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number={10},
pages={959-962},
note={Cited By :43},
language={English},
url={www.scopus.com},
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year={2018},
title={Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement},
journal={Nature communications},
volume={9},
number={1},
pages={4877},
language={English},
url={www.scopus.com},
}

@article{mezger2018,
author={Mezger,A. and Klemm,S. and Mann,I. and Brower,K. and Mir,A. and Bostick,M. and Farmer,A. and Fordyce,P. and Linnarsson,S. and Greenleaf,W.},
year={2018},
title={High-throughput chromatin accessibility profiling at single-cell resolution},
journal={Nature Communications},
volume={9},
number={1},
language={English},
url={www.scopus.com},
}

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year={2018},
title={Mapping gene regulatory networks from single-cell omics data},
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pages={246-254},
language={English},
url={www.scopus.com},
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}

@article{cole2018,
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language={English},
url={www.scopus.com},
}

@article{azizi2014,
author={Azizi,F. and Clouthier,S.G. and Wicha,M. S.},
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url={www.scopus.com},
}

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volume={16},
number={1},
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url={www.scopus.com},
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number={6222},
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@article{yuan2018,
author={Yuan,J. and Sheng,J. and Sims,P. A.},
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number={1},
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}

@article{picelli2017,
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year={2017},
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number={5},
pages={637-650},
language={English},
url={www.scopus.com},
}

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language={English},
url={www.scopus.com},
}

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volume={88},
number={2},
pages={1-3},
language={English},
url={www.scopus.com},
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@article{ahn2006a,
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year={2006},
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volume={88},
number={26},
language={English},
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number={5},
pages={870-891},
language={English},
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@article{grun2014,
author={Gr\"{u}n,D. and Kester,L. and Van Oudenaarden,A.},
year={2014},
title={Validation of noise models for single-cell transcriptomics},
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volume={11},
number={6},
pages={637-640},
language={English},
url={www.scopus.com},
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@article{streets2014,
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pages={7048-7053},
language={English},
url={www.scopus.com},
}

@article{zhang2019,
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title={Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems},
journal={Molecular cell},
volume={73},
number={1},
pages={130-142.e5},
language={English},
url={www.scopus.com},
}

@article{stuart2019,
author={Stuart,T. and Satija,R.},
year={2019},
title={Integrative single-cell analysis},
journal={Nature Reviews Genetics},
language={English},
url={www.scopus.com},
}

@article{farrell2018,
author={Farrell,J. A. and Wang,Y. and Riesenfeld,S. J. and Shekhar,K. and Regev,A. and Schier,A. F.},
year={2018},
title={Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis},
journal={Science},
volume={360},
number={6392},
language={English},
url={www.scopus.com},
}



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number={5696},
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language={English},
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}

@article{patti2012,
author={Patti,G. J. and Yanes,O. and Siuzdak,G.},
year={2012},
title={Innovation: Metabolomics: the apogee of the omics trilogy},
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volume={13},
number={4},
pages={263-269},
language={English},
url={www.scopus.com},
}

@article{patterson2003,
author={Patterson,S. D. and Aebersold,R. H.},
year={2003},
title={Proteomics: The first decade and beyond},
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language={English},
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}

@article{wang2010,
author={Wang,D. and Bodovitz,S.},
year={2010},
title={Single cell analysis: The new frontier in 'omics'},
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language={English},
url={www.scopus.com},
}

@article{kalisky2018,
author={Kalisky,T. and Oriel,S. and Bar-Lev,T. H. and Ben-Haim,N. and Trink,A. and Wineberg,Y. and Kanter,I. and Gilad,S. and Pyne,S.},
year={2018},
title={A brief review of single-cell transcriptomic technologies},
journal={Briefings in Functional Genomics},
volume={17},
number={1},
pages={64-76},
language={English},
url={www.scopus.com},
}

@article{hca2017,
author={{The Human Cell Atlas Consortium}},
year={2017},
title={The Human Cell Atlas Whitepaper},
}

@article{regev2017,
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year={2017},
title={The human cell atlas},
journal={eLife},
volume={6},
language={English},
url={www.scopus.com},
}

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author={Brouzes,E. and Medkova,M. and Savenelli,N. and Marran,D. and Twardowski,M. and Hutchison,J. B. and Rothberg,J. M. and Link,D. R. and Perrimon,N. and Samuels,M. L.},
year={2009},
title={Droplet microfluidic technology for single-cell high-throughput screening},
journal={Proceedings of the National Academy of Sciences of the United States of America},
volume={106},
number={34},
pages={14195-14200},
language={English},
url={www.scopus.com},
}

