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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
.... ( 2006 ) A gene-centered C. elegans protein–DNA interaction network . Cell 125 : 1193 – 1205 . ↵ Dupuy, D. , Li, Q. , Deplancke, B. , Boxem, M. , Hao, T. , Lamesch, P. , Sequerra, R. , Bosak, S. , Doucette-Stam, L. , Hope, I.A. , et al. ( 2004 ) A first version of the Caenorhabditis elegans promoterome...
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LETTER: Identification and analysis of internal promoters in Caenorhabditis elegans operons
- Peiming Huang,
- Erin D. Pleasance,
- Jason S. Maydan,
- Rebecca Hunt-Newbury,
- Nigel J. O’Neil,
- Allan Mah,
- David L. Baillie,
- Marco A. Marra,
- Donald G. Moerman,
- and Steven J.M. Jones
Genome Res. October 2007 17: 1478-1485; Published in Advance August 21, 2007, doi:10.1101/gr.6824707
....R. , Deplancke, B. , Boxem, M. , Hao, T. , Lamesch, P. , Sequerra, R. , Bosak, S. , Doucette-Stamm, L. , Hope, I.A. , et al. ( 2004 ) A first version of the Caenorhabditis elegans Promoterome . Genome Res. 14 : 2169 – 2175 . ↵ Evans, D. , Blumenthal, T. ( 2000 ) trans splicing of polycistronic Caenorhabditis...
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Methods: Identification of muscle-specific regulatory modules in Caenorhabditis elegans
- Guoyan Zhao,
- Lawrence A. Schriefer,
- and Gary D. Stormo
Genome Res. March 2007 17: 348-357; Published in Advance February 6, 2007, doi:10.1101/gr.5989907
...Identification of muscle-specific regulatory modules in Caenorhabditis elegans Guoyan Zhao , Lawrence A. Schriefer , and Gary D. Stormo 1 Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA...
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Research: Complex expression dynamics and robustness in C. elegans insulin networks
- Ashlyn D. Ritter,
- Yuan Shen,
- Juan Fuxman Bass,
- Sankarganesh Jeyaraj,
- Bart Deplancke,
- Arnab Mukhopadhyay,
- Jian Xu,
- Monica Driscoll,
- Heidi A. Tissenbaum,
- and Albertha J.M. Walhout
Genome Res. June 2013 23: 954-965; Published in Advance March 28, 2013, doi:10.1101/gr.150466.112
...–1193. Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA, et al. 2004. A first version of the Caenorhabditis elegans Promoterome. Genome Res 14: 2169–2175. Duret L, Guex N, Peitsch MC, Bairoch A. 1998. New insulin-like proteins with atypical disulfide bond...
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Resource: The transcription start site landscape of C. elegans
- Taro Leo Saito,
- Shin-ichi Hashimoto,
- Sam Guoping Gu,
- J. Jason Morton,
- Michael Stadler,
- Thomas Blumenthal,
- Andrew Fire,
- and Shinichi Morishita
Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
..., CO 80045, USA. Abstract More than half of Caenorhabditis elegans pre-mRNAs lose their original 5′ ends in a process termed “ trans -splicing” in which the RNA extending from the transcription start site (TSS) to the site of trans -splicing of the primary transcript, termed the “outron...
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Research: Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray,
- Thomas J. Boyle,
- Elicia Preston,
- Dionne Vafeados,
- Barbara Mericle,
- Peter Weisdepp,
- Zhongying Zhao,
- Zhirong Bao,
- Max Boeck,
- and Robert H. Waterston
Genome Res. July 2012 22: 1282-1294; Published in Advance April 16, 2012, doi:10.1101/gr.131920.111
...compendium could address the question of how transcription factors influence expression patterning. The nematode Caenorhabditis elegans is an ideal system in which to measure developmental expression with cellular resolution because it allows whole-animal microscopy, and its invariant embryogenesis proceeds...
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RESOURCE: Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library
- Jean-François Rual,
- Julian Ceron,
- John Koreth,
- Tong Hao,
- Anne-Sophie Nicot,
- Tomoko Hirozane-Kishikawa,
- Jean Vandenhaute,
- Stuart H. Orkin,
- David E. Hill,
- Sander van den Heuvel,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2162-2168; doi:10.1101/gr.2505604
...., Hao, T., Lamesch, P., Sequerra, R., Bosak, S., Doucette-Stamm, L., Hope, I.A., et al. 2004 . A first version of the Caenorhabditis elegans promoterome. Genome Res . (this issue). ↵ Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998 . Potent and specific genetic...
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LETTER: Feasibility of Genome-Scale Construction of Promoter::Reporter Gene Fusions for Expression in Caenorhabditis elegans Using a MultiSite Gateway Recombination System
- Ian A. Hope,
- Jonathan Stevens,
- Anna Garner,
- Josie Hayes,
- David L. Cheo,
- Michael A. Brasch,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2070-2075; doi:10.1101/gr.2463804
....A., and Thomason, L.C. 2002 . Genetic engineering using homologous recombination. Annu. Rev. Genet. 36 : 361 -388. ↵ Dupuy, D., Li, Q.-R., Deplancke, B., Boxem, M., Hao, T., Lamesch, P., Sequerra, R., Bozak, S., Doucette-Stamm, L., Hope, I.A., et al. 2004 . A first version of the Caenorhabditis elegans promoterome...
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Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions Eric L. Van Nostrand 1 and Stuart K. Kim 2 Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...4 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA Abstract The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data...

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