13 References

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990. “Basic Local Alignment Search Tool.” Journal of Molecular Biology 215 (3): 403–10. https://doi.org/10.1016/s0022-2836(05)80360-2.

Anders, Simon, and Wolfgang Huber. 2010. “Differential Expression Analysis for Sequence Count Data.” Genome Biol 11 (10): R106. https://doi.org/10.1186/gb-2010-11-10-r106.

Archer, Nathan, Mark D. Walsh, Vahid Shahrezaei, and Daniel Hebenstreit. 2016. “Modeling Enzyme Processivity Reveals That RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.” Cell Systems 3 (5): 467–479.e12. https://doi.org/10.1016/j.cels.2016.10.012.

Bray, Nicolas L, Harold Pimentel, Páll Melsted, and Lior Pachter. 2016. “Near-Optimal Probabilistic Rna-Seq Quantification.” Nat Biotechnol 34 (5): 525–27. https://doi.org/10.1038/nbt.3519.

Bullard, James H, Elizabeth Purdom, Kasper D Hansen, and Sandrine Dudoit. 2010. “Evaluation of Statistical Methods for Normalization and Differential Expression in mRNA-Seq Experiments.” BMC Bioinformatics 11 (1): 94. https://doi.org/10.1186/1471-2105-11-94.

Buttner, Maren, Zhichao Miao, Alexander Wolf, Sarah A Teichmann, and Fabian J Theis. 2017. “Assessment of Batch-Correction Methods for scRNA-seq Data with a New Test Metric.” bioRxiv, October, 200345.

Cannoodt, Robrecht, Wouter Saelens, and Yvan Saeys. 2016. “Computational Methods for Trajectory Inference from Single-Cell Transcriptomics.” Eur. J. Immunol. 46 (11): 2496–2506. https://doi.org/10.1002/eji.201646347.

Deng, Q., D. Ramskold, B. Reinius, and R. Sandberg. 2014. “Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells.” Science 343 (6167): 193–96. https://doi.org/10.1126/science.1245316.

Dijk, David van, Juozas Nainys, Roshan Sharma, Pooja Kathail, Ambrose J Carr, Kevin R Moon, Linas Mazutis, Guy Wolf, Smita Krishnaswamy, and Dana Pe’er. 2017. “MAGIC: A Diffusion-Based Imputation Method Reveals Gene-Gene Interactions in Single-Cell RNA-sequencing Data.” bioRxiv, February, 111591.

Gierahn, Todd M, Marc H Wadsworth 2nd, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, and Alex K Shalek. 2017. “Seq-Well: Portable, Low-Cost RNA Sequencing of Single Cells at High Throughput.” Nat. Methods 14 (4): 395–98.

Guo, Minzhe, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, and Yan Xu. 2015. “SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis.” PLoS Comput Biol 11 (11): e1004575. https://doi.org/10.1371/journal.pcbi.1004575.

Haghverdi, Laleh, Aaron T L Lun, Michael D Morgan, and John C Marioni. 2017. “Correcting Batch Effects in Single-Cell RNA Sequencing Data by Matching Mutual Nearest Neighbours.” bioRxiv, July, 165118.

Hashimshony, Tamar, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, et al. 2016. “CEL-Seq2: Sensitive Highly-Multiplexed Single-Cell RNA-Seq.” Genome Biol 17 (1). https://doi.org/10.1186/s13059-016-0938-8.

Hashimshony, Tamar, Florian Wagner, Noa Sher, and Itai Yanai. 2012. “CEL-Seq: Single-cell RNA-Seq by Multiplexed Linear Amplification.” Cell Reports 2 (3): 666–73. https://doi.org/10.1016/j.celrep.2012.08.003.

Islam, Saiful, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, and Sten Linnarsson. 2013. “Quantitative Single-Cell RNA-Seq with Unique Molecular Identifiers.” Nat Meth 11 (2): 163–66. https://doi.org/10.1038/nmeth.2772.

Jaitin, Diego Adhemar, Ephraim Kenigsberg, Hadas Keren-Shaul, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, et al. 2014. “Massively Parallel Single-Cell RNA-seq for Marker-Free Decomposition of Tissues into Cell Types.” Science 343 (6172): 776–79.

Kharchenko, Peter V, Lev Silberstein, and David T Scadden. 2014. “Bayesian Approach to Single-Cell Differential Expression Analysis.” Nat Meth 11 (7): 740–42. https://doi.org/10.1038/nmeth.2967.

Kiselev, Vladimir Yu, and Martin Hemberg. 2017. “Scmap - a Tool for Unsupervised Projection of Single Cell RNA-seq Data.” bioRxiv, July, 150292.

Kiselev, Vladimir Yu, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, et al. 2017. “SC3: Consensus Clustering of Single-Cell RNA-Seq Data.” Nat Meth 14 (5): 483–86. https://doi.org/10.1038/nmeth.4236.

Klein, Allon M., Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A. Weitz, and Marc W. Kirschner. 2015. “Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells.” Cell 161 (5): 1187–1201. https://doi.org/10.1016/j.cell.2015.04.044.

