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A compendium of Caenhorabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks
John S Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A Grove, Ian A Hope, Albertha JM Walhout
Genome Biol. 2005; 6(13): R110. Published online 2005 December 30. doi: 10.1186/gb-2005-6-13-r110
PMCID:
PMC1414109
Abstract Full Text PDF–550K Supplementary Material
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 Is Cited by the Following 36 Articles in this Archive:
A Genome-Wide Survey on Basic Helix-Loop-Helix Transcription Factors in Giant Panda
Chunwang Dang, Yong Wang, Debao Zhang, Qin Yao, Keping Chen
PLoS One. 2011; 6(11): e26878. Published online 2011 November 9. doi: 10.1371/journal.pone.0026878
PMCID:
PMC3212526
Abstract Full Text PDF–116K Supplementary Material
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR
Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice David, Frederik Decouttere, Jacques Rougemont, Bart Deplancke
Database (Oxford) 2011; 2011: bar040. Published online 2011 September 14. doi: 10.1093/database/bar040
PMCID:
PMC3173022
Abstract Full Text PDF–1.3M
The Homeobox Protein CEH-23 Mediates Prolonged Longevity in Response to Impaired Mitochondrial Electron Transport Chain in C. elegans
Ludivine Walter, Aiswarya Baruah, Hsin-Wen Chang, Heather Mae Pace, Siu Sylvia Lee
PLoS Biol. 2011 June; 9(6): e1001084. Published online 2011 June 21. doi: 10.1371/journal.pbio.1001084
PMCID:
PMC3119657
Abstract Full Text PDF–729K Supplementary Material
OrthoList: A Compendium of C. elegans Genes with Human Orthologs
Daniel D. Shaye, Iva Greenwald
PLoS One. 2011; 6(5): e20085. Published online 2011 May 25. doi: 10.1371/journal.pone.0020085
PMCID:
PMC3102077
Abstract Full Text PDF–530K Supplementary Material
Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants
Federico De Masi, Christian A. Grove, Anastasia Vedenko, Andreu Alibés, Stephen S. Gisselbrecht, Luis Serrano, Martha L. Bulyk, Albertha J. M. Walhout
Nucleic Acids Res. 2011 June; 39(11): 4553–4563. Published online 2011 February 18. doi: 10.1093/nar/gkr070
PMCID:
PMC3113581
Abstract Full Text PDF–876K Supplementary Material
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Wei Niu, Zhi John Lu, Mei Zhong, Mihail Sarov, John I. Murray, Cathleen M. Brdlik, Judith Janette, Chao Chen, Pedro Alves, Elicia Preston, Cindie Slightham, Lixia Jiang, Anthony A. Hyman, Stuart K. Kim, Robert H. Waterston, Mark Gerstein, Michael Snyder, Valerie Reinke
Genome Res. 2011 February; 21(2): 245–254. doi: 10.1101/gr.114587.110
PMCID:
PMC3032928
Abstract Full Text PDF–1.3M
Integrating one-dimensional and three-dimensional maps of genomes
Natalia Naumova, Job Dekker
J Cell Sci. 2010 June 15; 123(12): 1979–1988. Published online 2010 June 2. doi: 10.1242/jcs.051631
PMCID:
PMC2880011
Abstract Full Text Supplementary Material
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network
H Efsun Arda, Stefan Taubert, Lesley T MacNeil, Colin C Conine, Ben Tsuda, Marc Van Gilst, Reynaldo Sequerra, Lynn Doucette-Stamm, Keith R Yamamoto, Albertha J M Walhout
Mol Syst Biol. 2010; 6: 367. Published online 2010 May 11. doi: 10.1038/msb.2010.23
PMCID:
PMC2890327
Abstract Full Text PDF–1.5M Supplementary Material
The matrix peptide exporter HAF-1 signals a mitochondrial unfolded protein response by activating the transcription factor ZC376.7 in C. elegans
Cole M. Haynes, Yun Yang, Steven P. Blais, Thomas A. Neubert, David Ron
Mol Cell. Author manuscript; available in PMC 2011 February 26.
