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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2014 5
2015 6
2016 4
2017 3
2018 1
2019 1
2020 0
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19 results
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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. 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.
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. Pertea M, et al. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. Nat Biotechnol. 2015. PMID: 25690850 Free PMC article.
How to share data for collaboration.
Ellis SE, Leek JT. Ellis SE, et al. Am Stat. 2018;72(1):53-57. doi: 10.1080/00031305.2017.1375987. Epub 2018 Apr 24. Am Stat. 2018. PMID: 32981941 Free PMC article.
svaseq: removing batch effects and other unwanted noise from sequencing data.
Leek JT. Leek JT. Nucleic Acids Res. 2014 Dec 1;42(21):e161. doi: 10.1093/nar/gku864. Epub 2014 Oct 7. Nucleic Acids Res. 2014. PMID: 25294822 Free PMC article.
Reproducible RNA-seq analysis using recount2.
Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Collado-Torres L, et al. Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. Nat Biotechnol. 2017. PMID: 28398307 Free PMC article. No abstract available.
Addressing confounding artifacts in reconstruction of gene co-expression networks.
Parsana P, Ruberman C, Jaffe AE, Schatz MC, Battle A, Leek JT. Parsana P, et al. Genome Biol. 2019 May 16;20(1):94. doi: 10.1186/s13059-019-1700-9. Genome Biol. 2019. PMID: 31097038 Free PMC article.
qSVA framework for RNA quality correction in differential expression analysis.
Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR. Jaffe AE, et al. Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. doi: 10.1073/pnas.1617384114. Epub 2017 Jun 20. Proc Natl Acad Sci U S A. 2017. PMID: 28634288 Free PMC article.
Test set bias affects reproducibility of gene signatures.
Patil P, Bachant-Winner PO, Haibe-Kains B, Leek JT. Patil P, et al. Bioinformatics. 2015 Jul 15;31(14):2318-23. doi: 10.1093/bioinformatics/btv157. Epub 2015 Mar 18. Bioinformatics. 2015. PMID: 25788628 Free PMC article.
Polyester: simulating RNA-seq datasets with differential transcript expression.
Frazee AC, Jaffe AE, Langmead B, Leek JT. Frazee AC, et al. Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28. Bioinformatics. 2015. PMID: 25926345 Free PMC article.
Ballgown bridges the gap between transcriptome assembly and expression analysis.
Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Frazee AC, et al. Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. Nat Biotechnol. 2015. PMID: 25748911 Free PMC article. No abstract available.
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