tech.bib

@article{love2014moderated,
  title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
  author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
  journal={Genome biology},
  volume={15},
  number={12},
  pages={1--21},
  year={2014},
  publisher={BioMed Central}
}

@article{hafemeister2019normalization,
  title={Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression},
  author={Hafemeister, Christoph and Satija, Rahul},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={1--15},
  year={2019},
  publisher={Springer}
}

@article{vallejos2015basics,
  title={BASiCS: Bayesian analysis of single-cell sequencing data},
  author={Vallejos, Catalina A and Marioni, John C and Richardson, Sylvia},
  journal={PLoS computational biology},
  volume={11},
  number={6},
  pages={e1004333},
  year={2015},
  publisher={Public Library of Science San Francisco, CA USA}
}

@Article{Kurtz2021,
  author={Kurtz, David M.
    and Soo, Joanne
    and Co Ting Keh, Lyron
    and Alig, Stefan
    and Chabon, Jacob J.
    and Sworder, Brian J.
    and Schultz, Andre
    and Jin, Michael C.
    and Scherer, Florian
    and Garofalo, Andrea
    and Macaulay, Charles W.
    and Hamilton, Emily G.
    and Chen, Binbin
    and Olsen, Mari
    and Schroers-Martin, Joseph G.
    and Craig, Alexander F. M.
    and Moding, Everett J.
    and Esfahani, Mohammad S.
    and Liu, Chih Long
    and D{\"u}hrsen, Ulrich
and H{\"u}ttmann, Andreas
and Casasnovas, Ren{\'e}-Olivier
and Westin, Jason R.
and Roschewski, Mark
and Wilson, Wyndham H.
and Gaidano, Gianluca
and Rossi, Davide
and Diehn, Maximilian
and Alizadeh, Ash A.},
title={Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA},
journal={Nature Biotechnology},
year={2021},
month={Jul},
day={22},
abstract={Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25{\%} have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors.},
issn={1546-1696},
doi={10.1038/s41587-021-00981-w},
url={https://doi.org/10.1038/s41587-021-00981-w}
}


@article{tran2020benchmark,
  title={A benchmark of batch-effect correction methods for single-cell RNA sequencing data},
  author={Tran, Hoa Thi Nhu and Ang, Kok Siong and Chevrier, Marion and Zhang, Xiaomeng and Lee, Nicole Yee Shin and Goh, Michelle and Chen, Jinmiao},
  journal={Genome biology},
  volume={21},
  number={1},
  pages={1--32},
  year={2020},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13059-019-1850-9}
}

@article{robinson2010edger,
  title={edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
  author={Robinson, Mark D and McCarthy, Davis J and Smyth, Gordon K},
  journal={Bioinformatics},
  volume={26},
  number={1},
  pages={139--140},
  year={2010},
  publisher={Oxford University Press}
}


@article{breda2021bayesian,
  title={Bayesian inference of gene expression states from single-cell RNA-seq data},
  author={Breda, J{\'e}r{\'e}mie and Zavolan, Mihaela and van Nimwegen, Erik},
  journal={Nature Biotechnology},
  pages={1--9},
  year={2021},
  publisher={Nature Publishing Group}
}


@article{mccarthy2012differential,
  title={Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation},
  author={McCarthy, Davis J and Chen, Yunshun and Smyth, Gordon K},
  journal={Nucleic acids research},
  volume={40},
  number={10},
  pages={4288--4297},
  year={2012},
  publisher={Oxford University Press}
}