Research & Publications

Research Projects

As a research-focused company, we are actively engaged in various research projects. Our solution is adaptable and can be customized to meet the unique requirements and challenges of different research questions. Through our collaborative research projects, you can explore concrete examples that illustrate how our technology can be effectively applied in diverse fields. These real-world examples highlight the versatility and practicality of our solutions in diverse research contexts.

• Modeling Protein Abundance's Impact on Postsynaptic Protein Network Organization 

The collaborative project with Pázmány Péter Catholic University's Faculty of Information Technology and Bionics aims to investigate how postsynaptic protein complexes form. The goal is to understand the diversity of synaptic protein complexes in the postsynaptic density (PSD), which is a dense protein network critical for learning, memory, and it is involved in neurological disorders. The abundance of constituent proteins in the PSD can vary greatly in different brain areas, depending on the developmental stage, circadian rhythm, and in response to stimuli, making it challenging to characterize its molecular organization.   

The project uses large-scale stochastic simulations of protein binding events to predict the presence and distribution of PSD complexes. Seven major PSD proteins are modeled based on experimental protein abundance data from various brain areas of patients. The results show that the relative ratio of protein complexes can be influenced by subtle changes in protein abundances, and simulations are crucial to understand the relationship between protein availability and complex formation. 

Further information and updates on other ongoing projects will be provided later. 

Publications

Below you can find the scientific papers written by Cytocast scientists introducing the fundamental science behind our product.These papers illustrate how our research has contributed to the advancement of scientific knowledge in the field of biology, bioinformatics and health sciences.

List of publications

• Miski, Marcell, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy, and Zoltán Gáspári. "Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach." PLOS Computational Biology 18, no. 1 (2022): e1009758. 
• Quaglia, Federica, Bálint Mészáros, Edoardo Salladini, András Hatos, Rita Pancsa, Lucía B. Chemes, Mátyás Pajkos et al. "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation." Nucleic Acids Research 50, no. D1 (2022): D480-D487. 
• Pancsa, Rita, Erzsébet Fichó, Dániel Molnár, Éva Viola Surányi, Tamás Trombitás, Dóra Füzesi, Hanna Lóczi et al. "dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples." Nucleic Acids Research 50, no. D1 (2022): D1508-D1514. 
• Reguly, István Z., Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, Bence Keömley-Horváth et al. "Microsimulation based quantitative analysis of COVID-19 management strategies." PLoS computational biology 18, no. 1 (2022): e1009693. 
• Rizzetto, Simone, and Attila Csikász-Nagy. "Toward large-scale computational prediction of protein complexes." Computational Cell Biology: Methods and Protocols (2018): 271-295. 
• Rizzetto, Simone, Petros Moyseos, Bianca Baldacci, Corrado Priami, and Attila Csikász-Nagy. "Context-dependent prediction of protein complexes by SiComPre." NPJ Systems Biology and Applications 4, no. 1 (2018): 37. 
• Rizzetto, Simone, Corrado Priami, and Attila Csikász-Nagy. "Qualitative and quantitative protein complex prediction through proteome-wide simulations." PLOS Computational Biology 11, no. 10 (2015): e1004424. 
  

We recognize that the work we do at Cytocast is only made possible through the hard work and contributions of many individuals, including our past employees and collaborators. We want to acknowledge the work of those who have contributed to our mission. As such, we have compiled a list of publications from these individuals, highlighting their valuable work.

List of publications, research projects