Albertha J. Walhout, Ph.D. - Publications

Program in Systems Biology University of Massachussetts Medical School, Worcester, MA, United States 

102 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Basu J, Reis BS, Peri S, Zha J, Hua X, Ge L, Ferchen K, Nicolas E, Czyzewicz P, Cai KQ, Tan Y, Fuxman Bass JI, Walhout AJM, Grimes HL, Grivennikov SI, et al. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4 T cell identity and function. Nature Immunology. 22: 969-982. PMID 34312548 DOI: 10.1038/s41590-021-00980-8  1
2021 Walker MD, Giese GE, Holdorf AD, Bhattacharya S, Diot C, García-González AP, Horowitz BB, Lee YU, Leland T, Li X, Mirza Z, Na H, Nanda S, Ponomarova O, Zhang H, ... ... Walhout AJM, et al. WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. Genetics. PMID 34117752 DOI: 10.1093/genetics/iyab089  1
2020 Walker MD, Giese GE, Holdorf AD, Bhattacharya S, Diot C, García-González AP, Horowitz B, Lee YU, Leland T, Li X, Mirza Z, Na H, Nanda S, Ponomarova O, Zhang H, ... ... Walhout AJM, et al. WormPaths: metabolic pathway annotation and visualization. Biorxiv : the Preprint Server For Biology. PMID 33398287 DOI: 10.1101/2020.12.22.424026  1
2019 Zhang J, Li X, Olmedo M, Holdorf AD, Shang Y, Artal-Sanz M, Yilmaz LS, Walhout AJM. A Delicate Balance between Bacterial Iron and Reactive Oxygen Species Supports Optimal C. elegans Development. Cell Host & Microbe. PMID 31444089 DOI: 10.1016/J.Chom.2019.07.010  1
2019 Bulcha JT, Giese GE, Ali MZ, Lee YU, Walker MD, Holdorf AD, Yilmaz LS, Brewster RC, Walhout AJM. A Persistence Detector for Metabolic Network Rewiring in an Animal. Cell Reports. 26: 460-468.e4. PMID 30625328 DOI: 10.1016/j.celrep.2018.12.064  1
2018 Hu Q, D'Amora DR, MacNeil LT, Walhout AJM, Kubiseski TJ. The Oxidative Stress Response Requires the NHR-49 Transcription Factor. G3 (Bethesda, Md.). PMID 30297383 DOI: 10.1534/g3.118.200727  1
2018 Reece-Hoyes JS, Walhout AJM. Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays. Cold Spring Harbor Protocols. 2018: pdb.top094953. PMID 29967278 DOI: 10.1101/pdb.top094953  1
2018 Reece-Hoyes JS, Walhout AJM. High-Efficiency Yeast Transformation. Cold Spring Harbor Protocols. 2018: pdb.prot094995. PMID 29967274 DOI: 10.1101/pdb.prot094995  1
2018 Reece-Hoyes JS, Walhout AJM. Identifying Interactors from an Activation Domain Prey Library. Cold Spring Harbor Protocols. 2018: pdb.prot094987. PMID 29967273 DOI: 10.1101/pdb.prot094987  1
2018 Reece-Hoyes JS, Walhout AJM. Generating Yeast Two-Hybrid Bait Strains. Cold Spring Harbor Protocols. 2018: pdb.prot094979. PMID 29967272 DOI: 10.1101/pdb.prot094979  1
2018 Reece-Hoyes JS, Walhout AJM. Generating Yeast One-Hybrid DNA-Bait Strains. Cold Spring Harbor Protocols. 2018: pdb.prot094961. PMID 29967271 DOI: 10.1101/pdb.prot094961  1
2018 Na H, Ponomarova O, Giese GE, Walhout AJM. C. elegans MRP-5 Exports Vitamin B12 from Mother to Offspring to Support Embryonic Development. Cell Reports. 22: 3126-3133. PMID 29562169 DOI: 10.1016/j.celrep.2018.02.100  1
2018 Reece-Hoyes JS, Walhout AJM. Gateway Recombinational Cloning. Cold Spring Harbor Protocols. 2018: pdb.top094912. PMID 29295908 DOI: 10.1101/pdb.top094912  1
2018 Reece-Hoyes JS, Walhout AJM. Using Multisite LR Cloning to Generate a Destination Clone. Cold Spring Harbor Protocols. 2018: pdb.prot094946. PMID 29295906 DOI: 10.1101/pdb.prot094946  1
2018 Reece-Hoyes JS, Walhout AJM. Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone. Cold Spring Harbor Protocols. 2018: pdb.prot094938. PMID 29295905 DOI: 10.1101/pdb.prot094938  1
2018 Reece-Hoyes JS, Walhout AJM. Propagating Gateway Vectors. Cold Spring Harbor Protocols. 2018: pdb.prot094920. PMID 29295904 DOI: 10.1101/pdb.prot094920  1
2017 Mori A, Holdorf AD, Walhout AJM. Many transcription factors contribute to C. elegans growth and fat storage. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. PMID 28791781 DOI: 10.1111/gtc.12516  1
2017 Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM. PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. Translation (Austin, Tex.). 5: e1295130. PMID 28702278 DOI: 10.1080/21690731.2017.1295130  1
2017 Hu Q, D'Amora DR, MacNeil LT, Walhout AJM, Kubiseski TJ. The Oxidative Stress Response in Caenorhabditis elegans Requires the GATA Transcription Factor ELT-3 and SKN-1/Nrf2. Genetics. PMID 28600327 DOI: 10.1534/genetics.116.198788  1
2017 García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM. Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics. Cell. 169: 431-441.e8. PMID 28431244 DOI: 10.1016/J.Cell.2017.03.046  1
2017 Yilmaz LS, Walhout AJ. Metabolic network modeling with model organisms. Current Opinion in Chemical Biology. 36: 32-39. PMID 28088694 DOI: 10.1016/j.cbpa.2016.12.025  1
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  1
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  1
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  1
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  1
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  1
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  1
2016 Walhout AJ, Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. Elife. 5. PMID 27383050 DOI: 10.7554/Elife.17670  1
2016 Yilmaz LS, Walhout AJ. A Caenorhabditis elegans Genome-Scale Metabolic Network Model. Cell Systems. 2: 297-311. PMID 27211857 DOI: 10.1016/j.cels.2016.04.012  1
