Latest Research

Bacteria modulate host chemotherapeutic drug response by active metabolic mechanisms
April 20, 2017

García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM. (2017) Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics. Cell 169, 431-441.

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A new method for detecting RNA binding protien-3′ UTR interactions
March 10, 2017

Tamburino AM, Kaymak E, Shresta S, Holdorf AD, Ryder SP, Walhout AJM (2017) PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. Translation 5, e1295130.

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msb-oct-2016A protein–DNA interaction map for 15% of C. elegans promoters
October 24, 2016

Fuxman Bass, JI, Pons, C, Kozlowski, L, Reece‐Hoyes, JS, Shrestha, S, Holdorf, AD, Mori, A, Myers, CL, Walhout, AJM. (2016). A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions. Mol. Sys. Biol. 12: 884.

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All Publications

2016 2015  2014  2013  2012  2011  2010  2009  2008  2007  2006  2005  2004  2003  2002  2001  2000  1990s

2017

García-González AP, Walhout AJM (2017) Worms, bugs and drugs: Caenorhabditis elegans as a model for host-microbe-drug interactions. Curr. Opin. Sys. Biol. 6, 46-50.

Mori A, Holdorf AD, Walhout AJM. (2017) Many transcription factors contribute to C. elegans growth and fat storage. Genes to Cells 22, 770-784.

Hu Q, D’Amora DR, MacNeil LT, Walhout AJM, Kubiseski TJ. (2017) The Oxidative Stress Response in Caenorhabditis elegans Requires the GATA Transcription Factor ELT-3 and SKN-1/Nrf2. Genetics 206, 1909-1922.

García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM. (2017) Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics. Cell 169, 431-441.

Tamburino AM, Kaymak E, Shresta S, Holdorf AD, Ryder SP, Walhout AJM (2017) PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. Translation 5, e1295130.

Zhang J, Holdorf AD, Walhout AJ. (2017) C. elegans and its bacterial diet as a model for systems-level understanding of host–microbiota interactions. Curr. Opin. Biotechnol. 46, 74-80. PDF

Yilmaz LS, Walhout AJM (2017) Metabolic network modeling with model organisms. Curr. Opin. Chem. Biol. 36, 32-39. PDF

2016

Fuxman Bass JI, Reece-Hoyes JS, Walhout AMJ. (2016). Gene-Centered Yeast One-Hybrid Assay. Cold Spring Harb Protoc. 2016(12):pdb.top077669.

Fuxman Bass, JI, Pons, C, Kozlowski, L, Reece‐Hoyes,JS, Shrestha, S, Holdorf, AD, Mori, A, Myers, CL, Walhout, AJM. (2016). A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions. Mol. Sys. Biol. 12: 884. PDF

Andrews BJ, Walhout AJM, Iyengar R, The Human Cells Project Working Group. (2016). Quantitative human cell encyclopedia. Sci. Signal. 9, mr1.

Watson E, Olin-Sandoval V, Hoy MJ, Li C, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJM. (2016). Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. eLife 2016;5:e17670. PDF

Yilmaz LS, Walhout AJM. (2016). A Caenorhabditis elegans Genome-Scale Metabolic Network Model. Cell Systems 2, 297–31. PDF

2015

Watson E, Yilmas LS, Walhout AJ. (2015). Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms. Annu. Rev. Genet. 49, 553-575. PDF

MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM. (2015). Transcription Factor Activity Mapping of a Tissue-Specific In Vivo Gene Regulatory Network. Cell Systems 1, 152-162. PDF

Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM. (2015). Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants. Cell 161, 661–73. PDF

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, Khurana V, Sharma A, Liu Y, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási A, Charloteaux B, Hill DE, Hao T, Roth FP, Yu X, Walhout AJM, Lindquist S, Vidal M. (2015). Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders. Cell 161, 647–60. PDF

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. (2015). Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife 10.7554/eLife.06967.

