@article{Patro2017,
  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 = {https://doi.org/10.1038/nmeth.4197},
  year = 2017
}

@article{Soneson2015,
  url =          {https://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{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,
  volume = 16,
  issue = 2,
  pages = {e1007664}
}

@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}
}

@article{ensembldb,
    author = {Rainer, Johannes and Gatto, Laurent and Weichenberger, Christian X},
    title = "{ensembldb: an R package to create and use Ensembl-based annotation resources}",
    journal = {Bioinformatics},
    year = {2019},
    month = {01}
}

@article{granges,
    author = {Lawrence, Michael AND Huber, Wolfgang AND Pagès, Hervé AND Aboyoun, Patrick AND Carlson, Marc AND Gentleman, Robert AND Morgan, Martin T. AND Carey, Vincent J.},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {{Software for Computing and Annotating Genomic Ranges}},
    year = {2013},
    month = {08},
    volume = {9},
    pages = {1-10},
    number = {8}
}

@article {Orjuelag2019,
	author = {Orjuela, Stephany and Huang, Ruizhu and Hembach, Katharina M. and Robinson, Mark D. and Soneson, Charlotte},
	title = {{ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data}},
	year = {2019},
	publisher = {G3: Genes, Genomes, Genetics},
	journal = {G3: Genes, Genomes, Genetics}
}

@article{oarfish,
    author = {Zare Jousheghani, Zahra and Singh, Noor Pratap and Patro, Rob},
    title = {Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification},
    journal = {Bioinformatics},
    volume = {41},
    number = {Supplement_1},
    pages = {i304-i313},
    year = {2025},
    month = {07},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btaf240}
 }

@article{baldoni2025dtu,
  author={Baldoni, Pedro L. and Chen, Lizhong and Li, Mengbo and Chen, Yunshun and Smyth, Gordon K.},
  year={2025},
  title={Dividing out quantification uncertainty enables assessment of differential transcript usage with {limma} and {edgeR}},
  journal={Nucleic Acids Research},
  volume={53},
  number={22},
  pages={gkaf1305},
  doi={10.1093/nar/gkaf1305}
}

@ARTICLE{baldoni2024dividing,
  author = {Baldoni, Pedro L. and Chen, Yunshun and Hediyeh-zadeh, Soroor and Liao, Yang and Dong, Xueyi and Rithie, Matthew E. and Shi, Wei and Smyth, Gordon K.},
  title = {Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with {edgeR}},
  journal = {Nucleic Acids Research},
  year = {2024},
  volume = {52},
  number = {3},
  pages = {e13},
  doi = {10.1093/nar/gkad1167}
}
