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Items: 14

1.

Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.

Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ.

Genome Res. 2019 Jul;29(7):1100-1114. doi: 10.1101/gr.245159.118. Epub 2019 Jun 21.

PMID:
31227602
2.

Comprehensive Integration of Single-Cell Data.

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R.

Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6.

PMID:
31178118
3.

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.

Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov SB, Smibert P.

Nat Methods. 2019 May;16(5):409-412. doi: 10.1038/s41592-019-0392-0. Epub 2019 Apr 22.

4.

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.

Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM 3rd, Smibert P, Satija R.

Genome Biol. 2018 Dec 19;19(1):224. doi: 10.1186/s13059-018-1603-1.

5.

Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.

Ruf-Zamojski F, Ge Y, Nair V, Zamojski M, Pincas H, Toufaily C, Tome-Garcia J, Stoeckius M, Stephenson W, Smith GR, Bernard DJ, Tsankova NM, Hartmann BM, Fribourg M, Smibert P, Swerdlow H, Turgeon JL, Sealfon SC.

Nucleic Acids Res. 2018 Nov 30;46(21):11370-11380. doi: 10.1093/nar/gky991.

6.

Simultaneous epitope and transcriptome measurement in single cells.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P.

Nat Methods. 2017 Sep;14(9):865-868. doi: 10.1038/nmeth.4380. Epub 2017 Jul 31.

7.

Paternal diet defines offspring chromatin state and intergenerational obesity.

Öst A, Lempradl A, Casas E, Weigert M, Tiko T, Deniz M, Pantano L, Boenisch U, Itskov PM, Stoeckius M, Ruf M, Rajewsky N, Reuter G, Iovino N, Ribeiro C, Alenius M, Heyne S, Vavouri T, Pospisilik JA.

Cell. 2014 Dec 4;159(6):1352-64. doi: 10.1016/j.cell.2014.11.005.

8.

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism.

Stoeckius M, Grün D, Kirchner M, Ayoub S, Torti F, Piano F, Herzog M, Selbach M, Rajewsky N.

EMBO J. 2014 Aug 18;33(16):1751-66. doi: 10.15252/embj.201488769. Epub 2014 Jun 23.

9.

Paternal RNA contributions in the Caenorhabditis elegans zygote.

Stoeckius M, Grün D, Rajewsky N.

EMBO J. 2014 Aug 18;33(16):1740-50. doi: 10.15252/embj.201488117. Epub 2014 Jun 3.

10.

Conservation of mRNA and protein expression during development of C. elegans.

Grün D, Kirchner M, Thierfelder N, Stoeckius M, Selbach M, Rajewsky N.

Cell Rep. 2014 Feb 13;6(3):565-77. doi: 10.1016/j.celrep.2014.01.001. Epub 2014 Jan 23.

11.

Essential roles of Raf/extracellular signal-regulated kinase/mitogen-activated protein kinase pathway, YY1, and Ca2+ influx in growth arrest of human vascular smooth muscle cells by bilirubin.

Stoeckius M, Erat A, Fujikawa T, Hiromura M, Koulova A, Otterbein L, Bianchi C, Tobiasch E, Dagon Y, Sellke FW, Usheva A.

J Biol Chem. 2012 May 4;287(19):15418-26. doi: 10.1074/jbc.M111.266510. Epub 2012 Jan 18.

12.

Select microRNAs are essential for early development in the sea urchin.

Song JL, Stoeckius M, Maaskola J, Friedländer M, Stepicheva N, Juliano C, Lebedeva S, Thompson W, Rajewsky N, Wessel GM.

Dev Biol. 2012 Feb 1;362(1):104-13. doi: 10.1016/j.ydbio.2011.11.015. Epub 2011 Dec 3.

13.

In vivo and transcriptome-wide identification of RNA binding protein target sites.

Jungkamp AC, Stoeckius M, Mecenas D, Grün D, Mastrobuoni G, Kempa S, Rajewsky N.

Mol Cell. 2011 Dec 9;44(5):828-40. doi: 10.1016/j.molcel.2011.11.009.

14.

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.

Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedländer MR, Li N, Chen W, Piano F, Rajewsky N.

Nat Methods. 2009 Oct;6(10):745-51. doi: 10.1038/nmeth.1370. Epub 2009 Sep 6.

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