2015 Watson E, Yilmaz LS, Walhout AJ. Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms. Annual Review of Genetics. 49: 553-75. PMID 26631516 DOI: 10.1146/annurev-genet-112414-055257  1
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  1
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  1
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  0.04
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  1
2015 Conte D, MacNeil LT, Walhout AJ, Mello CC. RNA Interference in Caenorhabditis elegans. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 109: 26.3.1-26.3.30. PMID 25559107 DOI: 10.1002/0471142727.Mb2603S109  1
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  1
2014 Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJM. Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits. Cell. 156: 1336-1337. PMID 28898637 DOI: 10.1016/j.cell.2014.02.036  1
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  1
2014 Yilmaz LS, Walhout AJ. Worms, bacteria, and micronutrients: an elegant model of our diet. Trends in Genetics : Tig. 30: 496-503. PMID 25172020 DOI: 10.1016/j.tig.2014.07.010  1
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  1
2014 Watson E, Walhout AJ. Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy. Trends in Endocrinology and Metabolism: Tem. 25: 502-8. PMID 24731597 DOI: 10.1016/j.tem.2014.03.004  1
2014 Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJ. Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. Cell. 156: 759-70. PMID 24529378 DOI: 10.1016/J.Cell.2014.01.047  1
2014 Walhout AJ. Genetic adaptation to diet preserves longevity. Cell Metabolism. 19: 177-8. PMID 24506862 DOI: 10.1016/j.cmet.2014.01.006  0.01
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  1
2013 Macneil LT, Walhout AJ. Food, pathogen, signal: The multifaceted nature of a bacterial diet. Worm. 2: e26454. PMID 24744980 DOI: 10.4161/worm.26454  1
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  1
2013 Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, ... Walhout AJ, et al. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Molecular Cell. 51: 116-27. PMID 23791784 DOI: 10.1016/j.molcel.2013.05.018  1
2013 Watson E, MacNeil LT, Arda HE, Zhu LJ, Walhout AJ. Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell. 153: 253-66. PMID 23540702 DOI: 10.1016/j.cell.2013.02.050  1
2013 MacNeil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ. Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell. 153: 240-52. PMID 23540701 DOI: 10.1016/j.cell.2013.02.049  1
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  1
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  1
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  1
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  1
2011 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 Biology. 12: 137. PMID 22204305 DOI: 10.1186/Gb-2011-12-12-137  0.04
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  0.01
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  1
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  1
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  1
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  1
2011 Walhout AJ. What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biology. 12: 109. PMID 21489330 DOI: 10.1186/gb-2011-12-4-109  0.01
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  1
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  1
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  1
2010 Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJM. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network Molecular Systems Biology. 6. PMID 20461074 DOI: 10.1038/Msb.2010.23  1
2010 Arda HE, Walhout AJ. Gene-centered regulatory networks. Briefings in Functional Genomics. 9: 4-12. PMID 20008400 DOI: 10.1093/bfgp/elp049  1
2009 Walhout AJ. Getting an edge on human disease. Molecular Systems Biology. 5: 322. PMID 19888217 DOI: 10.1038/msb.2009.81  0.01
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  1
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  1
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  1
2008 Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ. Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Research. 18: 2005-15. PMID 18981266 DOI: 10.1101/gr.083055.108  1
2008 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 & Development. 22: 2535-49. PMID 18794350 DOI: 10.1101/Gad.1678608  1
2008 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 & Development. 22: 2520-34. PMID 18794349 DOI: 10.1101/gad.1678808  1
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  1
2008 Grove CA, Walhout AJ. Transcription factor functionality and transcription regulatory networks. Molecular Biosystems. 4: 309-14. PMID 18354784 DOI: 10.1039/b715909a  1
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  1
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  1
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  1
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  1
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  1
2006 Walhout AJ. Networking at the second Interactome Meeting. Expert Review of Proteomics. 3: 477-9. PMID 17078761 DOI: 10.1586/14789450.3.5.477  0.01
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  0.01
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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