Center for Bioinformatics and Computational Biology

 
photograph not shown

Mihaela Pertea's home page 

Assistant Research Scientist
Center for Bioinformatics & Computational Biology
3109 Biomolecular Sciences Building #296
University of Maryland
College Park, MD 20742
Phone: 301-405-9762

Email: mpertea [at] umiacs.umd.edu


Education

  1. PhD, Computer Science, Johns Hopkins University,  2001
  2. MSE, Computer Science, Johns Hopkins University,  1998
  3. MS, Computer Science, University of Bucharest, 1995
  4. BS, Computer Science, University of Bucharest, 1994
  5. BS, Psychology, University of Bucharest, 1995

Selected software

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).

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.


 

Publications

  1. Majoros WH, Pertea M, Salzberg SL. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding, Bioinformatics 2005 21(9):1782-1788. 

  2. Majoros WH, Pertea M, Delcher AL, Salzberg SL. Efficient decoding algorithms for generalized hidden Markov model gene finders, BMC Bioinformatics, 2005 Jan 24;6(1):16.

  3. Loftus BJ, Fung E, Roncaglia P, et al. The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus Neoformans, SCIENCE 2005 Feb 25;307(5713):1321-4.

  4. Feingold EA, Good PJ, Guyer MS, et al. The ENCODE (ENCyclopedia of DNA elements) Project SCIENCE 306 (5696): 636-640 Oct 22 2004

  5. Pertea M, "Searching for genes and biologically related signals in DNA sequences" (book chapter), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons Limited (to appear)

  6. Majoros WH, Pertea M, and Salzberg SL, TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders, Bioinformatics 2004 May 14

  7. Pain A, Woodward J, et al. Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genet Biol. 2004 Apr;41(4):443-53.

  8. Allen JE, Pertea M, Salzberg SL, Computational gene prediction using multiple sources of evidence, GENOME RES 14 (1): 142-148 JAN 2004

  9. Pertea M, Salzberg SL, "Using GlimmerM to find genes in eukaryotic genomes" (book chapter), Current Protocols in Bioinformatics, John Wiley & Sons, Inc, Volume 1: 4.4.1-4.4.20, 2003

  10. Majoros WH, Pertea M, Antonescu C, et al. GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders, NUCLEIC ACIDS RES 31 (13): 3601-3604 JUL 1 2003

  11. Yu YS, Rambo T, Currie J, et al. "In-depth view of structure, activity, and evolution of rice chromosome 10", SCIENCE 300 (5625): 1566-1569 JUN 6 2003

  12. Pertea M, Salzberg SL, "A method to improve the performance of translation start site detection and its application for gene finding", LECT NOTES COMPUT SC 2452: 210-219 2002

  13. Gardner MJ, Hall N, Fung E, et al. Genome sequence of the human malaria parasite Plasmodium falciparum, NATURE 419 (6906): 498-511 OCT 3 2002

  14. Carlton JM, Angiuoli SV, Suh BB, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii, NATURE 419 (6906): 512-519 OCT 3 2002

  15. Gardner MJ, Shallom SJ, Carlton JM, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14, NATURE 419 (6906): 531-534 OCT 3 2002

  16. Pertea M. and Salzberg S.L. Computational gene finding in plants. Plant Molecular Biology. 2002 48(1-2):39-48.

  17. Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR. Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species, Plant Physiol. 2001 Mar;125(3):1166-74.

  18. Pertea M, Lin X, Salzberg SL. GeneSplicer: a new computational method for splice site prediction, Nucleic Acids Res. 2001 Mar 1; 29(5):1185-90.

  19. The Arabidopsis Genome Initiative, "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. 2000 Dec 14; 408(6814):796-815.

  20. Pertea M, Salzberg SL, Gardner MJ, Finding genes in Plasmodium falciparum,Nature, 2000 Mar 2;404(6773):34.

  21. Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H, Interpolated Markov models for eukaryotic gene finding, Genomics. 1999 Jul 1;59(1):24-31.

  22. Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Peterson J, Shen K, Jing J, Aston C, Lai Z, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Hoffman SL, et al., Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum, Science. 1998 Nov 6;282(5391):1126-32.