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Items: 1 to 50 of 54

1.

SAVER: gene expression recovery for single-cell RNA sequencing.

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR.

Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25.

PMID:
29941873
2.

Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo.

Murray JI.

Wiley Interdiscip Rev Dev Biol. 2018 May;7(3):e314. doi: 10.1002/wdev.314. Epub 2018 Jan 25. Review.

PMID:
29369536
3.

Kinetic Resolution of 2-Substituted Indolines by N-Sulfonylation using an Atropisomeric 4-DMAP-N-oxide Organocatalyst.

Murray JI, Flodén NJ, Bauer A, Fessner ND, Dunklemann DL, Bob-Egbe O, Rzepa HS, Bürgi T, Richardson J, Spivey AC.

Angew Chem Int Ed Engl. 2017 May 15;56(21):5760-5764. doi: 10.1002/anie.201700977. Epub 2017 Apr 26.

4.

Crystal structure of 1-methylimidazole 3-oxide monohydrate.

Frampton CS, Murray JI, Spivey AC.

Acta Crystallogr E Crystallogr Commun. 2017 Feb 14;73(Pt 3):372-374. doi: 10.1107/S2056989017002079. eCollection 2017 Mar 1.

5.

The Lipocalin LPR-1 Cooperates with LIN-3/EGF Signaling To Maintain Narrow Tube Integrity in Caenorhabditis elegans.

Pu P, Stone CE, Burdick JT, Murray JI, Sundaram MV.

Genetics. 2017 Mar;205(3):1247-1260. doi: 10.1534/genetics.116.195156. Epub 2016 Dec 30.

6.

Overlapping cell population expression profiling and regulatory inference in C. elegans.

Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI.

BMC Genomics. 2016 Feb 29;17:159. doi: 10.1186/s12864-016-2482-z.

7.

Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time.

Zacharias AL, Murray JI.

Genesis. 2016 Apr;54(4):182-97. doi: 10.1002/dvg.22928. Epub 2016 Mar 19. Review.

8.

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M.

Nature. 2015 Dec 3;528(7580):152. doi: 10.1038/nature16075. Epub 2015 Nov 11. No abstract available.

PMID:
26560031
9.

Quantitative Differences in Nuclear β-catenin and TCF Pattern Embryonic Cells in C. elegans.

Zacharias AL, Walton T, Preston E, Murray JI.

PLoS Genet. 2015 Oct 21;11(10):e1005585. doi: 10.1371/journal.pgen.1005585. eCollection 2015 Oct.

10.

The Bicoid class homeodomain factors ceh-36/OTX and unc-30/PITX cooperate in C. elegans embryonic progenitor cells to regulate robust development.

Walton T, Preston E, Nair G, Zacharias AL, Raj A, Murray JI.

PLoS Genet. 2015 Mar 4;11(3):e1005003. doi: 10.1371/journal.pgen.1005003. eCollection 2015 Mar.

11.

Intratumoural inflammation and endocrine resistance in breast cancer.

Murray JI, West NR, Murphy LC, Watson PH.

Endocr Relat Cancer. 2015 Feb;22(1):R51-67. doi: 10.1530/ERC-14-0096. Epub 2014 Nov 17. Review.

12.
13.

Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M.

Nature. 2014 Aug 28;512(7515):400-5. doi: 10.1038/nature13497. Erratum in: Nature. 2015 Dec 3;528(7580):152.

14.

Construction of a system for single-cell transgene induction in Caenorhabditis elegans using a pulsed infrared laser.

Churgin MA, He L, Murray JI, Fang-Yen C.

Methods. 2014 Aug 1;68(3):431-6. doi: 10.1016/j.ymeth.2014.05.001. Epub 2014 May 14.

15.

Alternative synthetic tools to phospho-specific antibodies for phosphoproteome analysis: progress and prospects.

Murray JI, Spivey AC, Woscholski R.

J Chem Biol. 2013 Jul 9;6(4):175-84. doi: 10.1007/s12154-013-0100-y. eCollection 2013 Jul 9. Review.

16.

Efficient single-cell transgene induction in Caenorhabditis elegans using a pulsed infrared laser.

Churgin MA, He L, Murray JI, Fang-Yen C.

G3 (Bethesda). 2013 Oct 3;3(10):1827-32. doi: 10.1534/g3.113.007682.

