A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding. - Mihaela Pertea; Steven Salzberg (WABI, 2002)

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. - William H. Majoros; Mihaela Pertea; Corina Antonescu; Steven Salzberg (Nucleic Acids Res., 2003)

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. - William H. Majoros; Mihaela Pertea; Steven Salzberg (Bioinform., 2004)

Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. - William H. Majoros; Mihaela Pertea; Sihaela Salzberg (Bioinform., 2005)

Efficient decoding algorithms for generalized hidden Markov model gene finders. - William H. Majoros; Mihaela Pertea; Arthur L. Delcher; Steven Salzberg (BMC Bioinform., 2005)

Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding. - Mihaela Pertea; Steven Salzberg (WABI, 2007)

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. - Mihaela Pertea; Stephen M. Mount; Steven L. Salzberg (BMC Bioinform., 2007)

Problems and Solutions in Biological Sequence Analysis, Mark Borodovsky, Svetlana Ekisheva. - Mihaela Pertea (Briefings Bioinform., 2008)

OperonDB: a comprehensive database of predicted operons in microbial genomes. - Mihaela Pertea; Kunmi Ayanbule; Megan Smedinghoff; Steven L. Salzberg (Nucleic Acids Res., 2009)

Detection of Lineage-Specific Evolutionary Changes among Primate Species. - Mihaela Pertea; Geo Pertea; Steven L. Salzberg (BMC Bioinform., 2011)

TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets. - Ales Varabyou; Geo Pertea; Christopher Pockrandt; Mihaela Pertea (Bioinform., 2021)

Improved transcriptome assembly using a hybrid of long and short reads with StringTie. - Alaina Shumate; Brandon M. Wong; Geo Pertea; Mihaela Pertea (PLoS Comput. Biol., 2022)

Investigating open reading frames in known and novel transcripts using ORFanage. - Ales Varabyou; Beril Erdogdu; Steven L. Salzberg; Mihaela Pertea (Nat. Comput. Sci., 2023)