Mihaela Pertea

Mihaela Pertea, PhD, is an Associate Professor in the Department of Biomedical Engineering at Johns Hopkins University, with affiliations in Genetic Medicine and the Computer Science department. She leads the Pertea Lab, focusing on computational methods for analyzing genomic and transcriptomic data to understand cellular function, particularly in gene finding, alternative splicing, and RNA-seq analysis. Her work integrates machine learning and statistical techniques to improve gene annotation and maintain genomic catalogues.

• Education: PhD in Computer Science (Johns Hopkins University, 2001); multiple degrees from University of Bucharest (BS in Psychology, BS and MS in Computer Science).
• Affiliations: Center for Computational Biology at Johns Hopkins.

Research interests include developing algorithms for transcriptome assembly, splice site prediction (e.g., Splam tool), and tools like StringTie for RNA-seq analysis. Her lab’s work has contributed to genome projects of malaria parasites, nematodes, and other pathogens. Recent achievements include an AIMBE College of Fellows recognition (2025) and innovations in AI-driven gene splicing analysis.

Publications span over 70 peer-reviewed articles, emphasizing computational biology tools and genomic studies. Notable collaborations include work on the ENCODE project and genome sequencing of Plasmodium falciparum. Her lab’s tools (e.g., CHESS, GFF Utilities) are widely used in genomic research.