Published in final edited form as: Mol Cell. 2010 February 26; 37(4): 529–540. doi: 10.1016/j.molcel.2010.01.015
PMCID:
PMC2846537
Abstract Full Text PDF–1.3M Supplementary Material
bZIP transcription factor zip-2 mediates an early response to Pseudomonas aeruginosa infection in Caenorhabditis elegans
Kathleen A. Estes, Tiffany L. Dunbar, Jennifer R. Powell, Frederick M. Ausubel, Emily R. Troemel
Proc Natl Acad Sci U S A. 2010 February 2; 107(5): 2153–2158. Published online 2010 January 21. doi: 10.1073/pnas.0914643107
PMCID:
PMC2836710
Abstract Full Text PDF–913K Supplementary Material
Gene-centered regulatory networks
H. Efsun Arda, Albertha J.M. Walhout
Brief Funct Genomics. 2010 January; 9(1): 4–12. Published online 2009 December 11. doi: 10.1093/bfgp/elp049
PMCID:
PMC3096532
Abstract Full Text PDF–387K
Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
Itai Yanai, Craig P. Hunter
Genome Res. 2009 December; 19(12): 2214–2220. doi: 10.1101/gr.093815.109
PMCID:
PMC2792179
Abstract Full Text PDF–800K
In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean
Keiichi Mochida, Takuhiro Yoshida, Tetsuya Sakurai, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam-Son Phan Tran
DNA Res. 2009 December; 16(6): 353–369. Published online 2009 November 2. doi: 10.1093/dnares/dsp023
PMCID:
PMC2780956
Abstract Full Text PDF–412K Supplementary Material
A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses
Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K. Kim, Eugene Myers
Nat Methods. Author manuscript; available in PMC 2010 June 8.
Published in final edited form as: Nat Methods. 2009 September; 6(9): 667–672. Published online 2009 August 16. doi: 10.1038/nmeth.1366
PMCID:
PMC2882208
Abstract Full Text PDF–2.6M Supplementary Material
Does negative auto-regulation increase gene duplicability?
Tobias Warnecke, Guang-Zhong Wang, Martin J Lercher, Laurence D Hurst
BMC Evol Biol. 2009; 9: 193. Published online 2009 August 7. doi: 10.1186/1471-2148-9-193
PMCID:
PMC2739200
Abstract Full Text PDF–302K Supplementary Material
A Multi-Parameter Network Reveals Extensive Divergence Between C. elegans bHLH Transcription Factors
Christian A. Grove, Federico de Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, Albertha J.M. Walhout
Cell. Author manuscript; available in PMC 2010 July 23.
Published in final edited form as: Cell. 2009 July 23; 138(2): 314–327. doi: 10.1016/j.cell.2009.04.058
PMCID:
PMC2774807
Abstract Full Text PDF–4.0M Supplementary Material
Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in Caenorhabditis
Richard Jovelin
Mol Biol Evol. 2009 October; 26(10): 2373–2386. Published online 2009 July 9. doi: 10.1093/molbev/msp142
PMCID:
PMC2766936
Abstract Full Text PDF–175K Supplementary Material
Unlocking the secrets of the genome
Susan E. Celniker, Laura A. L. Dillon, Mark B. Gerstein, Kristin C. Gunsalus, Steven Henikoff, Gary H. Karpen, Manolis Kellis, Eric C. Lai, Jason D. Lieb, David M. MacAlpine, Gos Micklem, Fabio Piano, Michael Snyder, Lincoln Stein, Kevin P. White, Robert H. Waterston
Nature. Author manuscript; available in PMC 2010 March 22.
Published in final edited form as: Nature. 2009 June 18; 459(7249): 927–930. doi: 10.1038/459927a
PMCID:
PMC2843545
Abstract Full Text PDF–635K Supplementary Material
The interplay between transcription factors and microRNAs in genome-scale regulatory networks
Natalia J. Martinez, Albertha J. M. Walhout
Bioessays. Author manuscript; available in PMC 2011 June 20.
