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Genome Research|May 9, 2019
Human contamination in bacterial genomes has created thousands of spurious proteinsFlorian P Breitwieser, Mihaela Pertea, Aleksey V Zimin, et al.Genome Biology|August 24, 2006
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regionsJonathan E Allen, William H Majoros, Mihaela Pertea, et al.Biorxiv : the Preprint Server for Biology|April 1, 2025
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human speciesKuan-Hao Chao, Alan Mao, Anqi Liu, et al.Elife|October 30, 2025
OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman speciesKuan-Hao Chao, Alan Mao, Anqi Liu, et al.Cell Reports Methods|March 20, 2024
Detecting differential transcript usage in complex diseases with SPITBeril Erdogdu, Ales Varabyou, Stephanie C Hicks, et al.Biorxiv : the Preprint Server for Biology|July 28, 2023
Detecting differential transcript usage in complex diseases with SPITBeril Erdogdu, Ales Varabyou, Stephanie C Hicks, et al.Nature Methods|July 3, 2026
Efficient evidence-based genome annotation with EviAnnAleksey V Zimin, Daniela Puiu, Mihaela Pertea, et al.Biorxiv : the Preprint Server for Biology|July 14, 2025
Isoswitching drives the aging process in human brainsBeril Erdogdu, Hyun Joo Ji, Zoe C Rudnick, et al.Nature Protocols|August 26, 2016
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and BallgownMihaela Pertea, Daehwan Kim, Geo M Pertea, et al.Genome Research|August 21, 2015
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanismsTsung-Cheng Chang, Mihaela Pertea, Sungyul Lee, et al.Pageof 33