Conte D, MacNeil LT, Walhout AJ, Mello CC. (2015). RNA Interference in Caenorhabditis elegans. Curr. Protoc. Mol. Biol. 109:26.3.1-26.3.30.

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, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158:1431-43.

Yilmaz LS and Walhout AJ. (2014). Worms, bacteria, and micronutrients: an elegant model of our diet. Trends Genetics 30, 496-503. PDF

Liu WJ, Reece-Hoyes JS, Walhout AJ, Eisenmann DM. (2014). 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 Dev. Bio. 14:17.

Watson E and Walhout AJ. (2014) Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy. Trends Endocrinol. Metab. 25, 502-508. PDF

Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJ. (2014). Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. Cell 156:759-70. PDF

Walhout AJ. (2014). Genetic adaptation to diet preserves longevity. Cell Metab. 19:177-8. PDF

Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. (2014). Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res. 42:153-62. PDF

2013

MacNeil LT, Walhout AJ. (2013). Food, pathogen, signal: The multifaceted nature of a bacterial diet. Worm 2:e26454. PDF

Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ. (2013). Using networks to measure similarity between genes: association index selection. Nat Methods. 10:1169–1176. Erratum in: Nat. Methods 11:349. PDF

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. (2013). Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Mol. Cell 51:116-27. PDF

Walhout lab research featured on 28 Mar 2013 cover of Cell.

Walhout lab research featured on 28 Mar 2013 cover of Cell.

MacNeil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ. (2013). Diet-Induced developmental acceleration independent of TOR and insulin in C. elegans. Cell 153:240-252. PDF

Watson E*, MacNeil LT*, Arda HE, Zhu LJ, Walhout AJ. (2013). Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell 153:253-266. PDF

Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJ. (2013). Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res. 23:954-65. PDF

Tamburino AM, Ryder SP, Walhout AJ. (2013). A Compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 3:297-304. PDF

2012

Reece-Hoyes JS, Walhout AJ. (2012). Gene-centered yeast one-hybrid assays. Methods Mol. Biol. 812:189-208.

Feng H, Reece-Hoyes JS, Walhout AJ, Hope IA. (2012). A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans. Gene 494:73-84.

2011

Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. (2011). Genomics in 2011: challenges and opportunities. Genome Biol. 12:137.

Walhout AJ. (2011). Gene-centered regulatory network mapping. Methods Cell Biol. 106:271-88. PDF

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. (2011). Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat. Methods 8:1050-52. PDF

Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ. (2011). Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat. Methods 8:1059-64. PDF

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. (2011). Enhanced Y1H assays for Arabidopsis. Nat. Methods. 8:1053-5.

Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. (2011). Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet. 7:e1002074.

Walhout AJ. (2011). What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biol. 12:109. PDF

De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ. (2011). Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res. 39:4553-63. PDF

MacNeil LT, Walhout AJ. (2011). Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 21:645-57. PDF

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. (2011). A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7:459.

2010

Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJ. (2010). Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol. Syst. Biol. 6:367. PDF

Arda HE, Walhout AJ. (2010). Gene-centered regulatory networks. Brief. Funct. Genomics 9:4-12. PDF

2009

Walhout lab research featured on 23 Jul 2009 cover of Cell.

Walhout lab research featured on 23 Jul 2009 cover of Cell.

Walhout AJ. (2009). Getting an edge on human disease. Mol. Syst. Biol. 5:322. PDF

Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ. (2009). A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 138:314-27. PDF

Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ. (2009). The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res. 37:3689-98. PDF

Martinez NJ, Walhout AJ. (2009). The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays 31:435-45. PDF

2008

Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ. (2008). Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res. 18:2005-15. PDF

Ow MC, Martinez NJ, Olsen PH, Silverman HS, Barrasa MI, Conradt B, Walhout AJ, Ambros V. (2008). The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev. 22:2520-34.

