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Items: 1 to 20 of 142

1.

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
2.

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.

Thompson OA, Snoek LB, Nijveen H, Sterken MG, Volkers RJ, Brenchley R, Van't Hof A, Bevers RP, Cossins AR, Yanai I, Hajnal A, Schmid T, Perkins JD, Spencer D, Kruglyak L, Andersen EC, Moerman DG, Hillier LW, Kammenga JE, Waterston RH.

Genetics. 2015 Jul;200(3):975-89. doi: 10.1534/genetics.115.175950. Epub 2015 May 19.

3.

Isolation of specific neurons from C. elegans larvae for gene expression profiling.

Spencer WC, McWhirter R, Miller T, Strasbourger P, Thompson O, Hillier LW, Waterston RH, Miller DM 3rd.

PLoS One. 2014 Nov 5;9(11):e112102. doi: 10.1371/journal.pone.0112102. eCollection 2014.

4.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

5.

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.

6.

The million mutation project: a new approach to genetics in Caenorhabditis elegans.

Thompson O, Edgley M, Strasbourger P, Flibotte S, Ewing B, Adair R, Au V, Chaudhry I, Fernando L, Hutter H, Kieffer A, Lau J, Lee N, Miller A, Raymant G, Shen B, Shendure J, Taylor J, Turner EH, Hillier LW, Moerman DG, Waterston RH.

Genome Res. 2013 Oct;23(10):1749-62. doi: 10.1101/gr.157651.113. Epub 2013 Jun 25.

7.

A high-fidelity cell lineage tracing method for obtaining systematic spatiotemporal gene expression patterns in Caenorhabditis elegans.

Mace DL, Weisdepp P, Gevirtzman L, Boyle T, Waterston RH.

G3 (Bethesda). 2013 May 20;3(5):851-63. doi: 10.1534/g3.113.005918.

8.

Genetic control of vulval development in Caenorhabditis briggsae.

Sharanya D, Thillainathan B, Marri S, Bojanala N, Taylor J, Flibotte S, Moerman DG, Waterston RH, Gupta BP.

G3 (Bethesda). 2012 Dec;2(12):1625-41. doi: 10.1534/g3.112.004598. Epub 2012 Dec 1.

9.

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.

10.

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.

11.

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM.

Nat Genet. 2011 Oct 23;43(12):1179-85. doi: 10.1038/ng.948.

12.

A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans.

Engelmann I, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ.

PLoS One. 2011;6(5):e19055. doi: 10.1371/journal.pone.0019055. Epub 2011 May 13.

13.

The Genome.

Waterston RH, Sulston JE, Coulson AR.

In: Riddle DL, Blumenthal T, Meyer BJ, Priess JR, editors. C. elegans II. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. No abstract available. Chapter 2.

14.

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.

15.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB.

Genome Res. 2011 Feb;21(2):276-85. doi: 10.1101/gr.110189.110. Epub 2010 Dec 22. Erratum in: Genome Res. 2011 May;21(5):811.

16.

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.

17.

A global analysis of C. elegans trans-splicing.

Allen MA, Hillier LW, Waterston RH, Blumenthal T.

Genome Res. 2011 Feb;21(2):255-64. doi: 10.1101/gr.113811.110. Epub 2010 Dec 22.

18.

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.

19.

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M.

BMC Genomics. 2010 Jun 17;11:383. doi: 10.1186/1471-2164-11-383.

20.

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.

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