Dynamic system explanation: DySE, a framework that evolves to reason about complex systems - lessons learned. - Cheryl A. Telmer; Khaled Sayed; Adam A. Butchy; Kara N. Bocan; Emilee Holtzapple; Casey E. Hansen; Gaoxiang Zhou; Yasmine Ahmed; Natasa Miskov-Zivanov (AIDR, 2019)

FLUTE: Fast and reliable knowledge retrieval from biomedical literature. - Emilee Holtzapple; Cheryl A. Telmer; Natasa Miskov-Zivanov (Database J. Biol. Databases Curation, 2020)

Context-aware query design combines knowledge and data for efficient reading and reasoning. - Emilee Holtzapple; Brent Cochran; Natasa Miskov-Zivanov (BioNLP@NAACL-HLT, 2021)