Mihaela Pertea, PhD

Associate Professor

Office: Wyman Park S257
Lab: Pertea Lab


PhD, Computer Science, Johns Hopkins University, 2001
MSE, Computer Science, Johns Hopkins University, 1998
MS, Computer Science, University of Bucharest, 1995
BS, Psychology, University of Bucharest, 1995
BS, Computer Science, University of Bucharest, 1994

Research Interests

Our group focuses on developing innovative and efficient methods to analyze large DNA and RNA sequence data sets in order to provide a genome-scale understanding of cellular function. Our research contributions integrate sophisticated machine learning techniques and statistical methods for identifying stretches of genomic DNA that have a biological function.This includes protein-coding genes, noncoding RNA genes, and regulatory regions that control the genes. A huge and still-growing number of genetic studies depend on accurate and complete gene descriptions, so our current research effort continues to be dedicated towards both the creation of computational pipelines that will improve the gene annotation as well as in maintaining the existing gene catalogues.

Publications Search

From Pub Med   |   Google Scholar Profile

Selected Publications

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A and Salzberg SL. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome Biology 2018, 19:208,

Pertea M, Kim D, Pertea GM, Leek JT, and Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 11, 1650-1667 (2016), doi:10.1038/nprot.2016.095.

Chang TC, Pertea M, Lee S, Salzberg SL, and Mendell J. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Research 2015, Sep;25(9):1401-9. doi: 10.1101/gr.193607.115.    

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell J, and Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 2015, 33 (3), 290-295. Publ. online 18 February 2015.

Pertea M. The Human Transcriptome: An Unfinished Story. Genes 2012, 3(3), 344-360