@article{Li2011RSEM,
   author = {Li, Bo and Dewey, Colin N.},
   doi = {10.1186/1471-2105-12-3231},
   journal = {BMC Bioinformatics},
   pages = {323+},
   title = {{RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.}}, 
   url = {http://dx.doi.org/10.1186/1471-2105-12-323},
   volume = {12},
   year = {2011}
}

@article{Patro2014Sailfish,
  author = {Patro, Rob and Mount, Stephen M. and Kingsford, Carl},
  journal = {Nature Biotechnology},
  pages = {462--464},
  title = {{Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms}},
  url = {http://dx.doi.org/10.1038/nbt.2862},
  volume = {32},
  year = {2014}
}

@article{Patro2017Salmon,
  author = {Patro, Rob and Duggal, Geet and Love, Michael I. and Irizarry, Rafael A. and Kingsford, Carl},
  journal = {Nature Methods},
  title = {Salmon provides fast and bias-aware quantification of transcript expression},
  url = {http://dx.doi.org/10.1038/nmeth.4197},
  year = 2017
}

@article{Bray2016Near,
  author = {Bray, Nicolas and Pimentel, Harold and Melsted, Pall and Pachter, Lior},
  journal = {Nature Biotechnology},
  pages = {525–-527},
  title = {Near-optimal probabilistic RNA-seq quantification},
  volume = {34},
  url = {http://dx.doi.org/10.1038/nbt.3519},
  year = 2016
}

@article{Robert2015Errors,
   author = {Robert, Christelle and Watson, Mick},
   doi = {10.1186/s13059-015-0734-x},
   journal = {Genome Biology},
   title = {{Errors in RNA-Seq quantification affect genes of relevance to human disease}},
   url = {http://dx.doi.org/10.1186/s13059-015-0734-x},
   year = {2015}
}

@article{Trapnell2013Differential,
   author = {Trapnell, Cole and Hendrickson, David G and Sauvageau, Martin and Goff, Loyal and Rinn, John L and Pachter, Lior},
   doi = {10.1038/nbt.2450},
   journal = {Nature Biotechnology},
   title = {{Differential analysis of gene regulation at transcript resolution with RNA-seq}},
   url = {http://dx.doi.org/10.1038/nbt.2450},
   year = {2013}
}

@article{Soneson2015,
  url =          {http://dx.doi.org/10.12688/f1000research.7563.1},
  author =       {Soneson, Charlotte and Love, Michael I. and Robinson, Mark},
  title =        {{Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences}},
  journal =      {F1000Research},
  year =         2015,
  Volume =       4,
  Issue =        1521
}

@article{Love2014,
  url =          {http://dx.doi.org/10.1186/s13059-014-0550-8},
  author =       {Love, Michael I. and Huber, Wolfgang and Anders, Simon},
  title =        {{Moderated estimation of fold change and dispersion 
                  for RNA-seq data with DESeq2}},
  journal =      {Genome Biology},
  year =         2014,
  Volume =       15,
  Issue =        12,
  Pages =        550
}

@article{Robinson2010,
  url =          {http://dx.doi.org/10.1093/bioinformatics/btp616},
  author =       {Robinson, Mark D. and McCarthy, Davis J. and Smyth, Gordon K.},
  title =        {{edgeR: a Bioconductor package for differential expression analysis of digital gene expression data}},
  journal =      {Bioinformatics},
  year =         2010,
  Volume =       26,
  Issue =        1,
  Pages =        139
}

@article{Law2014,
  url =          {http://dx.doi.org/10.1186/gb-2014-15-2-r29},
  author =       {Law, Charity W. and Chen, Yunshun and Shi, Wei and Smyth, Gordon K.},
  title =        {{voom: precision weights unlock linear model analysis tools for RNA-seq read counts}},
  journal =      {Genome Biology},
  year =         2014,
  Volume =       15,
  Issue =        2,
  Pages =        29
}

@article{Pertea2015,
  url =          {https://dx.doi.org/10.1038%2Fnbt.3122},
  author =       {Pertea, Mihaela and Pertea, Geo M and Antonescu, Corina M and Chang, Tsung-Cheng and Mendell, Joshua T and Salzberg, Steven L},
  title =        {{StringTie enables improved reconstruction of a transcriptome from RNA-seq reads}},
  journal =      {Nature Biotechnology},
  year =         2015,
  Volume =       33,
  Issue =        3,
  Pages =        {290--295}
}

@article{Love2020,
  url =          {https://doi.org/10.1371/journal.pcbi.1007664},
  author =       {Love, Michael I. and Soneson, Charlotte and Hickey, Peter F. and Johnson, Lisa K. and Pierce, N. Tessa and Shepherd, Lori and Morgan, Martin and Patro, Rob},
  title =        {{Tximeta: Reference sequence checksums for provenance identification in RNA-seq}},
  journal =      {PLOS Computational Biology},
  year =         2020
}

@article{Srivastava2019,
	title={{Alevin efficiently estimates accurate gene abundances from dscRNA-seq data}},
	author={Srivastava, Avi and Malik, Laraib and Smith, Tom Sean and Sudbery, Ian and Patro, Rob},
	journal={Genome Biology},
	year={2019},
	volume={20},
	number={65},
	url={https://doi.org/10.1186/s13059-019-1670-y}
}
