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Items: 46

1.

TMEM41B is a novel regulator of autophagy and lipid mobilization.

Moretti F, Bergman P, Dodgson S, Marcellin D, Claerr I, Goodwin JM, DeJesus R, Kang Z, Antczak C, Begue D, Bonenfant D, Graff A, Genoud C, Reece-Hoyes JS, Russ C, Yang Z, Hoffman GR, Mueller M, Murphy LO, Xavier RJ, Nyfeler B.

EMBO Rep. 2018 Sep;19(9). pii: e45889. doi: 10.15252/embr.201845889. Epub 2018 Aug 20.

PMID:
30126924
2.

Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jul 2;2018(7):pdb.top094953. doi: 10.1101/pdb.top094953.

PMID:
29967278
3.

High-Efficiency Yeast Transformation.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jul 2;2018(7):pdb.prot094995. doi: 10.1101/pdb.prot094995.

PMID:
29967274
4.

Identifying Interactors from an Activation Domain Prey Library.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jul 2;2018(7):pdb.prot094987. doi: 10.1101/pdb.prot094987.

PMID:
29967273
5.

Generating Yeast Two-Hybrid Bait Strains.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jul 2;2018(7):pdb.prot094979. doi: 10.1101/pdb.prot094979.

PMID:
29967272
6.

Generating Yeast One-Hybrid DNA-Bait Strains.

Reece-Hoyes JS, Walhout AJM.

Cold Spring Harb Protoc. 2018 Jul 2;2018(7):pdb.prot094961. doi: 10.1101/pdb.prot094961.

PMID:
29967271
7.

Gateway Recombinational Cloning.

Reece-Hoyes JS, Walhout AJM.

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

8.

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.

9.

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.

PMID:
29295905
10.

Propagating Gateway Vectors.

Reece-Hoyes JS, Walhout AJM.

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

11.

Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy.

Potting C, Crochemore C, Moretti F, Nigsch F, Schmidt I, Manneville C, Carbone W, Knehr J, DeJesus R, Lindeman A, Maher R, Russ C, McAllister G, Reece-Hoyes JS, Hoffman GR, Roma G, Müller M, Sailer AW, Helliwell SB.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):E180-E189. doi: 10.1073/pnas.1711023115. Epub 2017 Dec 21. Erratum in: Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8579.

12.

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization.

Surdziel E, Clay I, Nigsch F, Thiemeyer A, Allard C, Hoffman G, Reece-Hoyes JS, Phadke T, Gambert R, Keller CG, Ludwig MG, Baumgarten B, Frederiksen M, Schübeler D, Seuwen K, Bouwmeester T, Fodor BD.

PLoS One. 2017 Aug 24;12(8):e0183679. doi: 10.1371/journal.pone.0183679. eCollection 2017.

13.

Identification of a novel NAMPT inhibitor by CRISPR/Cas9 chemogenomic profiling in mammalian cells.

Estoppey D, Hewett JW, Guy CT, Harrington E, Thomas JR, Schirle M, Cuttat R, Waldt A, Gerrits B, Yang Z, Schuierer S, Pan X, Xie K, Carbone W, Knehr J, Lindeman A, Russ C, Frias E, Hoffman GR, Varadarajan M, Ramadan N, Reece-Hoyes JS, Wang Q, Chen X, McAllister G, Roma G, Bouwmeester T, Hoepfner D.

Sci Rep. 2017 Feb 16;7:42728. doi: 10.1038/srep42728.

14.

Gene-Centered Yeast One-Hybrid Assays.

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

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

15.

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). doi: 10.1101/pdb.prot088971.

16.

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). doi: 10.1101/pdb.prot088963.

17.

Performing Yeast One-Hybrid Library Screens.

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

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

18.

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). doi: 10.1101/pdb.prot088948.

19.

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.

20.

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks.

van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, Russ C, Reece-Hoyes JS, Nye C, Gradia S, Vidal B, Zheng J, Hoffman GR, Fuller CK, May AP.

