| Year |
Citation |
Score |
| 2016 |
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harbor Protocols. 2016: pdb.top077669. PMID 27934693 DOI: 10.1101/pdb.top077669 |
0.762 |
|
| 2016 |
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Zymolyase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast. Cold Spring Harbor Protocols. 2016: pdb.prot088971. PMID 27934686 DOI: 10.1101/pdb.prot088971 |
0.653 |
|
| 2016 |
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Colony Lift Colorimetric Assay for β-Galactosidase Activity. Cold Spring Harbor Protocols. 2016: pdb.prot088963. PMID 27934685 DOI: 10.1101/pdb.prot088963 |
0.692 |
|
| 2016 |
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Performing Yeast One-Hybrid Library Screens. Cold Spring Harbor Protocols. 2016: pdb.prot088955. PMID 27934684 DOI: 10.1101/pdb.prot088955 |
0.715 |
|
| 2016 |
Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Generating Bait Strains for Yeast One-Hybrid Assays. Cold Spring Harbor Protocols. 2016: pdb.prot088948. PMID 27934683 DOI: 10.1101/pdb.prot088948 |
0.698 |
|
| 2016 |
Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Molecular Systems Biology. 12: 884. PMID 27777270 DOI: 10.15252/msb.20167131 |
0.774 |
|
| 2015 |
MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJ. Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network. Cell Systems. 1: 152-162. PMID 26430702 DOI: 10.1016/j.cels.2015.08.003 |
0.403 |
|
| 2015 |
Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJ. Human gene-centered transcription factor networks for enhancers and disease variants. Cell. 161: 661-73. PMID 25910213 DOI: 10.1016/J.Cell.2015.03.003 |
0.771 |
|
| 2015 |
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, ... ... Walhout AJ, et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161: 647-60. PMID 25910212 DOI: 10.1016/J.Cell.2015.04.013 |
0.739 |
|
| 2015 |
Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 4. PMID 25905672 DOI: 10.7554/eLife.06967 |
0.74 |
|
| 2015 |
Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Bass JIF, Walhout AJ, Weirauch MT, Hughes TR. Author response: Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities Elife. DOI: 10.7554/Elife.06967.038 |
0.395 |
|
| 2014 |
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, ... ... Walhout AJ, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 158: 1431-43. PMID 25215497 DOI: 10.1016/J.Cell.2014.08.009 |
0.76 |
|
| 2014 |
Liu WJ, Reece-Hoyes JS, Walhout AJ, Eisenmann DM. Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6. Bmc Developmental Biology. 14: 17. PMID 24885717 DOI: 10.1186/1471-213X-14-17 |
0.354 |
|
| 2014 |
Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Research. 42: 153-62. PMID 24068555 DOI: 10.1093/Nar/Gkt858 |
0.755 |
|
| 2013 |
Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. Using networks to measure similarity between genes: association index selection. Nature Methods. 10: 1169-76. PMID 24296474 DOI: 10.1038/nmeth.2728 |
0.688 |
|
| 2013 |
Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJ. Complex expression dynamics and robustness in C. elegans insulin networks. Genome Research. 23: 954-65. PMID 23539137 DOI: 10.1101/Gr.150466.112 |
0.72 |
|
| 2013 |
Tamburino AM, Ryder SP, Walhout AJ. A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda, Md.). 3: 297-304. PMID 23390605 DOI: 10.1534/G3.112.004390 |
0.411 |
|
| 2012 |
Reece-Hoyes JS, Walhout AJ. Gene-centered yeast one-hybrid assays. Methods in Molecular Biology (Clifton, N.J.). 812: 189-208. PMID 22218861 DOI: 10.1007/978-1-61779-455-1_11 |
0.448 |
|
| 2012 |
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. 494: 73-84. PMID 22207033 DOI: 10.1016/j.gene.2011.11.042 |
0.371 |
|
| 2011 |
Walhout AJ. Gene-centered regulatory network mapping. Methods in Cell Biology. 106: 271-88. PMID 22118281 DOI: 10.1016/B978-0-12-544172-8.00010-4 |
0.452 |
|
| 2011 |
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. Nature Methods. 8: 1053-5. PMID 22037706 DOI: 10.1038/Nmeth.1750 |
0.331 |
|
| 2011 |
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. Nature Methods. 8: 1059-64. PMID 22037705 DOI: 10.1038/Nmeth.1748 |
0.475 |
|
| 2011 |
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. Nature Methods. 8: 1050-2. PMID 22037702 DOI: 10.1038/Nmeth.1764 |
0.467 |
|
| 2011 |
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 Genetics. 7: e1002074. PMID 21589891 DOI: 10.1371/Journal.Pgen.1002074 |
0.659 |
|
| 2011 |
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 Research. 39: 4553-63. PMID 21335608 DOI: 10.1093/Nar/Gkr070 |
0.386 |
|
| 2011 |
Macneil LT, Walhout AJ. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Research. 21: 645-57. PMID 21324878 DOI: 10.1101/gr.097378.109 |
0.342 |
|
| 2011 |
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. Molecular Systems Biology. 7: 459. PMID 21245844 DOI: 10.1038/Msb.2010.114 |
0.354 |
|
| 2010 |
Arda HE, Walhout AJ. Gene-centered regulatory networks. Briefings in Functional Genomics. 9: 4-12. PMID 20008400 DOI: 10.1093/bfgp/elp049 |
0.345 |
|
| 2009 |
