Pertea M - Search Results

1

Splam: a deep-learning-based splice site predictor that improves spliced alignments.

Chao KH, Mao A, Salzberg SL, Pertea M. Chao KH, et al. Among authors: pertea m. Genome Biol. 2024 Sep 16;25(1):243. doi: 10.1186/s13059-024-03379-4. Genome Biol. 2024. PMID: 39285451 Free PMC article.

2

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. Pertea M, et al. Among authors: pertea g. Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2. Genome Biol. 2018. PMID: 30486838 Free PMC article.

3

Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Kovaka S, et al. Among authors: pertea m, pertea gm. Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. Genome Biol. 2019. PMID: 31842956 Free PMC article.

4

Splam: a deep-learning-based splice site predictor that improves spliced alignments.

Chao KH, Mao A, Salzberg SL, Pertea M. Chao KH, et al. Among authors: pertea m. bioRxiv [Preprint]. 2023 Jul 29:2023.07.27.550754. doi: 10.1101/2023.07.27.550754. bioRxiv. 2023. Update in: Genome Biol. 2024 Sep 16;25(1):243. doi: 10.1186/s13059-024-03379-4. PMID: 37546880 Free PMC article. Updated. Preprint.

5

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.

Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M. Varabyou A, et al. Among authors: pertea m. Genome Biol. 2023 Oct 30;24(1):249. doi: 10.1186/s13059-023-03088-4. Genome Biol. 2023. PMID: 37904256 Free PMC article.

6

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

Allen JE, Majoros WH, Pertea M, Salzberg SL. Allen JE, et al. Among authors: pertea m. Genome Biol. 2006;7 Suppl 1(Suppl 1):S9.1-13. doi: 10.1186/gb-2006-7-s1-s9. Epub 2006 Aug 7. Genome Biol. 2006. PMID: 16925843 Free PMC article.

7

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.

Pertea M, Mount SM, Salzberg SL. Pertea M, et al. BMC Bioinformatics. 2007 May 21;8:159. doi: 10.1186/1471-2105-8-159. BMC Bioinformatics. 2007. PMID: 17517127 Free PMC article.

8

Between a chicken and a grape: estimating the number of human genes.

Pertea M, Salzberg SL. Pertea M, et al. Genome Biol. 2010;11(5):206. doi: 10.1186/gb-2010-11-5-206. Epub 2010 May 5. Genome Biol. 2010. PMID: 20441615 Free PMC article. Review.

9

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT. Chang TC, et al. Among authors: pertea m. Genome Res. 2015 Sep;25(9):1401-9. doi: 10.1101/gr.193607.115. Genome Res. 2015. PMID: 26290535 Free PMC article.

10

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Pertea M, et al. Among authors: pertea gm. Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11. Nat Protoc. 2016. PMID: 27560171 Free PMC article.

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