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Items: 1 to 50 of 187

1.

Challenges and Approaches to Genotyping Repetitive DNA.

Morton EA, Hall AN, Kwan E, Mok C, Queitsch K, Nandakumar V, Stamatoyannopoulos J, Brewer BJ, Waterston R, Queitsch C.

G3 (Bethesda). 2020 Jan 7;10(1):417-430. doi: 10.1534/g3.119.400771.

2.

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution.

Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI.

Science. 2019 Sep 20;365(6459). pii: eaax1971. doi: 10.1126/science.aax1971. Epub 2019 Sep 5.

PMID:
31488706
3.

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution.

Warner AD, Gevirtzman L, Hillier LW, Ewing B, Waterston RH.

Genome Res. 2019 Jun;29(6):1036-1045. doi: 10.1101/gr.243394.118. Epub 2019 May 23.

4.

Publisher Correction: DNA sequencing at 40: past, present and future.

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH.

Nature. 2019 Apr;568(7752):E11. doi: 10.1038/s41586-019-1120-8.

PMID:
30948799
5.

Mutational and transcriptional landscape of spontaneous gene duplications and deletions in Caenorhabditis elegans.

Konrad A, Flibotte S, Taylor J, Waterston RH, Moerman DG, Bergthorsson U, Katju V.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7386-7391. doi: 10.1073/pnas.1801930115. Epub 2018 Jun 25.

6.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH.

Genetics. 2018 Mar;208(3):937-949. doi: 10.1534/genetics.117.300657. Epub 2017 Dec 28.

7.

DNA sequencing at 40: past, present and future.

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH.

Nature. 2017 Oct 19;550(7676):345-353. doi: 10.1038/nature24286. Epub 2017 Oct 11. Review. Erratum in: Nature. 2019 Apr;568(7752):E11.

PMID:
29019985
8.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes.

Mok CA, Au V, Thompson OA, Edgley ML, Gevirtzman L, Yochem J, Lowry J, Memar N, Wallenfang MR, Rasoloson D, Bowerman B, Schnabel R, Seydoux G, Moerman DG, Waterston RH.

Genetics. 2017 Oct;207(2):447-463. doi: 10.1534/genetics.117.300179. Epub 2017 Aug 21.

9.

Comprehensive single-cell transcriptional profiling of a multicellular organism.

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J.

Science. 2017 Aug 18;357(6352):661-667. doi: 10.1126/science.aam8940.

10.

Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V.

Mol Biol Evol. 2017 Jun 1;34(6):1319-1334. doi: 10.1093/molbev/msx051. Erratum in: Mol Biol Evol. 2017 Mar 1;34(3):778.

11.

The time-resolved transcriptome of C. elegans.

Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH.

Genome Res. 2016 Oct;26(10):1441-1450. Epub 2016 Aug 16.

12.

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
13.

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.

14.

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.

15.

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.

16.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

17.

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.

18.

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.

19.

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.

20.

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.

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.

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.

23.

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.

24.

Specific roles for the GATA transcription factors end-1 and end-3 during C. elegans E-lineage development.

Boeck ME, Boyle T, Bao Z, Murray J, Mericle B, Waterston R.

Dev Biol. 2011 Oct 15;358(2):345-55. doi: 10.1016/j.ydbio.2011.08.002. Epub 2011 Aug 10.

25.

Interaction in online interprofessional education case discussions.

Waterston R.

J Interprof Care. 2011 Jul;25(4):272-9. doi: 10.3109/13561820.2011.566647.

PMID:
21688952
26.

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.

27.

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.

28.

The C. elegans SoxC protein SEM-2 opposes differentiation factors to promote a proliferative blast cell fate in the postembryonic mesoderm.

Tian C, Shi H, Colledge C, Stern M, Waterston R, Liu J.

Development. 2011 Mar;138(6):1033-43. doi: 10.1242/dev.062240. Epub 2011 Feb 9.

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.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.
37.

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.

38.

Unlocking the secrets of the genome.

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium.

Nature. 2009 Jun 18;459(7249):927-30. doi: 10.1038/459927a. No abstract available.

39.

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.

Genome Res. 2009 Apr;19(4):657-66. doi: 10.1101/gr.088112.108. Epub 2009 Jan 30.

40.

Rapid high resolution single nucleotide polymorphism-comparative genome hybridization mapping in Caenorhabditis elegans.

Flibotte S, Edgley ML, Maydan J, Taylor J, Zapf R, Waterston R, Moerman DG.

Genetics. 2009 Jan;181(1):33-7. doi: 10.1534/genetics.108.096487. Epub 2008 Oct 28.

41.

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.

42.

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.

43.

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.

44.

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.

45.

Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.

Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, Waterston RH.

PLoS Biol. 2007 Jul;5(7):e167. Epub 2007 Jul 3.

46.

Completing the map of human genetic variation.

Human Genome Structural Variation Working Group, Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, Lupski JR, Mullikin JC, Pritchard JK, Sebat J, Sherry ST, Smith D, Valle D, Waterston RH.

Nature. 2007 May 10;447(7141):161-5. No abstract available.

47.

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
48.

Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development.

Fukushige T, Brodigan TM, Schriefer LA, Waterston RH, Krause M.

Genes Dev. 2006 Dec 15;20(24):3395-406. Epub 2006 Dec 1.

49.
50.

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.

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