Kolodziejczyk, Aleksandra A., Jong Kyoung Kim, Valentine Svensson, John C. Marioni, and Sarah A. Teichmann. 2015. “The Technology and Biology of Single-Cell RNA Sequencing.” Molecular Cell 58 (4): 610–20. https://doi.org/10.1016/j.molcel.2015.04.005.

Levine, Jacob H., Erin F. Simonds, Sean C. Bendall, Kara L. Davis, El-ad D. Amir, Michelle D. Tadmor, Oren Litvin, et al. 2015. “Data-Driven Phenotypic Dissection of AML Reveals Progenitor-Like Cells That Correlate with Prognosis.” Cell 162 (1): 184–97. https://doi.org/10.1016/j.cell.2015.05.047.

Li, Wei Vivian, and Jingyi Jessica Li. 2017. “scImpute: Accurate and Robust Imputation for Single Cell RNA-Seq Data.” bioRxiv, June, 141598.

L. Lun, Aaron T., Karsten Bach, and John C. Marioni. 2016. “Pooling Across Cells to Normalize Single-Cell RNA Sequencing Data with Many Zero Counts.” Genome Biol 17 (1). https://doi.org/10.1186/s13059-016-0947-7.

Macosko, Evan Z., Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, et al. 2015. “Highly Parallel Genome-Wide Expression Profiling of Individual Cells Using Nanoliter Droplets.” Cell 161 (5): 1202–14. https://doi.org/10.1016/j.cell.2015.05.002.

McCarthy, Davis J., Kieran R. Campbell, Aaron T. L. Lun, and Quin F. Wills. 2017. “Scater: Pre-processing, Quality Control, Normalization and Visualization of Single-Cell RNA-Seq Data in R.” Bioinformatics, January, btw777. https://doi.org/10.1093/bioinformatics/btw777.

Muraro, Mauro J., Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, et al. 2016. “A Single-Cell Transcriptome Atlas of the Human Pancreas.” Cell Systems 3 (4): 385–394.e3. https://doi.org/10.1016/j.cels.2016.09.002.

Picelli, Simone, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, and Rickard Sandberg. 2013. “Smart-Seq2 for Sensitive Full-Length Transcriptome Profiling in Single Cells.” Nat Meth 10 (11): 1096–8. https://doi.org/10.1038/nmeth.2639.

Picelli, Simone, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, and Rickard Sandberg. 2014. “Full-Length RNA-seq from Single Cells Using Smart-Seq2.” Nat. Protoc. 9 (1): 171–81.

Regev, Aviv, Sarah Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, et al. 2017. “The Human Cell Atlas.” bioRxiv, May, 121202.

Robinson, Mark D, and Alicia Oshlack. 2010. “A Scaling Normalization Method for Differential Expression Analysis of RNA-Seq Data.” Genome Biol 11 (3): R25. https://doi.org/10.1186/gb-2010-11-3-r25.

Segerstolpe, Åsa, Athanasia Palasantza, Pernilla Eliasson, Eva-Marie Andersson, Anne-Christine Andréasson, Xiaoyan Sun, Simone Picelli, et al. 2016. “Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.” Cell Metabolism 24 (4): 593–607. https://doi.org/10.1016/j.cmet.2016.08.020.

Soumillon, Magali, Davide Cacchiarelli, Stefan Semrau, Alexander van Oudenaarden, and Tarjei S Mikkelsen. 2014. “Characterization of Directed Differentiation by High-Throughput Single-Cell RNA-Seq.” bioRxiv, March, 003236.

Stegle, Oliver, Sarah A. Teichmann, and John C. Marioni. 2015. “Computational and Analytical Challenges in Single-Cell Transcriptomics.” Nat Rev Genet 16 (3): 133–45. https://doi.org/10.1038/nrg3833.

Svensson, Valentine, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo J Miragaia, Charlotte Labalette, Iain C Macaulay, Ana Cvejic, and Sarah A Teichmann. 2017. “Power Analysis of Single-Cell RNA-Sequencing Experiments.” Nat Meth 14 (4): 381–87. https://doi.org/10.1038/nmeth.4220.

Tang, Fuchou, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, et al. 2009. “mRNA-Seq Whole-Transcriptome Analysis of a Single Cell.” Nat Meth 6 (5): 377–82. https://doi.org/10.1038/nmeth.1315.

Tung, Po-Yuan, John D. Blischak, Chiaowen Joyce Hsiao, David A. Knowles, Jonathan E. Burnett, Jonathan K. Pritchard, and Yoav Gilad. 2017. “Batch Effects and the Effective Design of Single-Cell Gene Expression Studies.” Sci. Rep. 7 (January): 39921. https://doi.org/10.1038/srep39921.

Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. 2016. “SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-Seq Data.” Genome Biol 17 (1). https://doi.org/10.1186/s13059-016-0975-3.

Wickham, Hadley. 2014. “Tidy Data.” J Stat Softw 59 (10). https://doi.org/10.18637/jss.v059.i10.

Ziegenhain, Christoph, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, and Wolfgang Enard. 2017. “Comparative Analysis of Single-Cell RNA Sequencing Methods.” Molecular Cell 65 (4): 631–643.e4. https://doi.org/10.1016/j.molcel.2017.01.023.