Published in final edited form as: Bioessays. 2009 April; 31(4): 435–445. doi: 10.1002/bies.200800212
PMCID:
PMC3118512
Abstract Full Text PDF–649K
TFCat: the curated catalog of mouse and human transcription factors
Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek
Genome Biol. 2009; 10(3): R29. Published online 2009 March 12. doi: 10.1186/gb-2009-10-3-r29
PMCID:
PMC2691000
Abstract Full Text PDF–295K Supplementary Material
Universal protein binding microarrays for the comprehensive characterization of the DNA binding specificities of transcription factors
Michael F. Berger, Martha L. Bulyk
Nat Protoc. Author manuscript; available in PMC 2010 July 22.
Published in final edited form as: Nat Protoc. 2009; 4(3): 393–411. doi: 10.1038/nprot.2008.195
PMCID:
PMC2908410
Abstract Full Text PDF–4.1M
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity
Natalia J. Martinez, Maria C. Ow, M. Inmaculada Barrasa, Molly Hammell, Reynaldo Sequerra, Lynn Doucette-Stamm, Frederick P. Roth, Victor R. Ambros, Albertha J.M. Walhout
Genes Dev. 2008 September 15; 22(18): 2535–2549. doi: 10.1101/gad.1678608
PMCID:
PMC2546694
Abstract Full Text PDF–830K
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans
Maria C. Ow, Natalia J. Martinez, Philip H. Olsen, Howard S. Silverman, M. Inmaculada Barrasa, Barbara Conradt, Albertha J.M. Walhout, Victor Ambros
Genes Dev. 2008 September 15; 22(18): 2520–2534. doi: 10.1101/gad.1678808
PMCID:
PMC2546698
Abstract Full Text PDF–1.3M
Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution
Wilfried Haerty, Carlo Artieri, Navid Khezri, Rama S Singh, Bhagwati P Gupta
BMC Genomics. 2008; 9: 399. Published online 2008 August 27. doi: 10.1186/1471-2164-9-399
PMCID:
PMC2533025
Abstract Full Text PDF–1.9M Supplementary Material
Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides
Nathalie Pujol, Olivier Zugasti, Daniel Wong, Carole Couillault, C. Léopold Kurz, Hinrich Schulenburg, Jonathan J. Ewbank
PLoS Pathog. 2008 July; 4(7): e1000105. Published online 2008 July 18. doi: 10.1371/journal.ppat.1000105
PMCID:
PMC2453101
Abstract Full Text PDF–547K Supplementary Material
Transcription factor functionality and transcription regulatory networks
Christian A. Grove, Albertha J. M. Walhout
Mol Biosyst. Author manuscript; available in PMC 2009 April 27.
Published in final edited form as: Mol Biosyst. 2008 April; 4(4): 309–314. Published online 2008 February 21. doi: 10.1039/b715909a
PMCID:
PMC2673723
Abstract Full Text PDF–621K
Text-mining assisted regulatory annotation
Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium
Genome Biol. 2008; 9(2): R31. Published online 2008 February 13. doi: 10.1186/gb-2008-9-2-r31
PMCID:
PMC2374703
Abstract Full Text PDF–538K Supplementary Material
Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network
Vanessa Vermeirssen, M. Inmaculada Barrasa, César A. Hidalgo, Jenny Aurielle B. Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-László Barabási, Albertha J.M. Walhout
Genome Res. 2007 July; 17(7): 1061–1071. doi: 10.1101/gr.6148107
PMCID:
PMC1899117
Abstract Full Text PDF–909K
PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins
Sandra Richardt, Daniel Lang, Ralf Reski, Wolfgang Frank, Stefan A. Rensing
Plant Physiol. 2007 April; 143(4): 1452–1466. doi: 10.1104/pp.107.095760
PMCID:
PMC1851845
Abstract Full Text PDF–1.1M Supplementary Material
Identification of muscle-specific regulatory modules in Caenorhabditis elegans
Guoyan Zhao, Lawrence A. Schriefer, Gary D. Stormo
Genome Res. 2007 March; 17(3): 348–357. doi: 10.1101/gr.5989907
PMCID:
PMC1800926
Abstract Full Text PDF–384K
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