, S, Thompson W, and Papoutsakis ET. 2024. Engineered and hybrid human megakaryocytic extracellular vesicles for targeted non-viral cargo delivery to hematopoietic (blood) stem and progenitor cells. Frontiers Bioeng. Biotech. 12: Article Number1435228. DOI10.3389/fbioe.2024.1435228 

Thompson W, and Papoutsakis ET. 2023. The role of biomechanical stress in extracellular vesicle formation, composition and activity. Biotechnology Advances 66, 108158. doi.org/10.1016/j.biotechadv.2023.108158 320. 

Papoutsakis, E, C-Y Kao and J. Jiang Megakaryocytic particles and microparticles for cell therapy and fate modification of stem and progenitor cells. US patent 10,538,738. Issued: 1/21/2020. Assignees: Papoutsakis, E, C-Y Kao and J. Jiang. 

Papoutsakis, E., S., W. B. Whitaker, Bennett, R. K. Synthetic methylotrophs. US patent 10,640,746. Issued: 5/20/2020. Assignee: Univ. of Delaware. 

Papoutsakis, E., S. Nicolaou, A. Fast, V. Falara, R. K. Bennett, W. B. Whitaker, J. Gonzalez, M. Antoniewicz. Synthetic methylotrophy to liquid fuels and chemicals. US patent 10,717,964 B2 (divisional of US patent 10,059,920). Issued 7/21/2020. Assignee: Univ. of Delaware. 

Papoutsakis, E, C-Y Kao and J. Jiang. MEGAKARYOCYTIC PARTICLES AND MICROPARTICLES FOR IN VIVO HEMATOPOIETIC CELL AND GENE THERAPIES. US 11,820,968 B2. Date of Patent: Nov. 21, 2023 

ET Papoutsakis, K Charubin, AA Mitkas Syntrophic co-cultures and uses thereof - US Patent App. 16/327,695, Published 7/19/2019. PCT/US2017/048176 (August 23, 2017). WO2018039319A1 (March 1, 2018). Assignee: Univ. of Delaware. 

Papoutsakis, E, Day, E, Winter, E, Harris, J, C-Y Kao and Das, S. BIOMEMBRANE-COVERED NANOPARTICLES (BIONPS) FOR DELIVERING ACTIVE AGENTS TO STEM CELLS. PCT/US19/63685. filed 11/24/2019. Publication of World patent WO2020113059A1 (June 4, 2020). Assignee: Univ. of Delaware. 

Papoutsakis, E, C-Y Kao and J. Jiang. Megakaryocytic particles and microparticles for in vivo hematopoietic cell and gene therapies. Divisional application (number 16711396) filed 12/10/2019. Publication: Pub. No.: US 2020/0115681 Al (43). Pub. Date: Apr. 16, 2020. Assignees: Papoutsakis, E, C-Y Kao and J. Jiang. 

Papoutsakis, E, & C-Y Kao. MicroRNAs Enriched in Megakaryocytic Extracellular Vesicles and Uses Thereof. Filled 10/21/2020. PCT/US20/056593. EFS ID: 40902315 17. Papoutsakis E & S. Das. Cellular membrane vesicles and uses thereof. PCT/US2020/054967, filed 10/14/2021. Assignee: Univ. of Delaware. 

Papoutsakis ET, Seo, Y, Otten, J, Willis, N, Hill, H & Capece, S. ENGINEERED SYNTROPHIC MICROBIAL CONSORTIA AND USES THEREOF. PCT/US23/79827. Filed 11/15/2023 19. Papoutsakis E & S. Das. Cellular membrane vesicles and uses thereof. Filed 04/14/2023. US-2023-0390202-A 1