@article{nakamura2005,
author={Nakamura,M. and Kobayashi,A. and Takagi,F. and Watanabe,A. and Hiruma,Y. and Ohuchi,K. and Iwasaki,Y. and Horie,M. and Morita,I. and Takatani,S.},
year={2005},
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journal={Tissue engineering},
volume={11},
number={11-12},
pages={1658-1666},
language={English},
url={www.scopus.com},
}

@article{allazetta2015,
author={Allazetta,S. and Lutolf,M. P.},
year={2015},
title={Stem cell niche engineering through droplet microfluidics},
journal={Current opinion in biotechnology},
volume={35},
pages={86-93},
language={English},
url={www.scopus.com},
}

@article{huebner2007,
author={Huebner,A. and Srisa-Art,M. and Holt,D. and Abell,C. and Hollfelder,F. and DeMello,A. J. and Edel,J. B.},
year={2007},
title={Quantitative detection of protein expression in single cells using droplet microfluidics},
journal={Chemical Communications},
volume={12},
pages={1218-1220},
language={English},
url={www.scopus.com},
}

@book{goos2011, place={Hoboken, NJ}, title={Optimal design of experiments a case study approach}, publisher={Wiley}, author={Goos, Peter and Jones, Bradley}, year={2011}}

@article{lamanno2018,
author={La Manno,G. and Soldatov,R. and Zeisel,A. and Braun,E. and Hochgerner,H. and Petukhov,V. and Lidschreiber,K. and Kastriti,M. E. and L\"onnerberg,P. and Furlan,A. and Fan,J. and Borm,L. E. and Liu,Z. and van Bruggen,D. and Guo,J. and He,X. and Barker,R. and Sundstr\"om,E. and Castelo-Branco,G. and Cramer,P. and Adameyko,I. and Linnarsson,S. and Kharchenko,P. V.},
year={2018},
title={RNA velocity of single cells},
journal={Nature},
volume={560},
number={7719},
pages={494-498},
language={English},
url={www.scopus.com},
}

@article{mills2013,
author={Mills,J. D. and Kawahara,Y. and Janitz,M.},
year={2013},
title={Strand-specific RNA-Seq provides greater resolution of transcriptome profiling},
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volume={14},
number={3},
pages={173-181},
language={English},
url={www.scopus.com},
}

@article{butler2018,
author={Butler,A. and Hoffman,P. and Smibert,P. and Papalexi,E. and Satija,R.},
year={2018},
title={Integrating single-cell transcriptomic data across different conditions, technologies, and species},
journal={Nature biotechnology},
volume={36},
number={5},
pages={411-420},
language={English},
url={www.scopus.com},
}

@article{bowden2019,
author = {Bowden, Rory and Davies, Robert W and Heger, Andreas and Pagnamenta, Alistair T and Cesare, Mariateresa De and Oikkonen, Laura E and Parkes, Duncan and Freeman, Colin and Patel, Smita Y and Popitsch, Niko and Ip, Camilla L C and Roberts, Hannah E and Lunter, Gerton and Taylor, Jenny C and Buck, David and Simpson, Michael A},
doi = {10.1038/s41467-019-09637-5},
issn = {2041-1723},
journal = {Nature Communications},
pages = {1--9},
publisher = {Springer US},
title = {{Sequencing of human genomes with nanopore technology}},
url = {http://dx.doi.org/10.1038/s41467-019-09637-5},
year = {2019}
}

@article{martin2011,
author = {Marcel Martin},
title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
journal = {EMBnet.journal},
volume = {17},
number = {1},
year = {2011},
issn = {2226-6089},pages = {10--12},doi = {10.14806/ej.17.1.200},
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}

@article {lareau2019,
author = {Lareau, Caleb A. and Duarte, Fabiana M. and Chew, Jennifer G. and Kartha, Vinay K. and Burkett, Zach D. and Kohlway, Andrew S. and Pokholok, Dmitry and Aryee, Martin J. and Steemers, Frank J. and Lebofsky, Ronald and Buenrostro, Jason D.},
title = {Droplet-based combinatorial indexing for massive scale single-cell epigenomics},
elocation-id = {612713},
year = {2019},
doi = {10.1101/612713},
publisher = {Cold Spring Harbor Laboratory},
abstract = {While recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution, the throughput and quality of these methods have limited the widespread adoption of these technologies. Here, we describe a droplet microfluidics platform for single-cell assay for transposase accessible chromatin (scATAC-seq) for high-throughput single-cell profiling of chromatin accessibility. We use this approach for the unbiased discovery of cell types and regulatory elements within the mouse brain. Further, we extend the throughput of this approach by pairing combinatorial indexing with droplet microfluidics, enabling single-cell studies at a massive scale. With this approach, we measure chromatin accessibility across resting and stimulated human bone marrow derived cells to reveal changes in the cis- and trans- regulatory landscape across cell types and upon stimulation conditions at single-cell resolution. Altogether, we describe a total of 502,207 single-cell profiles, demonstrating the scalability and flexibility of this droplet-based platform.},
URL = {https://www.biorxiv.org/content/early/2019/04/18/612713},
eprint = {https://www.biorxiv.org/content/early/2019/04/18/612713.full.pdf},
journal = {bioRxiv}
}