Martinez NJ, Ow MC, Barrasa MI, Hammell M, Sequerra R, Doucette-Stamm L, Roth FP, Ambros VR, Walhout AJ. (2008). A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev. 22:2535-49. PDF

Grove CA, Walhout AJ. (2008). Transcription factor functionality and transcription regulatory networks. Mol. Biosyst. 4:309-14.

Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. (2008). Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nat. Protoc. 3:698-709.

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. (2007). Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat. Methods 4:659-64. PDF

Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JA, Sequerra R, Doucette-Stamm L, Barabási AL, Walhout AJ. (2007). Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res. 17:1061-71. PDF

Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJ, Vidal M, Hope IA. (2007). Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics 8:27.

Barrasa MI, Vaglio P, Cavasino F, Jacotot L, Walhout AJ. (2007). EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics 8:21. PDF

2006

Walhout AJ. (2006). Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 16:1445-54. PDF

Walhout AJ. (2006). Networking at the second Interactome Meeting. Expert Rev. Proteomics 3:477-9.

Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJ. (2006). Gateway-compatible yeast one-hybrid screens. CSH Protoc. 2006(5).

Wang Y, Oh SW, Deplancke B, Luo J, Walhout AJ, Tissenbaum HA. (2006). C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mech. Ageing Dev. 127:741-7.

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. (2006). A gene-centered C. elegans protein-DNA interaction network. Cell 125:1193-205. PDF

2005

Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. (2005). A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 6:R110. PDF

Davison EM, Harrison MM, Walhout AJ, Vidal M, Horvitz HR. (2005). 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.

Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. (2005). C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metab. 2:35-42.

2004

Deplancke B, Dupuy D, Vidal M, Walhout AJ. (2004). A gateway-compatible yeast one-hybrid system. Genome Res. 14:2093-101. PDF

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. (2004). A first version of the Caenorhabditis elegans promoterome. Genome Res. 14:2169-75.

Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M. (2004). Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93.

Fisk Green R, Lorson M, Walhout AJ, Vidal M, van den Heuvel S. (2004). Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5. Mol. Genet. Genomics. 271:532-44.

2003

Ge H, Walhout AJ, Vidal M. (2003). Integrating ‘omic’ information: a bridge between genomics and systems biology. Trends Genet. 19:551-60.

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, Vidal M. (2002). Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12:1952-8.

Huang NN, Mootz DE, Walhout AJ, Vidal M, Hunter CP. (2002) MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development 129:747-59.

Endoh H, Vincent S, Jacob Y, Réal E, Walhout AJ, Vidal M. (2002). Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol. 350:525-45.

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. (2001). A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2:821-8.

Walhout AJ, Vidal M. (2001). High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24:297-306.

Walhout AJ, Vidal M. (2001). Protein interaction maps for model organisms. Nat. Rev. Mol. Cell Biol. 2:55-62.

2000

Walhout AJ, Boulton SJ, Vidal M. (2000). Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17:88-94.

Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287:116-22.

Endoh H, Walhout AJ, Vidal M. (2000). A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions. Methods Enzymol. 328:74-88.

Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, van den Heuvel S, Vidal M. (2000). GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328:575-92.

1990s

Walhout AJ, Vidal M. (1999). A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 9:1128-34.

Walhout AJ, van der Vliet PC, Timmers HT. (1998). Sequences flanking the E-box contribute to cooperative binding by c-Myc/Max heterodimers to adjacent binding sites. Biochim. Biophys. Acta 1397:189-201.

Walhout AJ, Gubbels JM, Bernards R, van der Vliet PC, Timmers HT. (1997). 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. 25(8):1493-501.

Kruyt FA, Folkers GE, Walhout AJ, van der Leede BJ, van der Saag PT. (1993). E1A functions as a coactivator of retinoic acid-dependent retinoic acid receptor-beta 2 promoter activation. Mol. Endocrinol. 7:604-15.