Pitt Researchers Recognized for BioRECIPE

The American Chemical Society (ACS) has included University of Pittsburgh assistant professor Natasa Miskov-Zivanov and her students’ research in its collection celebrating International Day of Women and Girls in Science 2025. The paper, “The BioRECIPE Knowledge Representation Format,” describes a standardized format that researchers can use to write and share complex information more easily.

“It’s an honor to be selected by the ACS for this collection,” said Miskov-Zivanov. “As a woman scholar in electrical and computer engineering, we are a minority, so it is especially rewarding to see this acknowledgement of our efforts.”

At Pitt’s Swanson School of Engineering, Miskov-Zivanov runs the Mechanisms and Logic of Dynamics (MeLoDy) Lab. During her first years at Pitt, Miskov-Zivanov was the principal investigator (PI) for two Defense Advanced Research Projects Agency (DARPA) projects. She and her longtime collaborator Cheryl Telmer, a senior molecular biologist at Carnegie Mellon University, worked with students to develop “methods and tools for information retrieval, knowledge representation, model inference, and analysis of complex systems.”

“In systems and synthetic biology research, understanding the mechanisms of interaction and communication between cells, genes, and proteins within complex cellular networks is critically important,” Miskov-Zivanov explained.

The details of the mechanisms are available in the scientific literature, and machine reading can be used to extract information. However, many of the formats that are produced are only machine-readable and can be difficult for humans to interpret and evaluate. “To improve access to this information, biologists and computer scientists have developed standard representation formats of cell signaling and gene regulatory networks, a spreadsheet format that is both machine- and human-readable,” Miskov-Zivanov said.

The most recent version—Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution (BioRECIPE)—was released in spring 2024 and was developed using FAIR principles (findable, accessible, interoperable, and reusable). BioRECIPE is a knowledge representation format in spreadsheet form that is machine-readable. It can be used for analysis and modelling, and it is compatible with AI tools that can search and filter scientific literature and assist in curating knowledge. It represents an important step forward in making complex data more accessible to biologists.

This version of BioRECIPE was developed by a team of researchers, including five women, who wrote about it in “The BioRECIPE Knowledge Representation Format,” published in ACS Synthetic Biology in July 2024.

On February 11, International Day of Women and Girls in Science, Miskov-Zivanov learned that the paper had been included in an ACS collection that highlights “the latest achievements in research designed, performed, and published by women in chemistry.” The collection celebrates a day dedicated to promoting opportunities for women and girls worldwide to pursue education and careers in STEM-related fields.

“These women involved in BioRECIPE have played a vital role in developing it into what it is today. Having the opportunity to work with them and to get to watch them take these experiences and move into their future careers is so rewarding,” Miskov-Zivanov said.