Single cell multimodal data

Journal club on single-cell multimodal data technology and analysis

Details

• When and Where: TBD

Schedule

Paper	Date	Presenter
	2020-04-22
	2020-04-29
	2020-05-06
	2020-05-13
	2020-05-20

Article ideas

Here is a page with PDFs. If you use Paperpile, here is a shared folder you can add to and see any additions. Formatting below done by https://euangoddard.github.io/clipboard2markdown/.

Nature Methods January 2020 special issue

1. Method of the Year 2019: Single-cell multimodal omics. Nat. Methods 2020, 17:1.
2. Eisenstein M: The secret life of cells. Nat. Methods 2020, 17:7--10.
3. Schier AF: Single-cell biology: beyond the sum of its parts. Nat. Methods 2020, 17:17--20.
4. Efremova M, Teichmann SA: Computational methods for single-cell omics across modalities. Nat. Methods 2020, 17:14--17.
5. Zhu C, Preissl S, Ren B: Single-cell multimodal omics: the power of many. Nat. Methods 2020, 17:11--14.

Review papers

1. Navin NE: The first five years of single-cell cancer genomics and beyond. Genome Res. 2015, 25:1499--1507.
2. Hu Y, An Q, Sheu K, Trejo B, Fan S, Guo Y: Single Cell Multi-Omics Technology: Methodology and Application. Front Cell Dev Biol 2018, 6:28.
3. Macaulay IC, Ponting CP, Voet T: Single-Cell Multiomics: Multiple Measurements from Single Cells. Trends Genet. 2017, 33:155--168.
4. Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC: Orchestrating single-cell analysis with Bioconductor. Nat. Methods 2020, 17:137--145.

Technologies for RNA + DNA

1. Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN: Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature 2019, 568:49--54.
2. Bronner IF, Lorenz S: Combined Genome and Transcriptome (G&T) Sequencing of Single Cells. In Single Cell Methods: Sequencing and Proteomics. edited by Proserpio V New York, NY: Springer New York; 2019:319--362.
3. Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T: G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 2015, 12:519.
4. Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A: Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 2015, 33:285--289.

Technologies for RNA + protein

1. Peterson VM, Zhang KX, Kumar N, Wong J, Li L, Wilson DC, Moore R, McClanahan TK, Sadekova S, Klappenbach JA: Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 2017, 35:936--939.
2. 1. Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P: Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 2017, 14:865--868.

Technologies for RNA + epigenetics

1. Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W: Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat. Methods 2016, 13:229--232.

Technologies for DNA + epigenetics

1. Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B: Joint profiling of DNA methylation and chromatin architecture in single cells. Nat. Methods 2019, 16:991--993.

Technologies for 3+ modes

1. Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang F, Huang Y, Peng J: Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 2016, 26:304--319.