Mihaela Pertea, MS, MSE, PhD

Professional Titles

• Member, McKusick-Nathans Institute of Genetic Medicine

Primary Academic Title

Associate Professor of Biomedical Engineering

Background

Centers and Institutes

McKusick-Nathans Institute of Genetic Medicine

Additional Academic Titles

Associate Professor of Genetic Medicine

Contact for Research Inquiries

McKusick-Nathans Institute for Genetic Medicine
733 N Broadway
Baltimore, MD 21205

Phone: (443) 287-0972

Research Interests

Computational gene finding, Sequence motif finding, Splice site prediction

Lab Website

Mihaela Pertea Lab - Lab Website

• The Mihaela Pertea Lab develops computational tools for RNA sequence analysis, gene finding, splice-site prediction and sequence-motif finding. Previous research projects led to the development of open-source software systems related to finding genes.

Google Scholar

https://scholar.google.com/scholar?q=Pertea+M&btnG=&hl=en&as_sdt=0%2C21

PubMed

http://www.ncbi.nlm.nih.gov/pubmed?term=(pertea%20m)%20NOT%20%22romanian%22%5BLanguage%5D

Selected Publications

• 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-
  D482.

  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.

  
  
  

Honors

• Named among the top 1% most highly cited microbiology researchers in the world, Thomson Reuters., 1/1/14
• Graduate Student Award for excellence and research in Computational Molecular Biology, DIMACS and Celera Genomics, 1/1/01
• Featured in the Annual Report of The Whiting School of Engineering, 1/1/01
• Abel Wolman Fellowship, Johns Hopkins Univeristy, 1/1/96
• Second Prize at the National Computer Science Contest, 1/1/94
• Governmental Merit-Based Fellowship, University of Bucharest, 1/1/89

Lectures & Presentations

• A combining algorithm to improve the performance of gene finders, 12th International Genome Sequencing and Analysis Conference, Miami Beach, 1/12/00
• A method to improve the performance of translation start site detection and its application for gene finding, Second International Workshop, WABI, 1/17/02
• Gene Finding in Eukaryotes, DIMACS Workshop on Integration of Diverse Biological Data, DIMACS Center, Rutgers University, Piscataway, 1/21/01
• GlimmerM: A System to Find Genes in Plasmodium falciparum, Fourth Annual Conference on Computational Genomics, Baltimore, 1/19/00
• Splice Site Recognition in MORGAN, Fifth International Conference on Intelligent Systems for Molecular Biology, Halkidiki, 1/21/97
• TWAIN: a new tool for parallel gene finding, Gordon Research Conference on Bioinformatics: From predictive models to inference, Oxford, 1/1/03