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Gateway Recombinational Cloning.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.top094912. doi: 10.1101/pdb.top094912.


Using Multisite LR Cloning to Generate a Destination Clone.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.prot094946. doi: 10.1101/pdb.prot094946.


Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.prot094938. doi: 10.1101/pdb.prot094938.


Propagating Gateway Vectors.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jan 2;2018(1):pdb.prot094920. doi: 10.1101/pdb.prot094920.


Many transcription factors contribute to C. elegans growth and fat storage.

Mori A, Holdorf AD, Walhout AJM.

Genes Cells. 2017 Sep;22(9):770-784. doi: 10.1111/gtc.12516. Epub 2017 Aug 8.


PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions.

Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM.

Translation (Austin). 2017 Feb 28;5(1):e1295130. doi: 10.1080/21690731.2017.1295130. eCollection 2017.


The Oxidative Stress Response in Caenorhabditis elegans Requires the GATA Transcription Factor ELT-3 and SKN-1/Nrf2.

Hu Q, D'Amora DR, MacNeil LT, Walhout AJM, Kubiseski TJ.

Genetics. 2017 Aug;206(4):1909-1922. doi: 10.1534/genetics.116.198788. Epub 2017 Jun 9.


Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics.

García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM.

Cell. 2017 Apr 20;169(3):431-441.e8. doi: 10.1016/j.cell.2017.03.046.


C. elegans and its bacterial diet as a model for systems-level understanding of host-microbiota interactions.

Zhang J, Holdorf AD, Walhout AJ.

Curr Opin Biotechnol. 2017 Aug;46:74-80. doi: 10.1016/j.copbio.2017.01.008. Epub 2017 Feb 9. Review.


Metabolic network modeling with model organisms.

Yilmaz LS, Walhout AJ.

Curr Opin Chem Biol. 2017 Feb;36:32-39. doi: 10.1016/j.cbpa.2016.12.025. Epub 2017 Jan 12. Review.


Gene-Centered Yeast One-Hybrid Assays.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.top077669. doi: 10.1101/pdb.top077669.


Zymolyase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088971. doi: 10.1101/pdb.prot088971.


Colony Lift Colorimetric Assay for β-Galactosidase Activity.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088963. doi: 10.1101/pdb.prot088963.


Performing Yeast One-Hybrid Library Screens.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088955. doi: 10.1101/pdb.prot088955.


Generating Bait Strains for Yeast One-Hybrid Assays.

Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ.

Cold Spring Harb Protoc. 2016 Dec 1;2016(12):pdb.prot088948. doi: 10.1101/pdb.prot088948.


A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.

Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ.

Mol Syst Biol. 2016 Oct 24;12(10):884. doi: 10.15252/msb.20167131.


Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.

Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ.

Elife. 2016 Jul 6;5. pii: e17670. doi: 10.7554/eLife.17670.


A Caenorhabditis elegans Genome-Scale Metabolic Network Model.

Yilmaz LS, Walhout AJ.

Cell Syst. 2016 May 25;2(5):297-311. doi: 10.1016/j.cels.2016.04.012. Epub 2016 May 19.


Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms.

Watson E, Yilmaz LS, Walhout AJ.

Annu Rev Genet. 2015;49:553-75. doi: 10.1146/annurev-genet-112414-055257. Review.


Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network.

MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJ.

Cell Syst. 2015 Aug 26;1(2):152-162.


Human gene-centered transcription factor networks for enhancers and disease variants.

Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM.

Cell. 2015 Apr 23;161(3):661-673. doi: 10.1016/j.cell.2015.03.003.


Widespread macromolecular interaction perturbations in human genetic disorders.

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 YY, 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 AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.


Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.

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.

Elife. 2015 Apr 23;4. doi: 10.7554/eLife.06967.


RNA Interference in Caenorhabditis elegans.

Conte D Jr, MacNeil LT, Walhout AJ, Mello CC.

Curr Protoc Mol Biol. 2015 Jan 5;109:26.3.1-30. doi: 10.1002/0471142727.mb2603s109.


Determination and inference of eukaryotic transcription factor sequence specificity.

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 AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR.

Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009.


Worms, bacteria, and micronutrients: an elegant model of our diet.

Yilmaz LS, Walhout AJ.

Trends Genet. 2014 Nov;30(11):496-503. doi: 10.1016/j.tig.2014.07.010. Epub 2014 Aug 26. Review.


Food, pathogen, signal: The multifaceted nature of a bacterial diet.

Macneil LT, Walhout AJ.

