202_Das_SingleCellRNASeq.bib

@article{Street2017,
author = {Street, Kelly and Risso, Davide and Fletcher, Russell B and Das, Diya and Ngai, John and Yosef, Nir and Purdom, Elizabeth and Dudoit, Sandrine},
journal = {BMC Genomics},
title = {{Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics}},
volume = {19},
number = {1},
pages = {477},
year = {2018},
}

@article{Risso2017,
  title={A general and flexible method for signal extraction from single-cell RNA-seq data},
  author={Risso, Davide and Perraudeau, Fanny and Gribkova, Svetlana and Dudoit, Sandrine and Vert, Jean-Philippe},
  journal={Nature Communications},
  volume={9},
  number={1},
  pages={284},
  year={2018},
}

@article{Fletcher2017,
annote = {doi: 10.1016/j.stem.2017.04.003},
author = {Fletcher, Russell B and Das, Diya and Gadye, Levi and Street, Kelly N and Baudhuin, Ariane and Wagner, Allon and Cole, Michael B and Flores, Quetzal and Choi, Yoon Gi and Yosef, Nir and Purdom, Elizabeth and Dudoit, Sandrine and Risso, Davide and Ngai, John},
doi = {10.1016/j.stem.2017.04.003},
issn = {1934-5909},
journal = {Cell Stem Cell},
month = {jun},
number = {6},
pages = {817--830.e8},
publisher = {Elsevier},
title = {{Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution}},
url = {https://doi.org/10.1016/j.stem.2017.04.003},
volume = {20},
year = {2017}
}

@article{Risso2018,
  title={{clusterExperiment and RSEC}: A {Bioconductor} package and framework for clustering of single-cell and other large gene expression datasets},
  author={Risso, Davide and Purvis, Liam and Fletcher, Russell and Das, Diya and Ngai, John and Dudoit, Sandrine and Purdom, Elizabeth},
  journal={bioRxiv},
  pages={280545},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}
@article{Peer2017,
abstract = {Single-cell RNA-sequencing is fast becoming a major technology that is revolutionizing biological discovery in fields such as development, immunology and cancer. The ability to simultaneously measure thousands of genes at single cell resolution allows, among other prospects, for the possibility of learning gene regulatory networks at large scales. However, scRNA-seq technologies suffer from many sources of significant technical noise, the most prominent of which is 'dropout' due to inefficient mRNA capture. This results in data that has a high degree of sparsity, with typically only {\~{}}10{\%} non-zero values. To address this, we developed MAGIC (Markov Affinity-based Graph Imputation of Cells), a method for imputing missing values, and restoring the structure of the data. After MAGIC, we find that two-and three-dimensional gene interactions are restored and that MAGIC is able to impute complex and non-linear shapes of interactions. MAGIC also retains cluster structure, enhances cluster-specific gene interactions and restores trajectories, as demonstrated in mouse retinal bipolar cells, hematopoiesis, and our newly generated epithelial-to-mesenchymal transition dataset.},
author = {van Dijk, David and Nainys, Juozas and Sharma, Roshan and Kathail, Pooja and Carr, Ambrose J and Moon, Kevin R and Mazutis, Linas and Wolf, Guy and Krishnaswamy, Smita and Pe'er, Dana},
doi = {10.1101/111591},
journal = {bioRxiv},
title = {{MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data}},
url = {https://doi.org/10.1101/111591},
year = {2017}
}
@article{Pierson2015,
author = {Pierson, Emma and Yau, Christopher},
doi = {10.1186/s13059-015-0805-z},
issn = {1474-760X},
journal = {Genome Biology},
month = {dec},
number = {1},
pages = {241},
title = {{ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis}},
url = {http://genomebiology.com/2015/16/1/241},
volume = {16},
year = {2015}
}
@article{Tseng2005,
author = {Tseng, George C. and Wong, Wing H.},
doi = {10.1111/j.0006-341X.2005.031032.x},
issn = {0006-341X},
journal = {Biometrics},
month = {mar},
number = {1},
pages = {10--16},
title = {{Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data}},
url = {http://doi.wiley.com/10.1111/j.0006-341X.2005.031032.x},
volume = {61},
year = {2005}
}