John Isaac Murray - Publications

2004 Stanford University, Palo Alto, CA 

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Burdick J, Walton T, Preston E, Zacharias A, Raj A, Murray JI. Overlapping cell population expression profiling and regulatory inference in C. elegans. Bmc Genomics. 17: 159. PMID 26926147 DOI: 10.1186/S12864-016-2482-Z  0.36
2016 Zacharias AL, Murray JI. Combinatorial decoding of the invariant C. elegans embryonic lineage in space and time. Genesis (New York, N.Y. : 2000). PMID 26915329 DOI: 10.1002/Dvg.22928  0.36
2016 Surendran S, Jideonwo VN, Merchun C, Ahn M, Murray J, Ryan J, Dunn KW, Kota J, Morral N. Gene targets of mouse miR-709: regulation of distinct pools. Scientific Reports. 6: 18958. PMID 26743462 DOI: 10.1038/Srep18958  0.36
2015 Zacharias AL, Walton T, Preston E, Murray JI. Quantitative Differences in Nuclear β-catenin and TCF Pattern Embryonic Cells in C. elegans. Plos Genetics. 11: e1005585. PMID 26488501 DOI: 10.1371/Journal.Pgen.1005585  0.36
2015 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. 11: e1005003. PMID 25738873 DOI: 10.1371/Journal.Pgen.1005003  0.36
2014 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, et al. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 512: 400-5. PMID 25164749 DOI: 10.1038/Nature13497  0.36
2014 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 (San Diego, Calif.). 68: 431-6. PMID 24835576 DOI: 10.1016/J.Ymeth.2014.05.001  0.36
2013 Churgin MA, He L, Murray JI, Fang-Yen C. Efficient single-cell transgene induction in Caenorhabditis elegans using a pulsed infrared laser. G3 (Bethesda, Md.). 3: 1827-32. PMID 23979939 DOI: 10.1534/G3.113.007682  0.36
2013 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 (Cambridge, England). 140: 3385-94. PMID 23863485 DOI: 10.1242/Dev.098012  0.36
2013 Burdick JT, Murray JI. Deconvolution of gene expression from cell populations across the C. elegans lineage. Bmc Bioinformatics. 14: 204. PMID 23800200 DOI: 10.1186/1471-2105-14-204  0.36
2013 Richards JL, Zacharias AL, Walton T, Burdick JT, Murray JI. A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress. Developmental Biology. 374: 12-23. PMID 23220655 DOI: 10.1016/J.Ydbio.2012.11.034  0.36
2012 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, et al. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 150: 855-66. PMID 22901814 DOI: 10.1016/J.Cell.2012.08.001  0.36
2012 Murray JI, Bao Z. Automated lineage and expression profiling in live Caenorhabditis elegans embryos. Cold Spring Harbor Protocols. 2012. PMID 22854571 DOI: 10.1101/Pdb.Prot070615  0.36
2012 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, et al. Global analysis of RNA secondary structure in two metazoans. Cell Reports. 1: 69-82. PMID 22832108 DOI: 10.1016/J.Celrep.2011.10.002  0.36
2012 Abdus-Saboor I, Stone CE, Murray JI, Sundaram MV. The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system. Developmental Biology. 366: 298-307. PMID 22537498 DOI: 10.1016/J.Ydbio.2012.03.015  0.36
2012 Murray JI, Boyle TJ, Preston E, Vafeados D, Mericle B, Weisdepp P, Zhao Z, Bao Z, Boeck M, Waterston RH. Multidimensional regulation of gene expression in the C. elegans embryo. Genome Research. 22: 1282-94. PMID 22508763 DOI: 10.1101/Gr.131920.111  0.36
2011 Bao Z, Murray JI. Mounting Caenorhabditis elegans embryos for live imaging of embryogenesis. Cold Spring Harbor Protocols. 2011. PMID 21880814 DOI: 10.1101/Pdb.Prot065599  0.36
2011 Boeck ME, 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. 358: 345-355. PMID 21854766 DOI: 10.1016/J.Ydbio.2011.08.002  0.36
2011 Abdus-Saboor I, Mancuso VP, Murray JI, Palozola K, Norris C, Hall DH, Howell K, Huang K, Sundaram MV. Notch and Ras promote sequential steps of excretory tube development in C. elegans. Development (Cambridge, England). 138: 3545-55. PMID 21771815 DOI: 10.1242/Dev.068148  0.36
2011 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, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research. 21: 245-54. PMID 21177963 DOI: 10.1101/Gr.114587.110  0.36
