Mihaela Pertea, PhD

Assistant Professor, McKusick-Nathans Institute of Genetic Medicine and Department of Medicine
Contact | Education | Research | Software |  Publications |

Education:

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

Research Interests:   

Computational gene finding, splice site prediction, sequence motif finding    

Selected software:

GlimmerHMM, GHMM gene-finder like Genscan/Genie, which makes use of the techniques implemented previously by GlimmerM : splice site modules and IMMs. Fast and accurate. 

ELPH, Gibbs sampler for finding motifs in DNA; has been used for detecting exon splice enhancers (ESE's). Also applicable to other motif-detection tasks. 

GeneSplicer, a tool for splice site prediction in a wide range of eukaryotes.

OperonDB , a comprehensive database of predicted operons in microbial genomes. It implements an efficient computational method for operon prediction based on comparative analyses.

TWAIN , a new syntenic gene finder which employs a Generalized Pair Hidden Markov Model (GPHMM) to predict genes in two closely related eukaryotic genomes simultaneously (written together with Bill Majoros).

Selected Publications:

Pertea M, Pertea GM, Salzberg SL. "Detection of lineage-specific evolutionary changes among primate species", BMC Bioinformatics 2011, 12: 274, http://www.biomedcentral.com/1471-2105/12/274

Salzberg SL & Pertea M. “Do-it-yourself genetic testing”. Genome Biology 2010, 11:404, http://genomebiology.com/2010/11/10/404

Pertea M, Salzberg SL. “Between a chicken and a grape: estimating the number of human genes”. Genome Biol. 2010 May 5;11(5):206. http://genomebiology.com/2010/11/S1/I1

Berriman M , Haas BJ et. al.  “The genome of the blood fluke Schistosoma mansoni”. Nature 460(7253): 352-U65 Published: JUL 16 2009, http://www.ncbi.nlm.nih.gov/pubmed/19606141

Zhou LM, Pertea M, Delcher AL, Florea L. “Sim4cc: a cross-species spliced alignment program”.  Nucleic Acids Research 37(11) DOI: 10.1093/nar/gkp319 Published: JUN 2009, http://nar.oxfordjournals.org/content/37/11/e80

Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. “OperonDB: a comprehensive database of predicted operons in microbial genomes”. Nucleic Acids Research 37: D479-D482 Published: JAN 2009, http://nar.oxfordjournals.org/content/37/suppl_1/D479.full

BJ Haas, SL Salzberg, W Zhu, M Pertea, JE Allen, J Orvis, O White, CR Buell, JR Wortman, Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biology, 9:R7 (2008). 

E Ghedin, S Wang, et al. Draft genome of the filarial nematode parasite Brugia malayi, Science, 317:1756-60 (2007). 

M Pertea, S.L. Salzberg, Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding, Algorithms in Bioinformatics, Lecture Notes in Computer Science 4645:208-215 (2007). 

M Pertea, SM Mount, SL Salzberg, A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana, BMC Bioinformatics, 8:159 (2007). 

Contact:

Mihaela Pertea, PhD

McKusick-Nathans Institute for Genetic Medicine
Johns Hopkins University School of Medicine
733 N Broadway, BRB  455
Baltimore, MD 21205

Phone: 443-287-0972
E-mail: mpertea@jhu.edu