Research Publications

Peer-reviewed research contributions in synthetic biology, bioengineering, and biotechnology innovation using Google Scholar verified data.

2024Metabolic Engineering

Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942

María Santos-Merino, Jonathan K Sakkos, Amit K Singh, Daniel C Ducat

Investigated carbon partitioning in engineered cyanobacterial strains to optimize photosynthetic efficiency and biomass production.

2024Micropublication Biology

Population-level heterogeneity complicates utilization of Synechococcus elongatus PCC 7942 surface display platforms

Lisa Yun, Jonathan K Sakkos, Daniel C Ducat

Engineered cyanobacterial surface display platforms to facilitate interaction with other microorganisms.

2023PLOS Computational Biology

Predicting partner fitness based on spatial structuring in a light-driven microbial community

Jonathan K Sakkos, María Santos-Merino, Emmanuel J Kokarakis, Bowen Li, Miguel Fuentes-Cabrera, Paolo Zuliani, Daniel C Ducat

Computational modeling of spatial structuring in microbial communities to predict the fitness of engineered consortium partners.

2022The Journal of Physical Chemistry A

Investigating carboxysome morphology dynamics with a rotationally invariant variational autoencoder

Miguel Fuentes-Cabrera, Jonathan K Sakkos, Daniel C Ducat, Maxim Ziatdinov

Study of carboxysome morphology using high-resolution imaging and computational models to understand their dynamics and organization.

2022ACS Synthetic Biology

Developing cyanobacterial quorum sensing toolkits: toward interspecies coordination in mixed autotroph/heterotroph communities

Emmanuel J Kokarakis, Rees Rillema, Daniel C Ducat, Jonathan K Sakkos

Creation of modular quorum sensing tools for cyanobacteria enabling complex gene circuit design and cell-cell communication.

2022Plant Physiology

Rubisco regulation in response to altered carbon status in the cyanobacterium Synechococcus elongatus PCC 7942

Amit K Singh, María Santos-Merino, Jonathan K Sakkos, Berkley J Walker, Daniel C Ducat

Unraveling the complex regulatory mechanisms of Rubisco in cyanobacteria under varying carbon conditions.

2021ACS synthetic biology

Orthogonal degron system for controlled protein degradation in cyanobacteria

Jonathan K Sakkos, Sergio Hernandez-Ortiz, Katherine W Osteryoung, Daniel C Ducat

Developed tool for controlled protein degradation in cyanobacteria which can be used to study protein function, regulation, and also has potential applications in biotechnology.

2019Nano Letters

Visualizing in vivo dynamics of designer nanoscaffolds

Eric J. Young, Jonathan K. Sakkos, Jingcheng Huang, Jacob K. Wright, Benjamin Kachel, Miguel Fuentes-Cabrera, Cheryl A. Kerfeld, Daniel C. Ducat

Development of visualization tools for tracking nanoscaffold dynamics in live cells, combining microscopy automation with custom image analysis pipelines.

2019Frontiers in Microbiology

Signal disruption leads to changes in bacterial community population

Michael Schwab, Celine Bergonzi, Jonathan Sakkos, Christopher Staley, Qian Zhang, Michael J. Sadowsky, Alptekin Aksan, Mikael Elias

Investigated how signal disruption affects bacterial community population and biofilm formation.

2019Scientific Reports

Enhancement of biocatalyst activity and protection against stressors using a microbial exoskeleton

Jonathan K. Sakkos, Lawrence P. Wackett, Alptekin Aksan

Demonstrated a method to enhance biocatalyst activity and stability using a silica-based microbial exoskeleton.

2017ACS Applied Materials and Interfaces

Adsorption and biodegradation of aromatic chemicals by bacteria encapsulated in a hydrophobic silica gel

Jonathan K Sakkos, Baris R Mutlu, Lawrence P Wackett, Alptekin Aksan

Investigated the coupling of adsorption and biodegradation processes for the removal of aromatic pollutants.

2016Biotechnology and Bioengineering

Engineering of a silica encapsulation platform for hydrocarbon degradation using Pseudomonas sp. NCIB 9816‐4

Jonathan K Sakkos, Daniel P Kieffer, Baris R Mutlu, Lawrence P Wackett, Alptekin Aksan

Developed a silica encapsulation platform to stabilize proteins and enzymes for hydrocarbon degradation.