Mol Cell. 2016 Aug 18;63(4):633-646. doi: 10.1016/j.molcel.2016.06.037. Epub 2016 Aug 4.

21.

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62.

DeJesus R, Moretti F, McAllister G, Wang Z, Bergman P, Liu S, Frias E, Alford J, Reece-Hoyes JS, Lindeman A, Kelliher J, Russ C, Knehr J, Carbone W, Beibel M, Roma G, Ng A, Tallarico JA, Porter JA, Xavier RJ, Mickanin C, Murphy LO, Hoffman GR, Nyfeler B.

Elife. 2016 Jun 28;5. pii: e17290. doi: 10.7554/eLife.17290.

22.

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.

23.

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.

25.

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.

26.

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.

27.

Yeast one-hybrid assays: a historical and technical perspective.

Reece-Hoyes JS, Marian Walhout AJ.

Methods. 2012 Aug;57(4):441-7. doi: 10.1016/j.ymeth.2012.07.027. Epub 2012 Aug 3. Review.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.

Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D.

Mol Syst Biol. 2010 Aug 10;6:399. doi: 10.1038/msb.2010.54.

34.

The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors.

Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ.

Nucleic Acids Res. 2009 Jun;37(11):3689-98. doi: 10.1093/nar/gkp232. Epub 2009 Apr 16.

35.

Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity.

Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ.

Genome Res. 2008 Dec;18(12):2005-15. doi: 10.1101/gr.083055.108. Epub 2008 Nov 3.

36.

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.

Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ.

Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24.

PMID:
17589517
37.

Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns.

Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJ, Vidal M, Hope IA.

BMC Genomics. 2007 Jan 23;8:27.

38.

Components of both major axial patterning systems of the Bilateria are differentially expressed along the primary axis of a 'radiate' animal, the anthozoan cnidarian Acropora millepora.

de Jong DM, Hislop NR, Hayward DC, Reece-Hoyes JS, Pontynen PC, Ball EE, Miller DJ.

Dev Biol. 2006 Oct 15;298(2):632-43. Epub 2006 Aug 4.

39.

A gene-centered C. elegans protein-DNA interaction network.

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.

Cell. 2006 Jun 16;125(6):1193-205.

40.

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks.

Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ.

Genome Biol. 2005;6(13):R110. Epub 2005 Dec 30.

41.

A consensus Oct1 binding site is required for the activity of the Xenopus Cdx4 promoter.

Reece-Hoyes JS, Keenan ID, Pownall ME, Isaacs HV.

Dev Biol. 2005 Jun 15;282(2):509-23.

42.

Coral development: from classical embryology to molecular control.

Ball EE, Hayward DC, Reece-Hoyes JS, Hislop NR, Samuel G, Saint R, Harrison PL, Miller DJ.

Int J Dev Biol. 2002;46(4):671-8. Review.

43.

Cloning and expression of the Cdx family from the frog Xenopus tropicalis.

Reece-Hoyes JS, Keenan ID, Isaacs HV.

Dev Dyn. 2002 Jan;223(1):134-40.

44.

Gene structure and larval expression of cnox-2Am from the coral Acropora millepora.

Hayward DC, Catmull J, Reece-Hoyes JS, Berghammer H, Dodd H, Hann SJ, Miller DJ, Ball EE.

Dev Genes Evol. 2001 Jan;211(1):10-9.

PMID:
11277400
45.

Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): implications for the evolution of the Pax gene family.

Miller DJ, Hayward DC, Reece-Hoyes JS, Scholten I, Catmull J, Gehring WJ, Callaerts P, Larsen JE, Ball EE.

Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4475-80.

46.

Pax-6 origins--implications from the structure of two coral pax genes.

Catmull J, Hayward DC, McIntyre NE, Reece-Hoyes JS, Mastro R, Callaerts P, Ball EE, Miller DJ.

Dev Genes Evol. 1998 Aug;208(6):352-6.

PMID:
9716726

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