@article{davie2018,
author={Davie,K. and Janssens,J. and Koldere,D. and De Waegeneer,M. and Pech,U. and Kreft,Ł. and Aibar,S. and Makhzami,S. and Christiaens,V. and Bravo González-Blas,C. and Poovathingal,S. and Hulselmans,G. and Spanier,K. I. and Moerman,T. and Vanspauwen,B. and Geurs,S. and Voet,T. and Lammertyn,J. and Thienpont,B. and Liu,S. and Konstantinides,N. and Fiers,M. and Verstreken,P. and Aerts,S.},
year={2018},
title={A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain},
journal={Cell},
volume={174},
number={4},
pages={982-998.e20},
language={English},
url={www.scopus.com},
}

@article{schaum2019,
author="{Tabula Muris Consortium}",
year={2018},
title={Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris},
journal={Nature},
volume={562},
number={7727},
pages={367-372},
language={English},
url={www.scopus.com},
}

@article{mereu2019,
	author = {Mereu, Elisabetta and Lafzi, Atefeh and Moutinho, Catia and Ziegenhain, Christoph and MacCarthy, Davis J. and Alvarez, Adrian and Batlle, Eduard and Gr\"{u}n, Dominic and Lau, Julia K. and Boutet, St\'{e}phane C. and Sanada, Chad and Ooi, Aik and Jones, Robert C. and Kaihara, Kelly and Brampton, Chris and Talaga, Yasha and Sasagawa, Yohei and Tanaka, Kaori and Hayashi, Tetsutaro and Nikaido, Itoshi and Fischer, Cornelius and Sauer, Sascha and Trefzer, Timo and Conrad, Christian and Adiconis, Xian and Nguyen, Lan T. and Regev, Aviv and Levin, Joshua Z. and Parekh, Swati and Janjic, Aleksandar and Wange, Lucas E. and Bagnoli, Johannes W. and Enard, Wolfgang and Gut, Marta and Sandberg, Rickard and Gut, Ivo and Stegle, Oliver and Heyn, Holger},
	title = {Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects},
	elocation-id = {630087},
	year = {2019},
	doi = {10.1101/630087},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in-depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for drawing cell atlases of tissues, organs and organisms. We have generated benchmark datasets to systematically evaluate techniques in terms of their power to comprehensively describe cell types and states. We performed a multi-center study comparing 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. Comparative and integrative analysis at cell type and state level revealed marked differences in protocol performance, highlighting a series of key features for cell atlas projects. These should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project.},
	URL = {https://www.biorxiv.org/content/early/2019/05/13/630087},
	eprint = {https://www.biorxiv.org/content/early/2019/05/13/630087.full.pdf},
	journal = {bioRxiv}
}

@article{keren-shaul2019, title={MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing}, volume={14}, DOI={10.1038/s41596-019-0164-4}, number={6}, journal={Nature Protocols}, author={Keren-Shaul, Hadas and Kenigsberg, Ephraim and Jaitin, Diego Adhemar and David, Eyal and Paul, Franziska and Tanay, Amos and Amit, Ido}, year={2019}, pages={1841–1862}}

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@article {chen2019,
	author = {Chen, Song and Lake, Blue B and Zhang, Kun},
	title = {Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing},
	elocation-id = {692608},
	year = {2019},
	doi = {10.1101/692608},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Linked profiling of transcriptome and chromatin accessibility from single cells can provide unprecedented insights into cellular status. Here we developed a droplet-based Single-Nucleus chromatin Accessibility and mRNA Expression sequencing (SNARE-seq) assay, that we used to profile neonatal and adult mouse cerebral cortices. To demonstrate the strength of single-cell dual-omics profiling, we reconstructed transcriptome and epigenetic landscapes of cell types, uncovered lineage-specific accessible sites, and connected dynamics of promoter accessibility with transcription during neurogenesis.},
	URL = {https://www.biorxiv.org/content/early/2019/07/04/692608},
	eprint = {https://www.biorxiv.org/content/early/2019/07/04/692608.full.pdf},
	journal = {bioRxiv}
}

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year={2017},
title={Comparative Analysis of Single-Cell RNA Sequencing Methods},
journal={Molecular cell},
volume={65},
number={4},
pages={631-643.e4},
language={English},
url={www.scopus.com},
}

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