| Year |
Citation |
Score |
| 2024 |
Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the embryo reveals differential regulation of mRNA stability across stages and cell types. Genome Research. PMID 39142810 DOI: 10.1101/gr.278980.124 |
0.348 |
|
| 2024 |
Peng F, Nordgren CE, Murray JI. A spatiotemporally resolved atlas of mRNA decay in the embryo reveals differential regulation of mRNA stability across stages and cell types. Biorxiv : the Preprint Server For Biology. PMID 38293118 DOI: 10.1101/2024.01.15.575757 |
0.348 |
|
| 2023 |
Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics. PMID 37847877 DOI: 10.1093/genetics/iyad174 |
0.395 |
|
| 2023 |
Sivaramakrishnan P, Watkins C, Murray JI. Transcript accumulation rates in the early embryo. Science Advances. 9: eadi1270. PMID 37611097 DOI: 10.1126/sciadv.adi1270 |
0.375 |
|
| 2022 |
Patoori S, Barnada SM, Large C, Murray JI, Trizzino M. Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors. Development (Cambridge, England). PMID 36052683 DOI: 10.1242/dev.200413 |
0.334 |
|
| 2022 |
Rumley JD, Preston EA, Cook D, Peng FL, Zacharias AL, Wu L, Jileaeva I, Murray JI. pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo. Developmental Biology. PMID 35660370 DOI: 10.1016/j.ydbio.2022.05.019 |
0.783 |
|
| 2022 |
Murray JI, Preston E, Crawford JP, Rumley JD, Amom P, Anderson BD, Sivaramakrishnan P, Patel SD, Bennett BA, Lavon TD, Hsiao E, Peng F, Zacharias AL. The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo. Plos Genetics. 18: e1010187. PMID 35500030 DOI: 10.1371/journal.pgen.1010187 |
0.788 |
|
| 2021 |
Mizeracka K, Rogers JM, Rumley JD, Shaham S, Bulyk ML, Murray JI, Heiman MG. Lineage-specific control of convergent differentiation by a Forkhead repressor. Development (Cambridge, England). PMID 34423346 DOI: 10.1242/dev.199493 |
0.762 |
|
| 2020 |
Christensen EL, Beasley A, Radchuk J, Mielko ZE, Preston E, Stuckett S, Murray JI, Hudson ML. /neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Nervous System. G3 (Bethesda, Md.). PMID 32273286 DOI: 10.1534/G3.120.401126 |
0.473 |
|
| 2019 |
Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA. H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. Elife. 8. PMID 31573510 DOI: 10.7554/Elife.49278 |
0.412 |
|
| 2019 |
Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of embryogenesis at single-cell resolution. Science (New York, N.Y.). PMID 31488706 DOI: 10.1126/Science.Aax1971 |
0.642 |
|
| 2019 |
Sivaramakrishnan P, Murray JI. Silencing the alternative. Elife. 8. PMID 31386622 DOI: 10.7554/Elife.49635 |
0.412 |
|
| 2019 |
Murray JI. Decision letter: A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes Elife. DOI: 10.7554/Elife.46703.048 |
0.327 |
|
| 2018 |
Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR. Gene expression distribution deconvolution in single-cell RNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 29946020 DOI: 10.1073/Pnas.1721085115 |
0.487 |
|
| 2018 |
Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. SAVER: gene expression recovery for single-cell RNA sequencing. Nature Methods. PMID 29941873 DOI: 10.1038/S41592-018-0033-Z |
0.508 |
|
| 2018 |
Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A. Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Cell Systems. PMID 29454938 DOI: 10.1016/J.Cels.2018.01.014 |
0.439 |
|
| 2018 |
Murray JI. Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo. Wiley Interdisciplinary Reviews. Developmental Biology. PMID 29369536 DOI: 10.1002/Wdev.314 |
0.514 |
|
| 2016 |
Pu P, Stone CE, Burdick JT, Murray JI, Sundaram MV. The Lipocalin LPR-1 Cooperates with LIN-3/EGF Signaling To Maintain Narrow Tube Integrity in Caenorhabditis elegans. Genetics. PMID 28040739 DOI: 10.1534/Genetics.116.195156 |
0.336 |
|
| 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 |
0.549 |
|
| 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 |
0.556 |
|
| 2015 |
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. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. PMID 26560031 DOI: 10.1038/Nature16075 |
0.593 |
|
| 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 |
0.475 |
|
| 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 |
0.545 |
|
| 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 |
0.64 |
|
| 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 |
0.309 |
|
| 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 |
0.383 |
|
| 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 |
0.558 |
|
| 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 |
0.545 |
|
| 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 |
0.42 |
|
| 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 |
0.578 |
|
| 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 |
0.515 |
|
| 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 |
0.483 |
|
| 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 |
0.72 |
|
| 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 |
0.445 |
|
| 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 |
0.698 |
|
| 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 |
0.347 |
|
| 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 |
0.646 |
|
| 2010 |
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, ... ... Murray JI, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914 |
0.625 |
|
| 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 |
0.58 |
|
| 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 |
0.631 |
|
| 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 |
0.605 |
|
| 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 |
0.604 |
|
| 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 |
0.582 |
|
| 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 |
0.726 |
|
| 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 |
0.62 |
|
| 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 |
0.648 |
|
| 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 |
0.647 |
|
| 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 |
0.316 |
|
| 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 |
0.622 |
|
| 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 |
0.622 |
|
| 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 |
0.679 |
|
| 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 |
0.615 |
|
| 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 |
0.568 |
|
| 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 |
0.55 |
|
| 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 |
0.701 |
|
| 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 |
0.765 |
|
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