Albertha J. Walhout, Ph.D. - Publications

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

56 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
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  0.468
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  0.324
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  0.511
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  0.395
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  0.611
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  0.555
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  0.425
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  0.425
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  0.701
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  0.444
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  0.542
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  0.416
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  0.419
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  0.378
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  0.458
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  0.337
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  0.472
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  0.457
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  0.646
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  0.376
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  0.331
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  0.341
2010 Arda HE, Walhout AJ. Gene-centered regulatory networks. Briefings in Functional Genomics. 9: 4-12. PMID 20008400 DOI: 10.1093/bfgp/elp049  0.346
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  0.399
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  0.647
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  0.37
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  0.62
2008 Grove CA, Walhout AJ. Transcription factor functionality and transcription regulatory networks. Molecular Biosystems. 4: 309-14. PMID 18354784 DOI: 10.1039/b715909a  0.431
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  0.635
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  0.362
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  0.532
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  0.673
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  0.485
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  0.613
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  0.691
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  0.657
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  0.544
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  0.576
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  0.707
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  0.741
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  0.562
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  0.67
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  0.683
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  0.643
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  0.545
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  0.711
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  0.599
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  0.606
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  0.559
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  0.589
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  0.721
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  0.63
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  0.619
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