17.

Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification.

Nair G, Walton T, Murray JI, Raj A.

Development. 2013 Aug;140(16):3385-94. doi: 10.1242/dev.098012. Epub 2013 Jul 17.

18.

Deconvolution of gene expression from cell populations across the C. elegans lineage.

Burdick JT, Murray JI.

BMC Bioinformatics. 2013 Jun 22;14:204. doi: 10.1186/1471-2105-14-204.

19.

Oncostatin-M promotes phenotypic changes associated with mesenchymal and stem cell-like differentiation in breast cancer.

West NR, Murray JI, Watson PH.

Oncogene. 2014 Mar 20;33(12):1485-94. doi: 10.1038/onc.2013.105. Epub 2013 Apr 15.

PMID:
23584474
20.

A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress.

Richards JL, Zacharias AL, Walton T, Burdick JT, Murray JI.

Dev Biol. 2013 Feb 1;374(1):12-23. doi: 10.1016/j.ydbio.2012.11.034. Epub 2012 Dec 7.

21.

A genome-scale resource for in vivo tag-based protein function exploration in C. elegans.

Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA.

Cell. 2012 Aug 17;150(4):855-66. doi: 10.1016/j.cell.2012.08.001.

22.

Automated lineage and expression profiling in live Caenorhabditis elegans embryos.

Murray JI, Bao Z.

Cold Spring Harb Protoc. 2012 Aug 1;2012(8). pii: pdb.prot070615. doi: 10.1101/pdb.prot070615.

PMID:
22854571
23.

Global analysis of RNA secondary structure in two metazoans.

Li F, Zheng Q, Ryvkin P, Dragomir I, Desai Y, Aiyer S, Valladares O, Yang J, Bambina S, Sabin LR, Murray JI, Lamitina T, Raj A, Cherry S, Wang LS, Gregory BD.

Cell Rep. 2012 Jan 26;1(1):69-82. doi: 10.1016/j.celrep.2011.10.002. Epub 2012 Jan 26.

24.

Structural characterization of S100A15 reveals a novel zinc coordination site among S100 proteins and altered surface chemistry with functional implications for receptor binding.

Murray JI, Tonkin ML, Whiting AL, Peng F, Farnell B, Cullen JT, Hof F, Boulanger MJ.

BMC Struct Biol. 2012 Jul 2;12:16. doi: 10.1186/1472-6807-12-16.

25.

The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system.

Abdus-Saboor I, Stone CE, Murray JI, Sundaram MV.

Dev Biol. 2012 Jun 15;366(2):298-307. doi: 10.1016/j.ydbio.2012.03.015. Epub 2012 Apr 17.

26.

Multidimensional regulation of gene expression in the C. elegans embryo.

Murray JI, Boyle TJ, Preston E, Vafeados D, Mericle B, Weisdepp P, Zhao Z, Bao Z, Boeck M, Waterston RH.

Genome Res. 2012 Jul;22(7):1282-94. doi: 10.1101/gr.131920.111. Epub 2012 Apr 16.

27.

Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis.

Bao Z, Murray JI.

Cold Spring Harb Protoc. 2011 Sep 1;2011(9). pii: pdb.prot065599. doi: 10.1101/pdb.prot065599.

PMID:
21880814
28.

Notch and Ras promote sequential steps of excretory tube development in C. elegans.

Abdus-Saboor I, Mancuso VP, Murray JI, Palozola K, Norris C, Hall DH, Howell K, Huang K, Sundaram MV.

Development. 2011 Aug;138(16):3545-55. doi: 10.1242/dev.068148. Epub 2011 Jul 19.

29.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

30.

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V.

Genome Res. 2011 Feb;21(2):245-54. doi: 10.1101/gr.114587.110. Epub 2010 Dec 22.

31.

A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans.

Zhao Z, Boyle TJ, Liu Z, Murray JI, Wood WB, Waterston RH.

PLoS Genet. 2010 Sep 2;6(9):e1001089. doi: 10.1371/journal.pgen.1001089.

32.

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M.

PLoS Genet. 2010 Feb 19;6(2):e1000848. doi: 10.1371/journal.pgen.1000848.

33.
34.

New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegans.

