Mihaela Pertea's home page

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).

Publications

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).
V Nene, JR Wortman, et al. Genome sequence of Aedes aegypti, a major arbovirus vector,Science, 316:1718-23 (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).
JM Carlton, RP Hirt, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis, Science, 315:207-12 (2007).
JE Allen, WH Majoros, M Pertea, SL Salzberg JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions, Genome Biology, 7 Suppl 1:S9.1-13 (2006).
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.
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.
MJ Gardner, R Bishop, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes, Science, 309:134-7 2005.
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.
Feingold EA, Good PJ, Guyer MS, et al. The ENCODE (ENCyclopedia of DNA elements) Project SCIENCE 306 (5696): 636-640 Oct 22 2004
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)
Majoros WH, Pertea M, and Salzberg SL, TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders, Bioinformatics 2004 May 14
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.
Allen JE, Pertea M, Salzberg SL, Computational gene prediction using multiple sources of evidence, GENOME RES 14 (1): 142-148 JAN 2004
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
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
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
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
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
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
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
Pertea M. and Salzberg S.L. Computational gene finding in plants. Plant Molecular Biology. 2002 48(1-2):39-48.
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.
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.
The Arabidopsis Genome Initiative, "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. 2000 Dec 14; 408(6814):796-815.
Pertea M, Salzberg SL, Gardner MJ, Finding genes in Plasmodium falciparum,Nature, 2000 Mar 2;404(6773):34.
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.
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.