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Items: 18

1.

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.

Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR.

Cell. 2019 Feb 7;176(4):743-756.e17. doi: 10.1016/j.cell.2019.01.017.

PMID:
30735633
2.

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.

Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim DA, West JA, Leyrat AA, Kent WJ, Kriegstein AR.

Science. 2017 Dec 8;358(6368):1318-1323. doi: 10.1126/science.aap8809.

3.

Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence.

Wiley CD, Flynn JM, Morrissey C, Lebofsky R, Shuga J, Dong X, Unger MA, Vijg J, Melov S, Campisi J.

Aging Cell. 2017 Oct;16(5):1043-1050. doi: 10.1111/acel.12632. Epub 2017 Jul 11.

4.

Corrigendum: Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis.

Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NS, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JA.

Front Bioeng Biotechnol. 2017 Mar 14;5:11. doi: 10.3389/fbioe.2017.00011. eCollection 2017.

5.

Massively parallel digital transcriptional profiling of single cells.

Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH.

Nat Commun. 2017 Jan 16;8:14049. doi: 10.1038/ncomms14049.

6.

Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis.

Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NS, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JA.

Front Bioeng Biotechnol. 2016 Sep 21;4:70. eCollection 2016. Erratum in: Front Bioeng Biotechnol. 2017 Mar 14;5:11.

7.

Molecular identity of human outer radial glia during cortical development.

Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR.

Cell. 2015 Sep 24;163(1):55-67. doi: 10.1016/j.cell.2015.09.004.

8.

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.

Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, Li N, Szpankowski L, Fowler B, Chen P, Ramalingam N, Sun G, Thu M, Norris M, Lebofsky R, Toppani D, Kemp DW 2nd, Wong M, Clerkson B, Jones BN, Wu S, Knutsson L, Alvarado B, Wang J, Weaver LS, May AP, Jones RC, Unger MA, Kriegstein AR, West JA.

Nat Biotechnol. 2014 Oct;32(10):1053-8. doi: 10.1038/nbt.2967. Epub 2014 Aug 3.

9.

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A.

Nature. 2014 Jun 19;510(7505):363-9. doi: 10.1038/nature13437. Epub 2014 Jun 11.

10.

Modulation of Ras signaling alters the toxicity of hydroquinone, a benzene metabolite and component of cigarette smoke.

North M, Shuga J, Fromowitz M, Loguinov A, Shannon K, Zhang L, Smith MT, Vulpe CD.

BMC Cancer. 2014 Jan 5;14:6. doi: 10.1186/1471-2407-14-6.

11.

Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR.

Shuga J, Zeng Y, Novak R, Lan Q, Tang X, Rothman N, Vermeulen R, Li L, Hubbard A, Zhang L, Mathies RA, Smith MT.

Nucleic Acids Res. 2013 Sep;41(16):e159. doi: 10.1093/nar/gkt613. Epub 2013 Jul 19.

12.

Bone marrow genotoxicity of 2,5-dimethylfuran, a green biofuel candidate.

Fromowitz M, Shuga J, Wlassowsky AY, Ji Z, North M, Vulpe CD, Smith MT, Zhang L.

Environ Mol Mutagen. 2012 Jul;53(6):488-91. doi: 10.1002/em.21707. Epub 2012 Jun 25.

PMID:
22730236
13.

Integrated molecular analysis indicates undetectable change in DNA damage in mice after continuous irradiation at ~ 400-fold natural background radiation.

Olipitz W, Wiktor-Brown D, Shuga J, Pang B, McFaline J, Lonkar P, Thomas A, Mutamba JT, Greenberger JS, Samson LD, Dedon PC, Yanch JC, Engelward BP.

Environ Health Perspect. 2012 Aug;120(8):1130-6. doi: 10.1289/ehp.1104294. Epub 2012 Apr 26.

14.

Assessment of genetic damage in healthy and diseased tissue.

Shuga J, Hainaut P, Smith MT.

IARC Sci Publ. 2011;(163):63-97. Review.

PMID:
22997857
15.

Single-cell multiplex gene detection and sequencing with microfluidically generated agarose emulsions.

Novak R, Zeng Y, Shuga J, Venugopalan G, Fletcher DA, Smith MT, Mathies RA.

Angew Chem Int Ed Engl. 2011 Jan 10;50(2):390-5. doi: 10.1002/anie.201006089. No abstract available.

16.

Selected technologies for measuring acquired genetic damage in humans.

Shuga J, Zeng Y, Novak R, Mathies RA, Hainaut P, Smith MT.

Environ Mol Mutagen. 2010 Oct-Dec;51(8-9):851-70. doi: 10.1002/em.20630. Review.

PMID:
20872848
17.

High-performance single cell genetic analysis using microfluidic emulsion generator arrays.

Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA.

Anal Chem. 2010 Apr 15;82(8):3183-90. doi: 10.1021/ac902683t.

18.

In vitro erythropoiesis from bone marrow-derived progenitors provides a physiological assay for toxic and mutagenic compounds.

Shuga J, Zhang J, Samson LD, Lodish HF, Griffith LG.

Proc Natl Acad Sci U S A. 2007 May 22;104(21):8737-42. Epub 2007 May 14.

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