2010 Zhao Z, Boyle TJ, Liu Z, Murray JI, Wood WB, Waterston RH. A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans. Plos Genetics. 6: e1001089. PMID 20824072 DOI: 10.1371/Journal.Pgen.1001089  0.36
2010 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, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genetics. 6: e1000848. PMID 20174564 DOI: 10.1371/Journal.Pgen.1000848  0.36
2010 Aydin Z, Murray JI, Waterston RH, Noble WS. 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. 11: 84. PMID 20146825 DOI: 10.1186/1471-2105-11-84  0.36
2010 Zhao Z, Flibotte S, Murray JI, Blick D, Boyle TJ, Gupta B, Moerman DG, Waterston RH. New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegans. Genetics. 184: 853-63. PMID 20008572 DOI: 10.1534/Genetics.109.110270  0.36
2009 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. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell. 139: 623-33. PMID 19879847 DOI: 10.1016/J.Cell.2009.08.044  0.36
2008 Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nature Methods. 5: 703-9. PMID 18587405 DOI: 10.1038/Nmeth.1228  0.36
2008 Yoshimura S, Murray JI, Lu Y, Waterston RH, Shaham S. mls-2 and vab-3 Control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegans. Development (Cambridge, England). 135: 2263-75. PMID 18508862 DOI: 10.1242/Dev.019547  0.36
2008 Bao Z, Zhao Z, Boyle TJ, Murray JI, Waterston RH. Control of cell cycle timing during C. elegans embryogenesis. Developmental Biology. 318: 65-72. PMID 18430415 DOI: 10.1016/J.Ydbio.2008.02.054  0.36
2008 Zhao Z, Boyle TJ, Bao Z, Murray JI, Mericle B, Waterston RH. Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans. Developmental Biology. 314: 93-9. PMID 18164284 DOI: 10.1016/J.Ydbio.2007.11.015  0.36
2007 Jacobs SB, Basak S, Murray JI, Pathak N, Attardi LD. Siva is an apoptosis-selective p53 target gene important for neuronal cell death. Cell Death and Differentiation. 14: 1374-85. PMID 17464332 DOI: 10.1038/Sj.Cdd.4402128  0.36
2006 Murray JI, Bao Z, Boyle TJ, Waterston RH. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nature Protocols. 1: 1468-76. PMID 17406437 DOI: 10.1038/Nprot.2006.222  0.36
2006 Boyle TJ, Bao Z, Murray JI, Araya CL, Waterston RH. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. Bmc Bioinformatics. 7: 275. PMID 16740163 DOI: 10.1186/1471-2105-7-275  0.36
2006 Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH. Automated cell lineage tracing in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America. 103: 2707-12. PMID 16477039 DOI: 10.1073/Pnas.0511111103  0.36
2005 Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE, Waterston RH. Genomics in C. elegans: so many genes, such a little worm. Genome Research. 15: 1651-60. PMID 16339362 DOI: 10.1101/Gr.3729105  0.36
2004 Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. Diverse and specific gene expression responses to stresses in cultured human cells. Molecular Biology of the Cell. 15: 2361-74. PMID 15004229 DOI: 10.1091/Mbc.E03-11-0799  0.36
2004 Trinklein ND, Murray JI, Hartman SJ, Botstein D, Myers RM. The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Molecular Biology of the Cell. 15: 1254-61. PMID 14668476 DOI: 10.1091/Mbc.E03-10-0738  0.36
2003 Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proceedings of the National Academy of Sciences of the United States of America. 100: 12319-24. PMID 14530402 DOI: 10.1073/Pnas.1635114100  0.36
2002 Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell. 13: 1977-2000. PMID 12058064 DOI: 10.1091/Mbc.02-02-0030  0.36
1999 Murray J, Buard J, Neil DL, Yeramian E, Tamaki K, Hollies C, Jeffreys AJ. Comparative sequence analysis of human minisatellites showing meiotic repeat instability Genome Research. 9: 130-136. PMID 10022977  0.36
1998 Jeffreys AJ, Murray J, Neumann R. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot Molecular Cell. 2: 267-273. PMID 9734365 DOI: 10.1016/S1097-2765(00)80138-0  0.36
1997 Jeffreys AJ, Bois P, Buard J, Collick A, Dubrova Y, Hollies CR, May CA, Murray J, Neil DL, Neumann R, Stead JD, Tamaki K, Yardley J. Spontaneous and induced minisatellite instability. Electrophoresis. 18: 1501-11. PMID 9378111 DOI: 10.1002/Elps.1150180903  0.36
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