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. 138: 314-27. PMID 19632181 DOI: 10.1016/J.Cell.2009.04.058 |
0.398 |
|
| 2009 |
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 Research. 37: 3689-98. PMID 19372275 DOI: 10.1093/Nar/Gkp232 |
0.658 |
|
| 2009 |
Martinez NJ, Walhout AJ. The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 31: 435-45. PMID 19274664 DOI: 10.1002/bies.200800212 |
0.373 |
|
| 2008 |
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. Nature Protocols. 3: 698-709. PMID 18388953 DOI: 10.1038/Nprot.2008.38 |
0.632 |
|
| 2008 |
Grove CA, Walhout AJ. Transcription factor functionality and transcription regulatory networks. Molecular Biosystems. 4: 309-14. PMID 18354784 DOI: 10.1039/b715909a |
0.413 |
|
| 2007 |
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. Nature Methods. 4: 659-64. PMID 17589517 DOI: 10.1038/Nmeth1063 |
0.646 |
|
| 2007 |
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 Research. 17: 1061-71. PMID 17513831 DOI: 10.1101/Gr.6148107 |
0.363 |
|
| 2007 |
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. 8: 27. PMID 17244357 DOI: 10.1186/1471-2164-8-27 |
0.595 |
|
| 2007 |
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. 8: 21. PMID 17233892 DOI: 10.1186/1471-2164-8-21 |
0.526 |
|
| 2006 |
Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJ. Gateway-compatible yeast one-hybrid screens. Csh Protocols. 2006. PMID 22485967 DOI: 10.1101/Pdb.Prot4590 |
0.694 |
|
| 2006 |
Walhout AJ. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Research. 16: 1445-54. PMID 17053092 DOI: 10.1101/gr.5321506 |
0.472 |
|
| 2006 |
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. Mechanisms of Ageing and Development. 127: 741-7. PMID 16860373 DOI: 10.1016/J.Mad.2006.05.005 |
0.6 |
|
| 2006 |
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. 125: 1193-205. PMID 16777607 DOI: 10.1016/J.Cell.2006.04.038 |
0.7 |
|
| 2005 |
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 Biology. 6: R110. PMID 16420670 DOI: 10.1186/Gb-2005-6-13-R110 |
0.656 |
|
| 2005 |
Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metabolism. 2: 35-42. PMID 16054097 DOI: 10.1016/J.Cmet.2005.06.004 |
0.543 |
|
| 2005 |
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. 171: 1017-31. PMID 16020796 DOI: 10.1534/Genetics.104.034173 |
0.571 |
|
| 2004 |
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 Research. 14: 2169-75. PMID 15489340 DOI: 10.1101/Gr.2497604 |
0.703 |
|
| 2004 |
Deplancke B, Dupuy D, Vidal M, Walhout AJ. A gateway-compatible yeast one-hybrid system. Genome Research. 14: 2093-101. PMID 15489331 DOI: 10.1101/Gr.2445504 |
0.762 |
|
| 2004 |
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. 430: 88-93. PMID 15190252 DOI: 10.1038/Nature02555 |
0.554 |
|
| 2004 |
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. Molecular Genetics and Genomics : Mgg. 271: 532-44. PMID 15138888 DOI: 10.1007/S00438-004-1012-X |
0.55 |
|
| 2003 |
Ge H, Walhout AJ, Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends in Genetics : Tig. 19: 551-60. PMID 14550629 DOI: 10.1016/J.Tig.2003.08.009 |
0.669 |
|
| 2002 |
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, et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Current Biology : Cb. 12: 1952-8. PMID 12445390 DOI: 10.1016/S0960-9822(02)01279-4 |
0.673 |
|
| 2002 |
Endoh H, Vincent S, Jacob Y, Réal E, Walhout AJ, Vidal M. Integrated version of reverse two-hybrid system for the postproteomic era. Methods in Enzymology. 350: 525-45. PMID 12073334 DOI: 10.1016/S0076-6879(02)50983-6 |
0.614 |
|
| 2002 |
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 (Cambridge, England). 129: 747-59. PMID 11830574 |
0.542 |
|
| 2001 |
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 Reports. 2: 821-8. PMID 11559592 DOI: 10.1093/Embo-Reports/Kve184 |
0.701 |
|
| 2001 |
Walhout AJ, Vidal M. Protein interaction maps for model organisms. Nature Reviews. Molecular Cell Biology. 2: 55-62. PMID 11413466 DOI: 10.1038/35048107 |
0.561 |
|
| 2001 |
Walhout AJ, Vidal M. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods (San Diego, Calif.). 24: 297-306. PMID 11403578 DOI: 10.1006/Meth.2001.1190 |
0.575 |
|
| 2000 |
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 in Enzymology. 328: 575-92. PMID 11075367 DOI: 10.1016/S0076-6879(00)28419-X |
0.543 |
|
| 2000 |
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 in Enzymology. 328: 74-88. PMID 11075339 DOI: 10.1016/S0076-6879(00)28391-2 |
0.566 |
|
| 2000 |
Walhout AJ, Boulton SJ, Vidal M. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast (Chichester, England). 17: 88-94. PMID 10900455 DOI: 10.1002/1097-0061(20000630)17:2<88::Aid-Yea20>3.0.Co;2-Y |
0.713 |
|
| 2000 |
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 (New York, N.Y.). 287: 116-22. PMID 10615043 DOI: 10.1126/Science.287.5450.116 |
0.595 |
|
| 1999 |
Walhout AJ, Vidal M. A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Research. 9: 1128-34. PMID 10568752 DOI: 10.1101/Gr.9.11.1128 |
0.606 |
|
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