Zhao Z, Flibotte S, Murray JI, Blick D, Boyle TJ, Gupta B, Moerman DG, Waterston RH.

Genetics. 2010 Mar;184(3):853-63. doi: 10.1534/genetics.109.110270. Epub 2009 Dec 14.

35.

Analysis of cell fate from single-cell gene expression profiles in C. elegans.

Liu X, Long F, Peng H, Aerni SJ, Jiang M, Sánchez-Blanco A, Murray JI, Preston E, Mericle B, Batzoglou S, Myers EW, Kim SK.

Cell. 2009 Oct 30;139(3):623-33. doi: 10.1016/j.cell.2009.08.044.

36.

Structural and functional characterization of a triple mutant form of S100A7 defective for Jab1 binding.

West NR, Farnell B, Murray JI, Hof F, Watson PH, Boulanger MJ.

Protein Sci. 2009 Dec;18(12):2615-23. doi: 10.1002/pro.274.

37.

Identification and characterization of binding sites on S100A7, a participant in cancer and inflammation pathways.

León R, Murray JI, Cragg G, Farnell B, West NR, Pace TC, Watson PH, Bohne C, Boulanger MJ, Hof F.

Biochemistry. 2009 Nov 10;48(44):10591-600. doi: 10.1021/bi901330g.

PMID:
19810752
38.

Surface modification of upconverting NaYF4 nanoparticles with PEG-phosphate ligands for NIR (800 nm) biolabeling within the biological window.

Boyer JC, Manseau MP, Murray JI, van Veggel FC.

Langmuir. 2010 Jan 19;26(2):1157-64. doi: 10.1021/la902260j.

PMID:
19810725
39.

Automated analysis of embryonic gene expression with cellular resolution in C. elegans.

Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH.

Nat Methods. 2008 Aug;5(8):703-9. doi: 10.1038/nmeth.1228. Epub 2008 Jun 29.

40.

Identification of motifs that function in the splicing of non-canonical introns.

Murray JI, Voelker RB, Henscheid KL, Warf MB, Berglund JA.

Genome Biol. 2008;9(6):R97. doi: 10.1186/gb-2008-9-6-r97. Epub 2008 Jun 12.

41.

mls-2 and vab-3 Control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegans.

Yoshimura S, Murray JI, Lu Y, Waterston RH, Shaham S.

Development. 2008 Jul;135(13):2263-75. doi: 10.1242/dev.019547. Epub 2008 May 28.

42.

Control of cell cycle timing during C. elegans embryogenesis.

Bao Z, Zhao Z, Boyle TJ, Murray JI, Waterston RH.

Dev Biol. 2008 Jun 1;318(1):65-72. doi: 10.1016/j.ydbio.2008.02.054. Epub 2008 Mar 13.

43.

Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans.

Zhao Z, Boyle TJ, Bao Z, Murray JI, Mericle B, Waterston RH.

Dev Biol. 2008 Feb 1;314(1):93-9. doi: 10.1016/j.ydbio.2007.11.015. Epub 2007 Nov 22.

44.

Siva is an apoptosis-selective p53 target gene important for neuronal cell death.

Jacobs SB, Basak S, Murray JI, Pathak N, Attardi LD.

Cell Death Differ. 2007 Jul;14(7):1374-85. Epub 2007 Apr 20.

45.

The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree.

Murray JI, Bao Z, Boyle TJ, Waterston RH.

Nat Protoc. 2006;1(3):1468-76.

PMID:
17406437
46.

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

Boyle TJ, Bao Z, Murray JI, Araya CL, Waterston RH.

BMC Bioinformatics. 2006 Jun 1;7:275.

47.

Automated cell lineage tracing in Caenorhabditis elegans.

Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH.

Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2707-12. Epub 2006 Feb 13.

48.

Genomics in C. elegans: so many genes, such a little worm.

Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE, Waterston RH.

Genome Res. 2005 Dec;15(12):1651-60. Review.

49.

Diverse and specific gene expression responses to stresses in cultured human cells.

Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D.

Mol Biol Cell. 2004 May;15(5):2361-74. Epub 2004 Mar 5.

50.

The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.

Trinklein ND, Murray JI, Hartman SJ, Botstein D, Myers RM.

Mol Biol Cell. 2004 Mar;15(3):1254-61. Epub 2003 Dec 10.

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