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1.
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Macneil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ. Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans. Cell. 2013 Mar 28; 153(1):240-52.
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2.
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Watson E, Macneil LT, Arda HE, Zhu LJ, Walhout AJ. Integration of Metabolic and Gene Regulatory Networks Modulates the C. elegans Dietary Response. Cell. 2013 Mar 28; 153(1):253-66.
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3.
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Tamburino AM, Ryder SP, Walhout AJ. A Compendium of Caenorhabditis elegans RNA Binding Proteins Predicts Extensive Regulation at Multiple Levels. G3 (Bethesda). 2013 Feb; 3(2):297-304.
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4.
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Reece-Hoyes JS, Walhout AJ. Gene-centered yeast one-hybrid assays. Methods Mol Biol. 2012; 812:189-208.
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5.
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Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biol. 2011; 12(12):137.
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6.
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Feng H, Reece-Hoyes JS, Walhout AJ, Hope IA. A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. Gene. 2012 Feb 15; 494(1):73-84.
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7.
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Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, Macwilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJ. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011; 8(12):1050-2.
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8.
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Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Methods. 2011; 8(12):1059-64.
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9.
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Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L, Liu Z, Breton G, Pruneda-Paz JL, Kim D, Kay SA, Walhout AJ, Ware D, Brady SM. Enhanced Y1H assays for Arabidopsis. Nat Methods. 2011; 8(12):1053-5.
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10.
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Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex. PLoS Genet. 2011 May; 7(5):e1002074.
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11.
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Walhout AJ. What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biol. 2011 Apr 11; 12(4):109.
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12.
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De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ. Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res. 2011 Jun; 39(11):4553-63.
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13.
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Macneil LT, Walhout AJ. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011 May; 21(5):645-57.
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14.
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Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN. A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol. 2011 Jan 18; 7:459.
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15.
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Walhout AJ. Gene-centered regulatory network mapping. Methods Cell Biol. 2011; 106:271-88.
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16.
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Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJ. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol. 2010 May 11; 6:367.
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17.
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Arda HE, Walhout AJ. Gene-centered regulatory networks. Brief Funct Genomics. 2010 Jan; 9(1):4-12.
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18.
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Walhout AJ. Getting an edge on human disease. Mol Syst Biol. 2009; 5:322.
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19.
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Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell. 2009 Jul 23; 138(2):314-27.
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20.
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Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ. The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res. 2009 Jun; 37(11):3689-98.
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21.
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Martinez NJ, Walhout AJ. The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays. 2009 Apr; 31(4):435-45.
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22.
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Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ. Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res. 2008 Dec; 18(12):2005-15.
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23.
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Ow MC, Martinez NJ, Olsen PH, Silverman HS, Barrasa MI, Conradt B, Walhout AJ, Ambros V. The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev. 2008 Sep 15; 22(18):2520-34.
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24.
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Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJ. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 2008 Sep 15; 22(18):2535-49.
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25.
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Grove CA, Walhout AJ. Transcription factor functionality and transcription regulatory networks. Mol Biosyst. 2008 Apr; 4(4):309-14.
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26.
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Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat Protoc. 2008; 3(4):698-709.
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27.
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Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ. Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods. 2007 Aug; 4(8):659-64.
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28.
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Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JA, Sequerra R, Doucette-Stamm L, Barabási AL, Walhout AJ. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res. 2007 Jul; 17(7):1061-71.
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29.
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Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJ, Vidal M, Hope IA. Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics. 2007; 8:27.
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30.
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Barrasa MI, Vaglio P, Cavasino F, Jacotot L, Walhout AJ. EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics. 2007; 8:21.
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31.
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Walhout AJ. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 2006 Dec; 16(12):1445-54.
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32.
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Walhout AJ. Networking at the second Interactome Meeting. Expert Rev Proteomics. 2006 Oct; 3(5):477-9.
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33.
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Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJ. Gateway-compatible yeast one-hybrid screens. CSH Protoc. 2006; 2006(5).
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34.
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Wang Y, Oh SW, Deplancke B, Luo J, Walhout AJ, Tissenbaum HA. C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech Ageing Dev. 2006 Sep; 127(9):741-7.
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35.
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Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network. Cell. 2006 Jun 16; 125(6):1193-205.
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36.
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Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 2005; 6(13):R110.
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37.
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Davison EM, Harrison MM, Walhout AJ, Vidal M, Horvitz HR. lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics. 2005 Nov; 171(3):1017-31.
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38.
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Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab. 2005 Jul; 2(1):35-42.
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39.
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Deplancke B, Dupuy D, Vidal M, Walhout AJ. A gateway-compatible yeast one-hybrid system. Genome Res. 2004 Oct; 14(10B):2093-101.
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40.
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Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA, Hill DE, Walhout AJ, Vidal M. A first version of the Caenorhabditis elegans Promoterome. Genome Res. 2004 Oct; 14(10B):2169-75.
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41.
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Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004 Jul 1; 430(6995):88-93.
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42.
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Fisk Green R, Lorson M, Walhout AJ, Vidal M, van den Heuvel S. Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5. Mol Genet Genomics. 2004 Jun; 271(5):532-44.
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43.
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Ge H, Walhout AJ, Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 2003 Oct; 19(10):551-60.
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44.
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Walhout AJ, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Gunsalus KC, Schetter AJ, Morton DG, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol. 2002 Nov 19; 12(22):1952-8.
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45.
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Huang NN, Mootz DE, Walhout AJ, Vidal M, Hunter CP. MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development. 2002 Feb; 129(3):747-59.
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46.
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Endoh H, Vincent S, Jacob Y, Réal E, Walhout AJ, Vidal M. Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol. 2002; 350:525-45.
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47.
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Davy A, Bello P, Thierry-Mieg N, Vaglio P, Hitti J, Doucette-Stamm L, Thierry-Mieg D, Reboul J, Boulton S, Walhout AJ, Coux O, Vidal M. A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2001 Sep; 2(9):821-8.
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48.
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Walhout AJ, Vidal M. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods. 2001 Jul; 24(3):297-306.
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49.
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Walhout AJ, Vidal M. Protein interaction maps for model organisms. Nat Rev Mol Cell Biol. 2001 Jan; 2(1):55-62.
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50.
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Walhout AJ, Boulton SJ, Vidal M. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast. 2000 Jun 30; 17(2):88-94.
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51.
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Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 2000 Jan 7; 287(5450):116-22.
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52.
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Endoh H, Walhout AJ, Vidal M. A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions. Methods Enzymol. 2000; 328:74-88.
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53.
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Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, van den Heuvel S, Vidal M. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 2000; 328:575-92.
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54.
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Walhout AJ, Vidal M. A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 1999 Nov; 9(11):1128-34.
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55.
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Walhout AJ, van der Vliet PC, Timmers HT. Sequences flanking the E-box contribute to cooperative binding by c-Myc/Max heterodimers to adjacent binding sites. Biochim Biophys Acta. 1998 Apr 29; 1397(2):189-201.
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56.
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Walhout AJ, Gubbels JM, Bernards R, van der Vliet PC, Timmers HT. c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene. Nucleic Acids Res. 1997 Apr 15; 25(8):1493-501.
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57.
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Kruyt FA, Folkers GE, Walhout AJ, van der Leede BJ, van der Saag PT. E1A functions as a coactivator of retinoic acid-dependent retinoic acid receptor-beta 2 promoter activation. Mol Endocrinol. 1993 Apr; 7(4):604-15.
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