Worm. 2013 Oct 1;2(4):e26454. doi: 10.4161/worm.26454. Epub 2013 Sep 30.


Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy.

Watson E, Walhout AJ.

Trends Endocrinol Metab. 2014 Oct;25(10):502-8. doi: 10.1016/j.tem.2014.03.004. Epub 2014 Apr 12. Review.


Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits.

Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJM.

Cell. 2014 Mar 13;156(6):1336-1337. doi: 10.1016/j.cell.2014.02.036. Epub 2014 Mar 13. No abstract available.


Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits.

Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJ.

Cell. 2014 Feb 13;156(4):759-70. doi: 10.1016/j.cell.2014.01.047. Erratum in: Cell. 2014 Mar 13;156(6):1336-7.


Genetic adaptation to diet preserves longevity.

Walhout AJ.

Cell Metab. 2014 Feb 4;19(2):177-8. doi: 10.1016/j.cmet.2014.01.006.


Using networks to measure similarity between genes: association index selection.

Fuxman Bass JI, Diallo A, Nelson J, Soto JM, Myers CL, Walhout AJ.

Nat Methods. 2013 Dec;10(12):1169-76. doi: 10.1038/nmeth.2728. Erratum in: Nat Methods. 2014 Mar;11(3):349.


Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters.

Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ.

Nucleic Acids Res. 2014 Jan;42(1):153-62. doi: 10.1093/nar/gkt858. Epub 2013 Sep 24.


Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.

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.

Mol Cell. 2013 Jul 11;51(1):116-27. doi: 10.1016/j.molcel.2013.05.018. Epub 2013 Jun 20.


Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response.

Watson E, MacNeil LT, Arda HE, Zhu LJ, Walhout AJM.

Cell. 2013 Mar 28;153(1):253-66. doi: 10.1016/j.cell.2013.02.050. Erratum in: Cell. 2013 Jun 6;153(6):1406-7.


Diet-induced developmental acceleration independent of TOR and insulin in C. elegans.

MacNeil LT, Watson E, Arda HE, Zhu LJ, Walhout AJ.

Cell. 2013 Mar 28;153(1):240-52. doi: 10.1016/j.cell.2013.02.049.


Complex expression dynamics and robustness in C. elegans insulin networks.

Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJ.

Genome Res. 2013 Jun;23(6):954-65. doi: 10.1101/gr.150466.112. Epub 2013 Mar 28.


A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels.

Tamburino AM, Ryder SP, Walhout AJ.

G3 (Bethesda). 2013 Feb;3(2):297-304. doi: 10.1534/g3.112.004390. Epub 2013 Feb 1.


Gene-centered yeast one-hybrid assays.

Reece-Hoyes JS, Walhout AJ.

Methods Mol Biol. 2012;812:189-208. doi: 10.1007/978-1-61779-455-1_11.


A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans.

Feng H, Reece-Hoyes JS, Walhout AJ, Hope IA.

Gene. 2012 Feb 15;494(1):73-84. doi: 10.1016/j.gene.2011.11.042. Epub 2011 Dec 19.


Genomics in 2011: challenges and opportunities.

Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ.

Genome Biol. 2011 Dec 28;12(12):137. doi: 10.1186/gb-2011-12-12-137.


Gene-centered regulatory network mapping.

Walhout AJ.

Methods Cell Biol. 2011;106:271-88. doi: 10.1016/B978-0-12-544172-8.00010-4. Review.


Enhanced Y1H assays for Arabidopsis.

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.

Nat Methods. 2011 Oct 30;8(12):1053-5. doi: 10.1038/nmeth.1750.


Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.

Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ.

Nat Methods. 2011 Oct 30;8(12):1059-64. doi: 10.1038/nmeth.1748.


Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.

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.

Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764.


Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex.

Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA.

PLoS Genet. 2011 May;7(5):e1002074. doi: 10.1371/journal.pgen.1002074. Epub 2011 May 12.


What does biologically meaningful mean? A perspective on gene regulatory network validation.

Walhout AJ.

Genome Biol. 2011;12(4):109. doi: 10.1186/gb-2011-12-4-109. Epub 2011 Apr 11.


Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants.

De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ.

Nucleic Acids Res. 2011 Jun;39(11):4553-63. doi: 10.1093/nar/gkr070. Epub 2011 Feb 18.


Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression.

Macneil LT, Walhout AJ.

Genome Res. 2011 May;21(5):645-57. doi: 10.1101/gr.097378.109. Epub 2011 Feb 4. Erratum in: Genome Res. 2011 Jun;21(6):999.

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