Mihaela Pertea, Ph.D., M.S., M.S.E.

  • Member, McKusick-Nathans Institute of Genetic Medicine
  • Associate Professor of Biomedical Engineering

Research Interests

Sequence motif finding; Splice site prediction; Computational gene finding ...read more


Mihaela Pertea, Ph.D., is an assistant professor of medicine in the McKusick-Nathans Institute of Genetic Medicine. She currently teaches courses in programming for DNA analysis.

Dr. Pertea holds bachelor’s degrees in computer science and psychology and a master’s degree in computer science from the University of Bucharest in Romania. She also holds a master’s of science degree in engineering from The Johns Hopkins University, where she later completed a Ph.D. in computer science. She joined the Johns Hopkins faculty in 2011.

Dr. Pertea’s research interests include analyzing microbial genomes, computational tools for transcriptome reconstruction, computational gene modeling and genome sequencing.

She serves on the editorial board of PeerJ and reviews manuscripts for myriad peer-review journals, including Genome Biology, Journal of Computational Biology, Bioinformatics, BMC Bioinformatics, Machine Learning, Nucleic Acids Research, Genetics, Genomics, BMC Genomics, PLOS ONE, Journal of Molecular Biology, Journal of Theoretical Biology, Pattern Recognition Letters, Information and Software Technology.

Dr. Pertea’s work was recognized in 2001 when she was the featured computer science student in the Whiting School of Engineering’s annual report. That same year, she was also awarded the DIMACS and Celera Genomics Graduate Student Award for excellence and research in computational molecular biology.

In 2014, she was named one of the most highly cited researchers in the world, in the field of microbiology, by Thomson Reuters.

...read more


  • Member, McKusick-Nathans Institute of Genetic Medicine
  • Associate Professor of Biomedical Engineering
  • Associate Professor of Genetic Medicine

Departments / Divisions

Centers & Institutes



  • M.S.E.; Johns Hopkins University (Maryland) (1998)
  • Ph.D.; Johns Hopkins University (Maryland) (2001)
  • B.S.; University of Bucharest (Romania) (1944)
  • M.S.; University of Bucharest (Romania) (1995)

Research & Publications

Selected Publications

View all on PubMed

Pertea, M, Salzberg, SL. “Using protein domains to improve the accuracy of ab initio gene
finding”. LECTURE NOTES IN COMPUTER SCIENCE, 7th International Workshop, WABI
2007 Proceedings, Vol 4645: 208-215.

Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, the nGASP Consortium, and
Stein LD. “nGASP – the nematode genome annotation assessment project”. BMC Bioinformatics
2008, 9: 549.

Haas, BJ, Salzberg, SL, Zhu, W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR.
“Automated eukaryotic gene structure annotation using EVidenceModeler and the program to
assemble spliced alignments”. GENOME BIOLOGY 2008, 9(1):R7.

Pertea, M, Ayanbule, K; Smedinghoff, M, Salzberg SL. “OperonDB: a comprehensive database
of predicted operons in microbial genomes”. NUCLEIC ACIDS RESEARCH 2009, 37: D479-

Zhou, LM, Pertea, M, Delcher, AL, Florea L. “Sim4cc: a cross-species spliced alignment
program”. NUCLEIC ACIDS RESEARCH 2009 37(11):e80.

Berriman, M; Haas, BJ; LoVerde, PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-
Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR,
Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin
E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D,
Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ,
Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR,
White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell
BG, El-Sayed NM. “The genome of the blood fluke Schistosoma mansoni”. NATURE 2009,
460(7253): 352-U65.

Pertea M, Salzberg SL. “Between a chicken and a grape: estimating the number of human genes”.
GENOME BIOLOGY 2010 May 5;11(5):206.

Salzberg SL & Pertea M. “Do-it-yourself genetic testing”. Genome Biology 2010, 11:404.

Pertea M, Pertea GM, Salzberg SL. "Detection of lineage-specific evolutionary changes among
primate species", BMC BIONFORMATICS 2011, 12: 274

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

Salzberg SL, Pertea M, Fahrner JA, Sobreira N. “DIAMUND: Direct Comparison of Genomes to
Detect Mutations”, HUMAN MUTATION 2014, 35:283–288.

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell J, Salzberg SL. “The StringTie
approach to reconstructing a transcriptome from RNA-seq data”, NATURE BIOTECHNOLOGY
2014, to appear.

Deng K, Pertea M, Rongvaux A, Durand CM, Ghiaur G, Lai J, McHugh HL, Hao H, Kumar P,
Deeks SG, Siliciano JD, Salzberg SL, Flavell RA, Shan L & Siliciano RF. “Broad-spectrum CTL
response is required to clear latent HIV-1 due to dominance of escape mutations”, NATURE 2014,
to appear.

Contact for Research Inquiries

Johns Hopkins University School of Medicine
McKusick-Nathans Institute for Genetic Medicine
733 N Broadway
Baltimore, MD 21205 map
Phone: 443-287-0972

Activities & Honors


  • Named among the top 1% most highly cited microbiology researchers in the world, Thomson Reuters., 2014
  • Graduate Student Award for excellence and research in Computational Molecular Biology, DIMACS and Celera Genomics , 2001
  • Featured in the Annual Report of The Whiting School of Engineering, 2001
  • Abel Wolman Fellowship, Johns Hopkins Univeristy, 1996 - 1997
  • Second Prize at the National Computer Science Contest, 1994
  • Governmental Merit-Based Fellowship, University of Bucharest, 1989 - 1995

Videos & Media

Lectures and Presentations

  • TWAIN: a new tool for parallel gene finding
    Gordon Research Conference on Bioinformatics: From predictive models to inference, Oxford (01/01/2003)
  • A method to improve the performance of translation start site detection and its application for gene finding
    Second International Workshop (01/17/2002)
  • Gene Finding in Eukaryotes
    DIMACS Workshop on Integration of Diverse Biological Data,  DIMACS Center, Piscataway (01/21/2001)
    Rutgers University
  • GlimmerM: A System to Find Genes in Plasmodium falciparum
    Fourth Annual Conference on Computational Genomics, Baltimore (01/19/2000)
  • A combining algorithm to improve the performance of gene finders
    12th International Genome Sequencing and Analysis Conference, Miami Beach (01/12/2000)
  • Splice Site Recognition in MORGAN
    Fifth International Conference on Intelligent Systems for Molecular Biology, Halkidiki (01/21/1997)

Patient Ratings & Comments

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