Murray Lab



Zacharias AL,Murray JI. Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time. Genesis. 2016 Apr;54(4):182-97. .

Walton T, Preston E, Nair G, Zacharias AL, Raj A, Murray JI. The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development. PLoS Genetics. 2015 Mar 4;11(3):e1005003.

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. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 2014 Aug 28;512(7515):400-5

Churgin MA, He L, Murray JI, Fang-Yen C. Construction of a system for single-cell transgene induction in Caenorhabditis elegans using a pulsed infrared laser. Methods. 2014 Aug 1;68(3):431-6. 

Nair G, Walton T, Murray JI, Raj A. Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification. Development. 2013 Aug;140(16):3385-94.

Burdick JTMurray JI. Deconvolution of gene expression from cell populations across the C. elegans lineage. BMC Bioinformatics. 2013 Jun 22;14:204.

Richards J.L., Zacharias A.L., Walton T., Burdick J.T., Murray J.I. A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress. Developmental Biology. 2013 Feb 1;374(1).


Sarov M., Murray J.I., 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 R.K., Slightam C., Xu X., Kim S.K., Reinke V., Stewart A.F., Snyder M., Waterston R.H., Hyman A.A. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012, Aug 17. 150(4)

Murray J.I., Bao Z. Automated Lineage and Expression Profiling in Live Caenorhabditis elegans Embryos. Cold Spring Harbor Protocols. 2012 Aug 1;2012(8).

Li F., Zheng Q., Ryvkin P., Dragomir I., Desai Y., Aiyer S., Valladares O., Yang J., Bambina S., Sabin L.R., Murray J.I., Lamitina T., Raj A., Cherry S., Wang L.S., Gregory B.D. Global analysis of RNA secondary structure in two metazoans. Cell Reports. 2012 Jan 26;1(1):69-82.

Abdus-Saboor I., Stone C.E., Murray J.I., Sundaram M.V. The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system. Developmental Biology. 2012 Jun 15;366(2):298-307.

Murray J.I., Boyle T.J., Preston E., Vafeados D., Mericle B., Weisdepp P., Zhao Z., Bao Z., Boeck M., Waterston R.H. Multidimensional regulation of gene expression in the C. elegans embryo. Genome Research. 2012 Jul;22(7):1282-94.

Bao Z., Murray J.I. Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis. Cold Spring Harb Protoc. 2011 Sep 1;2011(9).

Boeck M.E., Boyle T., Bao Z., Murray J., Mericle B., Waterston R. Specific roles for the GATA transcription factors end-1 and end-3 during C. elegans E-lineage development. Developmental Biology. 2011 Oct 15;358(2):345-55.

Abdus-Saboor I., Mancuso V.P., Murray J.I., Palozola K., Norris C., Hall D.H., Howell K., Huang K., Sundaram M.V. Notch and Ras promote sequential steps of excretory tube development in C. elegans. Development. 2011 Aug;138(16):3545-55

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. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010; 330(6012):1775-87.

Niu W., Lu Z..J, Zhong M., Sarov M., Murray J.I., Brdlik C.M., Janette J., Chen C., Alves P., Preston E., Slightham C., Jiang L., Hyman A.A., Kim S.K., Waterston R.H., Gerstein M., Snyder M., Reinke V. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research. 2011; 21(2):245-54

Zhao, Z., Boyle, T., Murray, J.I., Wood, W., Waterston, RH. A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans. PLOS Genetics. 2010; 6(9).

Zhao, Z., Flibotte, S., Murray, J.I., Blick, D., Boyle, T.J., Gupta, B.P., Moerman, D.G., Waterston, R.H. New Tools for Investigating the Comparative Biology of Caenorhabditis briggsae and Caenorhabditis elegans. Genetics.  2010; 184(3):853063

Aydin, Z., Murray, J.I., Waterston, R.H., Noble, W.S. Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo. BMC Bioinformatics.  2010; 11:84

Liu, X., Long, F., Peng, H., Aerni, S.J., Jiang, M., Sanchez-Blanco, A., Murray, J.I., Waterston, R.H., Batzoglou, S., Myers, E.W., Kim, S.K. Analysis of gene regulation and cell fate from single-cell gene expression profiles in C. elegans. Cell. 2009; 139(3)623-33

Murray, J.I., Bao, Z., Boyle, T.J., Boeck, M.E., Mericle, B., Nicholas, T.J., Zhao, Z., Sandel, M.J., Waterston, R.H. Automated analysis of embryonic gene expression with cellular resolution in C. elegans.  Nature Methods. 2008; 5(8):703-9.

Yoshimura, S., Murray, J.I., Lu, Y., Waterston, R.H., Shaham, S.  mls-2 and vab-3 control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegans.  Development.  2008; 135(13):2263-75.

Zhao, Z., Boyle, T.J., Bao, Z., Murray, J.I., Mericle, B., Waterston, R.H. Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans.  Developmental Biology.  2008; 314(1):93-99

Bao, Z., Zhao, Z., Boyle, T.J., Murray, J.I., Waterston, R.H.  Control of cell cycle timing during C. elegans embryogenesis.  Developmental Biology.  2008; 318(1):65-72.

Jacobs, S.B., Basak, S., Murray, J.I., Pathak, M., Attardi, L.D. Siva is an apoptosis-selective p53 target gene important for neuronal cell death.  Cell Death and Differentiation2007; 14(7):1374-85

Boyle, T.J., Bao, Z., Murray, J.I., Araya, C.L., Waterston, R.H.  AceTree: a tool for visual analysis of Caenorhabditis elegans development.  BMC Bioinformatics. 2006; 7:275

Murray, J.I., Bao, Z., Boyle, T.J., Waterston, R.H. The lineageing of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree.  Nature Protocols2006; 1:1468-76

Bao, Z., Murray, J.I., Boyle, T., Ooi, S.L., Sandel, M.J., Waterston, R.H. Automated cell lineage tracing in Caenorhabditis elegans.  PNAS. 2006 Feb 21; 103(8):2707-12

Hillier, L.W., Coulson, A., Murray, J.I., Bao, Z., Sulston, J.E., Waterston, R.H. Genomics in C. elegans: so many genes, such a little worm. Genome Research. 2005 Dec; 15(12):1651-60

Murray, J.I., Whitfield, M.L.,Trinklein, N.D., Myers, R.M.,  Brown, P.O. and Botstein, D. Diverse gene expression responses to stress in human cell lines.  Molecular Biology of the Cell. 2004 May; 15(5):2361-74.

Trinklein, N.D., Murray, J.I., Hartman, S., Botstein, D. and  Myers, R.M. The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock responseMolecular Biology of the Cell. 2004 Mar; 15(3): 1254-61.

Whitfield,M.L., Finlay,D., Murray,J.I., A.Troyanskaya,O., Chi,J.A., Brown,P.O., Botstein,D. and Connolly,M.K. Systemic and cell-type specific gene expression patterns in scleroderma skin. PNAS. 2003 Oct 14; 100(21): 12319-24.

Whitfield,M.L., Sherlock, G., Saldanha, A.,Murray, J.I., Ball, C.A., Alexander, K.E., Matese, J.C., Perou, C.M., Hurt, M.M., Brown, P.O., Botstein, D. Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors Molecular Biology of the Cell.  2002 Jun; 13(6), 1977 - 2000